diff --git a/applications/lfric_atm/build/fortran/crayftn.mk b/applications/lfric_atm/build/fortran/crayftn.mk
index 49286c047..98e77d011 100644
--- a/applications/lfric_atm/build/fortran/crayftn.mk
+++ b/applications/lfric_atm/build/fortran/crayftn.mk
@@ -10,4 +10,4 @@ $(info Project specials for Cray compiler)
 
 export FFLAGS_UM_PHYSICS = -s real64
 
-include $(PROJECT_DIR)/build/fortran/crayftn/$(PROFILE).mk
\ No newline at end of file
+include $(PROJECT_DIR)/build/fortran/crayftn/$(PROFILE).mk
diff --git a/applications/linear_model/Makefile b/applications/linear_model/Makefile
index 7ad66520d..6b99b2116 100644
--- a/applications/linear_model/Makefile
+++ b/applications/linear_model/Makefile
@@ -1,15 +1,19 @@
 ##############################################################################
-# (c) Crown copyright 2023-2024 Met Office. All rights reserved.
+# (c) Crown copyright 2017-2026 Met Office. All rights reserved.
 # The file LICENCE, distributed with this code, contains details of the terms
 # under which the code may be used.
 ##############################################################################
 
 PROJECT_NAME = linear_model
+
 export PROFILE ?= fast-debug
 
 # Select option for PSyclone transformation. Select "none" for no transformation.
 export PSYCLONE_TRANSFORMATION ?= minimum
 
+# This makefile is almost identical to the lfric_atm makefile, but with
+# additions for the linear code.
+
 # This top level makefile is very order sensitive. Source code extraction and
 # generation must happen in a certain order. Due to this we turn off
 # multithreading for this file only. Any called recursively (i.e. with $(MAKE))
@@ -19,24 +23,51 @@ export PSYCLONE_TRANSFORMATION ?= minimum
 
 export PROJECT_DIR := $(realpath $(dir $(lastword $(MAKEFILE_LIST))))
 
+# The lfric_atm application project directory is used for the
+# optimisation options.
+# This is because it must be possible for the linear_model code to be in
+# the same exectuable as the nonlinear lfric_atm code, as is done in jedi.
+# Therefore the linear_model uses exactly the same optimisation
+# options as lfric_atm. Pointing to the lfric_atm options
+# means that the linear_model is always aligned with lfric_atm, even
+# if the lfric_atm options are updated.
+export LFRIC_ATM_DIR := $(APPS_ROOT_DIR)/applications/lfric_atm
+
+export EXTERNAL_DYNAMIC_LIBRARIES = shum
+
+# List of functions from shumlib that may be used by developers during debugging
+export IGNORE_DEPENDENCIES = c_shum_byteswap \
+                             f_shum_field_mod \
+                             f_shum_file_mod \
+                             f_shum_is_nan_mod \
+                             f_shum_is_inf_mod \
+                             f_shum_is_denormal_mod
+
 export EXTRA_ROSE_META = jules
 export META_DIR = $(WORKING_DIR)/../rose-meta
 export ROSE_META_DIRS = $(APPS_ROOT_DIR)/rose-meta $(META_DIR)
 
+# The physics components are extracted and built, even though they are not
+# actually used by the linear_model app. This is to ensure that the code runs
+# with the #ifdef UM_PHYSICS set to true, hence enabling both the linear
+# and nonlinear lfric_atm code to be run in the same executable.
+# Note - socrates_interface must come before jules_interface as there are dependencies on each other.
 export INTERNAL_DEPENDENCIES = $(CORE_ROOT_DIR)/infrastructure \
                                $(CORE_ROOT_DIR)/components/driver \
                                $(CORE_ROOT_DIR)/components/science \
                                $(CORE_ROOT_DIR)/components/inventory \
                                $(CORE_ROOT_DIR)/components/lfric-xios \
-                               $(APPS_ROOT_DIR)/science/gungho \
-                               $(APPS_ROOT_DIR)/science/linear
+                               $(APPS_ROOT_DIR)/science/shared \
+                               $(APPS_ROOT_DIR)/interfaces/socrates_interface \
+                               $(APPS_ROOT_DIR)/interfaces/jules_interface \
+                               $(APPS_ROOT_DIR)/interfaces/physics_schemes_interface
 
-META_VN       ?= HEAD
-META_FILE_DIR  = $(PROJECT_DIR)/rose-meta/lfric-$(PROJECT_NAME)/$(META_VN)
+META_VN             ?= HEAD
+export META_FILE_DIR = $(PROJECT_DIR)/rose-meta/lfric-$(PROJECT_NAME)/$(META_VN)
 
 # Check PSyclone transformation option is valid
 ifneq ("$(PSYCLONE_TRANSFORMATION)","none")
-  export OPTIMISATION_PATH ?= $(wildcard optimisation/$(PSYCLONE_TRANSFORMATION))
+  export OPTIMISATION_PATH ?= $(wildcard $(LFRIC_ATM_DIR)/optimisation/$(PSYCLONE_TRANSFORMATION))
   ifeq ("$(wildcard $(OPTIMISATION_PATH)/psykal/global.py)","")
     $(error PSyclone transformation dir "$(PSYCLONE_TRANSFORMATION)" does not have a global.py script)
   endif
@@ -44,38 +75,34 @@ endif
 
 .PHONY: default
 default: build
-
-.PHONY: documentation doc docs
-documentation doc docs: document-api
+	$(Q)echo > /dev/null
 
 include $(CORE_ROOT_DIR)/infrastructure/build/lfric.mk
 include $(INTERNAL_DEPENDENCIES:=/build/import.mk)
+include build/project.mk
 
-##############################################################################
-# Documentation
-#
-.PHONY: document-api
-document-api: PROJECT       = linear_model
-document-api: DOCUMENT_DIR ?= $(PROJECT_DIR)/documents/api
-document-api: CONFIG_DIR    = documentation
-document-api: SOURCE_DIR    = source
-document-api: WORKING_DIR  := $(WORKING_DIR)/api
-document-api: api-documentation
+# Include transmute list only if not using minimum or no transformations
+ifeq ($(filter "$(PSYCLONE_TRANSFORMATION)", "none" "minimum"),)
+  include build/psyclone_transmute_file_list.mk
+endif
 
 ##############################################################################
 # Build
 #
 .PHONY: build
 build: export BIN_DIR     ?= $(PROJECT_DIR)/bin
-build: export CXX_LINK     = TRUE
-build: export PROGRAMS    := $(basename $(notdir $(shell find source -maxdepth 1 -name '*.[Ff]90' -print)))
+build: export CXX_LINK     = YES
+build: export PROGRAMS    := $(basename $(notdir $(shell find source -maxdepth 1 -name '*.[Ff]90' -exec egrep -l "^\s*program" {} \;)))
+build: export PROJECT      = $(PROJECT_NAME)
+build: export SCRATCH_DIR := $(WORKING_DIR)/..
 build: export WORKING_DIR := $(WORKING_DIR)
 
