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implement restart for internal tides (#463)
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* implement restart for internal tides

* add a call to register restart diabatic in MOM

* register restart diabatic call register restart internal tides

* internal tides restart uses the extra_axes optional argument

* support for extra_axes added to MOM_restart/MOM_io

* implement 4d restart/ parallel_restart not working

* add proper documentation for extra axes

* fix read restart for 4d array

* passes global_file optional arg to allow reading
  in parallel restart files

* write one restart variable per vertical mode

  vertical modes >= 6 do not propagate hence there is no need for dynamic array size on this dimension

---------

Co-authored-by: Raphael Dussin <[email protected]>
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raphaeldussin and Raphael Dussin authored Sep 8, 2023
1 parent 1577ae1 commit 1d35fa1
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Showing 5 changed files with 371 additions and 101 deletions.
11 changes: 10 additions & 1 deletion src/core/MOM.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -62,6 +62,7 @@ module MOM
use MOM_coord_initialization, only : MOM_initialize_coord, write_vertgrid_file
use MOM_diabatic_driver, only : diabatic, diabatic_driver_init, diabatic_CS, extract_diabatic_member
use MOM_diabatic_driver, only : adiabatic, adiabatic_driver_init, diabatic_driver_end
use MOM_diabatic_driver, only : register_diabatic_restarts
use MOM_stochastics, only : stochastics_init, update_stochastics, stochastic_CS
use MOM_diagnostics, only : calculate_diagnostic_fields, MOM_diagnostics_init
use MOM_diagnostics, only : register_transport_diags, post_transport_diagnostics
Expand Down Expand Up @@ -94,6 +95,7 @@ module MOM
use MOM_interface_heights, only : find_eta, calc_derived_thermo, thickness_to_dz
use MOM_interface_filter, only : interface_filter, interface_filter_init, interface_filter_end
use MOM_interface_filter, only : interface_filter_CS
use MOM_internal_tides, only : int_tide_CS
use MOM_lateral_mixing_coeffs, only : calc_slope_functions, VarMix_init, VarMix_end
use MOM_lateral_mixing_coeffs, only : calc_resoln_function, calc_depth_function, VarMix_CS
use MOM_MEKE, only : MEKE_alloc_register_restart, step_forward_MEKE
Expand Down Expand Up @@ -409,6 +411,8 @@ module MOM
type(ALE_sponge_CS), pointer :: ALE_sponge_CSp => NULL()
!< Pointer to the oda incremental update control structure
type(oda_incupd_CS), pointer :: oda_incupd_CSp => NULL()
!< Pointer to the internal tides control structure
type(int_tide_CS), pointer :: int_tide_CSp => NULL()
!< Pointer to the ALE-mode sponge control structure
type(ALE_CS), pointer :: ALE_CSp => NULL()
!< Pointer to the Arbitrary Lagrangian Eulerian (ALE) vertical coordinate control structure
Expand Down Expand Up @@ -1964,6 +1968,7 @@ subroutine initialize_MOM(Time, Time_init, param_file, dirs, CS, &
type(ice_shelf_CS), optional, pointer :: ice_shelf_CSp !< A pointer to an ice shelf control structure
type(Wave_parameters_CS), &
optional, pointer :: Waves_CSp !< An optional pointer to a wave property CS

! local variables
type(ocean_grid_type), pointer :: G => NULL() ! A pointer to the metric grid use for the run
type(ocean_grid_type), pointer :: G_in => NULL() ! Pointer to the input grid
Expand Down Expand Up @@ -2774,6 +2779,10 @@ subroutine initialize_MOM(Time, Time_init, param_file, dirs, CS, &
call stoch_EOS_register_restarts(HI, param_file, CS%stoch_eos_CS, restart_CSp)
endif

if (.not. CS%adiabatic) then
call register_diabatic_restarts(G, US, param_file, CS%int_tide_CSp, restart_CSp)
endif

call callTree_waypoint("restart registration complete (initialize_MOM)")
call restart_registry_lock(restart_CSp)

