TR-BDF2 Timestepper by tommbendall · Pull Request #18 · tommbendall/lfric_apps

tommbendall · 2026-08-13T14:31:07Z

Shows the changes just relating to the TR-BDF2 branch

Copilot

Pull request overview

Adds TR-BDF2 timestepping support across GungHo dynamics, transport, solver infrastructure, configuration, tests, and documentation.

Changes:

Adds timestepper-aware transport, RHS, and solver operators.
Introduces per-outer-loop iteration configuration and migration.
Adds TR-BDF2 workflows and scientific/user documentation.

Reviewed changes

Copilot reviewed 89 out of 89 changed files in this pull request and generated 11 comments.

Show a summary per file

File	Description
`science/linear/source/algorithm/transport/control/tl_transport_controller_mod.x90`	Passes timestepper to TL transport controllers.
`science/linear/source/algorithm/transport/control/tl_transport_control_alg_mod.x90`	Extends TL transport API with timestepper selection.
`science/linear/source/algorithm/timestepping/tl_si_timestep_alg_mod.x90`	Supports per-outer SI iterations and timestepper propagation.
`science/linear/source/algorithm/timestepping/tl_rk_alg_timestep_mod.x90`	Identifies RK transport stages.
`science/linear/source/algorithm/core_dynamics/tl_rhs_alg_mod.x90`	Makes TL damping operators timestepper-aware.
`science/linear/integration-test/tl_test/tl_test_transport_control_mod.x90`	Updates transport integration tests.
`science/linear/integration-test/tl_test/tl_test_advect_theta_field_mod.x90`	Updates theta-advection test setup.
`science/linear/integration-test/tl_test/tl_test_advect_density_field_mod.x90`	Updates density-advection test setup.
`science/linear/integration-test/semi_implicit/resources/semi_implicit_configuration.nml`	Migrates SI iteration configuration.
`science/linear/integration-test/nwp_gal9/resources/nwp_gal9_configuration.nml`	Migrates NWP SI iteration configuration.
`science/gungho/unit-test/kernel/external_forcing/tidally_locked_earth_kernel_mod_test.pf`	Updates mocked iteration arrays.
`science/gungho/unit-test/kernel/external_forcing/shallow_hot_jupiter_kernel_mod_test.pf`	Updates mocked iteration arrays.
`science/gungho/unit-test/kernel/external_forcing/held_suarez_kernel_mod_test.pf`	Updates mocked iteration arrays.
`science/gungho/unit-test/kernel/external_forcing/earth_like_kernel_mod_test.pf`	Updates mocked iteration arrays.
`science/gungho/unit-test/kernel/external_forcing/deep_hot_jupiter_kernel_mod_test.pf`	Updates mocked iteration arrays.
`science/gungho/unit-test/kernel/diagnostics/compute_bottom_mass_from_flux_kernel_mod_test.pf`	Updates mocked iteration arrays.
`science/gungho/unit-test/kernel/diagnostics/cfl_kernel_mod_test.pf`	Updates mocked iteration arrays.
`science/gungho/unit-test/kernel/core_dynamics/compute_dl_matrix_kernel_mod_test.pf`	Updates mocked iteration arrays.
`science/gungho/source/driver/gungho_step_mod.x90`	Removes obsolete timestep-method imports.
`science/gungho/source/driver/gungho_model_mod.F90`	Registers and constructs TR-BDF2 timestepping.
`science/gungho/source/configuration/check_configuration_mod.F90`	Validates SI iteration arrays.
`science/gungho/source/algorithm/transport/control/transport_controller_mod.x90`	Selects stage-specific transport duration and wind.
`science/gungho/source/algorithm/transport/control/gungho_transport_control_alg_mod.X90`	Implements TR/BDF2 transport and flux handling.