 build: export LDFLAGS_GROUPS = OPENMP
 ifeq "$(PROFILE)" "full-debug"
-build: export FFLAG_GROUPS = OPENMP DEBUG WARNINGS INIT RUNTIME NO_OPTIMISATION FORTRAN_STANDARD
+build: export FFLAG_GROUPS = OPENMP DEBUG WARNINGS INIT RUNTIME NO_OPTIMISATION
 else ifeq "$(PROFILE)" "fast-debug"
-build: export FFLAG_GROUPS = OPENMP DEBUG WARNINGS FASTD_INIT FASTD_RUNTIME SAFE_OPTIMISATION FORTRAN_STANDARD
+# Use fast-debug environment vars from build/fortran/*.mk configs
+build: export FFLAG_GROUPS = OPENMP DEBUG WARNINGS FASTD_INIT FASTD_RUNTIME SAFE_OPTIMISATION
 else ifeq "$(PROFILE)" "production"
 build: export FFLAG_GROUPS = OPENMP DEBUG WARNINGS RISKY_OPTIMISATION
 else
@@ -88,6 +115,25 @@ build: ALWAYS
 	$(Q)for SUBPROJECT in $(INTERNAL_DEPENDENCIES) ; do \
 	    $(MAKE) $(QUIET_ARG) -f $$SUBPROJECT/build/import.mk ; done
 	$(call MESSAGE,========================================)
+	$(call MESSAGE,Extracting coupled_interface component)
+	$(call MESSAGE,========================================)
+	$Q$(MAKE) $(QUIET_ARG) -f $(LFRIC_BUILD)/extract.mk \
+	          SOURCE_DIR=$(APPS_ROOT_DIR)/interfaces/coupled_interface/source
+	$(call MESSAGE,========================================)
+	$(call MESSAGE,Extracting Gungho dynamical core)
+	$(call MESSAGE,========================================)
+	$Q$(MAKE) $(QUIET_ARG) -f $(LFRIC_BUILD)/extract.mk \
+	          SOURCE_DIR=$(APPS_ROOT_DIR)/science/gungho/source
+	$(call MESSAGE,========================================)
+	$(call MESSAGE,Extracting Linear)
+	$(call MESSAGE,========================================)
+	$Q$(MAKE) $(QUIET_ARG) -f $(LFRIC_BUILD)/extract.mk \
+	          SOURCE_DIR=$(APPS_ROOT_DIR)/science/linear/source
+	$(call MESSAGE,========================================)
+	$(call MESSAGE,Extracting UM physics )
+	$(call MESSAGE,========================================)
+	$Q$(MAKE) $(QUIET_ARG) -f $(APPS_ROOT_DIR)/build/extract/extract_physics.mk
+	$(call MESSAGE,========================================)
 	$(call MESSAGE,Extracting $(PROJECT_NAME))
 	$(call MESSAGE,========================================)
 	$Q$(MAKE) $(QUIET_ARG) -f $(LFRIC_BUILD)/extract.mk \
@@ -96,19 +142,59 @@ build: ALWAYS
 	$(call MESSAGE,Extracting External Rose Metadata)
 	$(call MESSAGE,========================================)
 	$Q$(MAKE) $(QUIET_ARG) -f $(APPS_ROOT_DIR)/build/extract/extract_meta.mk
-	$(call MESSAGE,=========================================================)
+	$(call MESSAGE,========================================)
 	$(call MESSAGE,Generating $(PROJECT) namelist loaders)
-	$(call MESSAGE,=========================================================)
+	$(call MESSAGE,========================================)
 	$Q$(MAKE) $(QUIET_ARG) -f $(LFRIC_BUILD)/configuration.mk \
-	          PROJECT=$(PROJECT)    \
-	          SOURCE_DIR=source \
+	          SOURCE_DIR=$(APPS_ROOT_DIR)/science/gungho/source \
 	          META_FILE_DIR=$(META_FILE_DIR)
 	$(call MESSAGE,========================================)
+	$(call MESSAGE,PSycloning interface components)
+	$(call MESSAGE,========================================)
+	$Q$(MAKE) $(QUIET_ARG) -f $(LFRIC_BUILD)/psyclone/psyclone_psykal.mk \
+	          SOURCE_DIR=$(APPS_ROOT_DIR)/interfaces/coupled_interface/source
+	$Q$(MAKE) $(QUIET_ARG) -f $(LFRIC_BUILD)/psyclone/psyclone_psykal.mk \
+	          SOURCE_DIR=$(APPS_ROOT_DIR)/interfaces/jules_interface/source
+	$Q$(MAKE) $(QUIET_ARG) -f $(LFRIC_BUILD)/psyclone/psyclone_psykal.mk \
+	          SOURCE_DIR=$(APPS_ROOT_DIR)/interfaces/socrates_interface/source
+	$Q$(MAKE) $(QUIET_ARG) -f $(LFRIC_BUILD)/psyclone/psyclone_psykal.mk \
+	          SOURCE_DIR=$(APPS_ROOT_DIR)/interfaces/physics_schemes_interface/source
+	$(call MESSAGE,========================================)
+	$(call MESSAGE,PSycloning Gungho dynamical core)
+	$(call MESSAGE,========================================)
+	$Q$(MAKE) $(QUIET_ARG) -f $(LFRIC_BUILD)/psyclone/psyclone_psykal.mk \
+	          SOURCE_DIR=$(APPS_ROOT_DIR)/science/gungho/source
+	$(call MESSAGE,========================================)
+	$(call MESSAGE,PSycloning Linear)
+	$(call MESSAGE,========================================)
+	$Q$(MAKE) $(QUIET_ARG) -f $(LFRIC_BUILD)/psyclone/psyclone_psykal.mk \
+	          SOURCE_DIR=$(APPS_ROOT_DIR)/science/linear/source
+	$(call MESSAGE,========================================)
 	$(call MESSAGE,PSycloning $(PROJECT_NAME))
 	$(call MESSAGE,========================================)
 	$Q$(MAKE) $(QUIET_ARG) -f $(LFRIC_BUILD)/psyclone/psyclone_psykal.mk \
-	          SOURCE_DIR=source \
-	          OPTIMISATION_PATH=$(OPTIMISATION_PATH)
+	          SOURCE_DIR=source
+	$(call MESSAGE,========================================)
+	$(call MESSAGE,Preprocess and PSyclone Transmute)
+	$(call MESSAGE,========================================)
+# Note depending on site target requirements, either all source or specific source will be affected
+# See application overrides and files exported there
+	$Q$(MAKE) $(QUIET_ARG) -f $(APPS_ROOT_DIR)/interfaces/build/pre_process_phys.mk \
+              SOURCE_DIR=$(WORKING_DIR) \
+              PSYCLONE_PHYSICS_FILES="$(PSYCLONE_PHYSICS_FILES)" \
+	          PSYCLONE_DIRECTORIES="$(PSYCLONE_DIRECTORIES)" \
+	          PSYCLONE_PHYSICS_EXCEPTION="$(PSYCLONE_PHYSICS_EXCEPTION)"
+	$Q$(MAKE) $(QUIET_ARG) -f $(APPS_ROOT_DIR)/interfaces/build/psyclone_transmute_pass.mk \
+	          SOURCE_DIR=$(WORKING_DIR) \
+	          OPTIMISATION_PATH_PSY=$(OPTIMISATION_PATH) \
+	          PSYCLONE_PASS_NO_SCRIPT="$(PSYCLONE_PASS_NO_SCRIPT)"
+	$Q$(MAKE) $(QUIET_ARG) -f $(APPS_ROOT_DIR)/interfaces/build/psyclone_transmute.mk \
+	          SOURCE_DIR=$(WORKING_DIR) \
+	          OPTIMISATION_PATH_PSY=$(OPTIMISATION_PATH) \
+	          PSYCLONE_PHYSICS_FILES="$(PSYCLONE_PHYSICS_FILES)" \
+	          PSYCLONE_PASS_NO_SCRIPT="$(PSYCLONE_PASS_NO_SCRIPT)" \
+	          PSYCLONE_DIRECTORIES="$(PSYCLONE_DIRECTORIES)" \
+	          PSYCLONE_PHYSICS_EXCEPTION="$(PSYCLONE_PHYSICS_EXCEPTION)"
 	$(call MESSAGE,=========================================================)
 	$(call MESSAGE,Analysing $(PROJECT) build dependencies)
 	$(call MESSAGE,=========================================================)
@@ -118,15 +204,45 @@ build: ALWAYS
 	$(call MESSAGE,=========================================================)
 	$Q$(MAKE) $(QUIET_ARG) -C $(WORKING_DIR) -f $(LFRIC_BUILD)/compile.mk
 
