From 52b018bb9adf9c026e8aa3b3bad2e09c75b07472 Mon Sep 17 00:00:00 2001 From: Gustavo Marques Date: Thu, 15 Aug 2019 14:46:33 -0600 Subject: [PATCH 01/72] Add time0 and timenow in MCT --- config_src/mct_driver/ocn_comp_mct.F90 | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/config_src/mct_driver/ocn_comp_mct.F90 b/config_src/mct_driver/ocn_comp_mct.F90 index 5b581e0427..d7d66b32f6 100644 --- a/config_src/mct_driver/ocn_comp_mct.F90 +++ b/config_src/mct_driver/ocn_comp_mct.F90 @@ -111,6 +111,7 @@ subroutine ocn_init_mct( EClock, cdata_o, x2o_o, o2x_o, NLFilename ) ! local variables type(time_type) :: time0 !< Model start time + type(time_type) :: timenow !< Model current time 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 @@ -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) + timenow = 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 @@ -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, timenow, input_restart_file = 'n') else ! hybrid or branch or continuos runs ! get output path root call seq_infodata_GetData( glb%infodata, outPathRoot=restartpath ) @@ -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, timenow, input_restart_file=trim(restartfile)) endif if (is_root_pe()) then write(glb%stdout,'(/12x,a/)') '======== COMPLETED MOM INITIALIZATION ========' From bd5760550192f146d4cd9e130fb91441c7d85d30 Mon Sep 17 00:00:00 2001 From: Gustavo Marques Date: Thu, 15 Aug 2019 15:18:02 -0600 Subject: [PATCH 02/72] Add time0 and timenow in NUOPC --- config_src/nuopc_driver/mom_cap.F90 | 27 ++++++++++++++++++++++----- 1 file changed, 22 insertions(+), 5 deletions(-) diff --git a/config_src/nuopc_driver/mom_cap.F90 b/config_src/nuopc_driver/mom_cap.F90 index d6a7837c83..b9ac3c0814 100644 --- a/config_src/nuopc_driver/mom_cap.F90 +++ b/config_src/nuopc_driver/mom_cap.F90 @@ -737,8 +737,9 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc) type(ice_ocean_boundary_type), pointer :: Ice_ocean_boundary => NULL() type(ocean_internalstate_wrapper) :: ocean_internalstate type(ocean_grid_type), pointer :: ocean_grid => NULL() - type(time_type) :: Run_len ! length of experiment - type(time_type) :: Time + type(time_type) :: Run_len !< length of experiment + type(time_type) :: time0 !< Model start time + type(time_type) :: timenow !< Model current time type(time_type) :: Time_restart type(time_type) :: DT integer :: DT_OCEAN @@ -841,7 +842,23 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc) ! this ocean connector will be driven at set interval DT = set_time (DT_OCEAN, 0) - Time = set_date (YEAR,MONTH,DAY,HOUR,MINUTE,SECOND) + ! get current time + timenow = set_date (YEAR,MONTH,DAY,HOUR,MINUTE,SECOND) + + ! get start/reference time + call ESMF_ClockGet(CLOCK, refTime=MyTime, RC=rc) + if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, & + line=__LINE__, & + file=__FILE__)) & + return ! bail out + + call ESMF_TimeGet (MyTime, YY=YEAR, MM=MONTH, DD=DAY, H=HOUR, M=MINUTE, S=SECOND, RC=rc ) + if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, & + line=__LINE__, & + file=__FILE__)) & + return ! bail out + + time0 = set_date (YEAR,MONTH,DAY,HOUR,MINUTE,SECOND) ! rsd need to figure out how to get this without share code !call shr_nuopc_get_component_instance(gcomp, inst_suffix, inst_index) @@ -971,9 +988,9 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc) ocean_public%is_ocean_pe = .true. if (len_trim(restartfile) > 0) then - call ocean_model_init(ocean_public, ocean_state, Time, Time, input_restart_file=trim(restartfile)) + call ocean_model_init(ocean_public, ocean_state, time0, timenow, input_restart_file=trim(restartfile)) else - call ocean_model_init(ocean_public, ocean_state, Time, Time) + call ocean_model_init(ocean_public, ocean_state, time0, timenow) endif call ocean_model_init_sfc(ocean_state, ocean_public) From 4191689d3d213190bef81a1bd8f94a376efc87fc Mon Sep 17 00:00:00 2001 From: Gustavo Marques Date: Fri, 16 Aug 2019 13:55:06 -0600 Subject: [PATCH 03/72] Deletes unecessary if statement --- config_src/nuopc_driver/mom_cap.F90 | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/config_src/nuopc_driver/mom_cap.F90 b/config_src/nuopc_driver/mom_cap.F90 index b9ac3c0814..e4afba6524 100644 --- a/config_src/nuopc_driver/mom_cap.F90 +++ b/config_src/nuopc_driver/mom_cap.F90 @@ -845,6 +845,10 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc) ! get current time timenow = set_date (YEAR,MONTH,DAY,HOUR,MINUTE,SECOND) + if (is_root_pe()) then + write(logunit,*) subname//'current time: y,m,d-',year,month,day,'h,m,s=',hour,minute,second + endif + ! get start/reference time call ESMF_ClockGet(CLOCK, refTime=MyTime, RC=rc) if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, & @@ -860,6 +864,10 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc) time0 = set_date (YEAR,MONTH,DAY,HOUR,MINUTE,SECOND) + if (is_root_pe()) then + write(logunit,*) subname//'start time: y,m,d-',year,month,day,'h,m,s=',hour,minute,second + endif + ! rsd need to figure out how to get this without share code !call shr_nuopc_get_component_instance(gcomp, inst_suffix, inst_index) !inst_name = "OCN"//trim(inst_suffix) @@ -987,11 +995,8 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc) endif ocean_public%is_ocean_pe = .true. - if (len_trim(restartfile) > 0) then - call ocean_model_init(ocean_public, ocean_state, time0, timenow, input_restart_file=trim(restartfile)) - else - call ocean_model_init(ocean_public, ocean_state, time0, timenow) - endif + + call ocean_model_init(ocean_public, ocean_state, time0, timenow, input_restart_file=trim(restartfile)) call ocean_model_init_sfc(ocean_state, ocean_public) From 52225e34a6d87bd26c7a9f57f79ab3c08d0f07cd Mon Sep 17 00:00:00 2001 From: Gustavo Marques Date: Fri, 16 Aug 2019 15:35:36 -0600 Subject: [PATCH 04/72] Deletes blank line contains spaces --- config_src/nuopc_driver/mom_cap.F90 | 1 - 1 file changed, 1 deletion(-) diff --git a/config_src/nuopc_driver/mom_cap.F90 b/config_src/nuopc_driver/mom_cap.F90 index e4afba6524..d1681bed25 100644 --- a/config_src/nuopc_driver/mom_cap.F90 +++ b/config_src/nuopc_driver/mom_cap.F90 @@ -995,7 +995,6 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc) endif ocean_public%is_ocean_pe = .true. - call ocean_model_init(ocean_public, ocean_state, time0, timenow, input_restart_file=trim(restartfile)) call ocean_model_init_sfc(ocean_state, ocean_public) From b61053bdf594357b5f6135ff9fde64fd481aa6b4 Mon Sep 17 00:00:00 2001 From: Gustavo Marques Date: Fri, 16 Aug 2019 16:04:23 -0600 Subject: [PATCH 05/72] Replaces timenow with time_start and corrects comments. --- config_src/mct_driver/ocn_comp_mct.F90 | 12 ++++++------ config_src/nuopc_driver/mom_cap.F90 | 8 ++++---- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/config_src/mct_driver/ocn_comp_mct.F90 b/config_src/mct_driver/ocn_comp_mct.F90 index d7d66b32f6..a7495d7a7f 100644 --- a/config_src/mct_driver/ocn_comp_mct.F90 +++ b/config_src/mct_driver/ocn_comp_mct.F90 @@ -109,9 +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 - type(time_type) :: timenow !< Model current 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 @@ -211,7 +211,7 @@ subroutine ocn_init_mct( EClock, cdata_o, x2o_o, o2x_o, NLFilename ) ! 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) - timenow = set_date(year, month, day, hour, minute, seconds, err_msg=err_msg) + time_start = set_date(year, month, day, hour, minute, seconds, err_msg=err_msg) ! Debugging clocks if (debug .and. is_root_pe()) then @@ -285,7 +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, timenow, 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 ) @@ -301,7 +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, timenow, 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 ========' diff --git a/config_src/nuopc_driver/mom_cap.F90 b/config_src/nuopc_driver/mom_cap.F90 index d1681bed25..aa034e7d36 100644 --- a/config_src/nuopc_driver/mom_cap.F90 +++ b/config_src/nuopc_driver/mom_cap.F90 @@ -738,8 +738,8 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc) type(ocean_internalstate_wrapper) :: ocean_internalstate type(ocean_grid_type), pointer :: ocean_grid => NULL() type(time_type) :: Run_len !< length of experiment - type(time_type) :: time0 !< Model start time - type(time_type) :: timenow !< Model current time + 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(time_type) :: Time_restart type(time_type) :: DT integer :: DT_OCEAN @@ -843,7 +843,7 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc) ! this ocean connector will be driven at set interval DT = set_time (DT_OCEAN, 0) ! get current time - timenow = set_date (YEAR,MONTH,DAY,HOUR,MINUTE,SECOND) + time_start = set_date (YEAR,MONTH,DAY,HOUR,MINUTE,SECOND) if (is_root_pe()) then write(logunit,*) subname//'current time: y,m,d-',year,month,day,'h,m,s=',hour,minute,second @@ -995,7 +995,7 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc) endif ocean_public%is_ocean_pe = .true. - call ocean_model_init(ocean_public, ocean_state, time0, timenow, input_restart_file=trim(restartfile)) + call ocean_model_init(ocean_public, ocean_state, time0, time_start, input_restart_file=trim(restartfile)) call ocean_model_init_sfc(ocean_state, ocean_public) From 6e145dfaa49f24c62e7fc1ff6e65aaf48cc0d227 Mon Sep 17 00:00:00 2001 From: Gustavo Marques Date: Tue, 20 Aug 2019 15:45:41 -0600 Subject: [PATCH 06/72] Obsolete parameter ADD_KV_SLOW --- src/core/MOM_variables.F90 | 2 -- src/diagnostics/MOM_obsolete_params.F90 | 3 +++ 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/src/core/MOM_variables.F90 b/src/core/MOM_variables.F90 index 3748684fd4..a0b31c37de 100644 --- a/src/core/MOM_variables.F90 +++ b/src/core/MOM_variables.F90 @@ -257,8 +257,6 @@ module MOM_variables real, pointer, dimension(:,:,:) :: TKE_turb => NULL() !< The turbulent kinetic energy per unit mass at the interfaces [m2 s-2]. !! This may be at the tracer or corner points - logical :: add_Kv_slow !< If True, add Kv_slow when calculating the 'coupling coefficient' (a_cpl) - !! at the interfaces in find_coupling_coef. end type vertvisc_type !> Container for information about the summed layer transports diff --git a/src/diagnostics/MOM_obsolete_params.F90 b/src/diagnostics/MOM_obsolete_params.F90 index 0e563648f5..4062d04fd9 100644 --- a/src/diagnostics/MOM_obsolete_params.F90 +++ b/src/diagnostics/MOM_obsolete_params.F90 @@ -47,6 +47,9 @@ subroutine find_obsolete_params(param_file) call obsolete_logical(param_file, "BT_CONT_BT_THICK", & hint="Instead use BT_THICK_SCHEME='FROM_BT_CONT'.") + call obsolete_logical(param_file, "ADD_KV_SLOW", & + hint="This option is no longer needed, nor supported.") + call obsolete_logical(param_file, "APPLY_OBC_U", & hint="Instead use OBC_NUMBER_SEGMENTS>0 and use the new segments protocol.") call obsolete_logical(param_file, "APPLY_OBC_V", & From 9f2f709151cc7b0a3023e493198c62fb55658957 Mon Sep 17 00:00:00 2001 From: Gustavo Marques Date: Tue, 20 Aug 2019 15:47:25 -0600 Subject: [PATCH 07/72] Removes visc%Kv_slow from restart files --- .../vertical/MOM_set_viscosity.F90 | 27 +++---------------- 1 file changed, 4 insertions(+), 23 deletions(-) diff --git a/src/parameterizations/vertical/MOM_set_viscosity.F90 b/src/parameterizations/vertical/MOM_set_viscosity.F90 index 1265067ef2..2180a62cc4 100644 --- a/src/parameterizations/vertical/MOM_set_viscosity.F90 +++ b/src/parameterizations/vertical/MOM_set_viscosity.F90 @@ -1735,11 +1735,10 @@ subroutine set_visc_register_restarts(HI, GV, param_file, visc, restart_CS) "Turbulent kinetic energy per unit mass at interfaces", "m2 s-2", z_grid='i') endif - ! MOM_bkgnd_mixing is always used, so always allocate visc%Kv_slow. GMM - call safe_alloc_ptr(visc%Kv_slow, isd, ied, jsd, jed, nz+1) - call register_restart_field(visc%Kv_slow, "Kv_slow", .false., restart_CS, & - "Vertical turbulent viscosity at interfaces due to slow processes", & - "m2 s-1", z_grid='i') + if (useKPP) then + ! MOM_bkgnd_mixing uses Kv_slow when KPP is defined. + call safe_alloc_ptr(visc%Kv_slow, isd, ied, jsd, jed, nz+1) + endif ! visc%MLD is used to communicate the state of the (e)PBL or KPP to the rest of the model call get_param(param_file, mdl, "MLE_USE_PBL_MLD", MLE_use_PBL_MLD, & @@ -1939,24 +1938,11 @@ subroutine set_visc_init(Time, G, GV, US, param_file, diag, visc, CS, restart_CS "The molecular value, ~1e-6 m2 s-1, may be used.", & units="m2 s-1", fail_if_missing=.true.) - call get_param(param_file, mdl, "ADD_KV_SLOW", visc%add_Kv_slow, & - "If true, the background vertical viscosity in the interior "//& - "(i.e., tidal + background + shear + convection) is added "//& - "when computing the coupling coefficient. The purpose of this "//& - "flag is to be able to recover previous answers and it will likely "//& - "be removed in the future since this option should always be true.", & - default=.false.) - call get_param(param_file, mdl, "USE_KPP", use_KPP, & "If true, turns on the [CVMix] KPP scheme of Large et al., 1994, "//& "to calculate diffusivities and non-local transport in the OBL.", & do_not_log=.true., default=.false.) - if (use_KPP .and. visc%add_Kv_slow) call MOM_error(FATAL,"set_visc_init: "//& - "When USE_KPP=True, ADD_KV_SLOW must be false. Otherwise vertical "//& - "viscosity due to slow processes will be double counted. Please set "//& - "ADD_KV_SLOW=False.") - call get_param(param_file, mdl, "KV_BBL_MIN", CS%KV_BBL_min, & "The minimum viscosities in the bottom boundary layer.", & units="m2 s-1", default=Kv_background, scale=US%m_to_Z**2) @@ -2049,11 +2035,6 @@ subroutine set_visc_init(Time, G, GV, US, param_file, diag, visc, CS, restart_CS enddo ; enddo ; enddo endif ; endif - if (associated(visc%Kv_slow)) then ; if (query_initialized(visc%Kv_slow, "Kv_slow", restart_CS)) then - do k=1,nz+1 ; do j=js,je ; do i=is,ie - visc%Kv_slow(i,j,k) = Z_rescale**2 * visc%Kv_slow(i,j,k) - enddo ; enddo ; enddo - endif ; endif endif end subroutine set_visc_init From 93727f8afe45340681c2b3c98ccfae77a8871ded Mon Sep 17 00:00:00 2001 From: Gustavo Marques Date: Thu, 22 Aug 2019 16:27:47 -0600 Subject: [PATCH 08/72] Fix first four loop indices suggested by Bob NOTE: we need to add a warning that MEKE_EQUILIBRIUM only works if MEKE_KHCOEFF > 0. --- src/parameterizations/lateral/MOM_hor_visc.F90 | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/parameterizations/lateral/MOM_hor_visc.F90 b/src/parameterizations/lateral/MOM_hor_visc.F90 index 5a31405268..e6a8a26631 100644 --- a/src/parameterizations/lateral/MOM_hor_visc.F90 +++ b/src/parameterizations/lateral/MOM_hor_visc.F90 @@ -407,7 +407,7 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, call barotropic_get_tav(BT, ubtav, vbtav, G) call pass_vector(ubtav, vbtav, G%Domain) - do j=js,je ; do i=is,ie + do j=js-1,je+1 ; do i=is-1,ie+1 dudx_bt(i,j) = CS%DY_dxT(i,j)*(G%IdyCu(I,j) * ubtav(I,j) - & G%IdyCu(I-1,j) * ubtav(I-1,j)) dvdy_bt(i,j) = CS%DX_dyT(i,j)*(G%IdxCv(i,J) * vbtav(i,J) - & @@ -417,7 +417,7 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, call pass_var(dudx_bt, G%Domain, complete=.true.) call pass_var(dvdy_bt, G%Domain, complete=.true.) - do j=Jsq-1,Jeq+2 ; do i=Isq-1,Ieq+2 + do j=Jsq,Jeq+1 ; do i=Isq,Ieq+1 sh_xx_bt(i,j) = dudx_bt(i,j) - dvdy_bt(i,j) enddo ; enddo @@ -433,11 +433,11 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, call pass_var(dudy_bt, G%Domain, position=CORNER, complete=.true.) if (CS%no_slip) then - do J=js-2,Jeq+1 ; do I=is-2,Ieq+1 + do J=js-1,Jeq ; do I=is-1,Ieq sh_xy_bt(I,J) = (2.0-G%mask2dBu(I,J)) * ( dvdx_bt(I,J) + dudy_bt(I,J) ) enddo ; enddo else - do J=js-2,Jeq+1 ; do I=is-2,Ieq+1 + do J=js-1,Jeq ; do I=is-1,Ieq sh_xy_bt(I,J) = G%mask2dBu(I,J) * ( dvdx_bt(I,J) + dudy_bt(I,J) ) enddo ; enddo endif From e7781917d054d40973a2848e7ba7215d2334a71e Mon Sep 17 00:00:00 2001 From: Gustavo Marques Date: Fri, 23 Aug 2019 11:18:39 -0600 Subject: [PATCH 09/72] Deletes max_diss_rate_bt since it is never used --- src/parameterizations/lateral/MOM_hor_visc.F90 | 9 --------- 1 file changed, 9 deletions(-) diff --git a/src/parameterizations/lateral/MOM_hor_visc.F90 b/src/parameterizations/lateral/MOM_hor_visc.F90 index e6a8a26631..a0ff1d96a0 100644 --- a/src/parameterizations/lateral/MOM_hor_visc.F90 +++ b/src/parameterizations/lateral/MOM_hor_visc.F90 @@ -251,7 +251,6 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, grad_vel_mag_h, & ! Magnitude of the velocity gradient tensor squared at h-points [s-2] grad_vel_mag_bt_h, & ! Magnitude of the barotropic velocity gradient tensor squared at h-points [s-2] grad_d2vel_mag_h, & ! Magnitude of the Laplacian of the velocity vector, squared [m-2 s-2] - max_diss_rate_bt, & ! maximum possible energy dissipated by barotropic lateral friction [m2 s-3] boundary_mask ! A mask that zeroes out cells with at least one land edge real, dimension(SZIB_(G),SZJB_(G)) :: & @@ -401,8 +400,6 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, str_xx_GME(:,:) = 0.0 str_xy_GME(:,:) = 0.0 -! call pass_var(boundary_mask, G%Domain, complete=.true.) - ! Get barotropic velocities and their gradients call barotropic_get_tav(BT, ubtav, vbtav, G) call pass_vector(ubtav, vbtav, G%Domain) @@ -451,12 +448,6 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, (0.25*(dudy_bt(I,J)+dudy_bt(I-1,J)+dudy_bt(I,J-1)+dudy_bt(I-1,J-1)) )**2) enddo ; enddo - if (associated(MEKE)) then ; if (associated(MEKE%mom_src)) then - do j=Jsq-1,Jeq+2 ; do i=Isq-1,Ieq+2 - max_diss_rate_bt(i,j) = 2.0*MEKE%MEKE(i,j) * grad_vel_mag_bt_h(i,j) - enddo ; enddo - endif ; endif - do J=js-2,Jeq+1 ; do I=is-2,Ieq+1 grad_vel_mag_bt_q(I,J) = boundary_mask(i,j) * (dvdx_bt(i,j)**2 + dudy_bt(i,j)**2 + & (0.25*(dudx_bt(i,j)+dudx_bt(i+1,j)+dudx_bt(i,j+1)+dudx_bt(i+1,j+1)))**2 + & From 3b7cb69a4352f66cadc42599e20821f679658fc2 Mon Sep 17 00:00:00 2001 From: Gustavo Marques Date: Fri, 23 Aug 2019 11:27:04 -0600 Subject: [PATCH 10/72] Fixes the remaining loop indices related to GME --- src/parameterizations/lateral/MOM_hor_visc.F90 | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/parameterizations/lateral/MOM_hor_visc.F90 b/src/parameterizations/lateral/MOM_hor_visc.F90 index a0ff1d96a0..8ad3e7f212 100644 --- a/src/parameterizations/lateral/MOM_hor_visc.F90 +++ b/src/parameterizations/lateral/MOM_hor_visc.F90 @@ -713,21 +713,21 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, call pass_var(div_xx, G%Domain, complete=.true.) ! Divergence gradient - do j=Jsq-1,Jeq+2 ; do I=is-2,Ieq+1 + do j=Jsq,Jeq+1 ; do I=Isq-1,Ieq+1 div_xx_dx(I,j) = G%IdxCu(I,j)*(div_xx(i+1,j) - div_xx(i,j)) enddo ; enddo - do J=js-2,Jeq+1 ; do i=Isq-1,Ieq+2 + do J=Jsq-1,Jeq+1 ; do i=Isq,Ieq+1 div_xx_dy(i,J) = G%IdyCv(i,J)*(div_xx(i,j+1) - div_xx(i,j)) enddo ; enddo call pass_vector(div_xx_dx, div_xx_dy, G%Domain) ! Magnitude of divergence