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Remove all usage of namelist collection object modeldb%configuration from LFRic Apps (Full Purge) #225

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121d1dc
Use the lfric_core with new config api
mo-rickywong Jan 9, 2026
9521e1d
Port as much across to new api without incurring a linked ticket
mo-rickywong Jan 9, 2026
5774478
Add some kinds
mo-rickywong Jan 12, 2026
7867f00
Remove configuration variables that weren't being used
mo-rickywong Jan 12, 2026
438c54d
Only changes that allow Apps to work with the purge of intermediate n…
mo-rickywong Jan 26, 2026
f146829
Link this branch to the LFRic Core Branch
mo-rickywong Jan 26, 2026
c763d41
Add changes to argument lists
mo-rickywong Jan 26, 2026
16931e0
Merge branch 'main' into AppsFloatJacobian
mo-rickywong Jan 26, 2026
02f3f03
Update patche to help adjoint build
mo-rickywong Jan 27, 2026
5376706
Merge branch 'main' into AppsFloatJacobian
mo-rickywong Jan 27, 2026
808e05e
Merge branch 'main' into AppsFloatJacobian
mo-rickywong Jan 27, 2026
b3edcf1
Update file for linked PR
mo-rickywong Jan 27, 2026
003f062
remove comments out of patch files
mo-rickywong Jan 27, 2026
3a1f6cc
Merge branch 'AppsConfigAccess' into AppsIntermediateApiFullPurge
mo-rickywong Jan 28, 2026
9a14b54
Merge branch 'AppsFloatJacobian' into AppsIntermediateApiFullPurge
mo-rickywong Jan 30, 2026
9ecb2d2
Merge branch 'main' into AppsIntermediateApiFullPurge
mo-rickywong Feb 3, 2026
2b19c6b
Point repo to corresponing lfric_core
mo-rickywong Feb 4, 2026
af5ac1e
Revert any change to CONTRIBUTORS file
mo-rickywong Feb 4, 2026
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1 change: 1 addition & 0 deletions CONTRIBUTORS.md
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Expand Up @@ -23,4 +23,5 @@
| mo-lottieturner | Lottie Turner | Met Office | 2026-01-27 |
| andrewcoughtrie | Andrew Coughtrie | Met Office | 2026-01-28 |
| tommbendall | Thomas Bendall | Met Office | 2026-01-13 |
| mo-jmanners | James Manners | Met Office | 2026-01-14 |
| maggiehendry | Maggie Hendry | Met Office | 2026-01-29 |
26 changes: 13 additions & 13 deletions applications/adjoint_tests/source/adjoint_tests.f90
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Expand Up @@ -11,6 +11,7 @@
program adjoint_tests

use cli_mod, only : parse_command_line
use constants_mod, only : l_def, str_max_filename
use driver_collections_mod, only : init_collections, final_collections
use driver_comm_mod, only : init_comm, final_comm
use driver_config_mod, only : init_config, final_config
Expand All @@ -25,25 +26,23 @@ program adjoint_tests
log_level_trace, &
log_scratch_space
use timing_mod, only: init_timing, final_timing
use io_config_mod, only: timer_output_path
use namelist_mod, only: namelist_type

implicit none

! Model run working data set
type (modeldb_type) :: modeldb

character(*), parameter :: application_name = "adjoint_tests"
character(:), allocatable :: filename
character(*), parameter :: application_name = "adjoint_tests"
character(:), allocatable :: filename

type(namelist_type), pointer :: io_nml

logical :: lsubroutine_timers
logical(l_def) :: subroutine_timers
character(str_max_filename) :: timer_output_path

call parse_command_line( filename )

modeldb%mpi => global_mpi

call modeldb%configuration%initialise( application_name, table_len=10 )
call modeldb%config%initialise( application_name )

call modeldb%values%initialise('values', 5)

Expand All @@ -65,14 +64,15 @@ program adjoint_tests
call init_comm( application_name, modeldb )

call init_config( filename, gungho_required_namelists, &
modeldb%configuration )
config=modeldb%config )

call init_logger( modeldb%mpi%get_comm(), application_name )

io_nml => modeldb%configuration%get_namelist('io')
call io_nml%get_value('subroutine_timers', lsubroutine_timers)
call init_timing( modeldb%mpi%get_comm(), lsubroutine_timers, &
subroutine_timers = modeldb%config%io%subroutine_timers()
timer_output_path = modeldb%config%io%timer_output_path()

call init_timing( modeldb%mpi%get_comm(), subroutine_timers, &
application_name, timer_output_path )
nullify( io_nml )

call init_collections()
call init_time( modeldb )
Expand Down
42 changes: 14 additions & 28 deletions applications/gravity_wave/source/algorithm/gravity_wave_alg_mod.x90
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Expand Up @@ -18,7 +18,6 @@ module gravity_wave_alg_mod
LOG_LEVEL_INFO, &
LOG_LEVEL_ERROR, &
LOG_LEVEL_TRACE
use namelist_mod, only: namelist_type