+
+##############################################################################
+# Pat_build step - This runs after the build step as relies on exe
+
+# Pass $(PROJECT_NAME) which is exe name linear_model which pat_report needs
+pat_build: build
+	$(call MESSAGE,=========================================================)
+	$(call MESSAGE, Begin Pat Build of $(PROJECT_NAME) executable)
+	$(call MESSAGE,=========================================================)
+	bash $(PAT_BUILD_PATH) $(PROJECT_NAME)
+	$(call MESSAGE,=========================================================)
+	$(call MESSAGE, Pat Build of $(PROJECT_NAME) complete as $(PROJECT_NAME)+pat)
+	$(call MESSAGE,=========================================================)
+
+##############################################################################
+# Unit tests
+#
+unit-tests:
+	$(call MESSAGE,Testing,"There are no unit tests.")
+
+
+##############################################################################
+# Integration tests
+#
+integration-tests:
+	$(call MESSAGE,Testing,"There are no integration tests.")
+
+
 ##############################################################################
 # Clean
 #
 .PHONY: clean
-clean: ALWAYS
-	$(call MESSAGE,Removing,"$(PROJECT_NAME) work space")
-	$(Q)-if [ $(WORKING_DIR) != *[\*]* ] && [ -d $(WORKING_DIR) ] ; then rm -r $(WORKING_DIR) ; fi
-	$(call MESSAGE,Removing,"$(PROJECT_NAME) documents")
-	$(Q)if [ -d documents ] ; then rm -r documents; fi
-	$(call MESSAGE,Removing,"$(PROJECT_NAME) binaries")
+clean: partial-clean
+	$(call MESSAGE,Removing,"UM work space")
+	$(Q)-rm -r $(WORKING_DIR)
+
+.PHONY: partial-clean pclean
+partial-clean pclean: ALWAYS
+	$(call MESSAGE,Removing,"LFRic atmosphere  workspace")
+	$(Q)-rm -r $(WORKING_DIR)
+	$(call MESSAGE,Removing,"LFRic atmosphere binaries")
 	$(Q)-if [ -d bin ] ; then rm -r bin ; fi
-	$(Q)-if [ -d test ] ; then rm -r test ; fi
diff --git a/applications/linear_model/build/compile_options.mk b/applications/linear_model/build/compile_options.mk
new file mode 100644
index 000000000..e4de43248
--- /dev/null
+++ b/applications/linear_model/build/compile_options.mk
@@ -0,0 +1,45 @@
+##############################################################################
+# (c) Crown copyright 2017-2026 Met Office. All rights reserved.
+# The file LICENCE, distributed with this code, contains details of the terms
+# under which the code may be used.
+##############################################################################
+
+# NOTE: Import of compile options from LFRic infrastructure is temporarily
+# suspended here as a workaround for #2340 in which application of the
+# -qoverride-limits option was preventing compilation of a UKCA module.
+# include $(LFRIC_BUILD)/compile_options.mk
+
+$(info UM physics specific compile options)
+
+include $(PROJECT_DIR)/build/fortran/$(FORTRAN_COMPILER).mk
+
+casim/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
+ukca/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
+jules/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
+socrates/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
+legacy/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
+AC_assimilation/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
+aerosols/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
+atmosphere_service/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
+boundary_layer/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
+carbon/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
+convection/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
+diffusion_and_filtering/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
+dynamics/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
+dynamics_advection/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
+electric/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
+free_tracers/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
+gravity_wave_drag/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
+idealised/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
+large_scale_cloud/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
+large_scale_precipitation/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
+PWS_diagnostics/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
+radiation_control/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
+stochastic_physics/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
+tracer_advection/%.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS)
+%/limited_area_constants_mod.o: private FFLAGS_EXTRA = $(FFLAGS_INTEL_FIX_ARG)
+
+$(info Disable warnings-turned-error caused by undeclared external functions - see ifort.mk)
+%mpi_mod.o: private FFLAGS_EXTRA = $(FFLAGS_INTEL_EXTERNALS)
+socrates/src/radiance_core/%.o: private FFLAGS_EXTRA = $(FFLAGS_INTEL_EXTERNALS)
+socrates/src/interface_core/%.o: private FFLAGS_EXTRA = $(FFLAGS_INTEL_EXTERNALS)
diff --git a/applications/linear_model/build/fortran/crayftn.mk b/applications/linear_model/build/fortran/crayftn.mk
new file mode 100644
index 000000000..98e77d011
--- /dev/null
+++ b/applications/linear_model/build/fortran/crayftn.mk
@@ -0,0 +1,13 @@
+##############################################################################
+# (c) Crown copyright 2017 Met Office. All rights reserved.
+# The file LICENCE, distributed with this code, contains details of the terms
+# under which the code may be used.
+##############################################################################
+# Various things specific to the Cray Fortran compiler.
+##############################################################################
+
+$(info Project specials for Cray compiler)
+
+export FFLAGS_UM_PHYSICS = -s real64
+
+include $(PROJECT_DIR)/build/fortran/crayftn/$(PROFILE).mk
diff --git a/applications/linear_model/build/fortran/crayftn/fast-debug.mk b/applications/linear_model/build/fortran/crayftn/fast-debug.mk
new file mode 100644
index 000000000..a627d2556
--- /dev/null
+++ b/applications/linear_model/build/fortran/crayftn/fast-debug.mk
@@ -0,0 +1,55 @@
+##############################################################################
+# (c) Crown copyright 2025 Met Office. All rights reserved.
+# The file LICENCE, distributed with this code, contains details of the terms
+# under which the code may be used.
+##############################################################################
+##############################################################################
+# Various things specific to fast-debug lfric_atm when using the
+# Cray Fortran compiler.
+# To override flags specified in LFRic Core, use
+# FFLAGS_SAFE_OPTIMISATION, to add an additional flag to what is specified
+# in Core, use FFLAGS_EXTRA. If you need to add debugging flags to a module,
+# modify FFLAGS_DEBUG for the target module.
+# All flag modification should be `private` so they are not inherited by
+# submodules.
+##############################################################################
+
+# ==========================================================================
+# NON-DEBUG FLAGS
+# ==========================================================================
+# UKCA
+%ukca_emiss_mode_mod.o: private FFLAGS_SAFE_OPTIMISATION = -O0
+%ukca_step_control_mod.o: private FFLAGS_SAFE_OPTIMISATION = -O0
+
+# UM
+%parcel_ascent_5a.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS) -hvector0
+
+# LFRic Apps
+%aerosol_ukca_alg_mod_psy.o: private FFLAGS_SAFE_OPTIMISATION = -O0
+%bl_exp_alg_mod_psy.o: private FFLAGS_SAFE_OPTIMISATION = -O0
+%bl_imp_alg_mod_psy.o: private FFLAGS_SAFE_OPTIMISATION = -O0
+%conv_comorph_alg_mod_psy.o: private FFLAGS_SAFE_OPTIMISATION = -O0
+%conv_comorph_kernel_mod.o: private FFLAGS_SAFE_OPTIMISATION = -O0
+%conv_gr_alg_mod_psy.o: private FFLAGS_SAFE_OPTIMISATION = -O0
+%gungho_model_mod.o: private FFLAGS_SAFE_OPTIMISATION = -O0
+%init_aerosol_fields_alg_mod_psy.o: private FFLAGS_SAFE_OPTIMISATION = -O0
+%jules_extra_kernel_mod.o: private FFLAGS_SAFE_OPTIMISATION = -O0
+large_scale_precipitation/%.o: private FFLAGS_SAFE_OPTIMISATION = -O2 -hfp0 -hflex_mp=strict
+
+# ==========================================================================
+# DEBUG FLAGS
+# ==========================================================================
+# UKCA
+%ukca_emiss_mode_mod.o: private FFLAGS_DEBUG = -G0
+%ukca_step_control_mod.o: private FFLAGS_DEBUG = -G0
+
+# LFRic Apps
+%aerosol_ukca_alg_mod_psy.o: private FFLAGS_DEBUG = -G0
+%bl_exp_alg_mod_psy.o: private FFLAGS_DEBUG = -G0
+%bl_imp_alg_mod_psy.o: private FFLAGS_DEBUG = -G0
+%conv_comorph_alg_mod_psy.o: private FFLAGS_DEBUG = -G0
+%conv_comorph_kernel_mod.o: private FFLAGS_DEBUG = -G0
+%conv_gr_alg_mod_psy.o: private FFLAGS_DEBUG = -G0
+%gungho_model_mod.o: private FFLAGS_DEBUG = -G0
+%init_aerosol_fields_alg_mod_psy.o: private FFLAGS_DEBUG = -G0
+%jules_extra_kernel_mod.o: private FFLAGS_DEBUG = -G0
diff --git a/applications/linear_model/build/fortran/crayftn/full-debug.mk b/applications/linear_model/build/fortran/crayftn/full-debug.mk
new file mode 100644
index 000000000..a5b3d45a3
--- /dev/null
+++ b/applications/linear_model/build/fortran/crayftn/full-debug.mk
@@ -0,0 +1,17 @@
+##############################################################################
+# (c) Crown copyright 2025 Met Office. All rights reserved.
+# The file LICENCE, distributed with this code, contains details of the terms
+# under which the code may be used.
+##############################################################################
+##############################################################################
+# Various things specific to full-debug lfric_atm when using the
+# Cray Fortran compiler.
+##############################################################################
+
+# ==========================================================================
+# NON-DEBUG FLAGS
+# ==========================================================================
+
+# ==========================================================================
+# DEBUG FLAGS
+# ==========================================================================
diff --git a/applications/linear_model/build/fortran/crayftn/production.mk b/applications/linear_model/build/fortran/crayftn/production.mk
new file mode 100644
index 000000000..ddf5ca86c
--- /dev/null
+++ b/applications/linear_model/build/fortran/crayftn/production.mk
@@ -0,0 +1,36 @@
+##############################################################################
+# (c) Crown copyright 2025 Met Office. All rights reserved.
+# The file LICENCE, distributed with this code, contains details of the terms
+# under which the code may be used.
+##############################################################################
+##############################################################################
+# Various things specific to production lfric_atm when using the
+# Cray Fortran compiler.
+##############################################################################
+
+# ==========================================================================
+# DIRECTORIES
+# ==========================================================================
+gravity_wave_drag/%.o: private FFLAGS_RISKY_OPTIMISATION = -O2 -hflex_mp=strict
+
+# ==========================================================================
+# MODULES
+# ==========================================================================