`science/gungho/source/algorithm/timestepping/timestepping_common_mod.x90`	Extracts shared timestepping utilities.
`science/gungho/source/algorithm/timestepping/semi_implicit_timestep_alg_mod.X90`	Uses shared utilities and variable SI iterations.
`science/gungho/source/algorithm/timestepping/rk_alg_timestep_mod.x90`	Passes the RK timestepper to transport.
`science/gungho/source/algorithm/solver/si_operators_alg_mod.x90`	Builds stage-specific SI operators.
`science/gungho/source/algorithm/solver/mixed_operator_alg_mod.x90`	Selects timestepper-specific mass matrices.
`science/gungho/source/algorithm/solver/lam_rhs_alg_mod.x90`	Adds timestepper-dependent LAM RHS coefficients.
`science/gungho/source/algorithm/runtime_constants/solver_constants_mod.x90`	Separates solver matrix inventories by timestepper.
`science/gungho/source/algorithm/runtime_constants/dycore_constants_mod.x90`	Defines steppers, TR-BDF2 coefficients, and matrix inventories.
`science/gungho/source/algorithm/diagnostics/si_diagnostics_mod.x90`	Clarifies increment diagnostics for TR-BDF2.
`science/gungho/source/algorithm/core_dynamics/rhs_alg_mod.x90`	Propagates timestepper selection through RHS calculation.
`science/gungho/rose-meta/lfric-gungho/versions.py`	Adds iteration-setting upgrade macro.
`science/gungho/rose-meta/lfric-gungho/HEAD/rose-meta.conf`	Defines TR-BDF2 configuration metadata.
`science/adjoint/source/algorithm/transport/control/atl_transport_control_alg_mod.x90`	Propagates timestepper through adjoint transport.
`science/adjoint/source/algorithm/timestepping/atl_si_timestep_alg_mod.x90`	Supports variable SI iterations in the adjoint.
`science/adjoint/source/algorithm/solver/adj_mixed_operator_alg_mod.x90`	Selects adjoint timestepper-specific matrices.
`science/adjoint/source/algorithm/core_dynamics/atl_rhs_alg_mod.x90`	Makes adjoint damping operators timestepper-aware.
`rose-stem/site/meto/lfric_atm/tasks_lfric_atm_ex1a.cylc`	Adds TR-BDF2 task resource settings.
`rose-stem/site/meto/groups/groups_lfric_atm.cylc`	Registers atmospheric TR-BDF2 tasks.
`rose-stem/site/meto/groups/groups_gungho_model.cylc`	Registers GungHo TR-BDF2 tasks.
`rose-stem/site/common/lfric_atm/tasks_lfric_atm.cylc`	Defines atmospheric TR-BDF2 test tasks.
`rose-stem/site/common/gungho_model/tasks_gungho_model.cylc`	Defines GungHo TR-BDF2 test tasks.
`rose-stem/site/common/gungho_model/tasks_gungho_model_weekly.cylc`	Adds weekly TR-BDF2 test coverage.
`rose-stem/app/lfric_atm/opt/rose-app-tr_bdf2.conf`	Adds atmospheric TR-BDF2 options.
`rose-stem/app/lfric_atm/opt/rose-app-tr_bdf2_big.conf`	Adds large-domain TR-BDF2 options.
`rose-stem/app/lfric_atm/opt/rose-app-tr_bdf2_big_ral.conf`	Adds regional TR-BDF2 options.
`rose-stem/app/gungho_model/opt/rose-app-tr_bdf2.conf`	Adds GungHo TR-BDF2 options.
`rose-stem/app/gungho_model/opt/rose-app-skamarock_klemp_gw_p0.conf`	Adjusts diagnostic frequency.
`rose-stem/app/gungho_model/opt/rose-app-schar_cart.conf`	Adjusts diagnostic frequency.
`documentation/source/user_guide/timestepping/index.rst`	Documents timestepping configuration.
`documentation/source/user_guide/index.rst`	Includes the timestepping user guide.
`documentation/source/science_guide/timestepping/tr_bdf2.rst`	Documents TR-BDF2 formulation and algorithm.
`documentation/source/science_guide/timestepping/semi_implicit.rst`	Documents SIQN formulation and coupling.
