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Modify LFRic Apps files that call native/coordinate Jacobian files #184

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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
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1 change: 1 addition & 0 deletions CONTRIBUTORS.md
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Expand Up @@ -6,6 +6,7 @@
| jennyhickson | Jenny Hickson | Met Office | 2025-12-10 |
| mike-hobson | Mike Hobson | Met Office | 2025-12-17 |
| mo-marqh | mark Hedley | Met Office | 2025-12-11 |
| mo-rickywong | Ricky Wong | Met Office | 2026-01-27 |
| yaswant | Yaswant Pradhan | Met Office | 2025-12-16 |
| oakleybrunt | Oakley Brunt | Met Office | 2025-12-19 |
| harry-shepherd | Harry Shepherd | Met Office | 2026-01-08 |
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2 changes: 1 addition & 1 deletion applications/gravity_wave/unit-test/kernel/initial_buoyancy_kernel_mod_test.pf
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Expand Up @@ -77,7 +77,7 @@ 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

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8 changes: 7 additions & 1 deletion applications/name_transport/source/kernel/set_name_field_kernel_mod.F90
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Expand Up @@ -21,6 +21,10 @@ module set_name_field_kernel_mod
use kernel_mod, only : kernel_type
use log_mod, only : log_event, LOG_LEVEL_ERROR

use base_mesh_config_mod, only: geometry, topology
use finite_element_config_mod, only: coord_system
use planet_config_mod, only: scaled_radius

implicit none

private
Expand Down Expand Up @@ -143,7 +147,9 @@ subroutine set_name_field_code(nlayers, tracer, &
chi_2_e(df1) = chi_2( map_chi(df1) + k )
chi_3_e(df1) = chi_3( map_chi(df1) + k )
end do
call coordinate_jacobian(ndf_chi, nqp_h, nqp_v, &
call coordinate_jacobian(coord_system, geometry, &
topology, scaled_radius, &
ndf_chi, nqp_h, nqp_v, &
chi_1_e, chi_2_e, chi_3_e, &
ipanel, chi_basis, chi_diff_basis, &
jac, dj)
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2 changes: 1 addition & 1 deletion applications/name_transport/unit-test/kernel/set_name_field_kernel_mod_test.pf
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Expand Up @@ -91,7 +91,7 @@ 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

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15 changes: 11 additions & 4 deletions applications/shallow_water/source/kernel/initial_swe_streamfunc_kernel_mod.F90
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Expand Up @@ -18,8 +18,13 @@ module initial_swe_streamfunc_kernel_mod
use constants_mod, only : r_def, i_def, PI
use fs_continuity_mod, only : W1
use kernel_mod, only : kernel_type

use base_mesh_config_mod, only: geometry, topology, &
geometry_spherical
use finite_element_config_mod, only: coord_system
use planet_config_mod, only: scaled_radius
use shallow_water_settings_config_mod, &
only : swe_test
only: swe_test

implicit none

Expand Down Expand Up @@ -86,8 +91,6 @@ subroutine initial_swe_streamfunc_code(nlayers, rhs, chi_1, chi_2, chi_3, panel_

use analytic_swe_streamfunction_profiles_mod, &
only: analytic_swe_streamfunction
use base_mesh_config_mod, only: geometry, &
geometry_spherical
use sci_coordinate_jacobian_mod, only: coordinate_jacobian, &
coordinate_jacobian_inverse
use coord_transform_mod, only: sphere2cart_vector
Expand Down Expand Up @@ -135,7 +138,11 @@ subroutine initial_swe_streamfunc_code(nlayers, rhs, chi_1, chi_2, chi_3, panel_
chi_3_cell(df) = chi_3( map_chi(df) )
end do

call coordinate_jacobian( ndf_chi, &
call coordinate_jacobian( coord_system, &
geometry, &
topology, &
scaled_radius, &
ndf_chi, &
nqp_h, &
nqp_v, &
chi_1_cell, &
Expand Down
22 changes: 14 additions & 8 deletions applications/shallow_water/source/kernel/initial_swe_u_kernel_mod.F90
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Expand Up @@ -19,13 +19,17 @@ module initial_swe_u_kernel_mod
ANY_DISCONTINUOUS_SPACE_3
use constants_mod, only : r_def, PI, i_def
use fs_continuity_mod, only : W2
use initial_wind_config_mod, only : profile_sin_uv, &
profile, sbr_angle_lat, sbr_angle_lon, &
u0, v0, shear, wavelength

use kernel_mod, only : kernel_type

use base_mesh_config_mod, only: geometry, topology, &
geometry_spherical
use finite_element_config_mod, only: coord_system
use initial_wind_config_mod, only: profile_sin_uv, &
profile, sbr_angle_lat, sbr_angle_lon, &
u0, v0, shear, wavelength
use planet_config_mod, only: scaled_radius
use shallow_water_settings_config_mod, &
only : swe_test
only: swe_test