+# UKCA
+%ukca_emiss_mode_mod.o: private FFLAGS_RISKY_OPTIMISATION = -O0
+%ukca_step_control_mod.o: private FFLAGS_RISKY_OPTIMISATION = -O0
+
+# UM
+%parcel_ascent_5a.o: private FFLAGS_EXTRA = $(FFLAGS_UM_PHYSICS) -hvector0
+
+# LFRic Apps
+%aerosol_ukca_alg_mod_psy.o: private FFLAGS_RISKY_OPTIMISATION = -O0
+%bl_exp_alg_mod_psy.o: private FFLAGS_RISKY_OPTIMISATION = -O0
+%bl_imp_alg_mod_psy.o: private FFLAGS_RISKY_OPTIMISATION = -O0
+%conv_comorph_alg_mod_psy.o: private FFLAGS_RISKY_OPTIMISATION = -O0
+%conv_comorph_kernel_mod.o: private FFLAGS_RISKY_OPTIMISATION = -O0
+%conv_gr_alg_mod_psy.o: private FFLAGS_RISKY_OPTIMISATION = -O0
+%gungho_model_mod.o: private FFLAGS_RISKY_OPTIMISATION = -O0
+%init_aerosol_fields_alg_mod_psy.o: private FFLAGS_RISKY_OPTIMISATION = -O0
+%jules_extra_kernel_mod.o: private FFLAGS_RISKY_OPTIMISATION = -O0
+large_scale_precipitation/%.o: private FFLAGS_SAFE_OPTIMISATION = -O3 -hipa3 -hflex_mp=conservative
diff --git a/applications/linear_model/build/fortran/gfortran.mk b/applications/linear_model/build/fortran/gfortran.mk
new file mode 100644
index 000000000..79f02dc5a
--- /dev/null
+++ b/applications/linear_model/build/fortran/gfortran.mk
@@ -0,0 +1,40 @@
+##############################################################################
+# (c) Crown copyright 2017 Met Office. All rights reserved.
+# The file LICENCE, distributed with this code, contains details of the terms
+# under which the code may be used.
+##############################################################################
+# Various things specific to the GNU Fortran compiler.
+##############################################################################
+
+$(info Project specials for GNU compiler)
+
+export FFLAGS_UM_PHYSICS = -fdefault-real-8 -fdefault-double-8
+# Most lfric_atm dependencies contain code with implicit lossy conversions and
+# unused variables.
+# We reset the FFLAGS_WARNINGS variable here in order to prevent
+# -Werror induced build failures.
+FFLAGS_WARNINGS          = -Wall -Werror=character-truncation -Werror=unused-value \
+                           -Werror=tabs
+# But, we can apply some more lfric infrastructure checking to socrates
+FFLAGS_SOCRATES_WARNINGS = -Werror=unused-variable
+
+science/src/socrates/%.o science/src/socrates/%.mod: private FFLAGS_EXTRA = $(FFLAGS_SOCRATES_WARNINGS)
+
+# We remove bounds checking (applied by -fcheck=all) and underflow checking. The
+# latter is due to regular permitting of exponents going to zero for small numbers
+# to imply total extinction of radiation passing through a medium
+FFLAGS_RUNTIME           = -fcheck=all,no-bounds -ffpe-trap=invalid,zero,overflow
+
+# The lfric_atm app defines an extra set of debug flags for
+# fast-debug which are the same as the full-debug settings
+# except for some platforms
+ifdef CRAY_ENVIRONMENT
+# On the EXZ these options are switched off for fast-debug
+# due to an unexpected FPE in the NetCDF library
+FFLAGS_FASTD_INIT               =
+FFLAGS_FASTD_RUNTIME            =
+else
+# Otherwise, use the same as the default full-debug settings
+FFLAGS_FASTD_INIT         = $(FFLAGS_INIT)
+FFLAGS_FASTD_RUNTIME      = $(FFLAGS_RUNTIME)
+endif
diff --git a/applications/linear_model/build/fortran/ifort.mk b/applications/linear_model/build/fortran/ifort.mk
new file mode 100644
index 000000000..dc9b4513c
--- /dev/null
+++ b/applications/linear_model/build/fortran/ifort.mk
@@ -0,0 +1,65 @@
+##############################################################################
+# (c) Crown copyright 2017 Met Office. All rights reserved.
+# The file LICENCE, distributed with this code, contains details of the terms
+# under which the code may be used.
+##############################################################################
+# Various things specific to the Intel Fortran compiler.
+##############################################################################
+
+$(info Project specials for Intel compiler)
+
+export FFLAGS_UM_PHYSICS = -r8
+
+# Set fast-debug and full-debug options for lfric_atm Intel that
+# differ from the setup in infrastructure used by other LFRic apps.
+# First, the -check all option is removed from all configurations as
+# it results in excessive numbers of warnings from UM code running
+# within LFRic
+FFLAGS_RUNTIME            = -fpe0
+# Second, certain fast-debug options cause XIOS failures on the Cray
+# in jobs that write diagnostic so they are removed. Note: the
+# full-debug test can still use these options as it avoids such XIOS
+# use.
+ifdef CRAY_ENVIRONMENT
+# On the Cray these options are switched off for fast-debug
+FFLAGS_FASTD_INIT               = 
+FFLAGS_FASTD_RUNTIME            =
+else
+# Otherwise, use the same as the default full-debug settings
+FFLAGS_FASTD_INIT         = $(FFLAGS_INIT) 
+FFLAGS_FASTD_RUNTIME      = $(FFLAGS_RUNTIME)
+endif
+
+# NOTE: The -qoverride-limits option contained in $(FFLAGS_INTEL_FIX_ARG) is
+# not currently applied here. This is a temporary workaround for #3465
+# which it was found to be inadvertently preventing compilation
+# openMP has also been removed from this routine via the optimisation script
+%bl_imp_alg_mod_psy.o %bl_imp_alg_mod_psy.mod:   private FFLAGS_EXTRA =
+%aerosol_ukca_alg_mod_psy.o %aerosol_ukca_alg_mod_psy.mod:   private FFLAGS_EXTRA =
+%conv_comorph_alg_mod_psy.o %conv_comorph_alg_mod_psy.mod:   private FFLAGS_EXTRA =
+
+$(info LFRic compile options required for files with OpenMP - see Ticket 1490)
+%psy.o %psy.mod:   private FFLAGS_EXTRA = $(FFLAGS_INTEL_FIX_ARG)
+# NOTE: The -qoverride-limits option contained in $(FFLAGS_INTEL_FIX_ARG) is
+# not currently applied here. This is a temporary workaround for #3205
+# which it was found to be inadvertently preventing compilation
+# psy/%.o psy/%.mod: private FFLAGS_EXTRA = $(FFLAGS_INTEL_FIX_ARG)
+
+
+# -warn noexternals applied to code that imports lfric_mpi_mod to avoid
+# a warning-turned-error about missing interfaces for MPI calls in
+# mpi.mod, such as MPI_Allreduce - switching to mpi_f08.mod resolves
+# this via polymorphic interface declarations. Some SOCRATES functions
+# do not currently declare interfaces either. Flag was introduced in
+# Intel Fortran v19.1.0 according to Intel release notes.
+ifeq ($(shell test "$(IFORT_VERSION)" -ge 0190100; echo $$?), 0)
+  $(info ** Activating externals warning override for selected source files)
+  export FFLAGS_INTEL_EXTERNALS = -warn noexternals
+else
+  export FFLAGS_INTEL_EXTERNALS =
+endif
+
+ifeq ($(shell test "$(IFORT_VERSION)" -ge 0190103; echo $$?), 0)
+  $(info ** Disabling OpenMP due to a compiler bug for intel-compiler newer than 2020.3.304 - see Ticket 3853)
+  %ls_ppnc.o %ls_ppnc.mod: FFLAGS:=${FFLAGS} -qno-openmp
+endif
diff --git a/applications/linear_model/build/fortran/ifx.mk b/applications/linear_model/build/fortran/ifx.mk
new file mode 100644
index 000000000..ff6251cde
--- /dev/null
+++ b/applications/linear_model/build/fortran/ifx.mk
@@ -0,0 +1,58 @@
+##############################################################################
+# (c) Crown copyright 2025 Met Office. All rights reserved.
+# The file LICENCE, distributed with this code, contains details of the terms
+# under which the code may be used.
+##############################################################################
+# Various things specific to the Intel oneAPI Fortran compiler.
+##############################################################################
+
+$(info Project specials for Intel oneAPI compiler)
+
+export FFLAGS_UM_PHYSICS = -r8
+
+# Set fast-debug and full-debug options for lfric_atm Intel that
+# differ from the setup in infrastructure used by other LFRic apps.
+# First, the -check all option is removed from all configurations as
+# it results in excessive numbers of warnings from UM code running
+# within LFRic
+FFLAGS_RUNTIME            = -fpe0
+# Second, certain fast-debug options cause XIOS failures on the Cray
+# in jobs that write diagnostic so they are removed. Note: the
+# full-debug test can still use these options as it avoids such XIOS
+# use.
+ifdef CRAY_ENVIRONMENT
+# On the Cray these options are switched off for fast-debug
+FFLAGS_FASTD_INIT               = 
+FFLAGS_FASTD_RUNTIME            =
+else
+# Otherwise, use the same as the default full-debug settings
+FFLAGS_FASTD_INIT         = $(FFLAGS_INIT) 
+FFLAGS_FASTD_RUNTIME      = $(FFLAGS_RUNTIME)
+endif
+
+# NOTE: The -qoverride-limits option contained in $(FFLAGS_INTEL_FIX_ARG) is
+# not currently applied here. This is a temporary workaround for #3465
+# which it was found to be inadvertently preventing compilation
+# openMP has also been removed from this routine via the optimisation script
+%bl_imp_alg_mod_psy.o %bl_imp_alg_mod_psy.mod:   private FFLAGS_EXTRA =
+%aerosol_ukca_alg_mod_psy.o %aerosol_ukca_alg_mod_psy.mod:   private FFLAGS_EXTRA =
+%conv_comorph_alg_mod_psy.o %conv_comorph_alg_mod_psy.mod:   private FFLAGS_EXTRA =
+
+$(info LFRic compile options required for files with OpenMP - see Ticket 1490)
+%psy.o %psy.mod:   private FFLAGS_EXTRA = $(FFLAGS_INTEL_FIX_ARG)
+# NOTE: The -qoverride-limits option contained in $(FFLAGS_INTEL_FIX_ARG) is
+# not currently applied here. This is a temporary workaround for #3205
+# which it was found to be inadvertently preventing compilation
+# psy/%.o psy/%.mod: private FFLAGS_EXTRA = $(FFLAGS_INTEL_FIX_ARG)
+
+
+# -warn noexternals applied to code that imports mpi_mod to avoid
+# a warning-turned-error about missing interfaces for MPI calls in
+# mpi.mod, such as MPI_Allreduce - switching to mpi_f08.mod resolves
+# this via polymorphic interface declarations. Some SOCRATES functions
+# do not currently declare interfaces either. Flag was introduced in
+# Intel Fortran v19.1.0 according to Intel release notes.
+export FFLAGS_INTEL_EXTERNALS = -warn noexternals
+
+$(info ** Disabling OpenMP due to a compiler bug for intel-compiler newer than 2020.3.304 - see Ticket 3853)
+%ls_ppnc.o %ls_ppnc.mod: FFLAGS:=${FFLAGS} -qno-openmp
diff --git a/applications/linear_model/build/fortran/nvfortran.mk b/applications/linear_model/build/fortran/nvfortran.mk
new file mode 100644
index 000000000..e4a25fe13
--- /dev/null
+++ b/applications/linear_model/build/fortran/nvfortran.mk
@@ -0,0 +1,17 @@
+#############################################################################
+#(c) Crown copyright 2024 Met Office. All rights reserved.
+#The file LICENCE, distributed with this code, contains details of the terms
+#under which the code may be used.
+#############################################################################
+# Various things specific to the NVIDIA Fortran compiler.
+#############################################################################
+
+$(info Project specials for NVIDIA compiler)
+
+export FFLAGS_UM_PHYSICS = -r8
+
+# The lfric_atm app defines an extra set of debug flags for
+# fast-debug. For this compiler use the same as the full-debug
+# settings
+FFLAGS_FASTD_INIT         = $(FFLAGS_INIT) 
+FFLAGS_FASTD_RUNTIME      = $(FFLAGS_RUNTIME)
diff --git a/applications/linear_model/build/fortran/pgfortran.mk b/applications/linear_model/build/fortran/pgfortran.mk
new file mode 100644
index 000000000..e95afff35
--- /dev/null
+++ b/applications/linear_model/build/fortran/pgfortran.mk
@@ -0,0 +1,17 @@
+##############################################################################
+# (c) Crown copyright 2017 Met Office. All rights reserved.
