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Merge branch 'dev/master' of github.com:NOAA-GFDL/MOM6 into dev/master
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@kshedstrom
kshedstrom committed Jun 30, 2016
2 parents 7ee3e4d + 14200da commit ad3219b
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110 changes: 68 additions & 42 deletions src/core/MOM.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -86,8 +86,9 @@ module MOM
use MOM_dyn_horgrid, only : dyn_horgrid_type, create_dyn_horgrid, destroy_dyn_horgrid
use MOM_EOS, only : EOS_init
use MOM_error_checking, only : check_redundant
use MOM_grid, only : MOM_grid_init, ocean_grid_type, MOM_grid_end
use MOM_hor_index, only : hor_index_type
use MOM_grid, only : ocean_grid_type, set_first_direction
use MOM_grid, only : MOM_grid_init, MOM_grid_end
use MOM_hor_index, only : hor_index_type, hor_index_init
use MOM_hor_visc, only : horizontal_viscosity, hor_visc_init
use MOM_interface_heights, only : find_eta
use MOM_lateral_mixing_coeffs, only : calc_slope_functions, VarMix_init
Expand Down Expand Up @@ -1366,10 +1367,11 @@ subroutine initialize_MOM(Time, param_file, dirs, CS, Time_in)
!! model is not being started from a restart file

! local
type(ocean_grid_type), pointer :: G ! pointer to a structure with metrics and related
type(ocean_grid_type), pointer :: G => NULL() ! A pointer to a structure with metrics and related
type(hor_index_type) :: HI ! A hor_index_type for array extents
type(verticalGrid_type), pointer :: GV => NULL()
type(dyn_horgrid_type), pointer :: dG => NULL()
type(diag_ctrl), pointer :: diag
type(diag_ctrl), pointer :: diag

character(len=4), parameter :: vers_num = 'v2.0'

Expand All @@ -1385,7 +1387,6 @@ subroutine initialize_MOM(Time, param_file, dirs, CS, Time_in)
real, allocatable, dimension(:,:) :: eta ! free surface height (m) or bottom press (Pa)
type(MOM_restart_CS), pointer :: restart_CSp_tmp => NULL()

integer :: nkml, nkbl, verbosity, write_geom
real :: default_val ! default value for a parameter
logical :: write_geom_files ! If true, write out the grid geometry files.
logical :: new_sim
Expand All @@ -1395,6 +1396,15 @@ subroutine initialize_MOM(Time, param_file, dirs, CS, Time_in)
logical :: save_IC ! If true, save the initial conditions.
logical :: do_unit_tests ! If true, call unit tests.
logical :: test_grid_copy = .false.
logical :: global_indexing ! If true use global horizontal index values instead
! of having the data domain on each processor start at 1.
logical :: bathy_at_vel ! If true, also define bathymetric fields at the
! the velocity points.
integer :: first_direction ! An integer that indicates which direction is to be
! updated first in directionally split parts of the
! calculation. This can be altered during the course
! of the run via calls to set_first_direction.
integer :: nkml, nkbl, verbosity, write_geom

type(time_type) :: Start_time
type(ocean_internal_state) :: MOM_internal_state
Expand Down Expand Up @@ -1487,6 +1497,11 @@ subroutine initialize_MOM(Time, param_file, dirs, CS, Time_in)
"If true, do thickness diffusion before dynamics.\n"//&
"This is only used if THICKNESSDIFFUSE is true.", &
default=.false.)
call get_param(param_file, "MOM", "BATHYMETRY_AT_VEL", bathy_at_vel, &
"If true, there are separate values for the basin depths \n"//&
"at velocity points. Otherwise the effects of topography \n"//&
"are entirely determined from thickness points.", &
default=.false.)

call get_param(param_file, "MOM", "DEBUG", CS%debug, &
"If true, write out verbose debugging data.", default=.false.)
Expand Down Expand Up @@ -1582,6 +1597,21 @@ subroutine initialize_MOM(Time, param_file, dirs, CS, Time_in)
default=2)
endif

call get_param(param_file, "MOM", "GLOBAL_INDEXING", global_indexing, &
"If true, use a global lateral indexing convention, so \n"//&
"that corresponding points on different processors have \n"//&
"the same index. This does not work with static memory.", &
default=.false., layoutParam=.true.)
#ifdef STATIC_MEMORY_
if (global_indexing) call MOM_error(FATAL, "initialize_MOM: "//&
"GLOBAL_INDEXING can not be true with STATIC_MEMORY.")
#endif
call get_param(param_file, "MOM", "FIRST_DIRECTION", first_direction, &
"An integer that indicates which direction goes first \n"//&
"in parts of the code that use directionally split \n"//&
"updates, with even numbers (or 0) used for x- first \n"//&
"and odd numbers used for y-first.", default=0)

