MetOffice/lfric_apps: vn3.1

LFRic Apps vn3.1 release notes Key Changes Fixes to incremental builds when using the local_build.py script. #162 Checkpoint dumps for NWP configurations with glomap_mode=dust_and_clim will additionally include ancil data soil_clay, soil_sand and dust_mrel. #202 Upgrades to GungHo linear and adjoint models including multigrid preconditioning, boundary layer drag scheme and optimisation of transport and timestepping algorithm. MPI ranks for cubed-sphere runs are no longer limited to a factor of 6, and can now run with a factor of 2 or 3. #138 Tanget Linear model computational improvements (split-Method of Lines, fixed linearisation state and 32-bit precision). Better testing of the validity of the linearisation (updated configuration for the linear integration tests). A new linear model boundary layer scheme (to match the UM). Breaking Changes These changes will affect suites upgrading to this release * No known breaking changes at this release. Known Issues Adjoint tests have been showing some instability that appears as an intermittent failed tolerance check. At vn3.1 an issue with some upgrade macro chains has been identified. This has been fixed, and the stable branch updated, with vn3.1.1 and 2026.03.2 tags added. Please see this announcement for details Linked Changes This release is part of the 2026.03.1 Simulation Systems Release.. All codebases required by LFRic Apps, including LFRic Core, JULES, UKCA etc, have been tagged 2026.03.1. What's Changed Create initial documentation by @andrewcoughtrie in https://github.com/MetOffice/lfric_apps/pull/2 add rose-stem docs by @james-bruten-mo in https://github.com/MetOffice/lfric_apps/pull/5 Correct link to simulation-systems discussions by @BHFock in https://github.com/MetOffice/lfric_apps/pull/6 remove incorrect line by @james-bruten-mo in https://github.com/MetOffice/lfric_apps/pull/7 #8 PSyclone transformation scripts documentation by @oakleybrunt in https://github.com/MetOffice/lfric_apps/pull/9 Add new option task option: task_ranks_depth_pad by @MetBenjaminWent in https://github.com/MetOffice/lfric_apps/pull/10 Update transmute docs for Developers working with Transmute PSyclone scripts by @MetBenjaminWent in https://github.com/MetOffice/lfric_apps/pull/15 Add banner by @jennyhickson in https://github.com/MetOffice/lfric_apps/pull/17 Add link to lfric_core docs to front page by @andrewcoughtrie in https://github.com/MetOffice/lfric_apps/pull/18 Add accessibility statement by @jennyhickson in https://github.com/MetOffice/lfric_apps/pull/19 Split workflows by @andrewcoughtrie in https://github.com/MetOffice/lfric_apps/pull/16 add local build instructions by @james-bruten-mo in https://github.com/MetOffice/lfric_apps/pull/21 Update issue templates by @andrewcoughtrie in https://github.com/MetOffice/lfric_apps/pull/24 Lfric apps rose stem by @james-bruten-mo in https://github.com/MetOffice/lfric_apps/pull/20 Moci port by @james-bruten-mo in https://github.com/MetOffice/lfric_apps/pull/27 lfric_atm checkpoint documentation by @stevemullerworth in https://github.com/MetOffice/lfric_apps/pull/22 GitHub files by @james-bruten-mo in https://github.com/MetOffice/lfric_apps/pull/28 change to c48 by @james-bruten-mo in https://github.com/MetOffice/lfric_apps/pull/32 add cla files by @james-bruten-mo in https://github.com/MetOffice/lfric_apps/pull/33 Prerelease v3.0 by @jennyhickson in https://github.com/MetOffice/lfric_apps/pull/35 Release vn3.0 by @jennyhickson in https://github.com/MetOffice/lfric_apps/pull/37 Stable to Main, vn3.0 by @james-bruten-mo in https://github.com/MetOffice/lfric_apps/pull/38 Docs deploy only triggers on upstream by @mo-marqh in https://github.com/MetOffice/lfric_apps/pull/39 fix local build script by @james-bruten-mo in https://github.com/MetOffice/lfric_apps/pull/43 Remove user contact question from issue template by @yaswant in https://github.com/MetOffice/lfric_apps/pull/63 Signed CLA by @oakleybrunt in https://github.com/MetOffice/lfric_apps/pull/78 Check config name by @mike-hobson in https://github.com/MetOffice/lfric_apps/pull/67 Add Harry Shepherd to CONTRIBUTORS.md by @harry-shepherd in https://github.com/MetOffice/lfric_apps/pull/96 Reformat pull request template by @yaswant in https://github.com/MetOffice/lfric_apps/pull/109 update symlink by @james-bruten-mo in https://github.com/MetOffice/lfric_apps/pull/102 raise error successfully from extract_source by @james-bruten-mo in https://github.com/MetOffice/lfric_apps/pull/122 Hotfix to rose-stem suite by @jennyhickson in https://github.com/MetOffice/lfric_apps/pull/131 Fixing adjoint failures with transport log_space config variable set to true by @DrTVockerodtMO in https://github.com/MetOffice/lfric_apps/pull/71 Add workflow to block direct merges to the stable branch by @yaswant in https://github.com/MetOffice/lfric_apps/pull/140 cla signed by @MetBenjaminWent in https://github.com/MetOffice/lfric_apps/pull/147 