+# The file LICENCE, distributed with this code, contains details of the terms
+# under which the code may be used.
+##############################################################################
+# Various things specific to the Portland Fortran compiler.
+##############################################################################
+
+$(info Project specials for Portland compiler)
+
+export FFLAGS_UM_PHYSICS = -r8
+
+# The lfric_atm app defines an extra set of debug flags for
+# fast-debug. For this compiler use the same as the full-debug
+# settings
+FFLAGS_FASTD_INIT         = $(FFLAGS_INIT) 
+FFLAGS_FASTD_RUNTIME      = $(FFLAGS_RUNTIME)
diff --git a/applications/linear_model/build/project.mk b/applications/linear_model/build/project.mk
new file mode 100644
index 000000000..e4a05cfed
--- /dev/null
+++ b/applications/linear_model/build/project.mk
@@ -0,0 +1,15 @@
+##############################################################################
+# (c) Crown copyright 2017 Met Office. All rights reserved.
+# The file LICENCE, distributed with this code, contains details of the terms
+# under which the code may be used.
+##############################################################################
+
+$(info UM physics project specials)
+
+export PRE_PROCESS_INCLUDE_DIRS = \
+        $(WORKING_DIR)/atmosphere_service/include \
+        $(WORKING_DIR)/boundary_layer/include \
+        $(WORKING_DIR)/large_scale_precipitation/include \
+        $(WORKING_DIR)/free_tracers/include
+
+export PRE_PROCESS_MACROS += UM_PHYSICS LFRIC USSPPREC_32B LSPREC_32B UM_JULES
diff --git a/applications/linear_model/build/psyclone_transmute_file_list.mk b/applications/linear_model/build/psyclone_transmute_file_list.mk
new file mode 100644
index 000000000..90e2556c0
--- /dev/null
+++ b/applications/linear_model/build/psyclone_transmute_file_list.mk
@@ -0,0 +1,70 @@
+##############################################################################
+# (c) Crown copyright 2025 Met Office. All rights reserved.
+# The file LICENCE, distributed with this code, contains details of the terms
+# under which the code may be used.
+##############################################################################
+
+# File lists provided will use the transmute PSyclone method.
+# https://code.metoffice.gov.uk/trac/lfric_apps/ticket/724
+
+
+##### TRANSMUTE_INCLUDE_METHOD specify_include #####
+# For CPU OMP, we want to choose which files get run through PSyclone,
+# and preserve existing hand coded optimisations.
+
+# Choose which files to Pre-proccess and PSyclone from physics_schemes / other source (e.g. UKCA)
+
+export PSYCLONE_PHYSICS_FILES = \
+                                bl_lsp \
+                                bm_tau_kernel_mod \
+                                btq_int \
+                                conv_gr_kernel_mod \
+                                ex_flux_tq \
+                                ex_flux_uv \
+                                fm_drag \
+                                gw_ussp_mod \
+                                imp_mix \
+                                jules_exp_kernel_mod \
+                                jules_extra_kernel_mod \
+                                jules_imp_kernel_mod \
+                                kmkh \
+                                kmkhz_9c_wtrac \
+                                lw_kernel_mod \
+                                mphys_kernel_mod \
+                                pc2_bl_forced_cu \
+                                pc2_bm_initiate \
+                                pc2_initiation_ctl \
+                                pc2_initiation_kernel_mod \
+                                pc2_conv_coupling_kernel_mod \
+                                sw_kernel_mod \
+                                ukca_aero_ctl \
+                                ukca_abdulrazzak_ghan \
+                                ukca_chemistry_ctl_full_mod \
+                                ukca_main1-ukca_main1 \
+                                sw_rad_tile_kernel_mod \
+                                jules_imp_kernel_mod \
+                                jules_exp_kernel_mod \
+                                jules_extra_kernel_mod
+
+##### TRANSMUTE_INCLUDE_METHOD specify_include #####
+
+# List to use PSyclone explicitly without any opt script
+# This will remove hand written (OMP) directives in the source
+# Used by both methods, specify_include and specify_exclude
+export PSYCLONE_PASS_NO_SCRIPT = ukca_abdulrazzak_ghan
+
+
+##### TRANSMUTE_INCLUDE_METHOD specify_exclude #####
+# For GPU, we may want to use more generic local.py transformation scripts and psyclone by directory.
+# Advise which directories to pass to PSyclone.
+# All files in these directories will be run through PSyclone using the transmute method.
+# Also provide an optional exception list.
+# These files will be filtered, and will NOT be run through PSyclone.
+
+# Directories to psyclone
+export PSYCLONE_DIRECTORIES =
+
+# A general file exception list
+export PSYCLONE_PHYSICS_EXCEPTION =
+
+##### TRANSMUTE_INCLUDE_METHOD specify_exclude #####
diff --git a/applications/linear_model/example/configuration.nml b/applications/linear_model/example/configuration.nml
index 40697eb6c..76dd2e7bd 100644
--- a/applications/linear_model/example/configuration.nml
+++ b/applications/linear_model/example/configuration.nml
@@ -13,8 +13,24 @@ transport_overwrite_freq='final'
 limit_cfl=.false.,
 /
 &section_choice
+aerosol='none',
+boundary_layer='none'
+chemistry='none',
+cloud='none',
+convection='none',
 dynamics='gungho',
+electric='none',
 external_forcing=.false.,
+iau=.false.,
+iau_sst=.false.,
+iau_surf=.false.,
+methane_oxidation=.false.,
+microphysics='none',
+orographic_drag='none',
+radiation='none',
+spectral_gwd='none',
+stochastic_physics='none',
+surface='none'
 /
 &departure_points
 horizontal_limit='none',
@@ -285,3 +301,4 @@ vertical_sl_order='cubic'
 wind_mono_top=.false.
 wind_mono_top_depth=5
 /
+
diff --git a/applications/linear_model/optimisation/esnz-cascade/psykal/global.py b/applications/linear_model/optimisation/esnz-cascade/psykal/global.py
deleted file mode 100644
index 125a77f40..000000000
--- a/applications/linear_model/optimisation/esnz-cascade/psykal/global.py
+++ /dev/null
@@ -1,32 +0,0 @@
-##############################################################################
-# Copyright (c) 2017,  Met Office, on behalf of HMSO and Queen's Printer
-# For further details please refer to the file LICENCE.original which you
-# should have received as part of this distribution.
-##############################################################################
-
-
-'''
-PSyclone transformation script for the LFRic (Dynamo0p3) API to apply
-colouring, OpenMP and redundant computation to the level-1 halo for
-the initialisation built-ins generically.
-
-'''
-
-from psyclone_tools import (redundant_computation_setval, colour_loops,
-                            openmp_parallelise_loops,
-                            view_transformed_schedule)
-
-
-def trans(psyir):
-    '''
-    Applies PSyclone colouring, OpenMP and redundant computation
-    transformations.
-
-    :param psyir: the PSyIR of the PSyIR-layer.
-    :type psyir: :py:class:`psyclone.psyir.nodes.FileContainer`
-
-    '''
-    redundant_computation_setval(psyir)
-    colour_loops(psyir)
-    openmp_parallelise_loops(psyir)
-    view_transformed_schedule(psyir)
diff --git a/applications/linear_model/optimisation/meto-azspice b/applications/linear_model/optimisation/meto-azspice
deleted file mode 120000
index 146775380..000000000
--- a/applications/linear_model/optimisation/meto-azspice
+++ /dev/null
@@ -1 +0,0 @@
-meto-ex1a/
\ No newline at end of file
diff --git a/applications/linear_model/optimisation/meto-ex1a/psykal/global.py b/applications/linear_model/optimisation/meto-ex1a/psykal/global.py
deleted file mode 100644
index 125a77f40..000000000
--- a/applications/linear_model/optimisation/meto-ex1a/psykal/global.py
+++ /dev/null
@@ -1,32 +0,0 @@
-##############################################################################
-# Copyright (c) 2017,  Met Office, on behalf of HMSO and Queen's Printer
-# For further details please refer to the file LICENCE.original which you
-# should have received as part of this distribution.
-##############################################################################
-
-
-'''
-PSyclone transformation script for the LFRic (Dynamo0p3) API to apply
-colouring, OpenMP and redundant computation to the level-1 halo for
-the initialisation built-ins generically.
-
-'''
-
-from psyclone_tools import (redundant_computation_setval, colour_loops,
-                            openmp_parallelise_loops,
-                            view_transformed_schedule)
-
-
-def trans(psyir):
-    '''
-    Applies PSyclone colouring, OpenMP and redundant computation
-    transformations.
-
-    :param psyir: the PSyIR of the PSyIR-layer.
-    :type psyir: :py:class:`psyclone.psyir.nodes.FileContainer`
-
-    '''
-    redundant_computation_setval(psyir)
-    colour_loops(psyir)
-    openmp_parallelise_loops(psyir)
-    view_transformed_schedule(psyir)
diff --git a/applications/linear_model/optimisation/minimum/psykal/global.py b/applications/linear_model/optimisation/minimum/psykal/global.py
deleted file mode 100644
index 5ea0bf84d..000000000
--- a/applications/linear_model/optimisation/minimum/psykal/global.py
+++ /dev/null
@@ -1,31 +0,0 @@
-##############################################################################
-# (c) Crown copyright 2023 Met Office. All rights reserved.
-# The file LICENCE, distributed with this code, contains details of the terms
-# under which the code may be used.
-##############################################################################
-
-
-'''
-PSyclone transformation script for the LFRic (Dynamo0p3) API to apply
-the minumum set of transformations required to permit the application
-to run safely in debug mode on all supported platforms.
-
-Applying the 'redundant_computation_setval' transformation for the
-initialisation built-ins permits developers to set safe values in halos.
-
-'''
-from psyclone_tools import (redundant_computation_setval,
-                            view_transformed_schedule)
-
-
-def trans(psyir):
-    '''
-    Applies PSyclone redundant computation transformations on
-    initialisation built-ins only.
-
-    :param psyir: the PSyIR of the PSyIR-layer.
-    :type psyir: :py:class:`psyclone.psyir.nodes.FileContainer`
-
-    '''
-    redundant_computation_setval(psyir)
-    view_transformed_schedule(psyir)
diff --git a/applications/linear_model/optimisation/nci-gadi/psykal/global.py b/applications/linear_model/optimisation/nci-gadi/psykal/global.py
deleted file mode 120000
index 7246d03a8..000000000
--- a/applications/linear_model/optimisation/nci-gadi/psykal/global.py
+++ /dev/null
@@ -1 +0,0 @@
-./../../meto-ex1a/psykal/global.py
\ No newline at end of file
diff --git a/rose-stem/flow.cylc b/rose-stem/flow.cylc
index de38992a1..02b40dfc6 100644
--- a/rose-stem/flow.cylc
+++ b/rose-stem/flow.cylc
@@ -91,6 +91,7 @@
 # Check if running physics - don't extract these if not
 {% if "lfric_atm" in requested_applications
       or "jules" in requested_applications
+      or "linear_model" in requested_applications
       or "ngarch" in requested_applications
       or "lfric_coupled" in requested_applications %}
 