gradient - do j=Jsq-1,Jeq+2 ; do i=Isq-1,Ieq+2 + do j=Jsq,Jeq+1 ; do i=Isq,Ieq+1 grad_div_mag_h(i,j) =sqrt((0.5*(div_xx_dx(I,j) + div_xx_dx(I-1,j)))**2 + & (0.5 * (div_xx_dy(i,J) + div_xx_dy(i,J-1)))**2) enddo ; enddo - do J=js-2,Jeq+1 ; do I=is-2,Ieq+1 + do J=js-1,Jeq ; do I=is-1,Ieq grad_div_mag_q(I,J) =sqrt((0.5*(div_xx_dx(I,j) + div_xx_dx(I,j+1)))**2 + & (0.5 * (div_xx_dy(i,J) + div_xx_dy(i+1,J)))**2) enddo ; enddo @@ -740,10 +740,10 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, do J=js-2,Jeq+1 ; do i=Isq-1,Ieq+2 div_xx_dy(i,J) = 0.0 enddo ; enddo - do j=Jsq-1,Jeq+2 ; do i=Isq-1,Ieq+2 + do j=Jsq,Jeq+1 ; do i=Isq,Ieq+1 grad_div_mag_h(i,j) = 0.0 enddo ; enddo - do J=js-2,Jeq+1 ; do I=is-2,Ieq+1 + do J=js-1,Jeq ; do I=is-1,Ieq grad_div_mag_q(I,J) = 0.0 enddo ; enddo From 32578013e14e5f96fc208672cf7bdb9e014c7a05 Mon Sep 17 00:00:00 2001 From: Gustavo Marques Date: Fri, 23 Aug 2019 13:49:56 -0600 Subject: [PATCH 11/72] Removes unneeded calls to pass_var and add calls to pass_vector --- src/parameterizations/lateral/MOM_hor_visc.F90 | 12 +++--------- 1 file changed, 3 insertions(+), 9 deletions(-) diff --git a/src/parameterizations/lateral/MOM_hor_visc.F90 b/src/parameterizations/lateral/MOM_hor_visc.F90 index 8ad3e7f212..7b1d7e00e2 100644 --- a/src/parameterizations/lateral/MOM_hor_visc.F90 +++ b/src/parameterizations/lateral/MOM_hor_visc.F90 @@ -5,7 +5,7 @@ module MOM_hor_visc use MOM_diag_mediator, only : post_data, register_diag_field, safe_alloc_ptr use MOM_diag_mediator, only : diag_ctrl, time_type -use MOM_domains, only : pass_var, CORNER, pass_vector +use MOM_domains, only : pass_var, CORNER, pass_vector, AGRID, BGRID_NE use MOM_error_handler, only : MOM_error, FATAL, WARNING, is_root_pe use MOM_file_parser, only : get_param, log_version, param_file_type use MOM_grid, only : ocean_grid_type @@ -411,8 +411,7 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, G%IdxCv(i,J-1) * vbtav(i,J-1)) enddo; enddo - call pass_var(dudx_bt, G%Domain, complete=.true.) - call pass_var(dvdy_bt, G%Domain, complete=.true.) + call pass_vector(dudx_bt, dvdy_bt, G%Domain, stagger=BGRID_NE) do j=Jsq,Jeq+1 ; do i=Isq,Ieq+1 sh_xx_bt(i,j) = dudx_bt(i,j) - dvdy_bt(i,j) @@ -426,8 +425,7 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, - ubtav(I,j)*G%IdxCu(I,j)) enddo ; enddo - call pass_var(dvdx_bt, G%Domain, position=CORNER, complete=.true.) - call pass_var(dudy_bt, G%Domain, position=CORNER, complete=.true.) + call pass_vector(dvdx_bt, dudy_bt, G%Domain, stagger=AGRID) if (CS%no_slip) then do J=js-1,Jeq ; do I=is-1,Ieq @@ -710,8 +708,6 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, (h(i,j,k) + GV%H_subroundoff) enddo ; enddo - call pass_var(div_xx, G%Domain, complete=.true.) - ! Divergence gradient do j=Jsq,Jeq+1 ; do I=Isq-1,Ieq+1 div_xx_dx(I,j) = G%IdxCu(I,j)*(div_xx(i+1,j) - div_xx(i,j)) @@ -720,8 +716,6 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, div_xx_dy(i,J) = G%IdyCv(i,J)*(div_xx(i,j+1) - div_xx(i,j)) enddo ; enddo - call pass_vector(div_xx_dx, div_xx_dy, G%Domain) - ! Magnitude of divergence gradient do j=Jsq,Jeq+1 ; do i=Isq,Ieq+1 grad_div_mag_h(i,j) =sqrt((0.5*(div_xx_dx(I,j) + div_xx_dx(I-1,j)))**2 + & From b339108f879b842a71ca19f6fe32ceda1af66210 Mon Sep 17 00:00:00 2001 From: Gustavo Marques Date: Fri, 23 Aug 2019 13:56:35 -0600 Subject: [PATCH 12/72] Groups terms for rotational invariance and deletes beta_h and beta_q (unused) --- src/parameterizations/lateral/MOM_hor_visc.F90 | 17 ++++------------- 1 file changed, 4 insertions(+), 13 deletions(-) diff --git a/src/parameterizations/lateral/MOM_hor_visc.F90 b/src/parameterizations/lateral/MOM_hor_visc.F90 index 7b1d7e00e2..fe1c069257 100644 --- a/src/parameterizations/lateral/MOM_hor_visc.F90 +++ b/src/parameterizations/lateral/MOM_hor_visc.F90 @@ -243,7 +243,6 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, FrictWorkIntz, & ! depth integrated energy dissipated by lateral friction [W m-2] Leith_Kh_h, & ! Leith Laplacian viscosity at h-points [m2 s-1] Leith_Ah_h, & ! Leith bi-harmonic viscosity at h-points [m4 s-1] - beta_h, & ! Gradient of planetary vorticity at h-points [m-1 s-1] grad_vort_mag_h, & ! Magnitude of vorticity gradient at h-points [m-1 s-1] grad_vort_mag_h_2d, & ! Magnitude of 2d vorticity gradient at h-points [m-1 s-1] grad_div_mag_h, & ! Magnitude of divergence gradient at h-points [m-1 s-1] @@ -264,7 +263,6 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, vort_xy, & ! Vertical vorticity (dv/dx - du/dy) including metric terms [s-1] Leith_Kh_q, & ! Leith Laplacian viscosity at q-points [m2 s-1] Leith_Ah_q, & ! Leith bi-harmonic viscosity at q-points [m4 s-1] - beta_q, & ! Gradient of planetary vorticity at q-points [m-1 s-1] grad_vort_mag_q, & ! Magnitude of vorticity gradient at q-points [m-1 s-1] grad_vort_mag_q_2d, & ! Magnitude of 2d vorticity gradient at q-points [m-1 s-1] grad_div_mag_q, & ! Magnitude of divergence gradient at q-points [m-1 s-1] @@ -442,14 +440,14 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, do j=Jsq-1,Jeq+2 ; do i=Isq-1,Ieq+2 grad_vel_mag_bt_h(i,j) = boundary_mask(i,j) * (dudx_bt(i,j)**2 + dvdy_bt(i,j)**2 + & - (0.25*(dvdx_bt(I,J)+dvdx_bt(I-1,J)+dvdx_bt(I,J-1)+dvdx_bt(I-1,J-1)) )**2 + & - (0.25*(dudy_bt(I,J)+dudy_bt(I-1,J)+dudy_bt(I,J-1)+dudy_bt(I-1,J-1)) )**2) + (0.25*((dvdx_bt(I,J)+dvdx_bt(I-1,J-1))+(dvdx_bt(I,J-1)+dvdx_bt(I-1,J)) )**2 + & + (0.25*((dudy_bt(I,J)+dudy_bt(I-1,J-1))+(dudy_bt(I,J-1)+dudy_bt(I-1,J)) )**2) enddo ; enddo do J=js-2,Jeq+1 ; do I=is-2,Ieq+1 grad_vel_mag_bt_q(I,J) = boundary_mask(i,j) * (dvdx_bt(i,j)**2 + dudy_bt(i,j)**2 + & - (0.25*(dudx_bt(i,j)+dudx_bt(i+1,j)+dudx_bt(i,j+1)+dudx_bt(i+1,j+1)))**2 + & - (0.25*(dvdy_bt(i,j)+dvdy_bt(i+1,j)+dvdy_bt(i,j+1)+dvdy_bt(i+1,j+1)) )**2) + (0.25*(dudx_bt(i,j)+dudx_bt(i+1,j+1))+(dudx_bt(i,j+1)+dudx_bt(i+1,j)))**2 + & + (0.25*(dvdy_bt(i,j)+dvdy_bt(i+1,j+1))+(dvdy_bt(i,j+1)+dvdy_bt(i+1,j)))**2) enddo ; enddo endif ! use_GME @@ -745,13 +743,6 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, ! Add in beta for the Leith viscosity if (CS%use_beta_in_Leith) then - do j=Jsq-1,Jeq+2 ; do i=Isq-1,Ieq+2 - beta_h(i,j) = sqrt( G%dF_dx(i,j)**2 + G%dF_dy(i,j)**2 ) - enddo; enddo - do J=js-2,Jeq+1 ; do I=is-2,Ieq+1 - beta_q(I,J) = sqrt( (0.25*(G%dF_dx(i,j)+G%dF_dx(i+1,j)+G%dF_dx(i,j+1)+G%dF_dx(i+1,j+1))**2) + & - (0.25*(G%dF_dy(i,j)+G%dF_dy(i+1,j)+G%dF_dy(i,j+1)+G%dF_dy(i+1,j+1))**2) ) - enddo ; enddo do J=js-2,Jeq+1 ; do i=is-1,Ieq+1 vort_xy_dx(i,J) = vort_xy_dx(i,J) + 0.5 * ( G%dF_dx(i,j) + G%dF_dx(i,j+1)) From 0aeec9de17270c86f19ac2c37bf90e48c7fe182f Mon Sep 17 00:00:00 2001 From: Gustavo Marques Date: Mon, 26 Aug 2019 15:15:03 -0600 Subject: [PATCH 13/72] Adds correct calculation of GME at q points --- .../lateral/MOM_hor_visc.F90 | 216 +++++++++--------- 1 file changed, 109 insertions(+), 107 deletions(-) diff --git a/src/parameterizations/lateral/MOM_hor_visc.F90 b/src/parameterizations/lateral/MOM_hor_visc.F90 index fe1c069257..44131952a1 100644 --- a/src/parameterizations/lateral/MOM_hor_visc.F90 +++ b/src/parameterizations/lateral/MOM_hor_visc.F90 @@ -250,7 +250,7 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, grad_vel_mag_h, & ! Magnitude of the velocity gradient tensor squared at h-points [s-2] grad_vel_mag_bt_h, & ! Magnitude of the barotropic velocity gradient tensor squared at h-points [s-2] grad_d2vel_mag_h, & ! Magnitude of the Laplacian of the velocity vector, squared [m-2 s-2] - boundary_mask ! A mask that zeroes out cells with at least one land edge + boundary_mask_h ! A mask that zeroes out cells with at least one land edge real, dimension(SZIB_(G),SZJB_(G)) :: & dvdx, dudy, & ! components in the shearing strain [s-1] @@ -269,13 +269,15 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, grad_vel_mag_q, & ! Magnitude of the velocity gradient tensor squared at q-points [s-2] hq, & ! harmonic mean of the harmonic means of the u- & v point thicknesses [H ~> m or kg m-2] ! This form guarantees that hq/hu < 4. - grad_vel_mag_bt_q ! Magnitude of the barotropic velocity gradient tensor squared at q-points [s-2] + grad_vel_mag_bt_q, & ! Magnitude of the barotropic velocity gradient tensor squared at q-points [s-2] + boundary_mask_q ! A mask that zeroes out cells with at least one land edge real, dimension(SZIB_(G),SZJB_(G),SZK_(G)) :: & Ah_q, & ! biharmonic viscosity at corner points [m4 s-1] Kh_q, & ! Laplacian viscosity at corner points [m2 s-1] vort_xy_q, & ! vertical vorticity at corner points [s-1] - GME_coeff_q !< GME coeff. at q-points [m2 s-1] + GME_coeff_q, & !< GME coeff. at q-points [m2 s-1] + max_diss_rate_q ! maximum possible energy dissipated by lateral friction [m2 s-3] real, dimension(SZIB_(G),SZJ_(G),SZK_(G)+1) :: & KH_u_GME !< interface height diffusivities in u-columns [m2 s-1] @@ -285,7 +287,7 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, Ah_h, & ! biharmonic viscosity at thickness points [m4 s-1] Kh_h, & ! Laplacian viscosity at thickness points [m2 s-1] diss_rate, & ! MKE dissipated by parameterized shear production [m2 s-3] - max_diss_rate, & ! maximum possible energy dissipated by lateral friction [m2 s-3] + max_diss_rate_h, & ! maximum possible energy dissipated by lateral friction [m2 s-3] target_diss_rate_GME, & ! the maximum theoretical dissipation plus the amount spuriously dissipated ! by friction [m2 s-3] FrictWork, & ! work done by MKE dissipation mechanisms [W m-2] @@ -293,7 +295,6 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, FrictWorkMax, & ! maximum possible work done by MKE dissipation mechanisms [W m-2] FrictWork_GME, & ! work done by GME [W m-2] div_xx_h ! horizontal divergence [s-1] - !real, dimension(SZI_(G),SZJ_(G),SZK_(G)+1) :: & real, dimension(SZI_(G),SZJ_(G),SZK_(G)) :: & KH_t_GME, & !< interface height diffusivities in t-columns [m2 s-1] GME_coeff_h !< GME coeff. at h-points [m2 s-1] @@ -312,8 +313,6 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, real :: hu, hv ! Thicknesses interpolated by arithmetic means to corner ! points; these are first interpolated to u or v velocity ! points where masks are applied [H ~> m or kg m-2]. -! real :: hq ! harmonic mean of the harmonic means of the u- & v- -! ! point thicknesses, in H; This form guarantees that hq/hu < 4. real :: h_neglect ! thickness so small it can be lost in roundoff and so neglected [H ~> m or kg m-2] real :: h_neglect3 ! h_neglect^3 [H3 ~> m3 or kg3 m-6] real :: hrat_min ! minimum thicknesses at the 4 neighboring @@ -382,10 +381,17 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, use_MEKE_Ku = associated(MEKE%Ku) use_MEKE_Au = associated(MEKE%Au) - do j=js,je ; do i=is,ie - boundary_mask(i,j) = (G%mask2dCu(I,j) * G%mask2dCv(i,J) * G%mask2dCu(I-1,j) * G%mask2dCv(i,J-1)) + do j = G%jsc, G%jec ; do i = G%isc, G%iec + boundary_mask_h(i,j) = (G%mask2dCu(I,j) * G%mask2dCv(i,J) * G%mask2dCu(I-1,j) * G%mask2dCv(i,J-1)) enddo ; enddo + do J = G%JscB, G%JecB ; do I = G%IscB, G%IecB + boundary_mask_q(I,J) = (G%mask2dCv(i,J) * G%mask2dCv(i+1,J) * G%mask2dCu(I,j) * G%mask2dCu(I,j-1)) + enddo; enddo + +! call pass_var(boundary_mask_h, G%Domain, complete=.true.) + + if (CS%use_GME) then ! GME tapers off above this depth H0 = 1000.0 @@ -411,6 +417,7 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, call pass_vector(dudx_bt, dvdy_bt, G%Domain, stagger=BGRID_NE) + do j=Jsq,Jeq+1 ; do i=Isq,Ieq+1 sh_xx_bt(i,j) = dudx_bt(i,j) - dvdy_bt(i,j) enddo ; enddo @@ -435,19 +442,16 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, enddo ; enddo endif - ! Get thickness diffusivity for use in GME -! call thickness_diffuse_get_KH(thickness_diffuse, KH_u_GME, KH_v_GME, G) - do j=Jsq-1,Jeq+2 ; do i=Isq-1,Ieq+2 - grad_vel_mag_bt_h(i,j) = boundary_mask(i,j) * (dudx_bt(i,j)**2 + dvdy_bt(i,j)**2 + & - (0.25*((dvdx_bt(I,J)+dvdx_bt(I-1,J-1))+(dvdx_bt(I,J-1)+dvdx_bt(I-1,J)) )**2 + & - (0.25*((dudy_bt(I,J)+dudy_bt(I-1,J-1))+(dudy_bt(I,J-1)+dudy_bt(I-1,J)) )**2) + grad_vel_mag_bt_h(i,j) = boundary_mask_h(i,j) * (dudx_bt(i,j)**2 + dvdy_bt(i,j)**2 + & + (0.25*((dvdx_bt(I,J)+dvdx_bt(I-1,J-1))+(dvdx_bt(I,J-1)+dvdx_bt(I-1,J))))**2 + & + (0.25*((dudy_bt(I,J)+dudy_bt(I-1,J-1))+(dudy_bt(I,J-1)+dudy_bt(I-1,J))))**2) enddo ; enddo do J=js-2,Jeq+1 ; do I=is-2,Ieq+1 - grad_vel_mag_bt_q(I,J) = boundary_mask(i,j) * (dvdx_bt(i,j)**2 + dudy_bt(i,j)**2 + & - (0.25*(dudx_bt(i,j)+dudx_bt(i+1,j+1))+(dudx_bt(i,j+1)+dudx_bt(i+1,j)))**2 + & - (0.25*(dvdy_bt(i,j)+dvdy_bt(i+1,j+1))+(dvdy_bt(i,j+1)+dvdy_bt(i+1,j)))**2) + grad_vel_mag_bt_q(I,J) = boundary_mask_h(I,J) * (dvdx_bt(i,j)**2 + dudy_bt(i,j)**2 + & + (0.25*((dudx_bt(i,j)+dudx_bt(i+1,j+1))+(dudx_bt(i,j+1)+dudx_bt(i+1,j))))**2 + & + (0.25*((dvdy_bt(i,j)+dvdy_bt(i+1,j+1))+(dvdy_bt(i,j+1)+dvdy_bt(i+1,j))))**2) enddo ; enddo endif ! use_GME @@ -555,6 +559,36 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, enddo endif endif + +! if (CS%use_GME) then +! call pass_var(dudx, G%Domain, complete=.true.) +! call pass_var(dvdy, G%Domain, complete=.true.) +! call pass_var(dvdx, G%Domain, position=CORNER, complete=.true.) +! call pass_var(dudy, G%Domain, position=CORNER, complete=.true.) +!! call pass_var(MEKE%MEKE, G%Domain, complete=.true.) +! + +! do j=Jsq-1,Jeq+2 ; do i=Isq-1,Ieq+2 +! do J=Jsq,Jeq+1 ; do i=Isq,Ieq+1 +! do j = js, je ; do i = is, ie +! grad_vel_mag_h(i,j) = boundary_mask_h(i,j) * (dudx(i,j)**2 + dvdy(i,j)**2 + & +! (0.25*((dvdx(I,J)+dvdx(I-1,J-1))+(dvdx(I,J-1)+dvdx(I-1,J))))**2 + & +! (0.25*((dudy(I,J)+dudy(I-1,J-1))+(dudy(I,J-1)+dudy(I-1,J))))**2) +! +! max_diss_rate_h(i,j,k) = 2.0 !*MEKE%MEKE(i,j) * sqrt(grad_vel_mag_h(i,j)) +! enddo ; enddo +! +! do J = G%JscB, G%JecB ; do I = G%IscB, G%IecB +! grad_vel_mag_q(I,J) = boundary_mask_h(I,J) * (dudx(i,j)**2 + dvdy(i,j)**2 + & +! (0.25*((dvdx(I,J)+dvdx(I-1,J-1))+(dvdx(I,J-1)+dvdx(I-1,J))))**2 + & +! (0.25*((dudy(I,J)+dudy(I-1,J-1))+(dudy(I,J-1)+dudy(I-1,J))))**2) +! +! max_diss_rate_q(I,J,k) = 0.5*(MEKE%MEKE(i,j)+MEKE%MEKE(i+1,j)+ & +! MEKE%MEKE(i,j+1)+MEKE%MEKE(i+1,j+1)) * sqrt(grad_vel_mag_q(I,J)) +! enddo ; enddo +! endif + + if (OBC%segment(n)%direction == OBC_DIRECTION_N) then ! There are extra wide halos here to accommodate the cross-corner-point ! OBC projections, but they might not be necessary if the accelerations @@ -659,25 +693,25 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, ! Note this a simple re-calculation of shearing components using the same discretization. ! We will consider using a circulation based calculation of vorticity later. ! Also note this will need OBC boundary conditions re-applied... - do J=js-2,Jeq+1 ; do I=is-2,Ieq+1 - DY_dxBu = G%dyBu(I,J) * G%IdxBu(I,J) - dvdx(I,J) = DY_dxBu * (v(i+1,J,k) * G%IdyCv(i+1,J) - v(i,J,k) * G%IdyCv(i,J)) - DX_dyBu = G%dxBu(I,J) * G%IdyBu(I,J) - dudy(I,J) = DX_dyBu * (u(I,j+1,k) * G%IdxCu(I,j+1) - u(I,j,k) * G%IdxCu(I,j)) - enddo ; enddo +! do J=js-2,Jeq+1 ; do I=is-2,Ieq+1 +! DY_dxBu = G%dyBu(I,J) * G%IdxBu(I,J) +! dvdx(I,J) = DY_dxBu * (v(i+1,J,k) * G%IdyCv(i+1,J) - v(i,J,k) * G%IdyCv(i,J)) +! DX_dyBu = G%dxBu(I,J) * G%IdyBu(I,J) +! dudy(I,J) = DX_dyBu * (u(I,j+1,k) * G%IdxCu(I,j+1) - u(I,j,k) * G%IdxCu(I,j)) +! enddo ; enddo ! Vorticity if (CS%no_slip) then do J=js-2,Jeq+1 ; do I=is-2,Ieq+1 vort_xy(I,J) = (2.0-G%mask2dBu(I,J)) * ( dvdx(I,J) - dudy(I,J) ) - dudy(I,J) = (2.0-G%mask2dBu(I,J)) * dudy(I,J) - dvdx(I,J) = (2.0-G%mask2dBu(I,J)) * dvdx(I,J) +! dudy(I,J) = (2.0-G%mask2dBu(I,J)) * dudy(I,J) +! dvdx(I,J) = (2.0-G%mask2dBu(I,J)) * dvdx(I,J) enddo ; enddo else do J=js-2,Jeq+1 ; do I=is-2,Ieq+1 vort_xy(I,J) = G%mask2dBu(I,J) * ( dvdx(I,J) - dudy(I,J) ) - dudy(I,J) = G%mask2dBu(I,J) * dudy(I,J) - dvdx(I,J) = G%mask2dBu(I,J) * dvdx(I,J) +! dudy(I,J) = G%mask2dBu(I,J) * dudy(I,J) +! dvdx(I,J) = G%mask2dBu(I,J) * dvdx(I,J) enddo ; enddo endif @@ -822,7 +856,6 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, visc_bound_rem = 0.0 Kh = hrat_min*CS%Kh_Max_xx(i,j) else - !visc_bound_rem = 1.0 - abs(Kh) / (hrat_min*CS%Kh_Max_xx(i,j)) visc_bound_rem = 1.0 - Kh / (hrat_min*CS%Kh_Max_xx(i,j)) endif endif @@ -988,7 +1021,6 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, visc_bound_rem = 0.0 Kh = hrat_min*CS%Kh_Max_xy(I,J) elseif (CS%Kh_Max_xy(I,J)>0.) then - !visc_bound_rem = 1.0 - abs(Kh) / (hrat_min*CS%Kh_Max_xy(I,J)) visc_bound_rem = 1.0 - Kh / (hrat_min*CS%Kh_Max_xy(I,J)) endif endif @@ -1051,85 +1083,46 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, enddo ; enddo - if (find_FrictWork) then - if (CS%biharmonic) call pass_vector(u0, v0, G%Domain) - call pass_var(dudx, G%Domain, complete=.true.) - call pass_var(dvdy, G%Domain, complete=.true.) - call pass_var(dvdx, G%Domain, position=CORNER, complete=.true.) - call pass_var(dudy, G%Domain, position=CORNER, complete=.true.) + if (CS%use_GME) then +! call pass_var(dudx, G%Domain, complete=.true.) +! call pass_var(dvdy, G%Domain, complete=.true.) +! call pass_var(dvdx, G%Domain, position=CORNER, complete=.true.) +! call pass_var(dudy, G%Domain, position=CORNER, complete=.true.) - if (CS%Laplacian) then - do j=js,je ; do i=is,ie - grad_vel_mag_h(i,j) = boundary_mask(i,j) * (dudx(i,j)**2 + dvdy(i,j)**2 + & - (0.25*(dvdx(I,J)+dvdx(I-1,J)+dvdx(I,J-1)+dvdx(I-1,J-1)) )**2 + & - (0.25*(dudy(I,J)+dudy(I-1,J)+dudy(I,J-1)+dudy(I-1,J-1)) )**2) - enddo ; enddo - else - do j=js,je ; do i=is,ie - grad_vel_mag_h(i,j) = 0.0 - enddo ; enddo - endif - if (CS%biharmonic) then - do j=js,je ; do i=is,ie - grad_d2vel_mag_h(i,j) = boundary_mask(i,j) * ((0.5*(u0(I,j) + u0(I-1,j)))**2 + & - (0.5*(v0(i,J) + v0(i,J-1)))**2) - enddo ; enddo - else - do j=js,je ; do i=is,ie - grad_d2vel_mag_h(i,j) = 0.0 - enddo ; enddo - endif + do j = js, je ; do i = is, ie + grad_vel_mag_h(i,j) = boundary_mask_h(i,j) * (dudx(i,j)**2 + dvdy(i,j)**2 + & + (0.25*((dvdx(I,J)+dvdx(I-1,J-1))+(dvdx(I,J-1)+dvdx(I-1,J))))**2 + & + (0.25*((dudy(I,J)+dudy(I-1,J-1))+(dudy(I,J-1)+dudy(I-1,J))))**2) - do j=js,je ; do i=is,ie - ! Diagnose -Kh * |del u|^2 - Ah * |del^2 u|^2 - diss_rate(i,j,k) = -Kh_h(i,j,k) * grad_vel_mag_h(i,j) - & - Ah_h(i,j,k) * grad_d2vel_mag_h(i,j) - - if (associated(MEKE)) then ; if (associated(MEKE%mom_src)) then - ! This is the maximum possible amount of energy that can be converted - ! per unit time, according to theory (multiplied by h) - max_diss_rate(i,j,k) = 2.0*MEKE%MEKE(i,j) * sqrt(grad_vel_mag_h(i,j)) - FrictWork_diss(i,j,k) = diss_rate(i,j,k) * h(i,j,k) * GV%H_to_kg_m2 - FrictWorkMax(i,j,k) = -max_diss_rate(i,j,k) * h(i,j,k) * GV%H_to_kg_m2 - - ! Determine how much work GME needs to do to reach the "target" ratio between - ! the amount of work actually done and the maximum allowed by theory. Note that - ! we need to add the FrictWork done by the dissipation operators, since this work - ! is done only for numerical stability and is therefore spurious - if (CS%use_GME) then - target_diss_rate_GME(i,j,k) = FWfrac * max_diss_rate(i,j,k) - diss_rate(i,j,k) - endif + max_diss_rate_h(i,j,k) = 2.0 * MEKE%MEKE(i,j) * sqrt(grad_vel_mag_h(i,j)) + enddo ; enddo - else - FrictWork_diss(i,j,k) = diss_rate(i,j,k) * h(i,j,k) * GV%H_to_kg_m2 - endif ; endif + do J = G%JscB, G%JecB ; do I = G%IscB, G%IecB + grad_vel_mag_q(I,J) = boundary_mask_q(I,J) * (dudx(i,j)**2 + dvdy(i,j)**2 + & + (0.25*((dvdx(I,J)+dvdx(I-1,J-1))+(dvdx(I,J-1)+dvdx(I-1,J))))**2 + & + (0.25*((dudy(I,J)+dudy(I-1,J-1))+(dudy(I,J-1)+dudy(I-1,J))))**2) - enddo ; enddo - endif + max_diss_rate_q(I,J,k) = 0.5*(MEKE%MEKE(i,j)+MEKE%MEKE(i+1,j)+ & + MEKE%MEKE(i,j+1)+MEKE%MEKE(i+1,j+1)) * sqrt(grad_vel_mag_q(I,J)) + enddo ; enddo + endif if (CS%use_GME) then - if (.not. (associated(MEKE))) call MOM_error(FATAL, & - "MEKE must be enabled for GME to be used.") - do J=Jsq,Jeq+1 ; do i=Isq,Ieq+1 - - if ((max_diss_rate(i,j,k) > 0) .and. (grad_vel_mag_bt_h(i,j)>0) ) then - GME_coeff = (MIN(G%bathyT(i,j)/H0,1.0)**2) * FWfrac*max_diss_rate(i,j,k) / grad_vel_mag_bt_h(i,j) -! GME_coeff = (MIN(G%bathyT(i,j)/H0,1.0)**2) * FWfrac*target_diss_rate_GME(i,j,k) / grad_vel_mag_bt_h(i,j) + if ((grad_vel_mag_bt_h(i,j)>0) .and. (max_diss_rate_h(i,j,k)>0)) then + GME_coeff = (MIN(G%bathyT(i,j)/H0,1.0)**2) * FWfrac*max_diss_rate_h(i,j,k) / grad_vel_mag_bt_h(i,j) else - GME_coeff = 0.0 + GME_coeff = 1.0 endif ! apply mask - GME_coeff = GME_coeff * boundary_mask(i,j) - + GME_coeff = GME_coeff * boundary_mask_h(i,j) GME_coeff = MIN(GME_coeff, GME_coeff_limiter) if ((CS%id_GME_coeff_h>0) .or. find_FrictWork) GME_coeff_h(i,j,k) = GME_coeff - str_xx_GME(i,j) = GME_coeff * sh_xx_bt(i,j) enddo ; enddo @@ -1137,16 +1130,14 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, do J=js-1,Jeq ; do I=is-1,Ieq - if ((max_diss_rate(i,j,k) > 0) .and. (grad_vel_mag_bt_q(i,j)>0) ) then - GME_coeff = (MIN(G%bathyT(i,j)/H0,1.0)**2) * FWfrac*max_diss_rate(i,j,k) / grad_vel_mag_bt_q(I,J) -! GME_coeff = (MIN(G%bathyT(i,j)/H0,1.0)**2) * FWfrac*target_diss_rate_GME(i,j,k) / grad_vel_mag_bt_q(I,J) + if ((grad_vel_mag_bt_q(I,J)>0) .and. (max_diss_rate_q(I,J,k)>0)) then + GME_coeff = (MIN(G%bathyT(i,j)/H0,1.0)**2) * FWfrac*max_diss_rate_q(I,J,k) / grad_vel_mag_bt_q(I,J) else GME_coeff = 0.0 endif ! apply mask - GME_coeff = GME_coeff * boundary_mask(i,j) - + GME_coeff = GME_coeff * boundary_mask_q(I,J) GME_coeff = MIN(GME_coeff, GME_coeff_limiter) if (CS%id_GME_coeff_q>0) GME_coeff_q(I,J,k) = GME_coeff @@ -1303,16 +1294,16 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, enddo ; enddo endif ! MEKE%backscatter - if (CS%use_GME) then - do j=js,je ; do i=is,ie - ! MEKE%mom_src now is sign definite because it only uses the dissipation - MEKE%mom_src(i,j) = MEKE%mom_src(i,j) + MAX(FrictWork_diss(i,j,k), FrictWorkMax(i,j,k)) - enddo ; enddo - else - do j=js,je ; do i=is,ie - MEKE%mom_src(i,j) = MEKE%mom_src(i,j) + FrictWork(i,j,k) - enddo ; enddo - endif ! CS%use_GME +! if (CS%use_GME) then +! do j=js,je ; do i=is,ie +! ! MEKE%mom_src now is sign definite because it only uses the dissipation +! MEKE%mom_src(i,j) = MEKE%mom_src(i,j) + MAX(FrictWork_diss(i,j,k), FrictWorkMax(i,j,k)) +! enddo ; enddo +! else + do j=js,je ; do i=is,ie + MEKE%mom_src(i,j) = MEKE%mom_src(i,j) + FrictWork(i,j,k) + enddo ; enddo +! endif ! CS%use_GME if (CS%use_GME .and. associated(MEKE)) then if (associated(MEKE%GME_snk)) then @@ -1405,6 +1396,9 @@ subroutine hor_visc_init(Time, G, US, param_file, diag, CS) ! valid parameters. logical :: split ! If true, use the split time stepping scheme. ! If false and USE_GME = True, issue a FATAL error. + logical :: use_MEKE ! If true, use the MEKE module for calculating eddy kinetic energy. + ! If false and USE_GME = True, issue a FATAL error. + character(len=64) :: inputdir, filename real :: deg2rad ! Converts degrees to radians real :: slat_fn ! sin(lat)**Kh_pwr_of_sine @@ -1659,6 +1653,14 @@ subroutine hor_visc_init(Time, G, US, param_file, diag, CS) do_not_log=.true.) if (.not. split) call MOM_error(FATAL,"ERROR: Currently, USE_GME = True "// & "cannot be used with SPLIT=False.") + + call get_param(param_file, mdl, "USE_MEKE", use_MEKE, & + "If true, turns on the MEKE scheme which calculates\n"// & + "a sub-grid mesoscale eddy kinetic energy budget.", & + default=.false.) + + if (.not. use_MEKE) call MOM_error(FATAL,"ERROR: Currently, USE_GME = True "// & + "cannot be used with USE_MEKE=False.") endif if (CS%bound_Kh .or. CS%bound_Ah .or. CS%better_bound_Kh .or. CS%better_bound_Ah) & From fa773cdefdcd3eb47b6a9f0e9d085eb91d83b1a3 Mon Sep 17 00:00:00 2001 From: Gustavo Marques Date: Mon, 26 Aug 2019 15:21:35 -0600 Subject: [PATCH 14/72] Created new variables dvdx3/dudy3 for shearing strain on the Laplacian --- src/parameterizations/lateral/MOM_hor_visc.F90 | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/src/parameterizations/lateral/MOM_hor_visc.F90 b/src/parameterizations/lateral/MOM_hor_visc.F90 index 44131952a1..b83ddd4432 100644 --- a/src/parameterizations/lateral/MOM_hor_visc.F90 +++ b/src/parameterizations/lateral/MOM_hor_visc.F90 @@ -254,6 +254,7 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, real, dimension(SZIB_(G),SZJB_(G)) :: & dvdx, dudy, & ! components in the shearing strain [s-1] + dvdx3, dudy3, & ! components in the shearing strain on the Laplacian [m-2 s-1] dvdx_bt, dudy_bt, & ! components in the barotropic shearing strain [s-1] sh_xy, & ! horizontal shearing strain (du/dy + dv/dx) including metric terms [s-1] sh_xy_bt, & ! barotropic horizontal shearing strain (du/dy + dv/dx) inc. metric terms [s-1] @@ -921,8 +922,8 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, if (CS%biharmonic) then ! Gradient of Laplacian, for use in bi-harmonic term do J=js-1,Jeq ; do I=is-1,Ieq - dvdx(I,J) = CS%DY_dxBu(I,J)*(v0(i+1,J)*G%IdyCv(i+1,J) - v0(i,J)*G%IdyCv(i,J)) - dudy(I,J) = CS%DX_dyBu(I,J)*(u0(I,j+1)*G%IdxCu(I,j+1) - u0(I,j)*G%IdxCu(I,j)) + dvdx3(I,J) = CS%DY_dxBu(I,J)*(v0(i+1,J)*G%IdyCv(i+1,J) - v0(i,J)*G%IdyCv(i,J)) + dudy3(I,J) = CS%DX_dyBu(I,J)*(u0(I,j+1)*G%IdxCu(I,j+1) - u0(I,j)*G%IdxCu(I,j)) enddo ; enddo ! Adjust contributions to shearing strain on open boundaries. if (apply_OBC) then ; if (OBC%zero_strain .or. OBC%freeslip_strain) then @@ -931,17 +932,17 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, if (OBC%segment(n)%is_N_or_S .and. (J >= js-1) .and. (J <= Jeq)) then do I=OBC%segment(n)%HI%IsdB,OBC%segment(n)%HI%IedB if (OBC%zero_strain) then - dvdx(I,J) = 0. ; dudy(I,J) = 0. + dvdx3(I,J) = 0. ; dudy3(I,J) = 0. elseif (OBC%freeslip_strain) then - dudy(I,J) = 0. + dudy3(I,J) = 0. endif enddo elseif (OBC%segment(n)%is_E_or_W .and. (I >= is-1) .and. (I <= Ieq)) then do J=OBC%segment(n)%HI%JsdB,OBC%segment(n)%HI%JedB if (OBC%zero_strain) then - dvdx(I,J) = 0. ; dudy(I,J) = 0. + dvdx3(I,J) = 0. ; dudy3(I,J) = 0. elseif (OBC%freeslip_strain) then - dvdx(I,J) = 0. + dvdx3(I,J) = 0. endif enddo endif @@ -1072,10 +1073,10 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, if (CS%id_Ah_q>0) Ah_q(I,J,k) = Ah - str_xy(I,J) = str_xy(I,J) + Ah * ( dvdx(I,J) + dudy(I,J) ) + str_xy(I,J) = str_xy(I,J) + Ah * ( dvdx3(I,J) + dudy3(I,J) ) ! Keep a copy of the biharmonic contribution for backscatter parameterization - bhstr_xy(I,J) = Ah * ( dvdx(I,J) + dudy(I,J) ) * & + bhstr_xy(I,J) = Ah * ( dvdx3(I,J) + dudy3(I,J) ) * & (hq(I,J) * G%mask2dBu(I,J) * CS%reduction_xy(I,J)) endif ! biharmonic From 2ac12ce6a5f609532eb519fabd18092c06cc2ef3 Mon Sep 17 00:00:00 2001 From: Gustavo Marques Date: Mon, 26 Aug 2019 15:24:33 -0600 Subject: [PATCH 15/72] Deleting comments --- .../lateral/MOM_hor_visc.F90 | 55 ------------------- 1 file changed, 55 deletions(-) diff --git a/src/parameterizations/lateral/MOM_hor_visc.F90 b/src/parameterizations/lateral/MOM_hor_visc.F90 index b83ddd4432..d4fa977cb9 100644 --- a/src/parameterizations/lateral/MOM_hor_visc.F90 +++ b/src/parameterizations/lateral/MOM_hor_visc.F90 @@ -561,34 +561,6 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, endif endif -! if (CS%use_GME) then -! call pass_var(dudx, G%Domain, complete=.true.) -! call pass_var(dvdy, G%Domain, complete=.true.) -! call pass_var(dvdx, G%Domain, position=CORNER, complete=.true.) -! call pass_var(dudy, G%Domain, position=CORNER, complete=.true.) -!! call pass_var(MEKE%MEKE, G%Domain, complete=.true.) -! - -! do j=Jsq-1,Jeq+2 ; do i=Isq-1,Ieq+2 -! do J=Jsq,Jeq+1 ; do i=Isq,Ieq+1 -! do j = js, je ; do i = is, ie -! grad_vel_mag_h(i,j) = boundary_mask_h(i,j) * (dudx(i,j)**2 + dvdy(i,j)**2 + & -! (0.25*((dvdx(I,J)+dvdx(I-1,J-1))+(dvdx(I,J-1)+dvdx(I-1,J))))**2 + & -! (0.25*((dudy(I,J)+dudy(I-1,J-1))+(dudy(I,J-1)+dudy(I-1,J))))**2) -! -! max_diss_rate_h(i,j,k) = 2.0 !*MEKE%MEKE(i,j) * sqrt(grad_vel_mag_h(i,j)) -! enddo ; enddo -! -! do J = G%JscB, G%JecB ; do I = G%IscB, G%IecB -! grad_vel_mag_q(I,J) = boundary_mask_h(I,J) * (dudx(i,j)**2 + dvdy(i,j)**2 + & -! (0.25*((dvdx(I,J)+dvdx(I-1,J-1))+(dvdx(I,J-1)+dvdx(I-1,J))))**2 + & -! (0.25*((dudy(I,J)+dudy(I-1,J-1))+(dudy(I,J-1)+dudy(I-1,J))))**2) -! -! max_diss_rate_q(I,J,k) = 0.5*(MEKE%MEKE(i,j)+MEKE%MEKE(i+1,j)+ & -! MEKE%MEKE(i,j+1)+MEKE%MEKE(i+1,j+1)) * sqrt(grad_vel_mag_q(I,J)) -! enddo ; enddo -! endif - if (OBC%segment(n)%direction == OBC_DIRECTION_N) then ! There are extra wide halos here to accommodate the cross-corner-point @@ -690,29 +662,14 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, if ((CS%Leith_Kh) .or. (CS%Leith_Ah)) then - ! Components for the vertical vorticity - ! Note this a simple re-calculation of shearing components using the same discretization. - ! We will consider using a circulation based calculation of vorticity later. - ! Also note this will need OBC boundary conditions re-applied... -! do J=js-2,Jeq+1 ; do I=is-2,Ieq+1 -! DY_dxBu = G%dyBu(I,J) * G%IdxBu(I,J) -! dvdx(I,J) = DY_dxBu * (v(i+1,J,k) * G%IdyCv(i+1,J) - v(i,J,k) * G%IdyCv(i,J)) -! DX_dyBu = G%dxBu(I,J) * G%IdyBu(I,J) -! dudy(I,J) = DX_dyBu * (u(I,j+1,k) * G%IdxCu(I,j+1) - u(I,j,k) * G%IdxCu(I,j)) -! enddo ; enddo - ! Vorticity if (CS%no_slip) then do J=js-2,Jeq+1 ; do I=is-2,Ieq+1 vort_xy(I,J) = (2.0-G%mask2dBu(I,J)) * ( dvdx(I,J) - dudy(I,J) ) -! dudy(I,J) = (2.0-G%mask2dBu(I,J)) * dudy(I,J) -! dvdx(I,J) = (2.0-G%mask2dBu(I,J)) * dvdx(I,J) enddo ; enddo else do J=js-2,Jeq+1 ; do I=is-2,Ieq+1 vort_xy(I,J) = G%mask2dBu(I,J) * ( dvdx(I,J) - dudy(I,J) ) -! dudy(I,J) = G%mask2dBu(I,J) * dudy(I,J) -! dvdx(I,J) = G%mask2dBu(I,J) * dvdx(I,J) enddo ; enddo endif @@ -1085,11 +1042,6 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, if (CS%use_GME) then -! call pass_var(dudx, G%Domain, complete=.true.) -! call pass_var(dvdy, G%Domain, complete=.true.) -! call pass_var(dvdx, G%Domain, position=CORNER, complete=.true.) -! call pass_var(dudy, G%Domain, position=CORNER, complete=.true.) - do j = js, je ; do i = is, ie grad_vel_mag_h(i,j) = boundary_mask_h(i,j) * (dudx(i,j)**2 + dvdy(i,j)**2 + & @@ -1295,16 +1247,9 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, enddo ; enddo endif ! MEKE%backscatter -! if (CS%use_GME) then -! do j=js,je ; do i=is,ie -! ! MEKE%mom_src now is sign definite because it only uses the dissipation -! MEKE%mom_src(i,j) = MEKE%mom_src(i,j) + MAX(FrictWork_diss(i,j,k), FrictWorkMax(i,j,k)) -! enddo ; enddo -! else do j=js,je ; do i=is,ie MEKE%mom_src(i,j) = MEKE%mom_src(i,j) + FrictWork(i,j,k) enddo ; enddo -! endif ! CS%use_GME if (CS%use_GME .and. associated(MEKE)) then if (associated(MEKE%GME_snk)) then From d29a4353fd10bab4e4b1215bb4d3df5b8b414a51 Mon Sep 17 00:00:00 2001 From: Gustavo Marques Date: Tue, 27 Aug 2019 11:05:23 -0600 Subject: [PATCH 16/72] Adds consistency check between mesh and mom6 grid Check for consistency of lat, lon and mask between mesh and mom6 grid --- config_src/nuopc_driver/mom_cap.F90 | 83 ++++++++++++++++++++++++++++- 1 file changed, 81 insertions(+), 2 deletions(-) diff --git a/config_src/nuopc_driver/mom_cap.F90 b/config_src/nuopc_driver/mom_cap.F90 index aa034e7d36..1d0b41b550 100644 --- a/config_src/nuopc_driver/mom_cap.F90 +++ b/config_src/nuopc_driver/mom_cap.F90 @@ -366,7 +366,7 @@ module MOM_cap_mod use ESMF, only: ESMF_METHOD_INITIALIZE, ESMF_MethodRemove, ESMF_State use ESMF, only: ESMF_LOGMSG_INFO, ESMF_RC_ARG_BAD, ESMF_VM, ESMF_Time use ESMF, only: ESMF_TimeInterval, ESMF_MAXSTR, ESMF_VMGetCurrent -use ESMF, only: ESMF_VMGet, ESMF_TimeGet, ESMF_TimeIntervalGet +use ESMF, only: ESMF_VMGet, ESMF_TimeGet, ESMF_TimeIntervalGet, ESMF_MeshGet use ESMF, only: ESMF_MethodExecute, ESMF_Mesh, ESMF_DeLayout, ESMF_Distgrid use ESMF, only: ESMF_DistGridConnection, ESMF_StateItem_Flag, ESMF_KIND_I4 use ESMF, only: ESMF_KIND_I8, ESMF_FAILURE, ESMF_DistGridCreate, ESMF_MeshCreate @@ -378,7 +378,8 @@ module MOM_cap_mod use ESMF, only: ESMF_FieldCreate, ESMF_LOGMSG_ERROR, ESMF_LOGMSG_WARNING use ESMF, only: ESMF_COORDSYS_SPH_DEG, ESMF_GridCreate, ESMF_INDEX_DELOCAL use ESMF, only: ESMF_MESHLOC_ELEMENT, ESMF_RC_VAL_OUTOFRANGE, ESMF_StateGet -use ESMF, only: ESMF_TimePrint, ESMF_AlarmSet, ESMF_FieldGet +use ESMF, only: ESMF_TimePrint, ESMF_AlarmSet, ESMF_FieldGet, ESMF_Array +use ESMF, only: ESMF_ArrayCreate use ESMF, only: operator(==), operator(/=), operator(+), operator(-) ! TODO ESMF_GridCompGetInternalState does not have an explicit Fortran interface. @@ -1181,6 +1182,14 @@ subroutine InitializeRealize(gcomp, importState, exportState, clock, rc) character(len=128) :: fldname character(len=256) :: cvalue character(len=*), parameter :: subname='(MOM_cap:InitializeRealize)' + integer :: spatialDim + integer :: numOwnedElements + type(ESMF_Array) :: elemMaskArray + real(ESMF_KIND_R8) , pointer :: ownedElemCoords(:) + real(ESMF_KIND_R8) , pointer :: lat(:), latMesh(:) + real(ESMF_KIND_R8) , pointer :: lon(:), lonMesh(:) + integer(ESMF_KIND_I4) , pointer :: mask(:), maskMesh(:) + real(ESMF_KIND_R8) :: diff_lon, diff_lat !-------------------------------- rc = ESMF_SUCCESS @@ -1326,6 +1335,76 @@ subroutine InitializeRealize(gcomp, importState, exportState, clock, rc) file=__FILE__)) & return + ! Check for consistency of lat, lon and mask between mesh and mom6 grid + call ESMF_MeshGet(Emesh, spatialDim=spatialDim, numOwnedElements=numOwnedElements, rc=rc) + if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, & + line=__LINE__, & + file=__FILE__)) & + return + + allocate(ownedElemCoords(spatialDim*numOwnedElements)) + allocate(lonMesh(numOwnedElements), lon(numOwnedElements)) + allocate(latMesh(numOwnedElements), lat(numOwnedElements)) + allocate(maskMesh(numOwnedElements), mask(numOwnedElements)) + + call ESMF_MeshGet(Emesh, ownedElemCoords=ownedElemCoords, rc=rc) + if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, & + line=__LINE__, & + file=__FILE__)) & + return + do n = 1,numOwnedElements + lonMesh(n) = ownedElemCoords(2*n-1) + latMesh(n) = ownedElemCoords(2*n) + end do + + elemMaskArray = ESMF_ArrayCreate(Distgrid, maskMesh, rc=rc) + if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, & + line=__LINE__, & + file=__FILE__)) & + return + call ESMF_MeshGet(Emesh, elemMaskArray=elemMaskArray, rc=rc) + if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, & + line=__LINE__, & + file=__FILE__)) & + return + + call mpp_get_compute_domain(ocean_public%domain, isc, iec, jsc, jec) + n = 0 + do j = jsc, jec + jg = j + ocean_grid%jsc - jsc + do i = isc, iec + ig = i + ocean_grid%isc - isc + n = n+1 + mask(n) = ocean_grid%mask2dT(ig,jg) + lon(n) = ocean_grid%geolonT(ig,jg) + lat(n) = ocean_grid%geolatT(ig,jg) + end do + end do + + do n = 1,numOwnedElements + diff_lon = abs(lonMesh(n) - lon(n)) + if (diff_lon > 1.e-2) then + write(6,100)n,lonMesh(n),lon(n), diff_lon +100 format('ERROR: MOM n, lonMesh(n), lon(n), diff_lon = ',i8,2(f21.13,3x),d21.5) + !call shr_sys_abort() + end if + diff_lat = abs(latMesh(n) - lat(n)) + if (diff_lat > 1.e-2) then + write(6,101)n,latMesh(n),lat(n), diff_lat +101 format('ERROR: CICE n, latMesh(n), lat(n), diff_lat = ',i8,2(f21.13,3x),d21.5) + !call shr_sys_abort() + end if + if (abs(maskMesh(n) - mask(n)) > 0) then + write(6,102)n,maskMesh(n),mask(n) +102 format('ERROR: CICE n, maskMesh(n), mask(n) = ',3(i8,2x)) + !call shr_sys_abort() + end if + end do + + deallocate(ownedElemCoords) + deallocate(lonMesh , lon ) + deallocate(latMesh , lat ) + deallocate(maskMesh, mask) ! realize the import and export fields using the mesh call MOM_RealizeFields(importState, fldsToOcn_num, fldsToOcn, "Ocn import", mesh=Emesh, rc=rc) if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, & From fb1133e7d2b3edeadda55941bcdbbab238f84f80 Mon Sep 17 00:00:00 2001 From: Gustavo Marques Date: Tue, 27 Aug 2019 11:14:36 -0600 Subject: [PATCH 17/72] Replaces CICE to MOM in error messages --- config_src/nuopc_driver/mom_cap.F90 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/config_src/nuopc_driver/mom_cap.F90 b/config_src/nuopc_driver/mom_cap.F90 index 1d0b41b550..360e8f833d 100644 --- a/config_src/nuopc_driver/mom_cap.F90 +++ b/config_src/nuopc_driver/mom_cap.F90 @@ -1391,12 +1391,12 @@ subroutine InitializeRealize(gcomp, importState, exportState, clock, rc) diff_lat = abs(latMesh(n) - lat(n)) if (diff_lat > 1.e-2) then write(6,101)n,latMesh(n),lat(n), diff_lat -101 format('ERROR: CICE n, latMesh(n), lat(n), diff_lat = ',i8,2(f21.13,3x),d21.5) +101 format('ERROR: MOM n, latMesh(n), lat(n), diff_lat = ',i8,2(f21.13,3x),d21.5) !call shr_sys_abort() end if if (abs(maskMesh(n) - mask(n)) > 0) then write(6,102)n,maskMesh(n),mask(n) -102 format('ERROR: CICE n, maskMesh(n), mask(n) = ',3(i8,2x)) +102 format('ERROR: MOM n, maskMesh(n), mask(n) = ',3(i8,2x)) !call shr_sys_abort() end if end do From 7ad72961103f4b436579dc34f78ab43d9d774641 Mon Sep 17 00:00:00 2001 From: alperaltuntas Date: Wed, 28 Aug 2019 15:30:09 -0600 Subject: [PATCH 18/72] remove labeled format specifiers --- config_src/nuopc_driver/mom_cap.F90 | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/config_src/nuopc_driver/mom_cap.F90 b/config_src/nuopc_driver/mom_cap.F90 index 360e8f833d..39ca8c2f66 100644 --- a/config_src/nuopc_driver/mom_cap.F90 +++ b/config_src/nuopc_driver/mom_cap.F90 @@ -1181,6 +1181,7 @@ subroutine InitializeRealize(gcomp, importState, exportState, clock, rc) integer, allocatable :: gindex(:) ! global index space character(len=128) :: fldname character(len=256) :: cvalue + character(len=256) :: frmt ! format specifier for several error msgs character(len=*), parameter :: subname='(MOM_cap:InitializeRealize)' integer :: spatialDim integer :: numOwnedElements @@ -1384,19 +1385,19 @@ subroutine InitializeRealize(gcomp, importState, exportState, clock, rc) do n = 1,numOwnedElements diff_lon = abs(lonMesh(n) - lon(n)) if (diff_lon > 1.e-2) then - write(6,100)n,lonMesh(n),lon(n), diff_lon -100 format('ERROR: MOM n, lonMesh(n), lon(n), diff_lon = ',i8,2(f21.13,3x),d21.5) + frmt = "('ERROR: MOM n, lonMesh(n), lon(n), diff_lon = ',i8,2(f21.13,3x),d21.5)" + write(6,frmt)n,lonMesh(n),lon(n), diff_lon !call shr_sys_abort() end if diff_lat = abs(latMesh(n) - lat(n)) if (diff_lat > 1.e-2) then - write(6,101)n,latMesh(n),lat(n), diff_lat -101 format('ERROR: MOM n, latMesh(n), lat(n), diff_lat = ',i8,2(f21.13,3x),d21.5) + frmt = "('ERROR: MOM n, latMesh(n), lat(n), diff_lat = ',i8,2(f21.13,3x),d21.5)" + write(6,frmt)n,latMesh(n),lat(n), diff_lat !call shr_sys_abort() end if if (abs(maskMesh(n) - mask(n)) > 0) then - write(6,102)n,maskMesh(n),mask(n) -102 format('ERROR: MOM n, maskMesh(n), mask(n) = ',3(i8,2x)) + frmt = "('ERROR: MOM n, maskMesh(n), mask(n) = ',3(i8,2x))" + write(6,frmt)n,maskMesh(n),mask(n) !call shr_sys_abort() end if end do From cc9e33d4da0eabacfbeeec826eff9e46c9ae01a6 Mon Sep 17 00:00:00 2001 From: Gustavo Marques Date: Wed, 28 Aug 2019 15:46:31 -0600 Subject: [PATCH 19/72] Adds new parameter, MEKE_EQUILIBRIUM_ALT This will use an alternative formula for computing the equilibrium (initial) value of MEKE. --- src/parameterizations/lateral/MOM_MEKE.F90 | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/src/parameterizations/lateral/MOM_MEKE.F90 b/src/parameterizations/lateral/MOM_MEKE.F90 index 8f947c4f68..3688c3dfea 100644 --- a/src/parameterizations/lateral/MOM_MEKE.F90 +++ b/src/parameterizations/lateral/MOM_MEKE.F90 @@ -45,6 +45,8 @@ module MOM_MEKE logical :: visc_drag !