Fix coupled model with 32bit compilation by @timgraham-Met in https://github.com/MetOffice/lfric_apps/pull/143 buffer_size_factor: fix broken XIOS attribute name in XML configs by @mo-marqh in https://github.com/MetOffice/lfric_apps/pull/144 Sign contributors by @mo-alistairp in https://github.com/MetOffice/lfric_apps/pull/155 Add project workflow by @james-bruten-mo in https://github.com/MetOffice/lfric_apps/pull/117 Timing Mod wrapper rewrite by @jedbakerMO in https://github.com/MetOffice/lfric_apps/pull/80 Update UKCA initialisation for dust only to include segment size by @oakleybrunt in https://github.com/MetOffice/lfric_apps/pull/83 update gitignore by @james-bruten-mo in https://github.com/MetOffice/lfric_apps/pull/75 Gregory-Rowntree convection - PSyclone optimisation and conversion from CELL_COLUMN to DOMAIN kernel by @ricky-lv426 in https://github.com/MetOffice/lfric_apps/pull/99 Remove use of deprecated XIOS context API by @EdHone in https://github.com/MetOffice/lfric_apps/pull/183 Stochastic Physics CPU and GPU Optimizations - NGARCH by @jasonjunweilyu in https://github.com/MetOffice/lfric_apps/pull/65 update jedi owners by @james-bruten-mo in https://github.com/MetOffice/lfric_apps/pull/173 Introducing cache for adjoint lookup tables by @DrTVockerodtMO in https://github.com/MetOffice/lfric_apps/pull/72 Performance test config by @mo-marqh in https://github.com/MetOffice/lfric_apps/pull/82 Bug in AOD diagnostics by @alanjhewitt in https://github.com/MetOffice/lfric_apps/pull/94 Removing populate_graph_lfricinputs.cylc by @mo-lottieturner in https://github.com/MetOffice/lfric_apps/pull/54 Update gitattributes diff to fortran-free-form by @andrewcoughtrie in https://github.com/MetOffice/lfric_apps/pull/190 Align adjoint_tests to linear_model by @tom-j-h in https://github.com/MetOffice/lfric_apps/pull/123 Fix Gungho Plots by @tommbendall in https://github.com/MetOffice/lfric_apps/pull/74 Transmute explicit no Transformation list and global.py by @MetBenjaminWent in https://github.com/MetOffice/lfric_apps/pull/56 Only build docs when docs files changed by @andrewcoughtrie in https://github.com/MetOffice/lfric_apps/pull/198 Improve negative mass error message by @tommbendall in https://github.com/MetOffice/lfric_apps/pull/187 Log to rank zero only by default by @tommbendall in https://github.com/MetOffice/lfric_apps/pull/186 #81: Fix unallocated arrays in ukca_volcanic_so2 by @mcdalvi in https://github.com/MetOffice/lfric_apps/pull/133 Calipers performance25 by @mo-marqh in https://github.com/MetOffice/lfric_apps/pull/176 Add standard suites by @james-bruten-mo in https://github.com/MetOffice/lfric_apps/pull/203 Add science guide section to documentation. by @andrewcoughtrie in https://github.com/MetOffice/lfric_apps/pull/204 Migrate metadata jules_model_environment remainder of jules_surface to jules-shared by @maggiehendry in https://github.com/MetOffice/lfric_apps/pull/181 Add a COSP timestep so diagnostics can be sampled less often by @mo-jmanners in https://github.com/MetOffice/lfric_apps/pull/158 Some of Boundary Layer PSyclone-d by @MetBenjaminWent in https://github.com/MetOffice/lfric_apps/pull/57 Weekly test fix - remove duplicate iodef.xml entry for cell_area field by @EdHone in https://github.com/MetOffice/lfric_apps/pull/209 Speed-up of adjoint transport by @DrTVockerodtMO in https://github.com/MetOffice/lfric_apps/pull/145 Replace model rh_crit with fixed value from config in glomap_aerosol by @stevemullerworth in https://github.com/MetOffice/lfric_apps/pull/193 Added Stability with Advective Tracers by @jameskent-metoffice in https://github.com/MetOffice/lfric_apps/pull/171 Remove redundant info from mesh configs by @cjohnson-pi in https://github.com/MetOffice/lfric_apps/pull/153 Add support for monsoon 3 by @t00sa in https://github.com/MetOffice/lfric_apps/pull/166 jelf adjoint test tolerance namelist variable by @tom-j-h in https://github.com/MetOffice/lfric_apps/pull/132 Generation of lfric2lfric lbcs by @ukmo-juan-castillo in https://github.com/MetOffice/lfric_apps/pull/55 Correct the sample_physics_winds_correction option by @tommbendall in https://github.com/MetOffice/lfric_apps/pull/69 Add link to milestones in readme by @andrewcoughtrie in https://github.com/MetOffice/lfric_apps/pull/235 update trigger project workflow by @james-bruten-mo in https://github.com/MetOffice/lfric_apps/pull/237 Stochastic Physics Fixes by @tommbendall in https://github.com/MetOffice/lfric_apps/pull/148 Floating-point precision conversions in jelf by @tom-j-h in https://github.com/MetOffice/lfric_apps/pull/142 Update checkpointing docs to include new functionality by @andrewcoughtrie in https://github.com/MetOffice/lfric_apps/pull/227 Decompose across panels by @thomasmelvin in https://github.com/MetOffice/lfric_apps/pull/138 Add crayhost to rose-stem for Genoa node selection by @oakleybrunt in https://github.com/MetOffice/lfric_apps/pull/230 run remote_ini