! Configuration options
use finite_element_config_mod, only: element_order_h, element_order_v
Expand Down Expand Up @@ -497,7 +496,6 @@ contains
use transpose_matrix_vector_kernel_mod, only: transpose_matrix_vector_kernel_type
use sci_enforce_bc_kernel_mod, only: enforce_bc_kernel_type
use fs_continuity_mod, only: W0, W2, W3, Wtheta
use boundaries_config_mod, only: limited_area

implicit none

Expand All @@ -514,44 +512,32 @@ contains
type( field_type ) :: rhs_p
type(mesh_type), pointer :: mesh => null()

! Namelists
type(namelist_type), pointer :: base_mesh_nml
type(namelist_type), pointer :: timestepping_nml
type(namelist_type), pointer :: initial_temperature_nml
type(namelist_type), pointer :: gravity_wave_constants_nml
type(namelist_type), pointer :: io_nml

! Namelist parameters
character(len=str_def) :: prime_mesh_name
real(kind=r_second) :: dt
real(kind=r_def) :: bvf_square
integer(kind=i_def) :: b_space
character(str_def) :: prime_mesh_name
real(r_second) :: dt
real(r_def) :: bvf_square
integer(i_def) :: b_space
logical(l_def) :: limited_area

! Auxiliary constants to group invokes
real(kind=r_def) :: const1, const2
integer(tik) :: id

if ( LPROF ) call start_timing( id, 'gravity_wave_alg' )
real(kind=r_def) :: const1, const2
integer(tik) :: id

! Pointers to namelists
timestepping_nml => modeldb%configuration%get_namelist('timestepping')
initial_temperature_nml => modeldb%configuration%get_namelist('initial_temperature')
io_nml => modeldb%configuration%get_namelist('io')
dt = modeldb%config%timestepping%dt()
bvf_square = modeldb%config%initial_temperature%bvf_square()
limited_area = modeldb%config%boundaries%limited_area()

! Obtain namelist parameters
call timestepping_nml%get_value( 'dt', dt )
call initial_temperature_nml%get_value( 'bvf_square', bvf_square )
if ( LPROF ) call start_timing( id, 'gravity_wave_alg')

!=== Do a single timestep ==============================================!
mesh => wind%get_mesh()
div => get_div(mesh%get_id())
m3_inv => get_inverse_mass_matrix_fe(W3, mesh%get_id())

if ( limited_area ) then
base_mesh_nml => modeldb%configuration%get_namelist('base_mesh')
gravity_wave_constants_nml => modeldb%configuration%get_namelist('gravity_wave_constants')
call base_mesh_nml%get_value( 'prime_mesh_name', prime_mesh_name )
call gravity_wave_constants_nml%get_value( 'b_space', b_space )

prime_mesh_name = modeldb%config%base_mesh%prime_mesh_name()
b_space = modeldb%config%gravity_wave_constants%b_space()

select case(b_space)
case(b_space_w0)
Expand Down
1 change: 0 additions & 1 deletion applications/gravity_wave/source/driver/gravity_wave_driver_mod.f90
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Expand Up @@ -47,7 +47,6 @@ module gravity_wave_driver_mod
log_scratch_space
use mesh_mod, only: mesh_type
use mesh_collection_mod, only: mesh_collection
use namelist_collection_mod, only: namelist_collection_type
use io_mod, only: ts_fname
use files_config_mod, only: checkpoint_stem_name