< If true use the vertvisc_type to calculate bottom drag. logical :: MEKE_GEOMETRIC !< If true, uses the GM coefficient formulation from the GEOMETRIC !! framework (Marshall et al., 2012) + logical :: MEKE_equilibrium_alt !< If true, use an alternative calculation for the + !! equilibrium value of MEKE. logical :: GM_src_alt !< If true, use the GM energy conversion form S^2*N^2*kappa rather !! than the streamfunction for the MEKE GM source term. logical :: Rd_as_max_scale !< If true the length scale can not exceed the @@ -744,8 +746,11 @@ subroutine MEKE_equilibrium(CS, MEKE, G, GV, US, SN_u, SN_v, drag_rate_visc, I_m else EKE = 0. endif - MEKE%MEKE(i,j) = EKE -! MEKE%MEKE(i,j) = (US%Z_to_m*G%bathyT(i,j)*SN / (8*CS%cdrag))**2 + if (CS%MEKE_equilibrium_alt) then + MEKE%MEKE(i,j) = (US%Z_to_m*G%bathyT(i,j)*SN / (8*CS%cdrag))**2 + else + MEKE%MEKE(i,j) = EKE + endif enddo ; enddo end subroutine MEKE_equilibrium @@ -973,6 +978,9 @@ logical function MEKE_init(Time, G, param_file, diag, CS, MEKE, restart_CS) call get_param(param_file, mdl, "MEKE_GEOMETRIC", CS%MEKE_GEOMETRIC, & "If MEKE_GEOMETRIC is true, uses the GM coefficient formulation "//& "from the GEOMETRIC framework (Marshall et al., 2012).", default=.false.) + call get_param(param_file, mdl, "MEKE_EQUILIBRIUM_ALT", CS%MEKE_equilibrium_alt, & + "If true, use an alternative formula for computing the (equilibrium)"//& + "initial value of MEKE.", default=.false.) call get_param(param_file, mdl, "MEKE_FRCOEFF", CS%MEKE_FrCoeff, & "The efficiency of the conversion of mean energy into "//& "MEKE. If MEKE_FRCOEFF is negative, this conversion "//& From d05235f901ca8890c04b69d250a7f3333f143e66 Mon Sep 17 00:00:00 2001 From: Gustavo Marques Date: Wed, 28 Aug 2019 15:48:09 -0600 Subject: [PATCH 20/72] Final GME code fix Changed the loop indices on boundary mask. Added three new runtime parameters for GME (GME_H0, GME_EFFICIENCY, GME_LIMITER) --- .../lateral/MOM_hor_visc.F90 | 40 ++++++++++++------- 1 file changed, 25 insertions(+), 15 deletions(-) diff --git a/src/parameterizations/lateral/MOM_hor_visc.F90 b/src/parameterizations/lateral/MOM_hor_visc.F90 index d4fa977cb9..8074fb2f7d 100644 --- a/src/parameterizations/lateral/MOM_hor_visc.F90 +++ b/src/parameterizations/lateral/MOM_hor_visc.F90 @@ -79,6 +79,10 @@ module MOM_hor_visc logical :: res_scale_MEKE !< If true, the viscosity contribution from MEKE is scaled by !! the resolution function. logical :: use_GME !< If true, use GME backscatter scheme. + real :: GME_h0 !< The strength of GME tapers quadratically to zero when the bathymetric + !! depth is shallower than GME_H0 [m] + real :: GME_efficiency !< The nondimensional prefactor multiplying the GME coefficient [nondim] + real :: GME_limiter !< The absolute maximum value the GME coefficient is allowed to take [m2 s-1]. real ALLOCABLE_, dimension(NIMEM_,NJMEM_) :: Kh_bg_xx !< The background Laplacian viscosity at h points [m2 s-1]. @@ -382,23 +386,15 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, use_MEKE_Ku = associated(MEKE%Ku) use_MEKE_Au = associated(MEKE%Au) - do j = G%jsc, G%jec ; do i = G%isc, G%iec + do j=Jsq-1,Jeq+2 ; do i=Isq-1,Ieq+2 boundary_mask_h(i,j) = (G%mask2dCu(I,j) * G%mask2dCv(i,J) * G%mask2dCu(I-1,j) * G%mask2dCv(i,J-1)) enddo ; enddo - do J = G%JscB, G%JecB ; do I = G%IscB, G%IecB + do J=js-2,Jeq+1 ; do I=is-2,Ieq+1 boundary_mask_q(I,J) = (G%mask2dCv(i,J) * G%mask2dCv(i+1,J) * G%mask2dCu(I,j) * G%mask2dCu(I,j-1)) enddo; enddo -! call pass_var(boundary_mask_h, G%Domain, complete=.true.) - - if (CS%use_GME) then - ! GME tapers off above this depth - H0 = 1000.0 - FWfrac = 1.0 - GME_coeff_limiter = 1e7 - ! initialize diag. array with zeros GME_coeff_h(:,:,:) = 0.0 GME_coeff_q(:,:,:) = 0.0 @@ -450,7 +446,7 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, enddo ; enddo do J=js-2,Jeq+1 ; do I=is-2,Ieq+1 - grad_vel_mag_bt_q(I,J) = boundary_mask_h(I,J) * (dvdx_bt(i,j)**2 + dudy_bt(i,j)**2 + & + grad_vel_mag_bt_q(I,J) = boundary_mask_q(I,J) * (dvdx_bt(i,j)**2 + dudy_bt(i,j)**2 + & (0.25*((dudx_bt(i,j)+dudx_bt(i+1,j+1))+(dudx_bt(i,j+1)+dudx_bt(i+1,j))))**2 + & (0.25*((dvdy_bt(i,j)+dvdy_bt(i+1,j+1))+(dvdy_bt(i,j+1)+dvdy_bt(i+1,j))))**2) enddo ; enddo @@ -1066,14 +1062,14 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, do J=Jsq,Jeq+1 ; do i=Isq,Ieq+1 if ((grad_vel_mag_bt_h(i,j)>0) .and. (max_diss_rate_h(i,j,k)>0)) then - GME_coeff = (MIN(G%bathyT(i,j)/H0,1.0)**2) * FWfrac*max_diss_rate_h(i,j,k) / grad_vel_mag_bt_h(i,j) + GME_coeff = (MIN(G%bathyT(i,j)/CS%GME_h0,1.0)**2) * CS%GME_efficiency*max_diss_rate_h(i,j,k) / grad_vel_mag_bt_h(i,j) else GME_coeff = 1.0 endif ! apply mask GME_coeff = GME_coeff * boundary_mask_h(i,j) - GME_coeff = MIN(GME_coeff, GME_coeff_limiter) + GME_coeff = MIN(GME_coeff, CS%GME_limiter) if ((CS%id_GME_coeff_h>0) .or. find_FrictWork) GME_coeff_h(i,j,k) = GME_coeff str_xx_GME(i,j) = GME_coeff * sh_xx_bt(i,j) @@ -1084,14 +1080,14 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, do J=js-1,Jeq ; do I=is-1,Ieq if ((grad_vel_mag_bt_q(I,J)>0) .and. (max_diss_rate_q(I,J,k)>0)) then - GME_coeff = (MIN(G%bathyT(i,j)/H0,1.0)**2) * FWfrac*max_diss_rate_q(I,J,k) / grad_vel_mag_bt_q(I,J) + GME_coeff = (MIN(G%bathyT(i,j)/CS%GME_h0,1.0)**2) * CS%GME_efficiency*max_diss_rate_q(I,J,k) / grad_vel_mag_bt_q(I,J) else GME_coeff = 0.0 endif ! apply mask GME_coeff = GME_coeff * boundary_mask_q(I,J) - GME_coeff = MIN(GME_coeff, GME_coeff_limiter) + GME_coeff = MIN(GME_coeff, CS%GME_limiter) if (CS%id_GME_coeff_q>0) GME_coeff_q(I,J,k) = GME_coeff str_xy_GME(I,J) = GME_coeff * sh_xy_bt(I,J) @@ -1607,6 +1603,20 @@ subroutine hor_visc_init(Time, G, US, param_file, diag, CS) if (.not. use_MEKE) call MOM_error(FATAL,"ERROR: Currently, USE_GME = True "// & "cannot be used with USE_MEKE=False.") + + call get_param(param_file, mdl, "GME_H0", CS%GME_h0, & + "The strength of GME tapers quadratically to zero when the bathymetric "//& + "depth is shallower than GME_H0.", units="m", & + default=1000.0) + + call get_param(param_file, mdl, "GME_EFFICIENCY", CS%GME_efficiency, & + "The nondimensional prefactor multiplying the GME coefficient.", & + units="nondim", default=1.0) + + call get_param(param_file, mdl, "GME_LIMITER", CS%GME_limiter, & + "The absolute maximum value the GME coefficient is allowed to take.", & + units="m2 s-1", default=1.0e7) + endif if (CS%bound_Kh .or. CS%bound_Ah .or. CS%better_bound_Kh .or. CS%better_bound_Ah) & From 18c6f1ebb8b3d27c4b666246c4717a9450417196 Mon Sep 17 00:00:00 2001 From: alperaltuntas Date: Wed, 28 Aug 2019 16:59:08 -0600 Subject: [PATCH 21/72] replace hard-coded mesh diff. limit with a param: eps_omesh --- config_src/nuopc_driver/mom_ocean_model_nuopc.F90 | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/config_src/nuopc_driver/mom_ocean_model_nuopc.F90 b/config_src/nuopc_driver/mom_ocean_model_nuopc.F90 index 95b1bcc6e3..abb6bb2679 100644 --- a/config_src/nuopc_driver/mom_ocean_model_nuopc.F90 +++ b/config_src/nuopc_driver/mom_ocean_model_nuopc.F90 @@ -80,6 +80,7 @@ module MOM_ocean_model_nuopc public ocean_public_type_chksum public ocean_model_data_get public get_ocean_grid +public get_eps_omesh !> This interface extracts a named scalar field or array from the ocean surface or public type interface ocean_model_data_get @@ -182,6 +183,9 @@ module MOM_ocean_model_nuopc logical :: diabatic_first !< If true, apply diabatic and thermodynamic !! processes before time stepping the dynamics. + real :: eps_omesh !< Max allowable difference between ESMF mesh and MOM6 + !! domain coordinates + type(directories) :: dirs !< A structure containing several relevant directory paths. type(mech_forcing) :: forces !< A structure with the driving mechanical surface forces type(forcing) :: fluxes !< A structure containing pointers to @@ -327,6 +331,9 @@ subroutine ocean_model_init(Ocean_sfc, OS, Time_init, Time_in, gas_fields_ocn, i else ; call MOM_error(FATAL,"ocean_model_init: OCEAN_SURFACE_STAGGER = "// & trim(stagger)//" is invalid.") ; endif + call get_param(param_file, mdl, "EPS_OMESH",OS%eps_omesh, & + "Maximum allowable difference between ESMF mesh and "//& + "MOM6 domain coordinates.", default=1.e-2) call get_param(param_file, mdl, "RESTORE_SALINITY",OS%restore_salinity, & "If true, the coupled driver will add a globally-balanced "//& "fresh-water flux that drives sea-surface salinity "//& @@ -353,7 +360,7 @@ subroutine ocean_model_init(Ocean_sfc, OS, Time_init, Time_in, gas_fields_ocn, i OS%press_to_z = 1.0/(Rho0*G_Earth) - call get_param(param_file, mdl, "HFREEZE", HFrz, & + call get_param(param_file, mdl, "HFREEZE", HFrz, & "If HFREEZE > 0, melt potential will be computed. The actual depth "//& "over which melt potential is computed will be min(HFREEZE, OBLD), "//& "where OBLD is the boundary layer depth. If HFREEZE <= 0 (default), "//& @@ -1174,4 +1181,10 @@ subroutine get_ocean_grid(OS, Gridp) return end subroutine get_ocean_grid +!> Returns eps_omesh read from param file +real function get_eps_omesh(OS) + type(ocean_state_type) :: OS + get_eps_omesh = OS%eps_omesh; return +end function + end module MOM_ocean_model_nuopc From 66f808bf8aec38fef9f5d5c293b8e91d7acd6fa5 Mon Sep 17 00:00:00 2001 From: alperaltuntas Date: Wed, 28 Aug 2019 17:20:39 -0600 Subject: [PATCH 22/72] add units to EPS_OMESH --- config_src/nuopc_driver/mom_ocean_model_nuopc.F90 | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/config_src/nuopc_driver/mom_ocean_model_nuopc.F90 b/config_src/nuopc_driver/mom_ocean_model_nuopc.F90 index abb6bb2679..83dfa0a4f8 100644 --- a/config_src/nuopc_driver/mom_ocean_model_nuopc.F90 +++ b/config_src/nuopc_driver/mom_ocean_model_nuopc.F90 @@ -333,7 +333,8 @@ subroutine ocean_model_init(Ocean_sfc, OS, Time_init, Time_in, gas_fields_ocn, i call get_param(param_file, mdl, "EPS_OMESH",OS%eps_omesh, & "Maximum allowable difference between ESMF mesh and "//& - "MOM6 domain coordinates.", default=1.e-2) + "MOM6 domain coordinates in nuopc cap.", & + units="degrees", default=1.e-2) call get_param(param_file, mdl, "RESTORE_SALINITY",OS%restore_salinity, & "If true, the coupled driver will add a globally-balanced "//& "fresh-water flux that drives sea-surface salinity "//& From c698b1a2864b3e2bf6006a5729c876506c5943ae Mon Sep 17 00:00:00 2001 From: alperaltuntas Date: Wed, 28 Aug 2019 17:21:34 -0600 Subject: [PATCH 23/72] call get_eps_omesh and remove hardcoded limit --- config_src/nuopc_driver/mom_cap.F90 | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/config_src/nuopc_driver/mom_cap.F90 b/config_src/nuopc_driver/mom_cap.F90 index 39ca8c2f66..642a7eb809 100644 --- a/config_src/nuopc_driver/mom_cap.F90 +++ b/config_src/nuopc_driver/mom_cap.F90 @@ -344,7 +344,8 @@ module MOM_cap_mod use MOM_grid, only: ocean_grid_type, get_global_grid_size use MOM_ocean_model_nuopc, only: ocean_model_restart, ocean_public_type, ocean_state_type use MOM_ocean_model_nuopc, only: ocean_model_init_sfc -use MOM_ocean_model_nuopc, only: ocean_model_init, update_ocean_model, ocean_model_end, get_ocean_grid +use MOM_ocean_model_nuopc, only: ocean_model_init, update_ocean_model, ocean_model_end +use MOM_ocean_model_nuopc, only: get_ocean_grid, get_eps_omesh use MOM_cap_time, only: AlarmInit use MOM_cap_methods, only: mom_import, mom_export, mom_set_geomtype #ifdef CESMCOUPLED @@ -1191,6 +1192,7 @@ subroutine InitializeRealize(gcomp, importState, exportState, clock, rc) real(ESMF_KIND_R8) , pointer :: lon(:), lonMesh(:) integer(ESMF_KIND_I4) , pointer :: mask(:), maskMesh(:) real(ESMF_KIND_R8) :: diff_lon, diff_lat + real :: eps_omesh !-------------------------------- rc = ESMF_SUCCESS @@ -1382,15 +1384,16 @@ subroutine InitializeRealize(gcomp, importState, exportState, clock, rc) end do end do + eps_omesh = get_eps_omesh(ocean_state) do n = 1,numOwnedElements diff_lon = abs(lonMesh(n) - lon(n)) - if (diff_lon > 1.e-2) then + if (diff_lon > eps_omesh) then frmt = "('ERROR: MOM n, lonMesh(n), lon(n), diff_lon = ',i8,2(f21.13,3x),d21.5)" write(6,frmt)n,lonMesh(n),lon(n), diff_lon !call shr_sys_abort() end if diff_lat = abs(latMesh(n) - lat(n)) - if (diff_lat > 1.e-2) then + if (diff_lat > eps_omesh) then frmt = "('ERROR: MOM n, latMesh(n), lat(n), diff_lat = ',i8,2(f21.13,3x),d21.5)" write(6,frmt)n,latMesh(n),lat(n), diff_lat !call shr_sys_abort() From d9a00d78175cc034aff47ae4fb0ff4f9f57af897 Mon Sep 17 00:00:00 2001 From: alperaltuntas Date: Wed, 28 Aug 2019 17:41:01 -0600 Subject: [PATCH 24/72] call MOM_error if mesh is inconsistent --- config_src/nuopc_driver/mom_cap.F90 | 27 +++++++++++++++------------ 1 file changed, 15 insertions(+), 12 deletions(-) diff --git a/config_src/nuopc_driver/mom_cap.F90 b/config_src/nuopc_driver/mom_cap.F90 index 642a7eb809..25dd9bde76 100644 --- a/config_src/nuopc_driver/mom_cap.F90 +++ b/config_src/nuopc_driver/mom_cap.F90 @@ -322,7 +322,6 @@ module MOM_cap_mod use mpp_domains_mod, only: mpp_get_ntile_count, mpp_get_pelist, mpp_get_global_domain use mpp_domains_mod, only: mpp_get_domain_npes use mpp_io_mod, only: mpp_open, MPP_RDONLY, MPP_ASCII, MPP_OVERWR, MPP_APPEND, mpp_close, MPP_SINGLE -use mpp_mod, only: input_nml_file, mpp_error, FATAL, NOTE, mpp_pe, mpp_npes, mpp_set_current_pelist use mpp_mod, only: stdlog, stdout, mpp_root_pe, mpp_clock_id use mpp_mod, only: mpp_clock_begin, mpp_clock_end, MPP_CLOCK_SYNC use mpp_mod, only: MPP_CLOCK_DETAILED, CLOCK_COMPONENT, MAXPES @@ -339,7 +338,7 @@ module MOM_cap_mod use MOM_file_parser, only: get_param, log_version, param_file_type, close_param_file use MOM_get_input, only: Get_MOM_Input, directories use MOM_domains, only: pass_var -use MOM_error_handler, only: is_root_pe +use MOM_error_handler, only: MOM_error, FATAL, is_root_pe use MOM_ocean_model_nuopc, only: ice_ocean_boundary_type use MOM_grid, only: ocean_grid_type, get_global_grid_size use MOM_ocean_model_nuopc, only: ocean_model_restart, ocean_public_type, ocean_state_type @@ -1182,7 +1181,8 @@ subroutine InitializeRealize(gcomp, importState, exportState, clock, rc) integer, allocatable :: gindex(:) ! global index space character(len=128) :: fldname character(len=256) :: cvalue - character(len=256) :: frmt ! format specifier for several error msgs + character(len=256) :: frmt ! format specifier for several error msgs + character(len=512) :: err_msg ! error messages character(len=*), parameter :: subname='(MOM_cap:InitializeRealize)' integer :: spatialDim integer :: numOwnedElements @@ -1388,20 +1388,23 @@ subroutine InitializeRealize(gcomp, importState, exportState, clock, rc) do n = 1,numOwnedElements diff_lon = abs(lonMesh(n) - lon(n)) if (diff_lon > eps_omesh) then - frmt = "('ERROR: MOM n, lonMesh(n), lon(n), diff_lon = ',i8,2(f21.13,3x),d21.5)" - write(6,frmt)n,lonMesh(n),lon(n), diff_lon - !call shr_sys_abort() + frmt = "('ERROR: Inconsistent coords - "//& + "MOM n, lonMesh(n), lon(n), diff_lon = ',i8,2(f21.13,3x),d21.5)" + write(err_msg, frmt)n,lonMesh(n),lon(n), diff_lon + call MOM_error(FATAL, err_msg) end if diff_lat = abs(latMesh(n) - lat(n)) if (diff_lat > eps_omesh) then - frmt = "('ERROR: MOM n, latMesh(n), lat(n), diff_lat = ',i8,2(f21.13,3x),d21.5)" - write(6,frmt)n,latMesh(n),lat(n), diff_lat - !call shr_sys_abort() + frmt = "('ERROR: Inconsistent coords - "//& + "MOM n, latMesh(n), lat(n), diff_lat = ',i8,2(f21.13,3x),d21.5)" + write(err_msg, frmt)n,latMesh(n),lat(n), diff_lat + call MOM_error(FATAL, err_msg) end if if (abs(maskMesh(n) - mask(n)) > 0) then - frmt = "('ERROR: MOM n, maskMesh(n), mask(n) = ',3(i8,2x))" - write(6,frmt)n,maskMesh(n),mask(n) - !call shr_sys_abort() + frmt = "('ERROR: Inconsistent masks - "//& + "MOM n, maskMesh(n), mask(n) = ',3(i8,2x))" + write(err_msg, frmt)n,maskMesh(n),mask(n) + call MOM_error(FATAL, err_msg) end if end do From e02b358ad6cb742de74cb84f7d6033ca9ad01779 Mon Sep 17 00:00:00 2001 From: alperaltuntas Date: Thu, 29 Aug 2019 11:46:23 -0600 Subject: [PATCH 25/72] compare mod 360 of diff and eps --- config_src/nuopc_driver/mom_cap.F90 | 2 +- config_src/nuopc_driver/mom_ocean_model_nuopc.F90 | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/config_src/nuopc_driver/mom_cap.F90 b/config_src/nuopc_driver/mom_cap.F90 index 25dd9bde76..d9400e0560 100644 --- a/config_src/nuopc_driver/mom_cap.F90 +++ b/config_src/nuopc_driver/mom_cap.F90 @@ -1386,7 +1386,7 @@ subroutine InitializeRealize(gcomp, importState, exportState, clock, rc) eps_omesh = get_eps_omesh(ocean_state) do n = 1,numOwnedElements - diff_lon = abs(lonMesh(n) - lon(n)) + diff_lon = abs(mod(lonMesh(n) - lon(n),360.0)) if (diff_lon > eps_omesh) then frmt = "('ERROR: Inconsistent coords - "//& "MOM n, lonMesh(n), lon(n), diff_lon = ',i8,2(f21.13,3x),d21.5)" diff --git a/config_src/nuopc_driver/mom_ocean_model_nuopc.F90 b/config_src/nuopc_driver/mom_ocean_model_nuopc.F90 index 83dfa0a4f8..426c7e9922 100644 --- a/config_src/nuopc_driver/mom_ocean_model_nuopc.F90 +++ b/config_src/nuopc_driver/mom_ocean_model_nuopc.F90 @@ -334,7 +334,7 @@ subroutine ocean_model_init(Ocean_sfc, OS, Time_init, Time_in, gas_fields_ocn, i call get_param(param_file, mdl, "EPS_OMESH",OS%eps_omesh, & "Maximum allowable difference between ESMF mesh and "//& "MOM6 domain coordinates in nuopc cap.", & - units="degrees", default=1.e-2) + units="degrees", default=1.e-4) call