`documentation/source/science_guide/timestepping/runge_kutta.rst`	Documents Runge–Kutta timestepping.
`documentation/source/science_guide/timestepping/index.rst`	Adds the timestepping science-guide index.
`documentation/source/science_guide/references.bib`	Adds timestepping references.
`applications/transport/source/algorithm/transport_control_alg_mod.x90`	Marks standalone transport as RK.
`applications/transport/example/configuration.nml`	Migrates iteration configuration.
`applications/shallow_water/source/algorithm/swe_transport_control_alg_mod.x90`	Propagates timestepper through SWE transport.
`applications/shallow_water/source/algorithm/swe_timestep_alg_mod.x90`	Uses stage-specific SWE transport settings.
`applications/shallow_water/example/configuration.nml`	Migrates iteration configuration.
`applications/ngarch/example/configuration_casim.nml`	Migrates CASIM configuration.
`applications/ngarch/example/configuration_bl.nml`	Migrates boundary-layer configuration.
`applications/name_transport/source/algorithm/name_transport_control_alg_mod.x90`	Marks name transport as RK.
`applications/name_transport/example/configuration.nml`	Migrates iteration configuration.
`applications/lfric_coupled/example/configuration.nml`	Migrates coupled configuration.
`applications/lfric_atm/example/configuration.nml`	Migrates atmospheric configuration.
`applications/jules/example/configuration.nml`	Migrates JULES configuration.
`applications/jedi_lfric_tests/example/configuration.nml`	Migrates JEDI configuration.
`applications/jedi_lfric_tests/example_tlm_tests/configuration.nml`	Migrates TLM test configuration.
`applications/jedi_lfric_tests/example_tlm_forecast_tl/configuration.nml`	Migrates TLM forecast configuration.
`applications/jedi_lfric_tests/example_tlm_forecast_tl/configuration_op.nml`	Migrates operational TLM configuration.
`applications/jedi_lfric_tests/example_id_tlm_tests/configuration.nml`	Migrates identity-TLM configuration.
`applications/jedi_lfric_tests/example_forecast/configuration.nml`	Migrates forecast configuration.
`applications/gungho_model/lam_example/straka/config_lam.nml`	Migrates Straka LAM configuration.
`applications/gungho_model/lam_example/straka/config_driver.nml`	Migrates Straka driver configuration.
`applications/gungho_model/lam_example/baroclinic/config_lam.nml`	Migrates baroclinic LAM configuration.
`applications/gungho_model/lam_example/baroclinic/config_driver.nml`	Migrates baroclinic driver configuration.
`applications/gungho_model/example/configuration.nml`	Migrates GungHo example configuration.
`applications/gravity_wave/example/configuration.nml`	Migrates gravity-wave configuration.
`applications/adjoint_tests/source/algorithm/transport/setup_test_alg_mod.x90`	Updates adjoint transport setup.
`applications/adjoint_tests/source/algorithm/transport/control/atlt_transport_controller_alg_mod.x90`	Updates TL controller tests.
`applications/adjoint_tests/source/algorithm/transport/control/atlt_transport_control_alg_mod.x90`	Updates TL/adjoint transport tests.
`applications/adjoint_tests/source/algorithm/transport/control/adjt_transport_controller_alg_mod.x90`	Updates adjoint controller tests.
`applications/adjoint_tests/source/algorithm/core_dynamics/atlt_rhs_alg_mod.x90`	Updates TL/adjoint RHS tests.
`applications/adjoint_tests/example/configuration.nml`	Migrates adjoint-test configuration.