call get_param(param_file, "MOM", "CHECK_BAD_SURFACE_VALS", &
CS%check_bad_surface_vals, &
"If true, check the surface state for ridiculous values.", &
Expand Down Expand Up @@ -1632,6 +1662,9 @@ subroutine initialize_MOM(Time, param_file, dirs, CS, Time_in)
"MOM: ENABLE_THERMODYNAMICS must be defined to use USE_EOS.")
if (CS%adiabatic .and. CS%bulkmixedlayer) call MOM_error(FATAL, &
"MOM: ADIABATIC and BULKMIXEDLAYER can not both be defined.")
if (CS%bulkmixedlayer .and. .not.use_EOS) call MOM_error(FATAL, &
"initialize_MOM: A bulk mixed layer can only be used with T & S as "//&
"state variables. Add USE_EOS = True to MOM_input.")

call callTree_waypoint("MOM parameters read (initialize_MOM)")

Expand All @@ -1652,20 +1685,18 @@ subroutine initialize_MOM(Time, param_file, dirs, CS, Time_in)
call callTree_waypoint("domains initialized (initialize_MOM)")

call MOM_checksums_init(param_file)

call diag_mediator_infrastructure_init()
call MOM_io_init(param_file)
call MOM_grid_init(G, param_file)

call create_dyn_horgrid(dG, G%HI)
dG%first_direction = G%first_direction
dG%bathymetry_at_vel = G%bathymetry_at_vel
call hor_index_init(G%Domain, HI, param_file, &
local_indexing=.not.global_indexing)

call create_dyn_horgrid(dG, HI, bathymetry_at_vel=bathy_at_vel)
call clone_MOM_domain(G%Domain, dG%Domain)

call verticalGridInit( param_file, CS%GV )
GV => CS%GV
dG%g_Earth = GV%g_Earth ; G%g_Earth = GV%g_Earth

! dG%g_Earth = GV%g_Earth

! Allocate the auxiliary non-symmetric domain for debugging or I/O purposes.
if (CS%debug .or. dG%symmetric) &
Expand All @@ -1678,10 +1709,6 @@ subroutine initialize_MOM(Time, param_file, dirs, CS, Time_in)

call tracer_registry_init(param_file, CS%tracer_Reg)

! Copy a common variable from the vertical grid to the horizontal grid.
! Consider removing this later?
! G%ke = GV%ke

is = dG%isc ; ie = dG%iec ; js = dG%jsc ; je = dG%jec ; nz = GV%ke
isd = dG%isd ; ied = dG%ied ; jsd = dG%jsd ; jed = dG%jed
IsdB = dG%IsdB ; IedB = dG%IedB ; JsdB = dG%JsdB ; JedB = dG%JedB
Expand All @@ -1702,8 +1729,8 @@ subroutine initialize_MOM(Time, param_file, dirs, CS, Time_in)
CS%vd_S = var_desc(name="S",units="PPT",longname="Salinity",&
cmor_field_name="so",cmor_units="ppt", &
conversion=0.001)
call register_tracer(CS%tv%T, CS%vd_T, param_file, G%HI, GV, CS%tracer_Reg, CS%vd_T)
call register_tracer(CS%tv%S, CS%vd_S, param_file, G%HI, GV, CS%tracer_Reg, CS%vd_S)
call register_tracer(CS%tv%T, CS%vd_T, param_file, dG%HI, GV, CS%tracer_Reg, CS%vd_T)
call register_tracer(CS%tv%S, CS%vd_S, param_file, dG%HI, GV, CS%tracer_Reg, CS%vd_S)
endif
if (CS%use_frazil) then
allocate(CS%tv%frazil(isd:ied,jsd:jed)) ; CS%tv%frazil(:,:) = 0.0
Expand All @@ -1713,11 +1740,7 @@ subroutine initialize_MOM(Time, param_file, dirs, CS, Time_in)
endif