get_param(param_file, mdl, "RESTORE_SALINITY",OS%restore_salinity, & "If true, the coupled driver will add a globally-balanced "//& "fresh-water flux that drives sea-surface salinity "//& From 7f7e8c081b6660031c0c6233c8b82c82607cb44f Mon Sep 17 00:00:00 2001 From: alperaltuntas Date: Thu, 29 Aug 2019 15:28:43 -0600 Subject: [PATCH 26/72] Add EPS_OMESH value in error message --- config_src/nuopc_driver/mom_cap.F90 | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/config_src/nuopc_driver/mom_cap.F90 b/config_src/nuopc_driver/mom_cap.F90 index d9400e0560..0caee9510e 100644 --- a/config_src/nuopc_driver/mom_cap.F90 +++ b/config_src/nuopc_driver/mom_cap.F90 @@ -1388,20 +1388,22 @@ subroutine InitializeRealize(gcomp, importState, exportState, clock, rc) do n = 1,numOwnedElements diff_lon = abs(mod(lonMesh(n) - lon(n),360.0)) if (diff_lon > eps_omesh) then - frmt = "('ERROR: Inconsistent coords - "//& - "MOM n, lonMesh(n), lon(n), diff_lon = ',i8,2(f21.13,3x),d21.5)" - write(err_msg, frmt)n,lonMesh(n),lon(n), diff_lon + frmt = "('ERROR: Difference between ESMF Mesh and MOM6 domain coords is "//& + "greater than parameter EPS_OMESH. n, lonMesh(n), lon(n), diff_lon, "//& + "EPS_OMESH= ',i8,2(f21.13,3x),2(d21.5))" + write(err_msg, frmt)n,lonMesh(n),lon(n), diff_lon, eps_omesh call MOM_error(FATAL, err_msg) end if diff_lat = abs(latMesh(n) - lat(n)) if (diff_lat > eps_omesh) then - frmt = "('ERROR: Inconsistent coords - "//& - "MOM n, latMesh(n), lat(n), diff_lat = ',i8,2(f21.13,3x),d21.5)" - write(err_msg, frmt)n,latMesh(n),lat(n), diff_lat + frmt = "('ERROR: Difference between ESMF Mesh and MOM6 domain coords is"//& + "greater than parameter EPS_OMESH. n, latMesh(n), lat(n), diff_lat, "//& + "EPS_OMESH= ',i8,2(f21.13,3x),2(d21.5))" + write(err_msg, frmt)n,latMesh(n),lat(n), diff_lat, eps_omesh call MOM_error(FATAL, err_msg) end if if (abs(maskMesh(n) - mask(n)) > 0) then - frmt = "('ERROR: Inconsistent masks - "//& + frmt = "('ERROR: ESMF mesh and MOM6 domain masks are inconsistent! - "//& "MOM n, maskMesh(n), mask(n) = ',3(i8,2x))" write(err_msg, frmt)n,maskMesh(n),mask(n) call MOM_error(FATAL, err_msg) From b810e26be32de73a5c176dd50d91c7e502547576 Mon Sep 17 00:00:00 2001 From: Gustavo Marques Date: Thu, 29 Aug 2019 15:37:15 -0600 Subject: [PATCH 27/72] Fixes line length exceeded --- src/parameterizations/lateral/MOM_hor_visc.F90 | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/parameterizations/lateral/MOM_hor_visc.F90 b/src/parameterizations/lateral/MOM_hor_visc.F90 index 8074fb2f7d..fe9073b7f1 100644 --- a/src/parameterizations/lateral/MOM_hor_visc.F90 +++ b/src/parameterizations/lateral/MOM_hor_visc.F90 @@ -1062,7 +1062,8 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, do J=Jsq,Jeq+1 ; do i=Isq,Ieq+1 if ((grad_vel_mag_bt_h(i,j)>0) .and. (max_diss_rate_h(i,j,k)>0)) then - GME_coeff = (MIN(G%bathyT(i,j)/CS%GME_h0,1.0)**2) * CS%GME_efficiency*max_diss_rate_h(i,j,k) / grad_vel_mag_bt_h(i,j) + GME_coeff = (MIN(G%bathyT(i,j)/CS%GME_h0,1.0)**2) * CS%GME_efficiency*max_diss_rate_h(i,j,k) / & + grad_vel_mag_bt_h(i,j) else GME_coeff = 1.0 endif @@ -1080,7 +1081,8 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, do J=js-1,Jeq ; do I=is-1,Ieq if ((grad_vel_mag_bt_q(I,J)>0) .and. (max_diss_rate_q(I,J,k)>0)) then - GME_coeff = (MIN(G%bathyT(i,j)/CS%GME_h0,1.0)**2) * CS%GME_efficiency*max_diss_rate_q(I,J,k) / grad_vel_mag_bt_q(I,J) + GME_coeff = (MIN(G%bathyT(i,j)/CS%GME_h0,1.0)**2) * CS%GME_efficiency*max_diss_rate_q(I,J,k) / & + grad_vel_mag_bt_q(I,J) else GME_coeff = 0.0 endif From 15a03c5aadfc8d2fd968a018dd07171c85451d05 Mon Sep 17 00:00:00 2001 From: Gustavo Marques Date: Tue, 3 Sep 2019 09:25:25 -0600 Subject: [PATCH 28/72] Commented out variables left over from merge These need to be cleaned before submitting a PR to dev/ncar --- .../lateral/MOM_hor_visc.F90 | 23 ++++++++++--------- 1 file changed, 12 insertions(+), 11 deletions(-) diff --git a/src/parameterizations/lateral/MOM_hor_visc.F90 b/src/parameterizations/lateral/MOM_hor_visc.F90 index 0498e34edf..f734bb2788 100644 --- a/src/parameterizations/lateral/MOM_hor_visc.F90 +++ b/src/parameterizations/lateral/MOM_hor_visc.F90 @@ -1002,7 +1002,7 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, if (CS%id_Kh_q>0 .or. CS%debug) Kh_q(I,J,k) = Kh if (CS%id_vort_xy_q>0) vort_xy_q(I,J,k) = vort_xy(I,J) - if (CS%debug) sh_xy_3d(I,J,k) = sh_xy(I,J) +! if (CS%debug) sh_xy_3d(I,J,k) = sh_xy(I,J) str_xy(I,J) = -Kh * sh_xy(I,J) else ! not Laplacian @@ -1048,10 +1048,10 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, if (CS%id_Ah_q>0 .or. CS%debug) Ah_q(I,J,k) = Ah - str_xy(I,J) = str_xy(I,J) + Ah * ( dvdx3(I,J) + dudy3(I,J) ) + str_xy(I,J) = str_xy(I,J) + Ah * ( dDel2vdx(I,J) + dDel2udy(I,J) ) ! Keep a copy of the biharmonic contribution for backscatter parameterization - bhstr_xy(I,J) = Ah * ( dvdx3(I,J) + dudy3(I,J) ) * & + bhstr_xy(I,J) = Ah * ( dDel2vdx(I,J) + dDel2udy(I,J) ) * & (hq(I,J) * G%mask2dBu(I,J) * CS%reduction_xy(I,J)) endif ! biharmonic @@ -1305,7 +1305,7 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, if (CS%Laplacian) then call hchksum(Kh_h, "Kh_h", G%HI, haloshift=0, scale=US%L_to_m**2*US%s_to_T) call Bchksum(Kh_q, "Kh_q", G%HI, haloshift=0, scale=US%L_to_m**2*US%s_to_T) - call Bchksum(sh_xy_3d, "shear_xy", G%HI, haloshift=0, scale=US%s_to_T) +! call Bchksum(sh_xy_3d, "shear_xy", G%HI, haloshift=0, scale=US%s_to_T) ! call hchksum(sh_xx_3d, "shear_xx", G%HI, haloshift=0, scale=US%s_to_T) endif if (CS%biharmonic) call hchksum(Ah_h, "Ah_h", G%HI, haloshift=0, scale=US%L_to_m**4*US%s_to_T) @@ -1426,13 +1426,14 @@ subroutine hor_visc_init(Time, G, US, param_file, diag, CS, MEKE) ! parameter spelling checks. call get_param(param_file, mdl, "GET_ALL_PARAMS", get_all, default=.false.) - call get_param(param_file, mdl, "DEFAULT_2018_ANSWERS", default_2018_answers, & - "This sets the default value for the various _2018_ANSWERS parameters.", & - default=.true.) - call get_param(param_file, mdl, "HOR_VISC_2018_ANSWERS", CS%answers_2018, & - "If true, use the order of arithmetic and expressions that recover the "//& - "answers from the end of 2018. Otherwise, use updated and more robust "//& - "forms of the same expressions.", default=default_2018_answers) +! call get_param(param_file, mdl, "DEFAULT_2018_ANSWERS", default_2018_answers, & +! "This sets the default value for the various _2018_ANSWERS parameters.", & +! default=.true.) +! call get_param(param_file, mdl, "HOR_VISC_2018_ANSWERS", CS%answers_2018, & +! "If true, use the order of arithmetic and expressions that recover the "//& +! "answers from the end of 2018. Otherwise, use updated and more robust "//& +! "forms of the same expressions.", default=default_2018_answers) + call get_param(param_file, mdl, "DEBUG", CS%debug, default=.false.) call get_param(param_file, mdl, "LAPLACIAN", CS%Laplacian, & From ab9bc8a3eebfaeefc45478743eeb1664d0c70f9b Mon Sep 17 00:00:00 2001 From: Gustavo Marques Date: Tue, 3 Sep 2019 09:27:46 -0600 Subject: [PATCH 29/72] Adds OS%US as argument in add_shelf_forces --- config_src/mct_driver/mom_ocean_model_mct.F90 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/config_src/mct_driver/mom_ocean_model_mct.F90 b/config_src/mct_driver/mom_ocean_model_mct.F90 index 4f1c7d963a..94bc15cec8 100644 --- a/config_src/mct_driver/mom_ocean_model_mct.F90 +++ b/config_src/mct_driver/mom_ocean_model_mct.F90 @@ -525,7 +525,7 @@ 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) & @@ -560,7 +560,7 @@ 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) & From 25b409bdcb3d0b2bc156093f967d5232b8d0e2eb Mon Sep 17 00:00:00 2001 From: Gustavo Marques Date: Tue, 3 Sep 2019 10:45:15 -0600 Subject: [PATCH 30/72] Adding back 2018_answers and cleanning the code --- .../lateral/MOM_hor_visc.F90 | 22 +++++++------------ 1 file changed, 8 insertions(+), 14 deletions(-) diff --git a/src/parameterizations/lateral/MOM_hor_visc.F90 b/src/parameterizations/lateral/MOM_hor_visc.F90 index f734bb2788..e9ff06d337 100644 --- a/src/parameterizations/lateral/MOM_hor_visc.F90 +++ b/src/parameterizations/lateral/MOM_hor_visc.F90 @@ -306,7 +306,6 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, FrictWork_GME, & ! work done by GME [W m-2] div_xx_h ! horizontal divergence [s-1] real, dimension(SZI_(G),SZJ_(G),SZK_(G)) :: & - ! KH_t_GME, & !< interface height diffusivities in t-columns [m2 s-1] GME_coeff_h !< GME coeff. at h-points [L2 T-1 ~> m2 s-1] real :: Ah ! biharmonic viscosity [L4 T-1 ~> m4 s-1] real :: Kh ! Laplacian viscosity [L2 T-1 ~> m2 s-1] @@ -363,11 +362,6 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, Ah_h(:,:,:) = 0.0 Kh_h(:,:,:) = 0.0 -! if (CS%debug) then -! sh_xx_3d(:,:,:) = 0.0 ; sh_xy_3d(:,:,:) = 0.0 -! Kh_q(:,:,:) = 0.0 ; Ah_q(:,:,:) = 0.0 -! endif - if (present(OBC)) then ; if (associated(OBC)) then ; if (OBC%OBC_pe) then apply_OBC = OBC%Flather_u_BCs_exist_globally .or. OBC%Flather_v_BCs_exist_globally apply_OBC = .true. @@ -1379,6 +1373,7 @@ subroutine hor_visc_init(Time, G, US, param_file, diag, CS, MEKE) ! If false and USE_GME = True, issue a FATAL error. logical :: use_MEKE ! If true, use the MEKE module for calculating eddy kinetic energy. ! If false and USE_GME = True, issue a FATAL error. + logical :: default_2018_answers character(len=64) :: inputdir, filename real :: deg2rad ! Converts degrees to radians @@ -1426,13 +1421,13 @@ subroutine hor_visc_init(Time, G, US, param_file, diag, CS, MEKE) ! parameter spelling checks. call get_param(param_file, mdl, "GET_ALL_PARAMS", get_all, default=.false.) -! call get_param(param_file, mdl, "DEFAULT_2018_ANSWERS", default_2018_answers, & -! "This sets the default value for the various _2018_ANSWERS parameters.", & -! default=.true.) -! call get_param(param_file, mdl, "HOR_VISC_2018_ANSWERS", CS%answers_2018, & -! "If true, use the order of arithmetic and expressions that recover the "//& -! "answers from the end of 2018. Otherwise, use updated and more robust "//& -! "forms of the same expressions.", default=default_2018_answers) + call get_param(param_file, mdl, "DEFAULT_2018_ANSWERS", default_2018_answers, & + "This sets the default value for the various _2018_ANSWERS parameters.", & + default=.true.) + call get_param(param_file, mdl, "HOR_VISC_2018_ANSWERS", CS%answers_2018, & + "If true, use the order of arithmetic and expressions that recover the "//& + "answers from the end of 2018. Otherwise, use updated and more robust "//& + "forms of the same expressions.", default=default_2018_answers) call get_param(param_file, mdl, "DEBUG", CS%debug, default=.false.) @@ -2142,7 +2137,6 @@ subroutine smooth_GME(CS,G,GME_flux_h,GME_flux_q) real :: wc, ww, we, wn, ws ! averaging weights for smoothing integer :: i, j, k, s - !do s=1,CS%n_smooth do s=1,1 ! Update halos From fe4428920a27aa4ca26071a6dfd394bd47f3290c Mon Sep 17 00:00:00 2001 From: Gustavo Marques Date: Thu, 12 Sep 2019 16:50:56 -0600 Subject: [PATCH 31/72] Fixes a bug when computing PE_release_h PE_release_h was being computed outside of a k-loop and, therefore, it was always zero. --- .../lateral/MOM_thickness_diffuse.F90 | 40 +++++++++---------- 1 file changed, 19 insertions(+), 21 deletions(-) diff --git a/src/parameterizations/lateral/MOM_thickness_diffuse.F90 b/src/parameterizations/lateral/MOM_thickness_diffuse.F90 index 3ebf159e3d..9d170e57c8 100644 --- a/src/parameterizations/lateral/MOM_thickness_diffuse.F90 +++ b/src/parameterizations/lateral/MOM_thickness_diffuse.F90 @@ -1263,26 +1263,27 @@ subroutine thickness_diffuse_full(h, e, Kh_u, Kh_v, tv, uhD, vhD, cg1, dt, G, GV enddo endif + if (find_work) then + do j=js,je ; do i=is,ie + Work_h = 0.5 * G%IareaT(i,j) * & + ((Work_u(I-1,j) + Work_u(I,j)) + (Work_v(i,J-1) + Work_v(i,J))) + if (associated(CS%GMwork)) CS%GMwork(i,j) = Work_h + if (associated(MEKE) .and. associated(MEKE%GM_src) .and. .not. CS%GM_src_alt ) then + MEKE%GM_src(i,j) = MEKE%GM_src(i,j) + Work_h + endif + enddo ; enddo - !if (find_work) then ; do j=js,je ; do i=is,ie ; do k=nz,1,-1 - if (find_work) then ; do j=js,je ; do i=is,ie - ! Note that the units of Work_v and Work_u are W, while Work_h is W m-2. - Work_h = 0.5 * G%IareaT(i,j) * & - ((Work_u(I-1,j) + Work_u(I,j)) + (Work_v(i,J-1) + Work_v(i,J))) - PE_release_h = -0.25*(Kh_u(I,j,k)*(Slope_x_PE(I,j,k)**2) * hN2_x_PE(I,j,k) + & - Kh_u(I-1,j,k)*(Slope_x_PE(I-1,j,k)**2) * hN2_x_PE(I-1,j,k) + & - Kh_v(i,J,k)*(Slope_y_PE(i,J,k)**2) * hN2_y_PE(i,J,k) + & - Kh_v(i,J-1,k)*(Slope_y_PE(i,J-1,k)**2) * hN2_y_PE(i,J-1,k)) - if (associated(CS%GMwork)) CS%GMwork(i,j) = Work_h - if (associated(MEKE)) then ; if (associated(MEKE%GM_src)) then - if (CS%GM_src_alt) then + if (associated(MEKE) .and. associated(MEKE%GM_src) .and. CS%GM_src_alt) then + do j=js,je ; do i=is,ie ; do k=nz,1,-1 + PE_release_h = -0.25*(Kh_u(I,j,k)*(Slope_x_PE(I,j,k)**2) * hN2_x_PE(I,j,k) + & + Kh_u(I-1,j,k)*(Slope_x_PE(I-1,j,k)**2) * hN2_x_PE(I-1,j,k) + & + Kh_v(i,J,k)*(Slope_y_PE(i,J,k)**2) * hN2_y_PE(i,J,k) + & + Kh_v(i,J-1,k)*(Slope_y_PE(i,J-1,k)**2) * hN2_y_PE(i,J-1,k)) + MEKE%GM_src(i,j) = MEKE%GM_src(i,j) + PE_release_h - else - MEKE%GM_src(i,j) = MEKE%GM_src(i,j) + Work_h - endif - endif ; endif - !enddo ; enddo ; enddo ; endif - enddo ; enddo ; endif + enddo ; enddo ; enddo + endif + endif if (CS%id_slope_x > 0) call post_data(CS%id_slope_x, CS%diagSlopeX, CS%diag) if (CS%id_slope_y > 0) call post_data(CS%id_slope_y, CS%diagSlopeY, CS%diag) @@ -2071,9 +2072,6 @@ end subroutine thickness_diffuse_end !! wave-speed or the equivalent barotropic mode wave-speed. !! \f$N_*^2 = \max(N^2,0)\f$ is a non-negative form of the square of the Brunt-Vaisala frequency. !! The parameter \f$\gamma_F\f$ is used to reduce the vertical smoothing length scale. -!! This elliptic form for \f$ \psi \f$ is turned on with the logical KHTH_USE_FGNV_STREAMFUNCTION. -!! -!! Thickness diffusivities are calculated independently at u- and v-points using the following expression !! \f[ !! \kappa_h = \left( \kappa_o + \alpha_{s} L_{s}^2 < S N > + \alpha_{M} \kappa_{M} \right) r(\Delta x,L_d) !! \f] From 584177f56e126218da3c189ad04ee98e40b8421d Mon Sep 17 00:00:00 2001 From: Gustavo Marques Date: Fri, 13 Sep 2019 09:33:59 -0600 Subject: [PATCH 32/72] Deletes whitespace --- src/parameterizations/lateral/MOM_thickness_diffuse.F90 | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/parameterizations/lateral/MOM_thickness_diffuse.F90 b/src/parameterizations/lateral/MOM_thickness_diffuse.F90 index 9d170e57c8..728e384f75 100644 --- a/src/parameterizations/lateral/MOM_thickness_diffuse.F90 +++ b/src/parameterizations/lateral/MOM_thickness_diffuse.F90 @@ -1268,9 +1268,9 @@ subroutine thickness_diffuse_full(h, e, Kh_u, Kh_v, tv, uhD, vhD, cg1, dt, G, GV Work_h = 0.5 * G%IareaT(i,j) * & ((Work_u(I-1,j) + Work_u(I,j)) + (Work_v(i,J-1) + Work_v(i,J))) if (associated(CS%GMwork)) CS%GMwork(i,j) = Work_h - if (associated(MEKE) .and. associated(MEKE%GM_src) .and. .not. CS%GM_src_alt ) then + if (associated(MEKE) .and. associated(MEKE%GM_src) .and. .not. CS%GM_src_alt ) then MEKE%GM_src(i,j) = MEKE%GM_src(i,j) + Work_h - endif + endif enddo ; enddo if (associated(MEKE) .and. associated(MEKE%GM_src) .and. CS%GM_src_alt) then @@ -1279,7 +1279,7 @@ subroutine thickness_diffuse_full(h, e, Kh_u, Kh_v, tv, uhD, vhD, cg1, dt, G, GV Kh_u(I-1,j,k)*(Slope_x_PE(I-1,j,k)**2) * hN2_x_PE(I-1,j,k) + & Kh_v(i,J,k)*(Slope_y_PE(i,J,k)**2) * hN2_y_PE(i,J,k) + & Kh_v(i,J-1,k)*(Slope_y_PE(i,J-1,k)**2) * hN2_y_PE(i,J-1,k)) - + MEKE%GM_src(i,j) = MEKE%GM_src(i,j) + PE_release_h enddo ; enddo ; enddo endif From 466903bd8a85b63ce7c849f9c5da8e700c867970 Mon Sep 17 00:00:00 2001 From: Gustavo Marques Date: Fri, 13 Sep 2019 10:58:44 -0600 Subject: [PATCH 33/72] Deletes more whitespace --- src/parameterizations/lateral/MOM_thickness_diffuse.F90 | 1 - 1 file changed, 1 deletion(-) diff --git a/src/parameterizations/lateral/MOM_thickness_diffuse.F90 b/src/parameterizations/lateral/MOM_thickness_diffuse.F90 index 728e384f75..9a5cfede6f 100644 --- a/src/parameterizations/lateral/MOM_thickness_diffuse.F90 +++ b/src/parameterizations/lateral/MOM_thickness_diffuse.F90 @@ -1279,7 +1279,6 @@ subroutine thickness_diffuse_full(h, e, Kh_u, Kh_v, tv, uhD, vhD, cg1, dt, G, GV Kh_u(I-1,j,k)*(Slope_x_PE(I-1,j,k)**2) * hN2_x_PE(I-1,j,k) + & Kh_v(i,J,k)*(Slope_y_PE(i,J,k)**2) * hN2_y_PE(i,J,k) + & Kh_v(i,J-1,k)*(Slope_y_PE(i,J-1,k)**2) * hN2_y_PE(i,J-1,k)) - MEKE%GM_src(i,j) = MEKE%GM_src(i,j) + PE_release_h enddo ; enddo ; enddo endif From 185235666d2e8799021cc88396849e91ec264bc9 Mon Sep 17 00:00:00 2001 From: Gustavo Marques Date: Mon, 16 Sep 2019 11:13:23 -0600 Subject: [PATCH 34/72] Removes white space --- src/parameterizations/lateral/MOM_hor_visc.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/parameterizations/lateral/MOM_hor_visc.F90 b/src/parameterizations/lateral/MOM_hor_visc.F90 index e9ff06d337..213e9a485f 100644 --- a/src/parameterizations/lateral/MOM_hor_visc.F90 +++ b/src/parameterizations/lateral/MOM_hor_visc.F90 @@ -263,7 +263,7 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, real, dimension(SZIB_(G),SZJB_(G)) :: & dvdx, dudy, & ! components in the shearing strain [s-1] - dDel2vdx, dDel2udy, & ! Components in the biharmonic equivalent of the shearing strain [L-2 T-1 ~> m-2 s-1] + dDel2vdx, dDel2udy, & ! Components in the biharmonic equivalent of the shearing strain [L-2 T-1 ~> m-2 s-1] dvdx_bt, dudy_bt, & ! components in the barotropic shearing strain [s-1] sh_xy, & ! horizontal shearing strain (du/dy + dv/dx) including metric terms [s-1] sh_xy_bt, & ! barotropic horizontal shearing strain (du/dy + dv/dx) inc. metric terms [s-1] From ba2f186aedb18320ca4110729ad65574c6c53e06 Mon Sep 17 00:00:00 2001 From: Gustavo Marques Date: Tue, 17 Sep 2019 09:43:33 -0600 Subject: [PATCH 35/72] Removed diagnostics related to FrictWork_diss and FrictWork_Max * We deleted these terms previously but forgot to remove posting the diagnostics. Thanks to Travis and .testing/tc0 we were able to identidy this mistake. --- .../lateral/MOM_hor_visc.F90 | 19 +------------------ 1 file changed, 1 insertion(+), 18 deletions(-) diff --git a/src/parameterizations/lateral/MOM_hor_visc.F90 b/src/parameterizations/lateral/MOM_hor_visc.F90 index 213e9a485f..b798fb4d86 100644 --- a/src/parameterizations/lateral/MOM_hor_visc.F90 +++ b/src/parameterizations/lateral/MOM_hor_visc.F90 @@ -180,8 +180,7 @@ module MOM_hor_visc integer :: id_GME_coeff_h = -1, id_GME_coeff_q = -1 integer :: id_vort_xy_q = -1, id_div_xx_h = -1 integer :: id_FrictWork = -1, id_FrictWorkIntz = -1 - integer :: id_FrictWorkMax = -1 - integer :: id_FrictWork_diss = -1, id_FrictWork_GME = -1 + integer :: id_FrictWork_GME = -1 !!