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Final changes before PR
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Andrew Shao committed Jun 16, 2017
1 parent ce44698 commit d96c87b
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1 change: 1 addition & 0 deletions src/core/MOM.F90
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Expand Up @@ -4214,3 +4214,4 @@ end subroutine MOM_end


end module MOM

6 changes: 4 additions & 2 deletions src/tracer/MOM_offline_aux.F90
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@@ -1,7 +1,8 @@
!> Contains routines related to offline transport of tracers
!> Contains routines related to offline transport of tracers. These routines are likely to be called from
!> the MOM_offline_main module
module MOM_offline_aux
! This file is part of MOM6. See LICENSE.md for the license.

! This file is part of MOM6. See LICENSE.md for the license.
use mpp_domains_mod, only : CENTER, CORNER, NORTH, EAST
use data_override_mod, only : data_override_init, data_override
use MOM_time_manager, only : time_type, operator(-)
Expand Down Expand Up @@ -800,3 +801,4 @@ function next_modulo_time(inidx, numtime)
end function next_modulo_time

end module MOM_offline_aux

101 changes: 58 additions & 43 deletions src/tracer/MOM_offline_main.F90
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@@ -1,6 +1,8 @@
!> The routines here implement the offline tracer algorithm used in MOM6. These are called from step_offline
!! Some routines called here can be found in the MOM_offline_aux module.
module MOM_offline_main

use mpp_domains_mod, only : CENTER, CORNER, NORTH, EAST
use mpp_domains_mod, only : CENTER, CORNER, NORTH, EAST
use MOM_ALE, only : ALE_CS, ALE_main_offline, ALE_offline_inputs, ALE_offline_tracer_final
use MOM_checksums, only : hchksum, uvchksum
use MOM_cpu_clock, only : cpu_clock_id, cpu_clock_begin, cpu_clock_end
Expand Down Expand Up @@ -41,34 +43,34 @@ module MOM_offline_main
type, public :: offline_transport_CS ; private

!> Pointers to relevant fields from the main MOM control structure
type(ALE_CS), pointer :: ALE_CSp => NULL()
type(diabatic_CS), pointer :: diabatic_CSp => NULL()
type(diag_ctrl), pointer :: diag => NULL()
type(ocean_OBC_type), pointer :: OBC => NULL()
type(tracer_advect_CS), pointer :: tracer_adv_CSp => NULL()
type(tracer_flow_control_CS), pointer :: tracer_flow_CSp => NULL()
type(tracer_registry_type), pointer :: tracer_Reg => NULL()
type(thermo_var_ptrs), pointer :: tv => NULL()
type(ocean_grid_type), pointer :: G => NULL()
type(verticalGrid_type), pointer :: GV => NULL()
type(optics_type), pointer :: optics => NULL()
type(opacity_CS), pointer :: opacity_CSp => NULL()
type(ALE_CS), pointer :: ALE_CSp => NULL()
type(diabatic_CS), pointer :: diabatic_CSp => NULL()
type(diag_ctrl), pointer :: diag => NULL()
type(ocean_OBC_type), pointer :: OBC => NULL()
type(tracer_advect_CS), pointer :: tracer_adv_CSp => NULL()
type(tracer_flow_control_CS), pointer :: tracer_flow_CSp => NULL()
type(tracer_registry_type), pointer :: tracer_Reg => NULL()
type(thermo_var_ptrs), pointer :: tv => NULL()
type(ocean_grid_type), pointer :: G => NULL()
type(verticalGrid_type), pointer :: GV => NULL()
type(optics_type), pointer :: optics => NULL()
type(opacity_CS), pointer :: opacity_CSp => NULL()

!> Variables related to reading in fields from online run
integer :: start_index !< Timelevel to start
integer :: iter_no !< Timelevel to start
integer :: numtime !< How many timelevels in the input fields
integer :: accumulated_time !< Length of time accumulated in the current offline interval
integer :: & !< Index of each of the variables to be read in
ridx_sum = -1, & !! Separate indices for each variabile if they are
ridx_sum = -1, & !! Separate indices for each variable if they are
ridx_snap = -1 !! setoff from each other in time
integer :: nk_input !! Number of input levels in the input fields
character(len=200) :: offlinedir ! Directory where offline fields are stored
character(len=200) :: & !< ! Names of input files
surf_file, &
snap_file, &
sum_file, &
mean_file
character(len=200) :: & ! Names of input files
surf_file, & !< Contains surface fields (2d arrays)
snap_file, & !< Snapshotted fields (layer thicknesses)
sum_file, & !< Fields which are accumulated over time
mean_file !< Fields averaged over time
character(len=20) :: redistribute_method !< 'barotropic' if evenly distributing extra flow
!! throughout entire watercolumn, 'upwards',
!! if trying to do it just in the layers above
Expand Down Expand Up @@ -137,21 +139,18 @@ module MOM_offline_main
real, allocatable, dimension(:,:,:) :: vhtr

! Fields at T-point
real ALLOCABLE_, dimension(NIMEM_,NJMEM_,NKMEM_) :: &
eatr, & ! Amount of fluid entrained from the layer above within
! one time step (m for Bouss, kg/m^2 for non-Bouss)
ebtr ! Amount of fluid entrained from the layer below within
! one time step (m for Bouss, kg/m^2 for non-Bouss)
real, allocatable, dimension(:,:,:) :: &
eatr, & !< Amount of fluid entrained from the layer above within
!! one time step (m for Bouss, kg/m^2 for non-Bouss)
ebtr !< Amount of fluid entrained from the layer below within
!! one time step (m for Bouss, kg/m^2 for non-Bouss)
! Fields at T-points on interfaces
real, allocatable, dimension(:,:,:) :: Kd
real, allocatable, dimension(:,:,:) :: Kd !< Vertical diffusivity
real, allocatable, dimension(:,:,:) :: h_end !< Thicknesses at the end of offline timestep