Expand Down
48 changes: 14 additions & 34 deletions applications/gravity_wave/source/driver/gravity_wave_infrastructure_mod.f90
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Expand Up @@ -30,7 +30,6 @@ module gravity_wave_infrastructure_mod
LOG_LEVEL_ALWAYS, &
LOG_LEVEL_ERROR
use mesh_collection_mod, only : mesh_collection
use namelist_mod, only : namelist_type
use field_mod, only : field_type
use driver_fem_mod, only : init_fem, init_function_space_chains
use driver_io_mod, only : init_io, final_io
Expand Down Expand Up @@ -89,43 +88,24 @@ subroutine initialise_infrastructure( program_name, &
real(r_def) :: domain_height
real(r_def) :: scaled_radius

type(namelist_type), pointer :: base_mesh_nml => null()
type(namelist_type), pointer :: formulation_nml => null()
type(namelist_type), pointer :: extrusion_nml => null()
type(namelist_type), pointer :: planet_nml => null()
type(namelist_type), pointer :: multigrid_nml => null()

integer(i_def) :: i
integer(i_def), parameter :: one_layer = 1_i_def

!=======================================================================
! 0.0 Extract configuration variables
!=======================================================================
base_mesh_nml => modeldb%configuration%get_namelist('base_mesh')
formulation_nml => modeldb%configuration%get_namelist('formulation')
extrusion_nml => modeldb%configuration%get_namelist('extrusion')
planet_nml => modeldb%configuration%get_namelist('planet')

call formulation_nml%get_value( 'l_multigrid', l_multigrid )

l_multigrid = modeldb%config%formulation%l_multigrid()
if (l_multigrid) then
multigrid_nml => modeldb%configuration%get_namelist('multigrid')
call multigrid_nml%get_value( 'chain_mesh_tags', chain_mesh_tags )
multigrid_nml => null()
chain_mesh_tags = modeldb%config%multigrid%chain_mesh_tags()
end if

call base_mesh_nml%get_value( 'prime_mesh_name', prime_mesh_name )
call base_mesh_nml%get_value( 'geometry', geometry )
call base_mesh_nml%get_value( 'prepartitioned', prepartitioned )
call extrusion_nml%get_value( 'method', method )
call extrusion_nml%get_value( 'domain_height', domain_height )
call extrusion_nml%get_value( 'number_of_layers', number_of_layers )
call planet_nml%get_value( 'scaled_radius', scaled_radius )

base_mesh_nml => null()
extrusion_nml => null()
formulation_nml => null()
planet_nml => null()
prime_mesh_name = modeldb%config%base_mesh%prime_mesh_name()
geometry = modeldb%config%base_mesh%geometry()
prepartitioned = modeldb%config%base_mesh%prepartitioned()
method = modeldb%config%extrusion%method()
domain_height = modeldb%config%extrusion%domain_height()
number_of_layers = modeldb%config%extrusion%number_of_layers()
scaled_radius = modeldb%config%planet%scaled_radius()

!-------------------------------------------------------------------------
! Initialise infrastructure
Expand Down Expand Up @@ -197,11 +177,11 @@ subroutine initialise_infrastructure( program_name, &
apply_partition_check = .true.
end if

call init_mesh( modeldb%configuration, &
modeldb%mpi%get_comm_rank(), &
modeldb%mpi%get_comm_size(), &
base_mesh_names, &
extrusion, stencil_depth, &
call init_mesh( modeldb%config, &
modeldb%mpi%get_comm_rank(), &
modeldb%mpi%get_comm_size(), &
base_mesh_names, &
extrusion, stencil_depth, &
apply_partition_check )

allocate( twod_names, source=base_mesh_names )
Expand Down
31 changes: 18 additions & 13 deletions applications/gravity_wave/source/gravity_wave.f90
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Expand Up @@ -12,6 +12,7 @@
program gravity_wave

use cli_mod, only: parse_command_line
use constants_mod, only: l_def, str_max_filename
use driver_modeldb_mod, only: modeldb_type
use driver_collections_mod, only: init_collections, final_collections
use driver_comm_mod, only: init_comm, final_comm
Expand All @@ -24,33 +25,37 @@ program gravity_wave
use log_mod, only: log_event, &
log_level_trace, &
log_scratch_space
use namelist_mod, only: namelist_type
use timing_mod, only: init_timing, final_timing
use io_config_mod, only: timer_output_path

implicit none

type(modeldb_type) :: modeldb
character(*), parameter :: program_name = "gravity_wave"
character(:), allocatable :: filename
type(namelist_type), pointer :: io_nml
logical :: lsubroutine_timers
type(modeldb_type) :: modeldb

character(*), parameter :: program_name = "gravity_wave"
character(:), allocatable :: filename

character(str_max_filename) :: timer_output_path
logical(l_def) :: subroutine_timers

call parse_command_line( filename )

call modeldb%configuration%initialise( program_name, table_len=10 )
call modeldb%config%initialise( program_name )