Expand Down Expand Up @@ -3139,7 +3148,7 @@ subroutine initialize_MOM(Time, Time_init, param_file, dirs, CS, &
else
call diabatic_driver_init(Time, G, GV, US, param_file, CS%use_ALE_algorithm, diag, &
CS%ADp, CS%CDp, CS%diabatic_CSp, CS%tracer_flow_CSp, &
CS%sponge_CSp, CS%ALE_sponge_CSp, CS%oda_incupd_CSp)
CS%sponge_CSp, CS%ALE_sponge_CSp, CS%oda_incupd_CSp, CS%int_tide_CSp)
endif

if (associated(CS%sponge_CSp)) &
Expand Down
71 changes: 51 additions & 20 deletions src/framework/MOM_io.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -148,6 +148,20 @@ module MOM_io
module procedure read_attribute_int32, read_attribute_int64
end interface read_attribute

!> Type that stores information that can be used to create a non-decomposed axis.
type :: axis_info
character(len=32) :: name = "" !< The name of this axis for use in files
character(len=256) :: longname = "" !< A longer name describing this axis
character(len=48) :: units = "" !< The units of the axis labels
character(len=8) :: cartesian = "N" !< A variable indicating which direction
!! this axis corresponds with. Valid values
!! include 'X', 'Y', 'Z', 'T', and 'N' for none.
integer :: sense = 0 !< This is 1 for axes whose values increase upward, or -1
!! if they increase downward. The default, 0, is ignored.
integer :: ax_size = 0 !< The number of elements in this axis
real, allocatable, dimension(:) :: ax_data !< The values of the data on the axis [arbitrary]
end type axis_info

!> Type for describing a 3-d variable for output
type, public :: vardesc
character(len=64) :: name !< Variable name in a NetCDF file
Expand All @@ -165,22 +179,9 @@ module MOM_io
character(len=32) :: dim_names(5) !< The names in the file of the axes for this variable
integer :: position = -1 !< An integer encoding the horizontal position, it may
!! CENTER, CORNER, EAST_FACE, NORTH_FACE, or 0.
type(axis_info) :: extra_axes(5) !< dimensions other than space-time
end type vardesc

!> Type that stores information that can be used to create a non-decomposed axis.
type :: axis_info ; private
character(len=32) :: name = "" !< The name of this axis for use in files
character(len=256) :: longname = "" !< A longer name describing this axis
character(len=48) :: units = "" !< The units of the axis labels
character(len=8) :: cartesian = "N" !< A variable indicating which direction
!! this axis corresponds with. Valid values
!! include 'X', 'Y', 'Z', 'T', and 'N' for none.
integer :: sense = 0 !< This is 1 for axes whose values increase upward, or -1
!! if they increase downward. The default, 0, is ignored.
integer :: ax_size = 0 !< The number of elements in this axis
real, allocatable, dimension(:) :: ax_data !< The values of the data on the axis [arbitrary]
end type axis_info

!> Type that stores for a global file attribute
type :: attribute_info ; private
character(len=:), allocatable :: name !< The name of this attribute
Expand Down Expand Up @@ -271,7 +272,8 @@ subroutine create_MOM_file(IO_handle, filename, vars, novars, fields, &
!! required if the new file uses any
!! vertical grid axes.
integer(kind=int64), optional, intent(in) :: checksums(:,:) !< checksums of vars
type(axis_info), optional, intent(in) :: extra_axes(:) !< Types with information about
type(axis_info), dimension(:), &
optional, intent(in) :: extra_axes !< Types with information about
!! some axes that might be used in this file
type(attribute_info), optional, intent(in) :: global_atts(:) !< Global attributes to
!! write to this file
Expand Down Expand Up @@ -1751,7 +1753,8 @@ end subroutine verify_variable_units
!! have default values that are empty strings or are appropriate for a 3-d
!! tracer field at the tracer cell centers.
function var_desc(name, units, longname, hor_grid, z_grid, t_grid, cmor_field_name, &
cmor_units, cmor_longname, conversion, caller, position, dim_names, fixed) result(vd)
cmor_units, cmor_longname, conversion, caller, position, dim_names, &
extra_axes, fixed) result(vd)
character(len=*), intent(in) :: name !< variable name
character(len=*), optional, intent(in) :: units !< variable units
character(len=*), optional, intent(in) :: longname !< variable long name
Expand All @@ -1772,6 +1775,8 @@ function var_desc(name, units, longname, hor_grid, z_grid, t_grid, cmor_field_na
!! NORTH_FACE, and 0 for no horizontal dimensions.
character(len=*), dimension(:), &
optional, intent(in) :: dim_names !< The names of the dimensions of this variable
type(axis_info), dimension(:), &
optional, intent(in) :: extra_axes !< dimensions other than space-time
logical, optional, intent(in) :: fixed !< If true, this does not evolve with time
type(vardesc) :: vd !< vardesc type that is created