diff --git a/rose-stem/site/meto/common/default_directives.cylc b/rose-stem/site/meto/common/default_directives.cylc
index f861939eb..21a2f8fb7 100644
--- a/rose-stem/site/meto/common/default_directives.cylc
+++ b/rose-stem/site/meto/common/default_directives.cylc
@@ -18,6 +18,9 @@
         "lfric_atm": {
             "build_wallclock": 45,
         },
+        "linear_model": {
+            "build_wallclock": 45,
+        },
         "jules": {
             "build_wallclock": 35,
         },
@@ -45,6 +48,9 @@
         "lfric_atm": {
             "build_wallclock": 60,
         },
+        "linear_model": {
+            "build_wallclock": 60,
+        },
         "lfric_coupled": {
             "build_wallclock": 60,
         },
diff --git a/science/gungho/source/algorithm/initialisation/init_physics_prognostics_alg_mod.X90 b/science/gungho/source/algorithm/initialisation/init_physics_prognostics_alg_mod.X90
index f43c0e5a0..9a116271c 100644
--- a/science/gungho/source/algorithm/initialisation/init_physics_prognostics_alg_mod.X90
+++ b/science/gungho/source/algorithm/initialisation/init_physics_prognostics_alg_mod.X90
@@ -22,9 +22,25 @@ module init_physics_prognostics_alg_mod
   use init_aerosol_fields_alg_mod,      only : init_aerosol_fields_alg
   use init_stph_fields_alg_mod,         only : init_stph_fields_alg
 