! Arrays for temperature and salinity
real, allocatable, dimension(NIMEM_,NJMEM_,NKMEM_) :: &
h_end
real ALLOCABLE_, dimension(NIMEM_,NJMEM_) :: &
netMassIn, netMassOut
real, allocatable, dimension(:,:) :: &
mld ! Mixed layer depths at thickness points, in H.
real, allocatable, dimension(:,:) :: netMassIn !< Freshwater fluxes into the ocean
real, allocatable, dimension(:,:) :: netMassOut !< Freshwater fluxes out of the ocean
real, allocatable, dimension(:,:) :: mld !< Mixed layer depths at thickness points, in H.

!> Allocatable arrays to read in entire fields during initialization
real, allocatable, dimension(:,:,:,:) :: &
Expand Down Expand Up @@ -611,6 +610,9 @@ real function remaining_transport_sum(CS, uhtr, vhtr)

end function remaining_transport_sum

!> The vertical/diabatic driver for offline tracers. First the eatr/ebtr associated with the interpolated
!! vertical diffusivities are calculated and then any tracer column functions are done which can include
!! vertical diffuvities and source/sink terms.
subroutine offline_diabatic_ale(fluxes, Time_start, Time_end, CS, h_pre, eatr, ebtr)

type(forcing), intent(inout) :: fluxes !< pointers to forcing fields
Expand Down Expand Up @@ -1356,11 +1358,11 @@ subroutine offline_transport_init(param_file, CS, diabatic_CSp, G, GV)
! Allocate arrays
allocate(CS%uhtr(IsdB:IedB,jsd:jed,nz)) ; CS%uhtr(:,:,:) = 0.0
allocate(CS%vhtr(isd:ied,JsdB:JedB,nz)) ; CS%vhtr(:,:,:) = 0.0
ALLOC_(CS%eatr(isd:ied,jsd:jed,nz)) ; CS%eatr(:,:,:) = 0.0
ALLOC_(CS%ebtr(isd:ied,jsd:jed,nz)) ; CS%ebtr(:,:,:) = 0.0
allocate(CS%eatr(isd:ied,jsd:jed,nz)) ; CS%eatr(:,:,:) = 0.0
allocate(CS%ebtr(isd:ied,jsd:jed,nz)) ; CS%ebtr(:,:,:) = 0.0
allocate(CS%h_end(isd:ied,jsd:jed,nz)) ; CS%h_end(:,:,:) = 0.0
ALLOC_(CS%netMassOut(G%isd:G%ied,G%jsd:G%jed)) ; CS%netMassOut(:,:) = 0.0
ALLOC_(CS%netMassIn(G%isd:G%ied,G%jsd:G%jed)) ; CS%netMassIn(:,:) = 0.0
allocate(CS%netMassOut(G%isd:G%ied,G%jsd:G%jed)) ; CS%netMassOut(:,:) = 0.0
allocate(CS%netMassIn(G%isd:G%ied,G%jsd:G%jed)) ; CS%netMassIn(:,:) = 0.0
allocate(CS%Kd(isd:ied,jsd:jed,nz+1)) ; CS%Kd = 0.
if (CS%read_mld) then
allocate(CS%mld(G%isd:G%ied,G%jsd:G%jed)) ; CS%mld(:,:) = 0.0
Expand All @@ -1380,6 +1382,8 @@ subroutine offline_transport_init(param_file, CS, diabatic_CSp, G, GV)

end subroutine offline_transport_init

!> Coordinates the allocation and reading in all time levels of uh, vh, hend, temp, and salt from files. Used
!! when read_all_ts_uvh
subroutine read_all_input(CS)
type(offline_transport_CS), pointer, intent(inout) :: CS

Expand Down Expand Up @@ -1425,13 +1429,23 @@ end subroutine read_all_input
subroutine offline_transport_end(CS)
type(offline_transport_CS), pointer, intent(inout) :: CS

DEALLOC_(CS%uhtr)
DEALLOC_(CS%vhtr)
DEALLOC_(CS%eatr)
DEALLOC_(CS%ebtr)
DEALLOC_(CS%h_end)
DEALLOC_(CS%netMassOut)
DEALLOC_(CS%netMassIn)
! Explicitly allocate all allocatable arrays
deallocate(CS%uhtr)
deallocate(CS%vhtr)
deallocate(CS%eatr)
deallocate(CS%ebtr)
deallocate(CS%h_end)
deallocate(CS%netMassOut)
deallocate(CS%netMassIn)
deallocate(CS%Kd)
if (CS%read_mld) deallocate(CS%mld)
if (CS%read_all_ts_uvh) then
deallocate(CS%uhtr_all)
deallocate(CS%vhtr_all)
deallocate(CS%hend_all)
deallocate(CS%temp_all)
deallocate(CS%salt_all)
endif

deallocate(CS)

Expand Down Expand Up @@ -1517,3 +1531,4 @@ end subroutine offline_transport_end
!! and 'none' which does no redistribution"

end module MOM_offline_main

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