Expand All @@ -1795,15 +1800,17 @@ function var_desc(name, units, longname, hor_grid, z_grid, t_grid, cmor_field_na
call modify_vardesc(vd, units=units, longname=longname, hor_grid=hor_grid, &
z_grid=z_grid, t_grid=t_grid, position=position, dim_names=dim_names, &
cmor_field_name=cmor_field_name, cmor_units=cmor_units, &
cmor_longname=cmor_longname, conversion=conversion, caller=cllr)
cmor_longname=cmor_longname, conversion=conversion, caller=cllr, &
extra_axes=extra_axes)

end function var_desc


!> This routine modifies the named elements of a vardesc type.
!! All arguments are optional, except the vardesc type to be modified.
subroutine modify_vardesc(vd, name, units, longname, hor_grid, z_grid, t_grid, &
cmor_field_name, cmor_units, cmor_longname, conversion, caller, position, dim_names)
cmor_field_name, cmor_units, cmor_longname, conversion, caller, position, dim_names, &
extra_axes)
type(vardesc), intent(inout) :: vd !< vardesc type that is modified
character(len=*), optional, intent(in) :: name !< name of variable
character(len=*), optional, intent(in) :: units !< units of variable
Expand All @@ -1825,6 +1832,8 @@ subroutine modify_vardesc(vd, name, units, longname, hor_grid, z_grid, t_grid, &
!! NORTH_FACE, and 0 for no horizontal dimensions.
character(len=*), dimension(:), &
optional, intent(in) :: dim_names !< The names of the dimensions of this variable
type(axis_info), dimension(:), &
optional, intent(in) :: extra_axes !< dimensions other than space-time

character(len=120) :: cllr
integer :: n
Expand Down Expand Up @@ -1877,6 +1886,12 @@ subroutine modify_vardesc(vd, name, units, longname, hor_grid, z_grid, t_grid, &
endif ; enddo
endif

if (present(extra_axes)) then
do n=1,size(extra_axes) ; if (len_trim(extra_axes(n)%name) > 0) then
vd%extra_axes(n) = extra_axes(n)
endif ; enddo
endif

end subroutine modify_vardesc

integer function position_from_horgrid(hor_grid)
Expand Down Expand Up @@ -2020,7 +2035,7 @@ end function cmor_long_std
!> This routine queries vardesc
subroutine query_vardesc(vd, name, units, longname, hor_grid, z_grid, t_grid, &
cmor_field_name, cmor_units, cmor_longname, conversion, caller, &
position, dim_names)
extra_axes, position, dim_names)
type(vardesc), intent(in) :: vd !< vardesc type that is queried
character(len=*), optional, intent(out) :: name !< name of variable
character(len=*), optional, intent(out) :: units !< units of variable
Expand All @@ -2035,6 +2050,8 @@ subroutine query_vardesc(vd, name, units, longname, hor_grid, z_grid, t_grid, &
!! convert from intensive to extensive
!! [various] or [a A-1 ~> 1]
character(len=*), optional, intent(in) :: caller !< calling routine?
type(axis_info), dimension(5), &
optional, intent(out) :: extra_axes !< dimensions other than space-time
integer, optional, intent(out) :: position !< A coded integer indicating the horizontal position
!! of this variable if it has such dimensions.
!! Valid values include CORNER, CENTER, EAST_FACE
Expand All @@ -2043,7 +2060,8 @@ subroutine query_vardesc(vd, name, units, longname, hor_grid, z_grid, t_grid, &
optional, intent(out) :: dim_names !< The names of the dimensions of this variable

integer :: n
character(len=120) :: cllr
integer, parameter :: nmax_extraaxes = 5
character(len=120) :: cllr, varname
cllr = "mod_vardesc"
if (present(caller)) cllr = trim(caller)

Expand Down Expand Up @@ -2076,6 +2094,19 @@ subroutine query_vardesc(vd, name, units, longname, hor_grid, z_grid, t_grid, &
enddo
endif

if (present(extra_axes)) then
! save_restart expects 5 extra axes (can be empty)
do n=1, nmax_extraaxes
if (vd%extra_axes(n)%ax_size>=1) then
extra_axes(n) = vd%extra_axes(n)
else
! return an empty axis
write(varname,"('dummy',i1.1)") n
call set_axis_info(extra_axes(n), name=trim(varname), ax_size=1)
endif
enddo
endif

end subroutine query_vardesc


Expand Down
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