@} @@ -301,8 +300,6 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, target_diss_rate_GME, & ! the maximum theoretical dissipation plus the amount spuriously dissipated ! by friction [m2 s-3] FrictWork, & ! work done by MKE dissipation mechanisms [W m-2] - FrictWork_diss, & ! negative definite work done by MKE dissipation mechanisms [W m-2] - FrictWorkMax, & ! maximum possible work done by MKE dissipation mechanisms [W m-2] FrictWork_GME, & ! work done by GME [W m-2] div_xx_h ! horizontal divergence [s-1] real, dimension(SZI_(G),SZJ_(G),SZK_(G)) :: & @@ -1283,8 +1280,6 @@ subroutine horizontal_viscosity(u, v, h, diffu, diffv, MEKE, VarMix, G, GV, US, if (CS%id_diffu>0) call post_data(CS%id_diffu, diffu, CS%diag) if (CS%id_diffv>0) call post_data(CS%id_diffv, diffv, CS%diag) if (CS%id_FrictWork>0) call post_data(CS%id_FrictWork, FrictWork, CS%diag) - if (CS%id_FrictWorkMax>0) call post_data(CS%id_FrictWorkMax, FrictWorkMax, CS%diag) - if (CS%id_FrictWork_diss>0) call post_data(CS%id_FrictWork_diss, FrictWork_diss, CS%diag) if (CS%id_FrictWork_GME>0) call post_data(CS%id_FrictWork_GME, FrictWork_GME, CS%diag) if (CS%id_Ah_h>0) call post_data(CS%id_Ah_h, Ah_h, CS%diag) if (CS%id_div_xx_h>0) call post_data(CS%id_div_xx_h, div_xx_h, CS%diag) @@ -2077,18 +2072,6 @@ subroutine hor_visc_init(Time, G, US, param_file, diag, CS, MEKE) CS%id_FrictWork = register_diag_field('ocean_model','FrictWork',diag%axesTL,Time,& 'Integral work done by lateral friction terms', 'W m-2', conversion=US%s_to_T**3*US%L_to_m**2) - CS%id_FrictWork_diss = register_diag_field('ocean_model','FrictWork_diss',diag%axesTL,Time,& - 'Integral work done by lateral friction terms (excluding diffusion of energy)', & - 'W m-2', conversion=US%s_to_T**3*US%L_to_m**2) - - if (associated(MEKE)) then - if (associated(MEKE%mom_src)) then - CS%id_FrictWorkMax = register_diag_field('ocean_model', 'FrictWorkMax', diag%axesTL, Time,& - 'Maximum possible integral work done by lateral friction terms', & - 'W m-2', conversion=US%s_to_T**3*US%L_to_m**2) - endif - endif - CS%id_FrictWorkIntz = register_diag_field('ocean_model','FrictWorkIntz',diag%axesT1,Time, & 'Depth integrated work done by lateral friction', 'W m-2', conversion=US%s_to_T**3*US%L_to_m**2, & cmor_field_name='dispkexyfo', & From 992e82652f73190b330eeec83f2375291e7f7c68 Mon Sep 17 00:00:00 2001 From: Gustavo Marques Date: Tue, 17 Sep 2019 10:23:21 -0600 Subject: [PATCH 36/72] Avoids posting Kv_slow when it is not initialized --- src/parameterizations/vertical/MOM_vert_friction.F90 | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/parameterizations/vertical/MOM_vert_friction.F90 b/src/parameterizations/vertical/MOM_vert_friction.F90 index 1bed36e75e..d286bc815a 100644 --- a/src/parameterizations/vertical/MOM_vert_friction.F90 +++ b/src/parameterizations/vertical/MOM_vert_friction.F90 @@ -1015,7 +1015,8 @@ subroutine vertvisc_coef(u, v, h, forces, visc, dt, G, GV, US, CS, OBC) endif ! Offer diagnostic fields for averaging. - if (CS%id_Kv_slow > 0) call post_data(CS%id_Kv_slow, visc%Kv_slow, CS%diag) + if (associated(visc%Kv_slow) .and. (CS%id_Kv_slow > 0)) & + call post_data(CS%id_Kv_slow, visc%Kv_slow, CS%diag) if (CS%id_Kv_u > 0) call post_data(CS%id_Kv_u, Kv_u, CS%diag) if (CS%id_Kv_v > 0) call post_data(CS%id_Kv_v, Kv_v, CS%diag) if (CS%id_au_vv > 0) call post_data(CS%id_au_vv, CS%a_u, CS%diag) From 353cea1d24689686480b3356f725666d291bc3f3 Mon Sep 17 00:00:00 2001 From: alperaltuntas Date: Tue, 17 Sep 2019 13:22:08 -0600 Subject: [PATCH 37/72] remove unused modules --- config_src/mct_driver/mom_ocean_model_mct.F90 | 1 - config_src/nuopc_driver/mom_ocean_model_nuopc.F90 | 1 - 2 files changed, 2 deletions(-) diff --git a/config_src/mct_driver/mom_ocean_model_mct.F90 b/config_src/mct_driver/mom_ocean_model_mct.F90 index ec894f1ebb..3dd302cf2d 100644 --- a/config_src/mct_driver/mom_ocean_model_mct.F90 +++ b/config_src/mct_driver/mom_ocean_model_mct.F90 @@ -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 diff --git a/config_src/nuopc_driver/mom_ocean_model_nuopc.F90 b/config_src/nuopc_driver/mom_ocean_model_nuopc.F90 index 426c7e9922..a99c1b60eb 100644 --- a/config_src/nuopc_driver/mom_ocean_model_nuopc.F90 +++ b/config_src/nuopc_driver/mom_ocean_model_nuopc.F90 @@ -52,7 +52,6 @@ module MOM_ocean_model_nuopc 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 From c295ce1bdb5760deaea84667eeb4ee6df98ebb2d Mon Sep 17 00:00:00 2001 From: alperaltuntas Date: Tue, 17 Sep 2019 13:24:27 -0600 Subject: [PATCH 38/72] add ncar version of Doxyfile --- docs/Doxyfile_ncar_rtd | 2437 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 2437 insertions(+) create mode 100644 docs/Doxyfile_ncar_rtd diff --git a/docs/Doxyfile_ncar_rtd b/docs/Doxyfile_ncar_rtd new file mode 100644 index 0000000000..46e06ef109 --- /dev/null +++ b/docs/Doxyfile_ncar_rtd @@ -0,0 +1,2437 @@ +# Doxyfile 1.8.12 + +# This file describes the settings to be used by the documentation system +# doxygen (www.doxygen.org) for a project. +# +# All text after a double hash (##) is considered a comment and is placed in +# front of the TAG it is preceding. +# +# All text after a single hash (#) is considered a comment and will be ignored. +# The format is: +# TAG = value [value, ...] +# For lists, items can also be appended using: +# TAG += value [value, ...] +# Values that contain spaces should be placed between quotes (\" \"). + +#--------------------------------------------------------------------------- +# Project related configuration options +#--------------------------------------------------------------------------- + +# This tag specifies the encoding used for all characters in the config file +# that follow. The default is UTF-8 which is also the encoding used for all text +# before the first occurrence of this tag. Doxygen uses libiconv (or the iconv +# built into libc) for the transcoding. See http://www.gnu.org/software/libiconv +# for the list of possible encodings. +# The default value is: UTF-8. + +DOXYFILE_ENCODING = UTF-8 + +# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by +# double-quotes, unless you are using Doxywizard) that should identify the +# project for which the documentation is generated. This name is used in the +# title of most generated pages and in a few other places. +# The default value is: My Project. + +PROJECT_NAME = "MOM6" + +# The PROJECT_NUMBER tag can be used to enter a project or revision number. This +# could be handy for archiving the generated documentation or if some version +# control system is used. + +PROJECT_NUMBER = + +# Using the PROJECT_BRIEF tag one can provide an optional one line description +# for a project that appears at the top of each page and should give viewer a +# quick idea about the purpose of the project. Keep the description short. + +PROJECT_BRIEF = + +# With the PROJECT_LOGO tag one can specify a logo or an icon that is included +# in the documentation. The maximum height of the logo should not exceed 55 +# pixels and the maximum width should not exceed 200 pixels. Doxygen will copy +# the logo to the output directory. + +PROJECT_LOGO = + +# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path +# into which the generated documentation will be written. If a relative path is +# entered, it will be relative to the location where doxygen was started. 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Setting this option to YES will make +# doxygen to replace the get and set methods by a property in the documentation. +# This will only work if the methods are indeed getting or setting a simple +# type. If this is not the case, or you want to show the methods anyway, you +# should set this option to NO. +# The default value is: YES. + +IDL_PROPERTY_SUPPORT = YES + +# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC +# tag is set to YES then doxygen will reuse the documentation of the first +# member in the group (if any) for the other members of the group. By default +# all members of a group must be documented explicitly. +# The default value is: NO. + +DISTRIBUTE_GROUP_DOC = YES + +# If one adds a struct or class to a group and this option is enabled, then also +# any nested class or struct is added to the same group. By default this option +# is disabled and one has to add nested compounds explicitly via \ingroup. +# The default value is: NO. + +GROUP_NESTED_COMPOUNDS = NO + +# Set the SUBGROUPING tag to YES to allow class member groups of the same type +# (for instance a group of public functions) to be put as a subgroup of that +# type (e.g. under the Public Functions section). Set it to NO to prevent +# subgrouping. Alternatively, this can be done per class using the +# \nosubgrouping command. +# The default value is: YES. + +SUBGROUPING = YES + +# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions +# are shown inside the group in which they are included (e.g. using \ingroup) +# instead of on a separate page (for HTML and Man pages) or section (for LaTeX +# and RTF). +# +# Note that this feature does not work in combination with +# SEPARATE_MEMBER_PAGES. +# The default value is: NO. + +INLINE_GROUPED_CLASSES = NO + +# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions +# with only public data fields or simple typedef fields will be shown inline in +# the documentation of the scope in which they are defined (i.e. file, +# namespace, or group documentation), provided this scope is documented. If set +# to NO, structs, classes, and unions are shown on a separate page (for HTML and +# Man pages) or section (for LaTeX and RTF). +# The default value is: NO. + +INLINE_SIMPLE_STRUCTS = NO + +# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or +# enum is documented as struct, union, or enum with the name of the typedef. So +# typedef struct TypeS {} TypeT, will appear in the documentation as a struct +# with name TypeT. When disabled the typedef will appear as a member of a file, +# namespace, or class. And the struct will be named TypeS. This can typically be +# useful for C code in case the coding convention dictates that all compound +# types are typedef'ed and only the typedef is referenced, never the tag name. +# The default value is: NO. + +TYPEDEF_HIDES_STRUCT = NO + +# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This +# cache is used to resolve symbols given their name and scope. Since this can be +# an expensive process and often the same symbol appears multiple times in the +# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small +# doxygen will become slower. If the cache is too large, memory is wasted. The +# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range +# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536 +# symbols. At the end of a run doxygen will report the cache usage and suggest +# the optimal cache size from a speed point of view. +# Minimum value: 0, maximum value: 9, default value: 0. + +LOOKUP_CACHE_SIZE = 0 + +#--------------------------------------------------------------------------- +# Build related configuration options +#--------------------------------------------------------------------------- + +# If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in +# documentation are documented, even if no documentation was available. Private +# class members and static file members will be hidden unless the +# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES. +# Note: This will also disable the warnings about undocumented members that are +# normally produced when WARNINGS is set to YES. +# The default value is: NO. + +EXTRACT_ALL = YES + +# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will +# be included in the documentation. +# The default value is: NO. + +EXTRACT_PRIVATE = YES + +# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal +# scope will be included in the documentation. +# The default value is: NO. + +EXTRACT_PACKAGE = YES + +# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be +# included in the documentation. +# The default value is: NO. + +EXTRACT_STATIC = YES + +# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined +# locally in source files will be included in the documentation. If set to NO, +# only classes defined in header files are included. Does not have any effect +# for Java sources. +# The default value is: YES. + +EXTRACT_LOCAL_CLASSES = YES + +# This flag is only useful for Objective-C code. If set to YES, local methods, +# which are defined in the implementation section but not in the interface are +# included in the documentation. If set to NO, only methods in the interface are +# included. +# The default value is: NO. + +EXTRACT_LOCAL_METHODS = YES + +# If this flag is set to YES, the members of anonymous namespaces will be +# extracted and appear in the documentation as a namespace called +# 'anonymous_namespace{file}', where file will be replaced with the base name of +# the file that contains the anonymous namespace. By default anonymous namespace +# are hidden. +# The default value is: NO. + +EXTRACT_ANON_NSPACES = YES + +# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all +# undocumented members inside documented classes or files. If set to NO these +# members will be included in the various overviews, but no documentation +# section is generated. This option has no effect if EXTRACT_ALL is enabled. +# The default value is: NO. + +HIDE_UNDOC_MEMBERS = NO + +# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all +# undocumented classes that are normally visible in the class hierarchy. If set +# to NO, these classes will be included in the various overviews. This option +# has no effect if EXTRACT_ALL is enabled. +# The default value is: NO. + +HIDE_UNDOC_CLASSES = NO + +# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend +# (class|struct|union) declarations. If set to NO, these declarations will be +# included in the documentation. +# The default value is: NO. + +HIDE_FRIEND_COMPOUNDS = NO + +# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any +# documentation blocks found inside the body of a function. If set to NO, these +# blocks will be appended to the function's detailed documentation block. +# The default value is: NO. + +HIDE_IN_BODY_DOCS = NO + +# The INTERNAL_DOCS tag determines if documentation that is typed after a +# \internal command is included. If the tag is set to NO then the documentation +# will be excluded. Set it to YES to include the internal documentation. +# The default value is: NO. + +INTERNAL_DOCS = YES + +# If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file +# names in lower-case letters. If set to YES, upper-case letters are also +# allowed. This is useful if you have classes or files whose names only differ +# in case and if your file system supports case sensitive file names. Windows +# and Mac users are advised to set this option to NO. +# The default value is: system dependent. + +CASE_SENSE_NAMES = YES + +# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with +# their full class and namespace scopes in the documentation. If set to YES, the +# scope will be hidden. +# The default value is: NO. + +HIDE_SCOPE_NAMES = NO + +# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will +# append additional text to a page's title, such as Class Reference. If set to +# YES the compound reference will be hidden. +# The default value is: NO. + +HIDE_COMPOUND_REFERENCE= NO + +# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of +# the files that are included by a file in the documentation of that file. +# The default value is: YES. + +SHOW_INCLUDE_FILES = YES + +# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each +# grouped member an include statement to the documentation, telling the reader +# which file to include in order to use the member. +# The default value is: NO. + +SHOW_GROUPED_MEMB_INC = NO + +# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include +# files with double quotes in the documentation rather than with sharp brackets. +# The default value is: NO. + +FORCE_LOCAL_INCLUDES = NO + +# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the +# documentation for inline members. +# The default value is: YES. + +INLINE_INFO = YES + +# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the +# (detailed) documentation of file and class members alphabetically by member +# name. If set to NO, the members will appear in declaration order. +# The default value is: YES. + +SORT_MEMBER_DOCS = YES + +# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief +# descriptions of file, namespace and class members alphabetically by member +# name. If set to NO, the members will appear in declaration order. Note that +# this will also influence the order of the classes in the class list. +# The default value is: NO. + +SORT_BRIEF_DOCS = NO + +# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the +# (brief and detailed) documentation of class members so that constructors and +# destructors are listed first. If set to NO the constructors will appear in the +# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS. +# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief +# member documentation. +# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting +# detailed member documentation. +# The default value is: NO. + +SORT_MEMBERS_CTORS_1ST = NO + +# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy +# of group names into alphabetical order. If set to NO the group names will +# appear in their defined order. +# The default value is: NO. + +SORT_GROUP_NAMES = NO + +# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by +# fully-qualified names, including namespaces. If set to NO, the class list will +# be sorted only by class name, not including the namespace part. +# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. +# Note: This option applies only to the class list, not to the alphabetical +# list. +# The default value is: NO. + +SORT_BY_SCOPE_NAME = NO + +# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper +# type resolution of all parameters of a function it will reject a match between +# the prototype and the implementation of a member function even if there is +# only one candidate or it is obvious which candidate to choose by doing a +# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still +# accept a match between prototype and implementation in such cases. +# The default value is: NO. + +STRICT_PROTO_MATCHING = NO + +# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo +# list. This list is created by putting \todo commands in the documentation. +# The default value is: YES. + +GENERATE_TODOLIST = NO + +# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test +# list. This list is created by putting \test commands in the documentation. +# The