if (CS%bulkmixedlayer) then
if (.not.use_EOS) call MOM_error(FATAL, &
"initialize_MOM: A bulk mixed layer can only be used with T & S as "//&
"state variables. Add #define USE_EOS.")
GV%nkml = nkml
GV%nk_rho_varies = nkml + nkbl
GV%nkml = nkml ; GV%nk_rho_varies = nkml + nkbl
allocate(CS%tv%Hml(isd:ied,jsd:jed)) ; CS%tv%Hml(:,:) = 0.0
else
GV%nkml = 0 ; GV%nk_rho_varies = 0
Expand Down Expand Up @@ -1770,30 +1793,30 @@ subroutine initialize_MOM(Time, param_file, dirs, CS, Time_in)
call set_restart_fields(GV, param_file, CS)
if (CS%split) then
if (CS%legacy_split) then
call register_restarts_dyn_legacy_split(G%HI, GV, param_file, &
call register_restarts_dyn_legacy_split(dG%HI, GV, param_file, &
CS%dyn_legacy_split_CSp, CS%restart_CSp, CS%uh, CS%vh)
else
call register_restarts_dyn_split_RK2(G%HI, GV, param_file, &
call register_restarts_dyn_split_RK2(dG%HI, GV, param_file, &
CS%dyn_split_RK2_CSp, CS%restart_CSp, CS%uh, CS%vh)
endif
else
if (CS%use_RK2) then
call register_restarts_dyn_unsplit_RK2(G%HI, GV, param_file, &
call register_restarts_dyn_unsplit_RK2(dG%HI, GV, param_file, &
CS%dyn_unsplit_RK2_CSp, CS%restart_CSp)
else
call register_restarts_dyn_unsplit(G%HI, GV, param_file, &
call register_restarts_dyn_unsplit(dG%HI, GV, param_file, &
CS%dyn_unsplit_CSp, CS%restart_CSp)
endif
endif

! This subroutine calls user-specified tracer registration routines.
! Additional calls can be added to MOM_tracer_flow_control.F90.
call call_tracer_register(G%HI, GV, param_file, CS%tracer_flow_CSp, &
call call_tracer_register(dG%HI, GV, param_file, CS%tracer_flow_CSp, &
CS%tracer_Reg, CS%restart_CSp)

call MEKE_alloc_register_restart(G%HI, param_file, CS%MEKE, CS%restart_CSp)
call set_visc_register_restarts(G%HI, GV, param_file, CS%visc, CS%restart_CSp)
call mixedlayer_restrat_register_restarts(G%HI, param_file, CS%mixedlayer_restrat_CSp, CS%restart_CSp)
call MEKE_alloc_register_restart(dG%HI, param_file, CS%MEKE, CS%restart_CSp)
call set_visc_register_restarts(dG%HI, GV, param_file, CS%visc, CS%restart_CSp)
call mixedlayer_restrat_register_restarts(dG%HI, param_file, CS%mixedlayer_restrat_CSp, CS%restart_CSp)

! Initialize fields
call callTree_waypoint("restart registration complete (initialize_MOM)")
Expand All @@ -1810,16 +1833,22 @@ subroutine initialize_MOM(Time, param_file, dirs, CS, Time_in)
call callTree_waypoint("returned from ALE_init() (initialize_MOM)")
endif

! Shift from using the temporary dynamic grid type to using the final (potentially
! static) ocean grid type.
! call clone_MOM_domain(dG%Domain, CS%G%Domain)
! call MOM_grid_init(CS%G, param_file)
! Shift from using the temporary dynamic grid type to using the final
! (potentially static) ocean-specific grid type.
! The next line would be needed if G%Domain had not already been init'd above:
! call clone_MOM_domain(dG%Domain, G%Domain)
call MOM_grid_init(G, param_file, HI, bathymetry_at_vel=bathy_at_vel)
call copy_dyngrid_to_MOM_grid(dG, G)
call destroy_dyn_horgrid(dG)

call copy_dyngrid_to_MOM_grid(dg, G)
! Set a few remaining fields that are specific to the ocean grid type.
call set_first_direction(G, first_direction)
! Allocate the auxiliary non-symmetric domain for debugging or I/O purposes.
if (CS%debug .or. G%symmetric) &
call clone_MOM_domain(G%Domain, G%Domain_aux, symmetric=.false.)
G%ke = GV%ke
! Copy common variables from the vertical grid to the horizontal grid.
! Consider removing this later?
G%ke = GV%ke ; G%g_Earth = GV%g_Earth

call MOM_initialize_state(CS%u, CS%v, CS%h, CS%tv, Time, G, GV, param_file, &
dirs, CS%restart_CSp, CS%ALE_CSp, CS%tracer_Reg, &
Expand All @@ -1828,7 +1857,7 @@ subroutine initialize_MOM(Time, param_file, dirs, CS, Time_in)
call callTree_waypoint("returned from MOM_initialize_state() (initialize_MOM)")

