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implement restart for internal tides #463

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merged 12 commits into from
Sep 8, 2023
Merged

implement restart for internal tides #463

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d51ecac
implement restart for internal tides
Jul 12, 2023
b1e6d4c
Merge branch 'dev/gfdl' into restart_internal_tides
raphaeldussin Aug 18, 2023
1e30897
implement 4d restart/ parallel_restart not working
Aug 22, 2023
66c5678
add proper documentation for extra axes
Aug 22, 2023
a19768d
Merge branch 'dev/gfdl' into restart_internal_tides
raphaeldussin Aug 22, 2023
337182e
fix read restart for 4d array
Aug 23, 2023
3489833
write one restart variable per vertical mode
Aug 23, 2023
bb28144
fix minor issues from review
Sep 6, 2023
95cbc78
revert changes to FMS1 infra
Sep 6, 2023
0e38327
Revert "revert changes to FMS1 infra"
Sep 6, 2023
5405c3b
remove changes to infra FMS1
Sep 6, 2023
ca7d82b
Merge branch 'dev/gfdl' into restart_internal_tides
marshallward Sep 8, 2023
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57 changes: 34 additions & 23 deletions config_src/infra/FMS1/MOM_io_infra.F90
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Expand Up @@ -739,7 +739,7 @@ end subroutine read_field_3d_region
!! 4-D data field named "fieldname" from file "filename". Valid values for
!! "position" include CORNER, CENTER, EAST_FACE and NORTH_FACE.
subroutine read_field_4d(filename, fieldname, data, MOM_Domain, &
timelevel, position, scale, global_file)
timelevel, position, scale, global_file, file_may_be_4d)
character(len=*), intent(in) :: filename !< The name of the file to read
character(len=*), intent(in) :: fieldname !< The variable name of the data in the file
real, dimension(:,:,:,:), intent(inout) :: data !< The 4-dimensional array into which the data
Expand All @@ -750,44 +750,55 @@ subroutine read_field_4d(filename, fieldname, data, MOM_Domain, &
real, optional, intent(in) :: scale !< A scaling factor that the field is multiplied
!! by before it is returned.
logical, optional, intent(in) :: global_file !< If true, read from a single global file
logical, optional, intent(in) :: file_may_be_4d !< If true, this file may have 4-d arrays,
!! in which case a more elaborate set of calls
!! is needed to read it due to FMS limitations.

! Local variables
character(len=80) :: varname ! The name of a variable in the file
type(fieldtype), allocatable :: fields(:) ! An array of types describing all the variables in the file
logical :: file_is_global
logical :: use_fms_read_data, file_is_global
integer :: n, unit, ndim, nvar, natt, ntime

! This single call does not work for a 4-d array due to FMS limitations, so multiple calls are
! needed.
! call read_data(filename, fieldname, data, MOM_Domain%mpp_domain, &
! timelevel=timelevel, position=position)

use_fms_read_data = .true. ; if (present(file_may_be_4d)) use_fms_read_data = .not.file_may_be_4d
file_is_global = .true. ; if (present(global_file)) file_is_global = global_file

if (file_is_global) then
call mpp_open(unit, trim(filename), form=NETCDF_FILE, action=READONLY_FILE, &
threading=MULTIPLE, fileset=SINGLE_FILE) !, domain=MOM_Domain%mpp_domain )
use_fms_read_data = .false. ! 4d arrays not working with FMS1

if (use_fms_read_data) then
call read_data(filename, fieldname, data, MOM_Domain%mpp_domain, &
timelevel=timelevel, position=position)
else
call mpp_open(unit, trim(filename), form=NETCDF_FILE, action=READONLY_FILE, &
threading=MULTIPLE, fileset=MULTIPLE, domain=MOM_Domain%mpp_domain )
endif
call mpp_get_info(unit, ndim, nvar, natt, ntime)
allocate(fields(nvar))
call mpp_get_fields(unit, fields(1:nvar))
do n=1, nvar
call mpp_get_atts(fields(n), name=varname)
if (lowercase(trim(varname)) == lowercase(trim(fieldname))) then
call MOM_error(NOTE, "Reading 4-d variable "//trim(fieldname)//" from file "//trim(filename))
! Maybe something should be done depending on the value of ntime.
call mpp_read(unit, fields(n), MOM_Domain%mpp_domain, data, timelevel)
exit
if (file_is_global) then
call mpp_open(unit, trim(filename), form=NETCDF_FILE, action=READONLY_FILE, &
threading=MULTIPLE, fileset=SINGLE_FILE) !, domain=MOM_Domain%mpp_domain )
else
call mpp_open(unit, trim(filename), form=NETCDF_FILE, action=READONLY_FILE, &
threading=MULTIPLE, fileset=MULTIPLE, domain=MOM_Domain%mpp_domain )
endif
enddo
if ((n == nvar+1) .or. (nvar < 1)) call MOM_error(WARNING, &
"read_field apparently did not find 4-d variable "//trim(fieldname)//" in file "//trim(filename))
call mpp_get_info(unit, ndim, nvar, natt, ntime)
allocate(fields(nvar))
call mpp_get_fields(unit, fields(1:nvar))
do n=1, nvar
call mpp_get_atts(fields(n), name=varname)
if (lowercase(trim(varname)) == lowercase(trim(fieldname))) then
call MOM_error(NOTE, "Reading 4-d variable "//trim(fieldname)//" from file "//trim(filename))
! Maybe something should be done depending on the value of ntime.
call mpp_read(unit, fields(n), MOM_Domain%mpp_domain, data, timelevel)
exit
endif
enddo
if ((n == nvar+1) .or. (nvar < 1)) call MOM_error(WARNING, &
"read_field apparently did not find 4-d variable "//trim(fieldname)//" in file "//trim(filename))

deallocate(fields)
call mpp_close(unit)
deallocate(fields)
call mpp_close(unit)
endif
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if (present(scale)) then ; if (scale /= 1.0) then
call rescale_comp_data(MOM_Domain, data, scale)
Expand Down
11 changes: 10 additions & 1 deletion src/core/MOM.F90
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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 @@ -1943,6 +1947,7 @@ 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 @@ -2758,6 +2763,10 @@ 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
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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 @@ -3123,7 +3132,7 @@ 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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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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