implicit none

Expand Down Expand Up @@ -94,8 +98,6 @@ subroutine initial_swe_u_code( nlayers, rhs, &
nqp_h, nqp_v, wqp_h, wqp_v )

use analytic_swe_wind_profiles_mod, only : analytic_swe_wind
use base_mesh_config_mod, only : geometry, &
geometry_spherical
use sci_coordinate_jacobian_mod, only : coordinate_jacobian
use coord_transform_mod, only : sphere2cart_vector
use sci_chi_transform_mod, only : chi2llr, chi2xyz
Expand Down Expand Up @@ -142,7 +144,11 @@ subroutine initial_swe_u_code( nlayers, rhs, &
chi_3_cell(df) = chi_3( map_chi(df) )
end do

call coordinate_jacobian(ndf_chi, &
call coordinate_jacobian( coord_system, &
geometry, &
topology, &
scaled_radius, &
ndf_chi, &
nqp_h, &
nqp_v, &
chi_1_cell, &
Expand Down
15 changes: 10 additions & 5 deletions applications/shallow_water/source/kernel/initial_vorticity_v2_kernel_mod.F90
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Expand Up @@ -25,12 +25,13 @@ module initial_vorticity_v2_kernel_mod
use kernel_mod, only: kernel_type
use sci_coordinate_jacobian_mod, only: coordinate_jacobian, &
coordinate_jacobian_inverse
use base_mesh_config_mod, only: geometry, &
geometry_spherical, &
f_lat
use rotation_vector_mod, only: rotation_vector_fplane, &
rotation_vector_sphere
use planet_config_mod, only: scaled_omega

use base_mesh_config_mod, only: geometry, topology, &
geometry_spherical, f_lat
use finite_element_config_mod, only: coord_system
use planet_config_mod, only: scaled_radius, scaled_omega

implicit none

Expand Down Expand Up @@ -165,7 +166,11 @@ subroutine initial_vorticity_v2_code(nlayers, r_q, curl_u, geopot, &
rotation_vector)
end if

call coordinate_jacobian(ndf_chi, &
call coordinate_jacobian(coord_system, &
geometry, &
topology, &
scaled_radius, &
ndf_chi, &
nqp_h, &
nqp_v, &
chi_1_e, &
Expand Down
2 changes: 1 addition & 1 deletion applications/shallow_water/unit-test/kernel/initial_geopot_kernel_mod_test.pf
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Expand Up @@ -96,7 +96,7 @@ contains
swe_test = swe_test_swe_geostr_balance, &
thermal_swe = .false. )

call init_chi_transforms()
call init_chi_transforms(geometry_planar, topology_fully_periodic)

end subroutine set_up

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2 changes: 1 addition & 1 deletion applications/shallow_water/unit-test/kernel/initial_swe_buoyancy_kernel_mod_test.pf
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Expand Up @@ -97,7 +97,7 @@ contains
swe_test = swe_test_swe_gaussian_hill, &
thermal_swe = .false.)

call init_chi_transforms()
call init_chi_transforms(geometry_planar, topology_fully_periodic)

end subroutine set_up

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2 changes: 1 addition & 1 deletion applications/shallow_water/unit-test/kernel/initial_swe_tracer_kernel_mod_test.pf
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Expand Up @@ -96,7 +96,7 @@ contains
swe_test = swe_test_swe_geostr_balance, &
thermal_swe = .false. )

call init_chi_transforms()
call init_chi_transforms(geometry_planar, topology_fully_periodic)

end subroutine set_up

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2 changes: 1 addition & 1 deletion applications/shallow_water/unit-test/kernel/initial_swe_u_kernel_mod_test.pf
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Expand Up @@ -96,7 +96,7 @@ contains
swe_test = swe_test_swe_gaussian_hill, &
ref_gp = 10000.0_r_def )

call init_chi_transforms()
call init_chi_transforms(geometry_planar, topology_fully_periodic)

end subroutine setUp

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10 changes: 8 additions & 2 deletions applications/transport/source/kernel/set_tracer_field_kernel_mod.F90
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Expand Up @@ -18,10 +18,14 @@ module set_tracer_field_kernel_mod
GH_QUADRATURE_XYoZ
use fs_continuity_mod, only : Wchi
use constants_mod, only : r_def, i_def
use idealised_config_mod, only : test
use kernel_mod, only : kernel_type
use log_mod, only : log_event, LOG_LEVEL_ERROR