! From this point, there may be pointers being set, so the final grid type
! that will persist through the run has to be used.
! that will persist throughout the run has to be used.

if (test_grid_copy) then
! Copy the data from the temporary grid to the dyn_hor_grid to CS%G.
Expand All @@ -1840,17 +1869,14 @@ subroutine initialize_MOM(Time, param_file, dirs, CS, Time_in)

call copy_MOM_grid_to_dyngrid(G, dg)
call copy_dyngrid_to_MOM_grid(dg, CS%G)
! Copy a common variable from the vertical grid to the horizontal grid.
! Consider removing this later?
CS%G%ke = GV%ke

call destroy_dyn_horgrid(dG)
call MOM_grid_end(G) ; deallocate(G)

G => CS%G

if (CS%debug .or. CS%G%symmetric) &
call clone_MOM_domain(CS%G%Domain, CS%G%Domain_aux, symmetric=.false.)
G%ke = GV%ke ; G%g_Earth = GV%g_Earth
endif


Expand Down
56 changes: 25 additions & 31 deletions src/core/MOM_grid.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -151,52 +151,36 @@ module MOM_grid

!~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~!
!> MOM_grid_init initializes the ocean grid array sizes and grid memory.
subroutine MOM_grid_init(G, param_file, HI)
subroutine MOM_grid_init(G, param_file, HI, global_indexing, bathymetry_at_vel)
type(ocean_grid_type), intent(inout) :: G !< The horizontal grid type
type(param_file_type), intent(in) :: param_file !< Parameter file handle
type(hor_index_type), optional, intent(in) :: HI !< A hor_index_type for array extents
! Arguments: G - The ocean's grid structure.
! (in) param_file - A structure indicating the open file to parse for
! model parameter values.
type(hor_index_type), &
optional, intent(in) :: HI !< A hor_index_type for array extents
logical, optional, intent(in) :: global_indexing !< If true use global index
!! values instead of having the data domain on each
!! processor start at 1.
logical, optional, intent(in) :: bathymetry_at_vel !< If true, there are
!! separate values for the ocean bottom depths at
!! velocity points. Otherwise the effects of topography
!! are entirely determined from thickness points.

! This include declares and sets the variable "version".
#include "version_variable.h"
integer :: isd, ied, jsd, jed, nk
integer :: IsdB, IedB, JsdB, JedB
integer :: ied_max, jed_max
integer :: niblock, njblock, nihalo, njhalo, nblocks, n, i, j
logical :: global_indexing ! If true use global index values instead of having
logical :: local_indexing ! If false use global index values instead of having
! the data domain on each processor start at 1.

integer, allocatable, dimension(:) :: ibegin, iend, jbegin, jend
character(len=40) :: mod_nm = "MOM_grid" ! This module's name.


! Read all relevant parameters and write them to the model log.
call log_version(param_file, mod_nm, version, &
"Parameters providing information about the lateral grid.")
! call get_param(param_file, "MOM", "G_EARTH", G%g_Earth, &
! "The gravitational acceleration of the Earth.", &
! units="m s-2", default = 9.80)
call get_param(param_file, mod_nm, "GLOBAL_INDEXING", global_indexing, &
"If true, use a global lateral indexing convention, so \n"//&
"that corresponding points on different processors have \n"//&
"the same index. This does not work with static memory.", &
default=.false., layoutParam=.true.)
#ifdef STATIC_MEMORY_
if (global_indexing) call MOM_error(FATAL, "MOM_grid_init : "//&
"GLOBAL_INDEXING can not be true with STATIC_MEMORY.")
#endif
call get_param(param_file, mod_nm, "FIRST_DIRECTION", G%first_direction, &
"An integer that indicates which direction goes first \n"//&
"in parts of the code that use directionally split \n"//&
"updates, with even numbers (or 0) used for x- first \n"//&
"and odd numbers used for y-first.", default=0)

call get_param(param_file, mod_nm, "BATHYMETRY_AT_VEL", G%bathymetry_at_vel, &
"If true, there are separate values for the basin depths \n"//&
"at velocity points. Otherwise the effects of of \n"//&
"topography are entirely determined from thickness points.", &
default=.false.)