-  use section_choice_config_mod, only: surface, surface_jules, &
-                                       aerosol, aerosol_um,    &
-                                       electric, electric_um
+  use section_choice_config_mod, only: surface, surface_jules,  &
+                                       surface_none,            &
+                                       aerosol, aerosol_um,     &
+                                       aerosol_none,            &
+                                       cloud, cloud_none,       &
+                                       microphysics,            &
+                                       microphysics_none,       &
+                                       radiation,               &
+                                       radiation_none,          &
+                                       convection,              &
+                                       convection_none,         &
+                                       orographic_drag,         &
+                                       orographic_drag_none,    &
+                                       boundary_layer,          &
+                                       boundary_layer_none,     &
+                                       stochastic_physics,      &
+                                       stochastic_physics_none, &
+                                       electric, electric_um,   &
+                                       electric_none
 
   use aerosol_config_mod,        only: glomap_mode,               &
                                        glomap_mode_dust_and_clim, &
@@ -87,37 +103,44 @@ contains
 
 #ifdef UM_PHYSICS
 
-    ! Only actually initialise the fields if we're using the external code
-    ! Most things need calling regardless of whether the scheme is on,
-    ! because we initialise fields used by other schemes if the scheme
-    ! is off. Jules however can only be initialised if it is switched on
-    ! as it uses things from the surface namelist which is not read if
-    ! it is switched off.
-    call init_radiation_fields_alg(radiation_fields)
-    call init_microphysics_fields_alg(microphysics_fields)
-    if (electric == electric_um) then
-      call init_electric_fields_alg(electric_fields)
+    if ( surface            /= surface_none             .or. &
+         radiation          /= radiation_none           .or. &
+         orographic_drag    /= orographic_drag_none     .or. &
+         stochastic_physics /= stochastic_physics_none  .or. &
+         boundary_layer     /= boundary_layer_none ) then
+
+      ! Only actually initialise the fields if we're using the external code
+      ! Most things need calling regardless of whether the scheme is on,
+      ! because we initialise fields used by other schemes if the scheme
+      ! is off. Jules however can only be initialised if it is switched on
+      ! as it uses things from the surface namelist which is not read if
+      ! it is switched off.
+      call init_radiation_fields_alg(radiation_fields)
+      call init_microphysics_fields_alg(microphysics_fields)
+      if (electric == electric_um) then
+        call init_electric_fields_alg(electric_fields)
+      end if
+      call init_orography_fields_alg(orography_fields)
+      call init_turbulence_fields_alg(turbulence_fields)
+      call init_convection_fields_alg(convection_fields)
+      call init_cloud_fields_alg(cloud_fields)
+      call init_surface_fields_alg(surface_fields)
+      if (surface == surface_jules) then
+        call init_soil_fields_alg(soil_fields)
+        call init_snow_fields_alg(snow_fields)
+      end if
+      if ( ( aerosol == aerosol_um .and.          &
+           ( glomap_mode == glomap_mode_ukca .or. &
+             glomap_mode == glomap_mode_dust_and_clim ) ) .or. &
+           ( chem_scheme == chem_scheme_flexchem ) ) then
+        call init_chemistry_fields_alg(chemistry_fields)
+      end if
+      call init_aerosol_fields_alg(aerosol_fields)
+
+      call init_stph_fields_alg(stph_fields)
+
+      call log_event( 'Physics field collections initialised', LOG_LEVEL_INFO )
     end if
-    call init_orography_fields_alg(orography_fields)
-    call init_turbulence_fields_alg(turbulence_fields)
-    call init_convection_fields_alg(convection_fields)
-    call init_cloud_fields_alg(cloud_fields)
-    call init_surface_fields_alg(surface_fields)
-    if (surface == surface_jules) then
-      call init_soil_fields_alg(soil_fields)
-      call init_snow_fields_alg(snow_fields)
-    end if
-    if ( ( aerosol == aerosol_um .and.          &
-         ( glomap_mode == glomap_mode_ukca .or. &
-           glomap_mode == glomap_mode_dust_and_clim ) ) .or. &
-         ( chem_scheme == chem_scheme_flexchem ) ) then
-      call init_chemistry_fields_alg(chemistry_fields)
-    end if
-    call init_aerosol_fields_alg(aerosol_fields)
-
-    call init_stph_fields_alg(stph_fields)
-
-    call log_event( 'Physics field collections initialised', LOG_LEVEL_INFO )
 
 #endif
 
diff --git a/science/gungho/source/driver/create_physics_prognostics_mod.F90 b/science/gungho/source/driver/create_physics_prognostics_mod.F90
index 6e6545f72..cc4e98025 100644
--- a/science/gungho/source/driver/create_physics_prognostics_mod.F90
+++ b/science/gungho/source/driver/create_physics_prognostics_mod.F90
@@ -52,18 +52,29 @@ module create_physics_prognostics_mod
                                              easyaerosol_sw, easyaerosol_lw,    &
                                              murk_prognostic, murk
   use section_choice_config_mod,      only : cloud, cloud_um,                   &
+                                             cloud_none,                        &
                                              aerosol, aerosol_um,               &
+                                             aerosol_none,                      &
                                              radiation, radiation_socrates,     &
+                                             radiation_none,                    &
                                              boundary_layer,                    &
                                              boundary_layer_um,                 &
+                                             boundary_layer_none,               &
                                              electric, electric_um,             &
+                                             electric_none,                     &
                                              iau_sst,                           &
                                              surface, surface_jules,            &
+                                             surface_none,                      &
                                              orographic_drag,                   &
                                              orographic_drag_um,                &
+                                             orographic_drag_none,              &
                                              convection, convection_um,         &
+                                             convection_none,                   &
+                                             microphysics,                      &
+                                             microphysics_none,                 &
                                              stochastic_physics,                &
-                                             stochastic_physics_um
+                                             stochastic_physics_um,             &
+                                             stochastic_physics_none
   use cloud_config_mod,               only : scheme,                            &
                                              scheme_pc2
   use convection_config_mod,          only : cv_scheme, cv_scheme_comorph
@@ -209,6 +220,13 @@ subroutine process_physics_prognostics(processor)
     end if
 
 #ifdef UM_PHYSICS
+
+  if ( surface            /= surface_none             .or. &
+       radiation          /= radiation_none           .or. &
+       orographic_drag    /= orographic_drag_none     .or. &
+       stochastic_physics /= stochastic_physics_none  .or. &
+       boundary_layer     /= boundary_layer_none ) then
+
     !========================================================================
     ! Fields owned by the radiation scheme
     !========================================================================
@@ -1882,6 +1900,8 @@ subroutine process_physics_prognostics(processor)
           twod=.true., is_int=.true., ckp=checkpoint_flag, empty=is_empty))
     end if
 
+  end if
+
 #endif
 
 
diff --git a/science/gungho/source/driver/gungho_driver_mod.F90 b/science/gungho/source/driver/gungho_driver_mod.F90
index cb77b425d..2aa6193e3 100644
--- a/science/gungho/source/driver/gungho_driver_mod.F90
+++ b/science/gungho/source/driver/gungho_driver_mod.F90
@@ -18,9 +18,10 @@ module gungho_driver_mod
   use gungho_diagnostics_driver_mod, &
                                    only : gungho_diagnostics_driver
   use iau_time_control_mod,        only : calc_iau_ts_end
-  use gungho_init_fields_mod,      only : create_model_data, &
-                                          initialise_model_data, &
-                                          output_model_data, &
+  use gungho_init_fields_mod,      only : create_model_data,         &
+                                          create_physics_model_data, &
+                                          initialise_model_data,     &
+                                          output_model_data,         &
                                           finalise_model_data
   use driver_modeldb_mod,          only : modeldb_type
   use gungho_model_mod,            only : initialise_infrastructure, &
@@ -229,6 +230,9 @@ subroutine initialise( program_name, modeldb )
     call create_model_data( modeldb,         &
                             mesh, twod_mesh, &
                             aerosol_mesh, aerosol_twod_mesh )
+    call create_physics_model_data( modeldb, &
+                            mesh, twod_mesh, &
+                            aerosol_mesh, aerosol_twod_mesh )
 
     ! Set up io for multifile reading
     if ( multifile_io ) then
diff --git a/science/gungho/source/driver/gungho_init_fields_mod.X90 b/science/gungho/source/driver/gungho_init_fields_mod.X90
index 829eaf802..f37186a85 100644
--- a/science/gungho/source/driver/gungho_init_fields_mod.X90
+++ b/science/gungho/source/driver/gungho_init_fields_mod.X90
@@ -158,7 +158,7 @@ module gungho_init_fields_mod
   ! Set these to select how to initialize model prognostic fields
   integer(i_def) :: prognostic_init_choice, ancil_choice
 
-  public create_model_data, finalise_model_data, &
+  public create_model_data, create_physics_model_data, finalise_model_data, &
          initialise_model_data, output_model_data
 
 contains
@@ -321,11 +321,11 @@ contains
   !> @param[in]    twod_mesh The current 2d mesh
   !> @param[in]    aerosol_mesh      Aerosol 3d mesh
   !> @param[in]    aerosol_twod_mesh Aerosol 2d mesh
-subroutine create_model_data( modeldb,      &
-                              mesh,         &
-                              twod_mesh,    &
-                              aerosol_mesh, &
-                              aerosol_twod_mesh )
+  subroutine create_model_data( modeldb,      &
+                                mesh,         &
+                                twod_mesh,    &
+                                aerosol_mesh, &
+                                aerosol_twod_mesh )
 
 
     implicit none
@@ -521,7 +521,45 @@ subroutine create_model_data( modeldb,      &
       call create_physics_prognostics( mesh, twod_mesh, aerosol_mesh, aerosol_twod_mesh, field_mapper, &
                                        modeldb%clock )
 
+    end if
+
+  end subroutine create_model_data
+
+  !------------------------------------------------------------------------------
+  !> @brief Create the additional fields contained in model_data that are
+  !!        only required by runs that use physics.
+  !> @param[inout] modeldb   The working data set for a model run
+  !> @param[in]    mesh      The current 3d mesh
+  !> @param[in]    twod_mesh The current 2d mesh
+  !> @param[in]    aerosol_mesh      Aerosol 3d mesh
+  !> @param[in]    aerosol_twod_mesh Aerosol 2d mesh
+  subroutine create_physics_model_data( modeldb,      &
+                                        mesh,         &
+                                        twod_mesh,    &
+                                        aerosol_mesh, &
+                                        aerosol_twod_mesh )
+
+
+    implicit none
+
+    type( modeldb_type ), intent(inout)       :: modeldb
+    type( mesh_type ),    intent(in), pointer :: mesh
+    type( mesh_type ),    intent(in), pointer :: twod_mesh
+    type( mesh_type ),    intent(in), pointer :: aerosol_mesh
+    type( mesh_type ),    intent(in), pointer :: aerosol_twod_mesh
+
+    type(field_collection_type), pointer :: depository
+    type(field_collection_type), pointer :: fd_fields
+    type(field_collection_type), pointer :: ancil_fields
+    type(gungho_time_axes_type), pointer :: model_axes
+
+    model_axes => get_time_axes_from_collection(modeldb%values, "model_axes" )
+    depository => modeldb%fields%get_field_collection("depository")
+    fd_fields => modeldb%fields%get_field_collection("fd_fields")
+    ancil_fields => modeldb%fields%get_field_collection("ancil_fields")
+
 #ifdef UM_PHYSICS
+    if (use_physics) then
       ! Create FD prognostic fields
       select case ( prognostic_init_choice )
         case ( init_option_fd_start_dump )
@@ -544,10 +582,10 @@ subroutine create_model_data( modeldb,      &
                                            ancil_fields, &
                                            mesh, twod_mesh )
       end select
-#endif
     end if
+#endif
 