use base_mesh_config_mod, only: geometry, topology
use finite_element_config_mod, only: coord_system
use idealised_config_mod, only: test
use planet_config_mod, only: scaled_radius

implicit none

private
Expand Down Expand Up @@ -148,7 +152,9 @@ subroutine set_tracer_field_code(nlayers, tracer, &
chi_2_e(df1) = chi_2( map_chi(df1) + k )
chi_3_e(df1) = chi_3( map_chi(df1) + k )
end do
call coordinate_jacobian(ndf_chi, nqp_h, nqp_v, &
call coordinate_jacobian(coord_system, geometry, &
topology, scaled_radius, &
ndf_chi, nqp_h, nqp_v, &
chi_1_e, chi_2_e, chi_3_e, &
ipanel, chi_basis, chi_diff_basis, &
jac, dj)
Expand Down
2 changes: 1 addition & 1 deletion applications/transport/unit-test/kernel/initial_tracer_field_sample_kernel_mod_test.pf
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Expand Up @@ -82,7 +82,7 @@ contains
f_lon_deg=0.0_r_def, perturb_init=.false., &
perturb_magnitude=0, perturb_seed=0 )

call init_chi_transforms()
call init_chi_transforms(geometry_planar, topology_fully_periodic)

end subroutine setUp

Expand Down
2 changes: 1 addition & 1 deletion applications/transport/unit-test/kernel/set_tracer_field_kernel_mod_test.pf
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Expand Up @@ -103,7 +103,7 @@ 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

Expand Down
4 changes: 2 additions & 2 deletions dependencies.yaml
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Expand Up @@ -30,8 +30,8 @@ lfric_apps:
ref:

lfric_core:
source: git@github.com:MetOffice/lfric_core.git
ref: bbb3d8a69a2671df93859f617bbe336c6715476f
source: git@github.com:mo-rickywong/lfric_core.git
ref: FloatJacobian

moci:
source: git@github.com:MetOffice/moci.git
Expand Down
13 changes: 7 additions & 6 deletions science/adjoint/patches/kernel/atl_kinetic_energy_gradient_kernel_mod.patch
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@@ -1,18 +1,19 @@
@@ -1,11 +1,11 @@
@@ -1,4 +1,4 @@
-module adj_kinetic_energy_gradient_kernel_mod
+module atl_kinetic_energy_gradient_kernel_mod
use argument_mod, only : any_discontinuous_space_3, any_space_9, arg_type, cell_column, func_type, gh_basis, gh_diff_basis, &
&gh_field, gh_inc, gh_quadrature_xyoz, gh_read, gh_real
use constants_mod, only : i_def, r_def
use fs_continuity_mod, only : w2
use kernel_mod, only : kernel_type
@@ -8,7 +8,7 @@
use finite_element_config_mod, only : coord_system
use planet_config_mod, only : scaled_radius
implicit none
- type, public, extends(kernel_type) :: adj_kinetic_energy_gradient_kernel_type
+ type, public, extends(kernel_type) :: atl_kinetic_energy_gradient_kernel_type
type(ARG_TYPE) :: META_ARGS(5) = (/ &
arg_type(gh_field, gh_real, gh_read, w2), &
arg_type(gh_field, gh_real, gh_inc, w2), &
@@ -18,15 +18,15 @@
@@ -21,15 +21,15 @@
INTEGER :: GH_SHAPE = gh_quadrature_xyoz
INTEGER :: OPERATES_ON = cell_column
CONTAINS
Expand All @@ -32,15 +33,15 @@
&w2_basis, w2_diff_basis, ndf_chi, undf_chi, map_chi, chi_basis, chi_diff_basis, ndf_pid, undf_pid, map_pid, nqp_h, nqp_v, wqp_h, &
&wqp_v)
use sci_coordinate_jacobian_mod, only : coordinate_jacobian
@@ -75,7 +75,6 @@
@@ -78,7 +78,6 @@
real(kind=r_def) :: dv
real(kind=r_def), dimension(3) :: mul1
real(kind=r_def), dimension(3) :: mul2
- integer :: i
real(kind=r_def) :: res_dot_product
integer :: idx
integer :: idx_1
@@ -153,6 +152,6 @@
@@ -156,6 +155,6 @@
enddo
enddo