modeldb%mpi => global_mpi

call init_comm( program_name, modeldb )
call init_config( filename, gravity_wave_required_namelists, &
modeldb%configuration )
config=modeldb%config )
deallocate( filename )

call init_logger( modeldb%mpi%get_comm(), program_name )
io_nml => modeldb%configuration%get_namelist('io')
call io_nml%get_value('subroutine_timers', lsubroutine_timers)
call init_timing( modeldb%mpi%get_comm(), lsubroutine_timers, program_name, timer_output_path )
nullify( io_nml )

subroutine_timers = modeldb%config%io%subroutine_timers()
timer_output_path = modeldb%config%io%timer_output_path()

call init_timing( modeldb%mpi%get_comm(), subroutine_timers, &
program_name, timer_output_path )

call init_collections()
call init_time( modeldb )

Expand Down
2 changes: 1 addition & 1 deletion applications/gravity_wave/unit-test/initialisation/analytic_buoyancy_profiles_mod_test.pf
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Expand Up @@ -116,7 +116,7 @@ contains
@after
subroutine tear_down()

use configuration_mod, only: final_configuration
use config_loader_mod, only: final_configuration

implicit none

Expand Down
2 changes: 1 addition & 1 deletion applications/gravity_wave/unit-test/kernel/compute_q_operator_kernel_mod_test.pf
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Expand Up @@ -52,7 +52,7 @@ contains
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
subroutine tearDown( this )

use configuration_mod, only: final_configuration
use config_loader_mod, only: final_configuration

implicit none

Expand Down
6 changes: 3 additions & 3 deletions applications/gravity_wave/unit-test/kernel/initial_buoyancy_kernel_mod_test.pf
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Expand Up @@ -77,16 +77,16 @@ contains
p_zero=100000.0_r_def, &
scaling_factor=1.0_r_def )

call init_chi_transforms()
call init_chi_transforms(geometry_planar, topology_fully_periodic)

end subroutine set_up

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
@after
subroutine tear_down()

use configuration_mod, only: final_configuration
use sci_chi_transform_mod, only: final_chi_transforms
use config_loader_mod, only: final_configuration
use sci_chi_transform_mod, only: final_chi_transforms

implicit none

Expand Down
30 changes: 16 additions & 14 deletions applications/gungho_model/source/gungho_model.f90
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Expand Up @@ -16,6 +16,7 @@
program gungho_model

use cli_mod, only: parse_command_line
use constants_mod, only: l_def, str_max_filename
use derived_config_mod, only: l_esm_couple
use driver_collections_mod, only: init_collections, final_collections
use driver_comm_mod, only: init_comm, final_comm
Expand All @@ -31,27 +32,24 @@ program gungho_model
log_level_info, &
log_level_trace, &
log_scratch_space
use namelist_mod, only: namelist_type
use timing_mod, only: init_timing, final_timing
use io_config_mod, only: timer_output_path


implicit none

! Model run working data set
type(modeldb_type) :: modeldb

character(*), parameter :: application_name = "gungho_model"
character(:), allocatable :: filename
type(namelist_type), pointer :: io_nml
logical :: lsubroutine_timers
character(*), parameter :: application_name = "gungho_model"
character(:), allocatable :: filename

logical(l_def) :: subroutine_timers
character(str_max_filename) :: timer_output_path

call parse_command_line( filename )

modeldb%mpi => global_mpi

call modeldb%configuration%initialise( application_name, &
table_len=10 )
call modeldb%config%initialise( application_name )
call modeldb%values%initialise( 'values', 5 )

! Create the depository, prognostics and diagnostics field collections
Expand All @@ -75,12 +73,16 @@ program gungho_model
call init_comm( application_name, modeldb )

call init_config( filename, gungho_required_namelists, &
modeldb%configuration )
config=modeldb%config )

call init_logger( modeldb%mpi%get_comm(), application_name )
io_nml => modeldb%configuration%get_namelist('io')
call io_nml%get_value('subroutine_timers', lsubroutine_timers)
call init_timing( modeldb%mpi%get_comm(), lsubroutine_timers, application_name, timer_output_path )
nullify( io_nml )

subroutine_timers = modeldb%config%io%subroutine_timers()
timer_output_path = modeldb%config%io%timer_output_path()

call init_timing( modeldb%mpi%get_comm(), subroutine_timers, &
application_name, timer_output_path )

call init_collections()
call init_time( modeldb )
call init_counters( application_name )
Expand Down
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