Suppressed comments (1)

science/gungho/rose-meta/lfric-gungho/HEAD/rose-meta.conf:6146

This description says density, but tau_u controls the velocity/momentum equation, as the help text immediately below explains.

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 subroutine tl_rhs_alg(rhs, alpha_dt, base_state, state, moist_dyn, &
                      ls_state, ls_moist_dyn, compute_eos,         &
-                      dlayer_rhs, model_clock)
+                      dlayer_rhs, stepper, model_clock)


+class vn32_t379(MacroUpgrade):
+    """Upgrade macro for ticket #379 by Thomas Bendall."""
+
+    BEFORE_TAG = "vn3.2"
+    AFTER_TAG = "vn3.2_t379"


+material derivative which preserves the numerical properties of the
+Crank-Nicolson scheme: high frequency (acoustic) waves are damped while low
+frequency waves (such as Rossby waves) are represented accurately.


Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

macro PR number

iboutle

A few minor comments (I realise I'm doing this in the wrong place, but it was easier to do here!)

iboutle · 2026-08-18T12:52:19Z

Not an issue for this PR, but I do have a worry that by having 2 timestepping routines, things will be added to 1 but not the other. I'm not sure if we can think of some way of grouping/simplifying things such that everything that is shared between the different methods only exists in 1 place, and the timestepping routines themselves only contain the differences which are relevant for SI/TRBDF2

Yes agreed, it will be a pain and could cause issues if something gets forgotten from one.

I've made steps towards that by adding the timestepping_common_mod.x90 file which contains some common things, but this was as far as I was comfortable going in this PR as I didn't want to completely refactor the semi-implicit timestepper!

I'll make a note for now that we'll need to take care to ensure the changes from MetOffice#709 are included in whoever's PR ends up going on 2nd

iboutle · 2026-08-18T13:07:54Z

+            outer, model_clock, dt                                             &
+        )
+
+        fast_smagorinsky = (                                                   &


Sorry - suggest calling this "outer_smagorinsky", because we also have the option of calling smagorinsky inside fast physics, which might get confusing!

iboutle · 2026-08-19T13:08:52Z

+    {% do task_dict.update({
+        "opt_confs": ["l70_40km","ral3","ral_opts","hh_solve","tr_bdf2_big_ral"],
+        "resolution": "seuk_MG",
+        "DT": 120,


Sorry, just noticed this. 2 minutes is a pain, because there are requirements for model output at 5min and 15min intervals. So it would be better if this was either 100s or 150s (i.e something that divides into 5min). n_radstep can then be set appropriately to still be 15min, and you'll also need to set n_inc_radstep (5min)

tommbendall added 20 commits August 4, 2026 16:17

rose-meta tidy up and upgrade macro

db22e60

fix upgrade macro

7376d41

fix upgrade macro again

c1cc154

more rose-meta fixes

340712d

TR-BDF2 compiling. Also add tasks

5917577

fixes, which get a local example running

bd7b8ab

fix typo in tasks

a3d4e15

fix task names

a20692e

tau_r_dt fix

2f2a264

some fixes, and first attempt at TR-BDF2 diagnostics

e151e8f

Merge branch 'si_operator_dt' into tr_bdf2

189e6b8

adopt new SI operator split

830205c

fix silly error

1c946e7

fixes to test cases

08396f3

linear and adjoint fixes

0a3cc39

adjustments for RAL task

35b1081

revert diagnostic changes, and add documentation

9e08fec

new lines at end of file

952d14d

fixes to shallow-water app and gungho unit-tests

88292d1

actually fix shallow water

89859c6

tommbendall added DO NOT MERGE Blocked labels Aug 13, 2026

tommbendall requested a balanced review from Copilot August 17, 2026 08:59

Copilot started reviewing on behalf of tommbendall August 17, 2026 09:00 View session

Copilot AI reviewed Aug 17, 2026

View reviewed changes

tommbendall and others added 5 commits August 17, 2026 10:23

copilot review suggestions

9d90abf

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

fix linear integration test, improve config checks, correct upgrade

d3cf600

macro PR number

Merge branch 'tr_bdf2' of github.com:tommbendall/lfric_apps into tr_bdf2

1a556dc

actually fix upgrade macro

ddaadcd

urgh silly typo

77c1268

iboutle reviewed Aug 18, 2026

View reviewed changes

tommbendall added 3 commits August 19, 2026 10:54

ian comments

b08c1e1

typo

4b3b8df

and update memory

de850ab

iboutle reviewed Aug 19, 2026

View reviewed changes

tommbendall added 4 commits August 19, 2026 14:30

change RAL settings

b30b42a

documentation improvements, and add solver flux to BDF tracer transport

b2a01f5

documentation improvements, and avoid unnecessary flux precomputations

be6cc39

fix precision issue

1d12ccf

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TR-BDF2 Timestepper - #18

TR-BDF2 Timestepper#18
tommbendall wants to merge 32 commits into
si_operator_dtfrom
tr_bdf2

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