Expand Down
15 changes: 9 additions & 6 deletions science/adjoint/patches/kernel/atl_project_eos_pressure_kernel_mod.patch
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@@ -1,19 +1,22 @@
@@ -1,11 +1,12 @@
@@ -1,4 +1,4 @@
-module adj_project_eos_pressure_kernel_mod
+module atl_project_eos_pressure_kernel_mod
use argument_mod, only : any_discontinuous_space_3, any_space_2, arg_type, cell_column, func_type, gh_basis, gh_diff_basis, &
&gh_field, gh_operator, gh_quadrature_xyoz, gh_read, gh_readwrite, gh_real, gh_write
use constants_mod, only : i_def, r_def
use fs_continuity_mod, only : w3, wtheta
@@ -6,9 +6,9 @@
use kernel_mod, only : kernel_type
+ use planet_config_mod, only : kappa, rd, p_zero
use base_mesh_config_mod, only : geometry, topology
use finite_element_config_mod, only : coord_system
- use planet_config_mod, only : scaled_radius
+ use planet_config_mod, only : scaled_radius, kappa, rd, p_zero
implicit none
- type, public, extends(kernel_type) :: adj_project_eos_pressure_kernel_type
+ type, public, extends(kernel_type) :: atl_project_eos_pressure_kernel_type
type(ARG_TYPE) :: META_ARGS(10) = (/ &
arg_type(gh_field, gh_real, gh_readwrite, w3), &
arg_type(gh_field, gh_real, gh_readwrite, w3), &
@@ -24,15 +25,15 @@
@@ -27,15 +27,15 @@
INTEGER :: GH_SHAPE = gh_quadrature_xyoz
INTEGER :: OPERATES_ON = cell_column
CONTAINS
Expand All @@ -33,7 +36,7 @@
&chi1, chi2, chi3, panel_id, ncell_3d, m3_inv, ndf_w3, undf_w3, map_w3, w3_basis, ndf_wt, undf_wt, map_wt, wt_basis, ndf_chi, &
&undf_chi, map_chi, chi_basis, chi_diff_basis, ndf_pid, undf_pid, map_pid, nqp_h, nqp_v, wqp_h, wqp_v)
use sci_coordinate_jacobian_mod, only : coordinate_jacobian
@@ -96,9 +97,6 @@
@@ -99,9 +99,6 @@
real(kind=r_def) :: ls_theta_vd_at_quad
real(kind=r_def) :: tmp_ls_exner
real(kind=r_def) :: tmp_exner
Expand All @@ -43,7 +46,7 @@

exner_e = 0.0_r_def
exner_at_quad = 0.0_r_def
@@ -176,6 +174,6 @@
@@ -179,6 +176,6 @@
enddo
enddo

Expand Down
13 changes: 7 additions & 6 deletions science/adjoint/patches/kernel/atl_rhs_project_eos_kernel_mod.patch
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@@ -1,18 +1,19 @@
@@ -1,11 +1,11 @@
@@ -1,4 +1,4 @@
-module adj_rhs_project_eos_kernel_mod
+module atl_rhs_project_eos_kernel_mod
use argument_mod, only : any_discontinuous_space_3, any_space_9, arg_type, cell_column, func_type, gh_basis, gh_diff_basis, &
&gh_field, gh_quadrature_xyoz, gh_read, gh_readwrite, gh_real, gh_scalar, gh_write
use constants_mod, only : i_def, r_def
use fs_continuity_mod, only : w3, wtheta
use kernel_mod, only : kernel_type
@@ -8,7 +8,7 @@
use finite_element_config_mod, only : coord_system
use planet_config_mod, only : scaled_radius
implicit none
- type, public, extends(kernel_type) :: adj_rhs_project_eos_kernel_type
+ type, public, extends(kernel_type) :: atl_rhs_project_eos_kernel_type
type(ARG_TYPE) :: META_ARGS(14) = (/ &
arg_type(gh_field, gh_real, gh_readwrite, w3), &
arg_type(gh_field, gh_real, gh_readwrite, w3), &
@@ -28,15 +28,15 @@
@@ -31,15 +31,15 @@
INTEGER :: GH_SHAPE = gh_quadrature_xyoz
INTEGER :: OPERATES_ON = cell_column
CONTAINS
Expand All @@ -31,8 +32,8 @@
+ subroutine atl_rhs_project_eos_code(nlayers, rhs_eos, exner, rho, theta, moist_dyn_gas, ls_exner, ls_rho, ls_theta, &
&ls_moist_dyn_gas, chi1, chi2, chi3, panel_id, kappa, rd, p_zero, ndf_w3, undf_w3, map_w3, w3_basis, ndf_wt, undf_wt, map_wt, &
&wt_basis, ndf_chi, undf_chi, map_chi, chi_basis, chi_diff_basis, ndf_pid, undf_pid, map_pid, nqp_h, nqp_v, wqp_h, wqp_v)
use coordinate_jacobian_mod, only : coordinate_jacobian
@@ -176,6 +176,6 @@
use sci_coordinate_jacobian_mod, only : coordinate_jacobian
@@ -179,6 +179,6 @@
enddo
enddo

Expand Down
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