default value is: YES. + +GENERATE_TESTLIST = YES + +# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug +# list. This list is created by putting \bug commands in the documentation. +# The default value is: YES. + +GENERATE_BUGLIST = YES + +# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO) +# the deprecated list. This list is created by putting \deprecated commands in +# the documentation. +# The default value is: YES. + +GENERATE_DEPRECATEDLIST= YES + +# The ENABLED_SECTIONS tag can be used to enable conditional documentation +# sections, marked by \if ... \endif and \cond +# ... \endcond blocks. + +ENABLED_SECTIONS = + +# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the +# initial value of a variable or macro / define can have for it to appear in the +# documentation. If the initializer consists of more lines than specified here +# it will be hidden. Use a value of 0 to hide initializers completely. The +# appearance of the value of individual variables and macros / defines can be +# controlled using \showinitializer or \hideinitializer command in the +# documentation regardless of this setting. +# Minimum value: 0, maximum value: 10000, default value: 30. + +MAX_INITIALIZER_LINES = 30 + +# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at +# the bottom of the documentation of classes and structs. If set to YES, the +# list will mention the files that were used to generate the documentation. +# The default value is: YES. + +SHOW_USED_FILES = YES + +# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This +# will remove the Files entry from the Quick Index and from the Folder Tree View +# (if specified). +# The default value is: YES. + +SHOW_FILES = YES + +# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces +# page. This will remove the Namespaces entry from the Quick Index and from the +# Folder Tree View (if specified). +# The default value is: YES. + +SHOW_NAMESPACES = YES + +# The FILE_VERSION_FILTER tag can be used to specify a program or script that +# doxygen should invoke to get the current version for each file (typically from +# the version control system). Doxygen will invoke the program by executing (via +# popen()) the command command input-file, where command is the value of the +# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided +# by doxygen. Whatever the program writes to standard output is used as the file +# version. For an example see the documentation. + +FILE_VERSION_FILTER = + +# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed +# by doxygen. The layout file controls the global structure of the generated +# output files in an output format independent way. To create the layout file +# that represents doxygen's defaults, run doxygen with the -l option. You can +# optionally specify a file name after the option, if omitted DoxygenLayout.xml +# will be used as the name of the layout file. +# +# Note that if you run doxygen from a directory containing a file called +# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE +# tag is left empty. + +LAYOUT_FILE = + +# The CITE_BIB_FILES tag can be used to specify one or more bib files containing +# the reference definitions. This must be a list of .bib files. The .bib +# extension is automatically appended if omitted. This requires the bibtex tool +# to be installed. See also http://en.wikipedia.org/wiki/BibTeX for more info. +# For LaTeX the style of the bibliography can be controlled using +# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the +# search path. See also \cite for info how to create references. + +CITE_BIB_FILES = + +#--------------------------------------------------------------------------- +# Configuration options related to warning and progress messages +#--------------------------------------------------------------------------- + +# The QUIET tag can be used to turn on/off the messages that are generated to +# standard output by doxygen. If QUIET is set to YES this implies that the +# messages are off. +# The default value is: NO. + +QUIET = NO + +# The WARNINGS tag can be used to turn on/off the warning messages that are +# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES +# this implies that the warnings are on. +# +# Tip: Turn warnings on while writing the documentation. +# The default value is: YES. + +WARNINGS = YES + +# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate +# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag +# will automatically be disabled. +# The default value is: YES. + +WARN_IF_UNDOCUMENTED = YES + +# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for +# potential errors in the documentation, such as not documenting some parameters +# in a documented function, or documenting parameters that don't exist or using +# markup commands wrongly. +# The default value is: YES. + +WARN_IF_DOC_ERROR = YES + +# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that +# are documented, but have no documentation for their parameters or return +# value. If set to NO, doxygen will only warn about wrong or incomplete +# parameter documentation, but not about the absence of documentation. +# The default value is: NO. + +WARN_NO_PARAMDOC = NO + +# If the WARN_AS_ERROR tag is set to YES then doxygen will immediately stop when +# a warning is encountered. +# The default value is: NO. + +WARN_AS_ERROR = NO + +# The WARN_FORMAT tag determines the format of the warning messages that doxygen +# can produce. The string should contain the $file, $line, and $text tags, which +# will be replaced by the file and line number from which the warning originated +# and the warning text. Optionally the format may contain $version, which will +# be replaced by the version of the file (if it could be obtained via +# FILE_VERSION_FILTER) +# The default value is: $file:$line: $text. + +WARN_FORMAT = "$file:$line: $text" + +# The WARN_LOGFILE tag can be used to specify a file to which warning and error +# messages should be written. If left blank the output is written to standard +# error (stderr). + +WARN_LOGFILE = doxygen.log + +#--------------------------------------------------------------------------- +# Configuration options related to the input files +#--------------------------------------------------------------------------- + +# The INPUT tag is used to specify the files and/or directories that contain +# documented source files. You may enter file names like myfile.cpp or +# directories like /usr/src/myproject. Separate the files or directories with +# spaces. +# Note: If this tag is empty the current directory is searched. + +INPUT = ../src \ + ../config_src/solo_driver \ + ../config_src/mct_driver \ + ../config_src/nuopc_driver \ + +# This tag can be used to specify the character encoding of the source files +# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses +# libiconv (or the iconv built into libc) for the transcoding. See the libiconv +# documentation (see: http://www.gnu.org/software/libiconv) for the list of +# possible encodings. +# The default value is: UTF-8. + +INPUT_ENCODING = UTF-8 + +# If the value of the INPUT tag contains directories, you can use the +# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and +# *.h) to filter out the source-files in the directories. +# +# Note that for custom extensions or not directly supported extensions you also +# need to set EXTENSION_MAPPING for the extension otherwise the files are not +# read by doxygen. +# +# If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cpp, +# *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h, +# *.hh, *.hxx, *.hpp, *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc, +# *.m, *.markdown, *.md, *.mm, *.dox, *.py, *.pyw, *.f90, *.f, *.for, *.tcl, +# *.vhd, *.vhdl, *.ucf and *.qsf. + +FILE_PATTERNS = *.c \ + *.cc \ + *.cxx \ + *.cpp \ + *.c++ \ + *.h \ + *.hh \ + *.hxx \ + *.hpp \ + *.h++ \ + *.inc \ + *.m \ + *.markdown \ + *.md \ + *.mm \ + *.dox \ + *.f90 \ + *.f \ + *.for \ + *.F90 + +# The RECURSIVE tag can be used to specify whether or not subdirectories should +# be searched for input files as well. +# The default value is: NO. + +RECURSIVE = YES + +# The EXCLUDE tag can be used to specify files and/or directories that should be +# excluded from the INPUT source files. This way you can easily exclude a +# subdirectory from a directory tree whose root is specified with the INPUT tag. +# +# Note that relative paths are relative to the directory from which doxygen is +# run. + +EXCLUDE = ../src/equation_of_state/TEOS10 + +# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or +# directories that are symbolic links (a Unix file system feature) are excluded +# from the input. +# The default value is: NO. + +EXCLUDE_SYMLINKS = NO + +# If the value of the INPUT tag contains directories, you can use the +# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude +# certain files from those directories. +# +# Note that the wildcards are matched against the file with absolute path, so to +# exclude all test directories for example use the pattern */test/* + +EXCLUDE_PATTERNS = makedep.py Makefile INSTALL + +# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names +# (namespaces, classes, functions, etc.) that should be excluded from the +# output. The symbol name can be a fully qualified name, a word, or if the +# wildcard * is used, a substring. Examples: ANamespace, AClass, +# AClass::ANamespace, ANamespace::*Test +# +# Note that the wildcards are matched against the file with absolute path, so to +# exclude all test directories use the pattern */test/* + +EXCLUDE_SYMBOLS = + +# The EXAMPLE_PATH tag can be used to specify one or more files or directories +# that contain example code fragments that are included (see the \include +# command). + +EXAMPLE_PATH = ../src + +# If the value of the EXAMPLE_PATH tag contains directories, you can use the +# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and +# *.h) to filter out the source-files in the directories. If left blank all +# files are included. + +EXAMPLE_PATTERNS = * + +# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be +# searched for input files to be used with the \include or \dontinclude commands +# irrespective of the value of the RECURSIVE tag. +# The default value is: NO. + +EXAMPLE_RECURSIVE = NO + +# The IMAGE_PATH tag can be used to specify one or more files or directories +# that contain images that are to be included in the documentation (see the +# \image command). + +IMAGE_PATH = images ../src + +# The INPUT_FILTER tag can be used to specify a program that doxygen should +# invoke to filter for each input file. Doxygen will invoke the filter program +# by executing (via popen()) the command: +# +# +# +# where is the value of the INPUT_FILTER tag, and is the +# name of an input file. Doxygen will then use the output that the filter +# program writes to standard output. If FILTER_PATTERNS is specified, this tag +# will be ignored. +# +# Note that the filter must not add or remove lines; it is applied before the +# code is scanned, but not when the output code is generated. If lines are added +# or removed, the anchors will not be placed correctly. +# +# Note that for custom extensions or not directly supported extensions you also +# need to set EXTENSION_MAPPING for the extension otherwise the files are not +# properly processed by doxygen. + +INPUT_FILTER = + +# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern +# basis. Doxygen will compare the file name with each pattern and apply the +# filter if there is a match. The filters are a list of the form: pattern=filter +# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how +# filters are used. If the FILTER_PATTERNS tag is empty or if none of the +# patterns match the file name, INPUT_FILTER is applied. +# +# Note that for custom extensions or not directly supported extensions you also +# need to set EXTENSION_MAPPING for the extension otherwise the files are not +# properly processed by doxygen. + +FILTER_PATTERNS = + +# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using +# INPUT_FILTER) will also be used to filter the input files that are used for +# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES). +# The default value is: NO. + +FILTER_SOURCE_FILES = NO + +# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file +# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and +# it is also possible to disable source filtering for a specific pattern using +# *.ext= (so without naming a filter). +# This tag requires that the tag FILTER_SOURCE_FILES is set to YES. + +FILTER_SOURCE_PATTERNS = + +# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that +# is part of the input, its contents will be placed on the main page +# (index.html). This can be useful if you have a project on for instance GitHub +# and want to reuse the introduction page also for the doxygen output. + +USE_MDFILE_AS_MAINPAGE = ../README.md + +#--------------------------------------------------------------------------- +# Configuration options related to source browsing +#--------------------------------------------------------------------------- + +# If the SOURCE_BROWSER tag is set to YES then a list of source files will be +# generated. Documented entities will be cross-referenced with these sources. +# +# Note: To get rid of all source code in the generated output, make sure that +# also VERBATIM_HEADERS is set to NO. +# The default value is: NO. + +SOURCE_BROWSER = YES + +# Setting the INLINE_SOURCES tag to YES will include the body of functions, +# classes and enums directly into the documentation. +# The default value is: NO. + +INLINE_SOURCES = YES + +# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any +# special comment blocks from generated source code fragments. Normal C, C++ and +# Fortran comments will always remain visible. +# The default value is: YES. + +STRIP_CODE_COMMENTS = NO + +# If the REFERENCED_BY_RELATION tag is set to YES then for each documented +# function all documented functions referencing it will be listed. +# The default value is: NO. + +REFERENCED_BY_RELATION = YES + +# If the REFERENCES_RELATION tag is set to YES then for each documented function +# all documented entities called/used by that function will be listed. +# The default value is: NO. + +REFERENCES_RELATION = YES + +# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set +# to YES then the hyperlinks from functions in REFERENCES_RELATION and +# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will +# link to the documentation. +# The default value is: YES. + +REFERENCES_LINK_SOURCE = NO + +# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the +# source code will show a tooltip with additional information such as prototype, +# brief description and links to the definition and documentation. Since this +# will make the HTML file larger and loading of large files a bit slower, you +# can opt to disable this feature. +# The default value is: YES. +# This tag requires that the tag SOURCE_BROWSER is set to YES. + +SOURCE_TOOLTIPS = YES + +# If the USE_HTAGS tag is set to YES then the references to source code will +# point to the HTML generated by the htags(1) tool instead of doxygen built-in +# source browser. The htags tool is part of GNU's global source tagging system +# (see http://www.gnu.org/software/global/global.html). You will need version +# 4.8.6 or higher. +# +# To use it do the following: +# - Install the latest version of global +# - Enable SOURCE_BROWSER and USE_HTAGS in the config file +# - Make sure the INPUT points to the root of the source tree +# - Run doxygen as normal +# +# Doxygen will invoke htags (and that will in turn invoke gtags), so these +# tools must be available from the command line (i.e. in the search path). +# +# The result: instead of the source browser generated by doxygen, the links to +# source code will now point to the output of htags. +# The default value is: NO. +# This tag requires that the tag SOURCE_BROWSER is set to YES. + +USE_HTAGS = NO + +# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a +# verbatim copy of the header file for each class for which an include is +# specified. Set to NO to disable this. +# See also: Section \class. +# The default value is: YES. + +VERBATIM_HEADERS = YES + +#--------------------------------------------------------------------------- +# Configuration options related to the alphabetical class index +#--------------------------------------------------------------------------- + +# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all +# compounds will be generated. Enable this if the project contains a lot of +# classes, structs, unions or interfaces. +# The default value is: YES. + +ALPHABETICAL_INDEX = YES + +# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in +# which the alphabetical index list will be split. +# Minimum value: 1, maximum value: 20, default value: 5. +# This tag requires that the tag ALPHABETICAL_INDEX is set to YES. + +COLS_IN_ALPHA_INDEX = 1 + +# In case all classes in a project start with a common prefix, all classes will +# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag +# can be used to specify a prefix (or a list of prefixes) that should be ignored +# while generating the index headers. +# This tag requires that the tag ALPHABETICAL_INDEX is set to YES. + +IGNORE_PREFIX = + +#--------------------------------------------------------------------------- +# Configuration options related to the HTML output +#--------------------------------------------------------------------------- + +# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output +# The default value is: YES. + +GENERATE_HTML = NO + +# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a +# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of +# it. +# The default directory is: html. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_OUTPUT = APIs + +# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each +# generated HTML page (for example: .htm, .php, .asp). +# The default value is: .html. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_FILE_EXTENSION = .html + +# The HTML_HEADER tag can be used to specify a user-defined HTML header file for +# each generated HTML page. If the tag is left blank doxygen will generate a +# standard header. +# +# To get valid HTML the header file that includes any scripts and style sheets +# that doxygen needs, which is dependent on the configuration options used (e.g. +# the setting GENERATE_TREEVIEW). It is highly recommended to start with a +# default header using +# doxygen -w html new_header.html new_footer.html new_stylesheet.css +# YourConfigFile +# and then modify the file new_header.html. See also section "Doxygen usage" +# for information on how to generate the default header that doxygen normally +# uses. +# Note: The header is subject to change so you typically have to regenerate the +# default header when upgrading to a newer version of doxygen. For a description +# of the possible markers and block names see the documentation. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_HEADER = dox_rtd_header.html + +# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each +# generated HTML page. If the tag is left blank doxygen will generate a standard +# footer. See HTML_HEADER for more information on how to generate a default +# footer and what special commands can be used inside the footer. See also +# section "Doxygen usage" for information on how to generate the default footer +# that doxygen normally uses. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_FOOTER = dox_rtd_footer.html + +# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style +# sheet that is used by each HTML page. It can be used to fine-tune the look of +# the HTML output. If left blank doxygen will generate a default style sheet. +# See also section "Doxygen usage" for information on how to generate the style +# sheet that doxygen normally uses. +# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as +# it is more robust and this tag (HTML_STYLESHEET) will in the future become +# obsolete. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_STYLESHEET = + +# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined +# cascading style sheets that are included after the standard style sheets +# created by doxygen. Using this option one can overrule certain style aspects. +# This is preferred over using HTML_STYLESHEET since it does not replace the +# standard style sheet and is therefore more robust against future updates. +# Doxygen will copy the style sheet files to the output directory. +# Note: The order of the extra style sheet files is of importance (e.g. the last +# style sheet in the list overrules the setting of the previous ones in the +# list). For an example see the documentation. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_EXTRA_STYLESHEET = + +# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or +# other source files which should be copied to the HTML output directory. Note +# that these files will be copied to the base HTML output directory. Use the +# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these +# files. In the HTML_STYLESHEET file, use the file name only. Also note that the +# files will be copied as-is; there are no commands or markers available. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_EXTRA_FILES = + +# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen +# will adjust the colors in the style sheet and background images according to +# this color. Hue is specified as an angle on a colorwheel, see +# http://en.wikipedia.org/wiki/Hue for more information. For instance the value +# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300 +# purple, and 360 is red again. +# Minimum value: 0, maximum value: 359, default value: 220. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_HUE = 220 + +# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors +# in the HTML output. For a value of 0 the output will use grayscales only. A +# value of 255 will produce the most vivid colors. +# Minimum value: 0, maximum value: 255, default value: 100. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_SAT = 100 + +# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the +# luminance component of the colors in the HTML output. Values below 100 +# gradually make the output lighter, whereas values above 100 make the output +# darker. The value divided by 100 is the actual gamma applied, so 80 represents +# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not +# change the gamma. +# Minimum value: 40, maximum value: 240, default value: 80. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_GAMMA = 80 + +# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML +# page will contain the date and time when the page was generated. Setting this +# to YES can help to show when doxygen was last run and thus if the +# to NO can help when comparing the output of multiple runs. +# The default value is: YES. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_TIMESTAMP = NO + +# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML +# documentation will contain sections that can be hidden and shown after the +# page has loaded. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_DYNAMIC_SECTIONS = NO + +# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries +# shown in the various tree structured indices initially; the user can expand +# and collapse entries dynamically later on. Doxygen will expand the tree to +# such a level that at most the specified number of entries are visible (unless +# a fully collapsed tree already exceeds this amount). So setting the number of +# entries 1 will produce a full collapsed tree by default. 0 is a special value +# representing an infinite number of entries and will result in a full expanded +# tree by default. +# Minimum value: 0, maximum value: 9999, default value: 100. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_INDEX_NUM_ENTRIES = 900 + +# If the GENERATE_DOCSET tag is set to YES, additional index files will be +# generated that can be used as input for Apple's Xcode 3 integrated development +# environment (see: http://developer.apple.com/tools/xcode/), introduced with +# OSX 10.5 (Leopard). To create a documentation set, doxygen will generate a +# Makefile in the HTML output directory. Running make will produce the docset in +# that directory and running make install will install the docset in +# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at +# startup. See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html +# for more information. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_DOCSET = NO + +# This tag determines the name of the docset feed. A documentation feed provides +# an umbrella under which multiple documentation sets from a single provider +# (such as a company or product suite) can be grouped. +# The default value is: Doxygen generated docs. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_FEEDNAME = "Doxygen generated docs" + +# This tag specifies a string that should uniquely identify the documentation +# set bundle. This should be a reverse domain-name style string, e.g. +# com.mycompany.MyDocSet. Doxygen will append .docset to the name. +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_BUNDLE_ID = org.doxygen.Project + +# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify +# the documentation publisher. This should be a reverse domain-name style +# string, e.g. com.mycompany.MyDocSet.documentation. +# The default value is: org.doxygen.Publisher. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_PUBLISHER_ID = org.doxygen.Publisher + +# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher. +# The default value is: Publisher. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_PUBLISHER_NAME = Publisher + +# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three +# additional HTML index files: index.hhp, index.hhc, and index.hhk. The +# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop +# (see: http://www.microsoft.com/en-us/download/details.aspx?id=21138) on +# Windows. +# +# The HTML Help Workshop contains a compiler that can convert all HTML output +# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML +# files are now used as the Windows 98 help format, and will replace the old +# Windows help format (.hlp) on all Windows platforms in the future. Compressed +# HTML files also contain an index, a table of contents, and you can search for +# words in the documentation. The HTML workshop also contains a viewer for +# compressed HTML files. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_HTMLHELP = NO + +# The CHM_FILE tag can be used to specify the file name of the resulting .chm +# file. You can add a path in front of the file if the result should not be +# written to the html output directory. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +CHM_FILE = + +# The HHC_LOCATION tag can be used to specify the location (absolute path +# including file name) of the HTML help compiler (hhc.exe). If non-empty, +# doxygen will try to run the HTML help compiler on the generated index.hhp. +# The file has to be specified with full path. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +HHC_LOCATION = + +# The GENERATE_CHI flag controls if a separate .chi index file is generated +# (YES) or that it should be included in the master .chm file (NO). +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +GENERATE_CHI = NO + +# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc) +# and project file content. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +CHM_INDEX_ENCODING = + +# The BINARY_TOC flag controls whether a binary table of contents is generated +# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it +# enables the Previous and Next buttons. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +BINARY_TOC = NO + +# The TOC_EXPAND flag can be set to YES to add extra items for group members to +# the table of contents of the HTML help documentation and to the tree view. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +TOC_EXPAND = NO + +# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and +# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that +# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help +# (.qch) of the generated HTML documentation. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_QHP = NO + +# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify +# the file name of the resulting .qch file. The path specified is relative to +# the HTML output folder. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QCH_FILE = + +# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help +# Project output. For more information please see Qt Help Project / Namespace +# (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#namespace). +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_NAMESPACE = org.doxygen.Project + +# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt +# Help Project output. For more information please see Qt Help Project / Virtual +# Folders (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#virtual- +# folders). +# The default value is: doc. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_VIRTUAL_FOLDER = doc + +# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom +# filter to add. For more information please see Qt Help Project / Custom +# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom- +# filters). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_CUST_FILTER_NAME = + +# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the +# custom filter to add. For more information please see Qt Help Project / Custom +# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom- +# filters). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_CUST_FILTER_ATTRS = + +# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this +# project's filter section matches. Qt Help Project / Filter Attributes (see: +# http://qt-project.org/doc/qt-4.8/qthelpproject.html#filter-attributes). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_SECT_FILTER_ATTRS = + +# The QHG_LOCATION tag can be used to specify the location of Qt's +# qhelpgenerator. If non-empty doxygen will try to run qhelpgenerator on the +# generated .qhp file. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHG_LOCATION = + +# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be +# generated, together with the HTML files, they form an Eclipse help plugin. To +# install this plugin and make it available under the help contents menu in +# Eclipse, the contents of the directory containing the HTML and XML files needs +# to be copied into the plugins directory of eclipse. The name of the directory +# within the plugins directory should be the same as the ECLIPSE_DOC_ID value. +# After copying Eclipse needs to be restarted before the help appears. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_ECLIPSEHELP = NO + +# A unique identifier for the Eclipse help plugin. When installing the plugin +# the directory name containing the HTML and XML files should also have this +# name. Each documentation set should have its own identifier. +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES. + +ECLIPSE_DOC_ID = org.doxygen.Project + +# If you want full control over the layout of the generated HTML pages it might +# be necessary to disable the index and replace it with your own. The +# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top +# of each HTML page. A value of NO enables the index and the value YES disables +# it. Since the tabs in the index contain the same information as the navigation +# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +DISABLE_INDEX = YES + +# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index +# structure should be generated to display hierarchical information. If the tag +# value is set to YES, a side panel will be generated containing a tree-like +# index structure (just like the one that is generated for HTML Help). For this +# to work a browser that supports JavaScript, DHTML, CSS and frames is required +# (i.e. any modern browser). Windows users are probably better off using the +# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can +# further fine-tune the look of the index. As an example, the default style +# sheet generated by doxygen has an example that shows how to put an image at +# the root of the tree instead of the PROJECT_NAME. Since the tree basically has +# the same information as the tab index, you could consider setting +# DISABLE_INDEX to YES when enabling this option. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_TREEVIEW = NO + +# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that +# doxygen will group on one line in the generated HTML documentation. +# +# Note that a value of 0 will completely suppress the enum values from appearing +# in the overview section. +# Minimum value: 0, maximum value: 20, default value: 4. +# This tag requires that the tag GENERATE_HTML is set to YES. + +ENUM_VALUES_PER_LINE = 4 + +# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used +# to set the initial width (in pixels) of the frame in which the tree is shown. +# Minimum value: 0, maximum value: 1500, default value: 250. +# This tag requires that the tag GENERATE_HTML is set to YES. + +TREEVIEW_WIDTH = 250 + +# If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to +# external symbols imported via tag files in a separate window. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +EXT_LINKS_IN_WINDOW = YES + +# Use this tag to change the font size of LaTeX formulas included as images in +# the HTML documentation. When you change the font size after a successful +# doxygen run you need to manually remove any form_*.png images from the HTML +# output directory to force them to be regenerated. +# Minimum value: 8, maximum value: 50, default value: 10. +# This tag requires that the tag GENERATE_HTML is set to YES. + +FORMULA_FONTSIZE = 10 + +# Use the FORMULA_TRANPARENT tag to determine whether or not the images +# generated for formulas are transparent PNGs. Transparent PNGs are not +# supported properly for IE 6.0, but are supported on all modern browsers. +# +# Note that when changing this option you need to delete any form_*.png files in +# the HTML output directory before the changes have effect. +# The default value is: YES. +# This tag requires that the tag GENERATE_HTML is set to YES. + +FORMULA_TRANSPARENT = YES + +# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see +# http://www.mathjax.org) which uses client side Javascript for the rendering +# instead of using pre-rendered bitmaps. Use this if you do not have LaTeX +# installed or if you want to formulas look prettier in the HTML output. When +# enabled you may also need to install MathJax separately and configure the path +# to it using the MATHJAX_RELPATH option. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +USE_MATHJAX = YES + +# When MathJax is enabled you can set the default output format to be used for +# the MathJax output. See the MathJax site (see: +# http://docs.mathjax.org/en/latest/output.html) for more details. +# Possible values are: HTML-CSS (which is slower, but has the best +# compatibility), NativeMML (i.e. MathML) and SVG. +# The default value is: HTML-CSS. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_FORMAT = HTML-CSS + +# When MathJax is enabled you need to specify the location relative to the HTML +# output directory using the MATHJAX_RELPATH option. The destination directory +# should contain the MathJax.js script. For instance, if the mathjax directory +# is located at the same level as the HTML output directory, then +# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax +# Content Delivery Network so you can quickly see the result without installing +# MathJax. However, it is strongly recommended to install a local copy of +# MathJax from http://www.mathjax.org before deployment. +# The default value is: http://cdn.mathjax.org/mathjax/latest. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_RELPATH = http://cdn.mathjax.org/mathjax/latest + +# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax +# extension names that should be enabled during MathJax rendering. For example +# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_EXTENSIONS = + +# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces +# of code that will be used on startup of the MathJax code. See the MathJax site +# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an +# example see the documentation. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_CODEFILE = + +# When the SEARCHENGINE tag is enabled doxygen will generate a search box for +# the HTML output. The underlying search engine uses javascript and DHTML and +# should work on any modern browser. Note that when using HTML help +# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET) +# there is already a search function so this one should typically be disabled. +# For large projects the javascript based search engine can be slow, then +# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to +# search using the keyboard; to jump to the search box use + S +# (what the is depends on the OS and browser, but it is typically +# , /