call get_param(param_file, mod_nm, "NIBLOCK", niblock, "The number of blocks "// &
"in the x-direction on each processor (for openmp).", default=1, &
Expand All @@ -220,16 +204,18 @@ subroutine MOM_grid_init(G, param_file, HI)
G%isd_global = G%isd + HI%idg_offset ; G%jsd_global = G%jsd + HI%jdg_offset
G%symmetric = HI%symmetric
else
local_indexing = .true.
if (present(global_indexing)) local_indexing = .not.global_indexing
call hor_index_init(G%Domain, G%HI, param_file, &
local_indexing=.not.global_indexing)
local_indexing=local_indexing)

! get_domain_extent ensures that domains start at 1 for compatibility between
! static and dynamically allocated arrays, unless global_indexing is true.
call get_domain_extent(G%Domain, G%isc, G%iec, G%jsc, G%jec, &
G%isd, G%ied, G%jsd, G%jed, &
G%isg, G%ieg, G%jsg, G%jeg, &
G%idg_offset, G%jdg_offset, G%symmetric, &
local_indexing=.not.global_indexing)
local_indexing=local_indexing)
G%isd_global = G%isd+G%idg_offset ; G%jsd_global = G%jsd+G%jdg_offset
endif

Expand All @@ -254,6 +240,9 @@ subroutine MOM_grid_init(G, param_file, HI)

isd = G%isd ; ied = G%ied ; jsd = G%jsd ; jed = G%jed
IsdB = G%IsdB ; IedB = G%IedB ; JsdB = G%JsdB ; JedB = G%JedB

G%bathymetry_at_vel = .false.
if (present(bathymetry_at_vel)) G%bathymetry_at_vel = bathymetry_at_vel
if (G%bathymetry_at_vel) then
ALLOC_(G%Dblock_u(IsdB:IedB, jsd:jed)) ; G%Dblock_u(:,:) = 0.0
ALLOC_(G%Dopen_u(IsdB:IedB, jsd:jed)) ; G%Dopen_u(:,:) = 0.0
Expand Down Expand Up @@ -535,6 +524,11 @@ subroutine MOM_grid_end(G)
DEALLOC_(G%dF_dx) ; DEALLOC_(G%dF_dy)
DEALLOC_(G%sin_rot) ; DEALLOC_(G%cos_rot)

if (G%bathymetry_at_vel) then
DEALLOC_(G%Dblock_u) ; DEALLOC_(G%Dopen_u)
DEALLOC_(G%Dblock_v) ; DEALLOC_(G%Dopen_v)
endif

deallocate(G%gridLonT) ; deallocate(G%gridLatT)
deallocate(G%gridLonB) ; deallocate(G%gridLatB)

Expand Down
2 changes: 0 additions & 2 deletions src/core/MOM_transcribe_grid.F90
View file
Original file line number Diff line number Diff line change
Expand Up @@ -139,7 +139,6 @@ subroutine copy_dyngrid_to_MOM_grid(dG, oG)
oG%south_lat = dG%south_lat ; oG%west_lon = dG%west_lon
oG%len_lat = dG%len_lat ; oG%len_lon = dG%len_lon
oG%Rad_Earth = dG%Rad_Earth ; oG%max_depth = dG%max_depth
oG%g_Earth = dG%g_Earth

! Update the halos in case the dynamic grid has smaller halos than the ocean grid.
call pass_var(oG%areaT, oG%Domain)
Expand Down Expand Up @@ -290,7 +289,6 @@ subroutine copy_MOM_grid_to_dyngrid(oG, dG)
dG%south_lat = oG%south_lat ; dG%west_lon = oG%west_lon
dG%len_lat = oG%len_lat ; dG%len_lon = oG%len_lon
dG%Rad_Earth = oG%Rad_Earth ; dG%max_depth = oG%max_depth
dG%g_Earth = oG%g_Earth

! Update the halos in case the dynamic grid has smaller halos than the ocean grid.
call pass_var(dG%areaT, dG%Domain)
Expand Down
2 changes: 1 addition & 1 deletion src/core/MOM_verticalGrid.F90
View file
Original file line number Diff line number Diff line change
Expand Up @@ -100,7 +100,7 @@ subroutine verticalGridInit( param_file, GV )
! Read all relevant parameters and write them to the model log.
call log_version(param_file, mod, version, &
"Parameters providing information about the vertical grid.")
call get_param(param_file, "MOM", "G_EARTH", GV%g_Earth, &
call get_param(param_file, mod, "G_EARTH", GV%g_Earth, &
"The gravitational acceleration of the Earth.", &
units="m s-2", default = 9.80)
call get_param(param_file, mod, "RHO_0", GV%Rho0, &
Expand Down
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