-  end subroutine create_model_data
+  end subroutine create_physics_model_data
 
   !------------------------------------------------------------------------------
   !> @brief Initialises the working data set dependent of namelist
diff --git a/science/linear/source/driver/linear_diagnostics_driver_mod.F90 b/science/linear/source/driver/linear_diagnostics_driver_mod.F90
index 287724c3b..fadbaa713 100644
--- a/science/linear/source/driver/linear_diagnostics_driver_mod.F90
+++ b/science/linear/source/driver/linear_diagnostics_driver_mod.F90
@@ -8,65 +8,166 @@
 
 module linear_diagnostics_driver_mod
 
-  use constants_mod,             only : i_def, str_def
+  use constants_mod,             only : i_def, str_def, l_def
+  use diagnostic_alg_mod,        only : column_total_diagnostics_alg,          &
+                                        calc_wbig_diagnostic_alg,              &
+                                        pressure_diag_alg
   use diagnostics_io_mod,        only : write_scalar_diagnostic, &
                                         write_vector_diagnostic
   use field_collection_mod,      only : field_collection_type
+  use field_collection_iterator_mod, &
+                                 only : field_collection_iterator_type
   use driver_modeldb_mod,        only : modeldb_type
   use field_array_mod,           only : field_array_type
   use field_mod,                 only : field_type
-  use formulation_config_mod,    only : moisture_formulation,    &
+  use field_parent_mod,          only : field_parent_type, write_interface
+  use formulation_config_mod,    only : use_physics,             &
+                                        moisture_formulation,    &
                                         moisture_formulation_dry
+  use fs_continuity_mod,         only : W3, Wtheta
   use mesh_mod,                  only : mesh_type
   use mr_indices_mod,            only : nummr, mr_names
   use initialization_config_mod, only : ls_option, &
                                         ls_option_file
+  use initialise_diagnostics_mod, &
+                                 only : diagnostic_to_be_sampled
+  use io_value_mod,              only : io_value_type, get_io_value
+  use io_config_mod,             only : use_xios_io, write_fluxes, &
+                                        write_diag
   use log_mod,                   only : log_event, &
                                         LOG_LEVEL_INFO
   use linear_config_mod,         only : ls_read_w2h
+  use lfric_xios_write_mod,      only : write_field_generic
+  use sci_geometric_constants_mod,                                             &
+                                 only : get_panel_id
 
   implicit none
 
   private
-  public linear_diagnostics_driver
+  public linear_write_initial_output, &
+         linear_diagnostics_driver
 
 contains
 
-  !> @brief Outputs simple diagnostics from Linear model
-  !> @param[in] mesh        The primary mesh
-  !> @param[in] modeldb     The working data set for the model run
-  !> @param[in] nodal_output_on_w3 Flag that determines if vector fields
+
+  !> @brief Outputs simple diagnostics from Gungho/LFRic
+  !>
+  !> @param[in,out] modeldb             Working data set of model.
+  !> @param[in]     mesh                The primary mesh
+  !> @param[in]     twod_mesh           The 2d mesh
+  !> @param[in]     io_context_name     The name of the IO context for writing
+  !> @param[in]     nodal_output_on_w3  Flag that determines if vector fields
   !>                  should be projected to W3 for nodal output
-  subroutine linear_diagnostics_driver( mesh,    &
-                                        modeldb, &
+  !>
+  subroutine linear_write_initial_output( modeldb, mesh, twod_mesh, &
+                                   io_context_name, nodal_output_on_w3 )
+
+#ifdef USE_XIOS
+    !>@todo This will be removed by #3321
+    use lfric_xios_context_mod, only : lfric_xios_context_type
+    use lfric_xios_action_mod,  only : advance
+#endif
+
+    implicit none
+
+    class(modeldb_type),      intent(inout) :: modeldb
+    type(mesh_type), pointer, intent(in)    :: mesh
+    type(mesh_type), pointer, intent(in)    :: twod_mesh
+    character(*),             intent(in)    :: io_context_name
+    logical(l_def),           intent(in)    :: nodal_output_on_w3
+#ifdef USE_XIOS
+    type(lfric_xios_context_type), pointer :: io_context
+    ! Call clock initial step before initial conditions output
+    if (modeldb%clock%is_initialisation() .and. use_xios_io) then
+      call modeldb%io_contexts%get_io_context(io_context_name, io_context)
+      call advance(io_context, modeldb%clock)
+    end if
+#endif
+
+    if (modeldb%clock%is_initialisation() .and. write_diag) then
+      ! Calculation and output of initial conditions
+      call linear_diagnostics_driver( modeldb,   &
+                                      mesh,      &
+                                      twod_mesh, &
+                                      nodal_output_on_w3 )
+
+    end if
+
+  end subroutine linear_write_initial_output
+
+  !> @brief Outputs simple diagnostics from linear model
+  !> @param[in,out] modeldb             Working data set of model run.
+  !> @param[in]     mesh                The primary mesh
+  !> @param[in]     twod_mesh           The 2d mesh
+  !> @param[in]     nodal_output_on_w3  Flag that determines if vector fields
+  !>                should be projected to W3 for nodal output
+  subroutine linear_diagnostics_driver( modeldb,   &
+                                        mesh,      &
+                                        twod_mesh, &
                                         nodal_output_on_w3 )
 
     implicit none
 
     type(mesh_type),      intent(in), pointer :: mesh
+    type(mesh_type),      intent(in), pointer :: twod_mesh
     type(modeldb_type),   intent(in), target  :: modeldb
     logical,              intent(in)          :: nodal_output_on_w3
+
+    type(field_collection_type), pointer :: prognostic_fields
     type(field_collection_type), pointer :: moisture_fields => null()
-    type(field_array_type), pointer      :: ls_mr_array => null()
+    type(field_type),            pointer :: mr(:)
+    type(field_collection_type), pointer :: derived_fields
+    type(field_array_type),      pointer :: ls_mr_array => null()
+    type(field_collection_type), pointer :: ls_fields
+    type(field_type),            pointer :: ls_mr(:) => null()
+
+    type(field_type), pointer :: theta
+    type(field_type), pointer :: u
+    type(field_type), pointer :: rho
+    type(field_type), pointer :: exner
+    type(field_type), pointer :: panel_id
+    type(field_type), pointer :: u_in_w2h
+    type(field_type), pointer :: v_in_w2h
+    type(field_type), pointer :: w_in_wth
+    type(field_type), pointer :: exner_in_wth
+
+    type(field_array_type), pointer :: mr_array
+
+    type(field_type), pointer :: ls_theta => null()
+    type(field_type), pointer :: ls_u => null()
+    type(field_type), pointer :: ls_rho => null()
+    type(field_type), pointer :: ls_exner => null()
+    type(field_type), pointer :: ls_v_u => null()
+    type(field_type), pointer :: ls_h_u => null()
 
-    type( field_collection_type ), pointer :: ls_fields
-    type( field_type ),            pointer :: ls_mr(:) => null()
+    ! Iterator for field collection
+    type(field_collection_iterator_type)  :: iterator
 
-    type( field_type), pointer :: ls_theta => null()
-    type( field_type), pointer :: ls_u => null()
-    type( field_type), pointer :: ls_rho => null()
-    type( field_type), pointer :: ls_exner => null()
-    type( field_type), pointer :: ls_v_u => null()
-    type( field_type), pointer :: ls_h_u => null()
+    ! A pointer used for retrieving fields from collections
+    ! when iterating over them
+    class(field_parent_type),   pointer :: field_ptr
+    procedure(write_interface), pointer :: tmp_write_ptr
+    type(io_value_type),        pointer :: temp_corr_io_value
 
-    integer :: i
+    integer :: i, fs
+    character(len=str_def) :: name
 
     call log_event("Linear: writing diagnostic output", LOG_LEVEL_INFO)
 
+    prognostic_fields => modeldb%fields%get_field_collection("prognostic_fields")
     ls_fields => modeldb%fields%get_field_collection("ls_fields")
     moisture_fields => modeldb%fields%get_field_collection("moisture_fields")
+    call moisture_fields%get_field("mr", mr_array)
+    mr => mr_array%bundle
     call moisture_fields%get_field("ls_mr", ls_mr_array)
     ls_mr => ls_mr_array%bundle
+    derived_fields => modeldb%fields%get_field_collection("derived_fields")
+    panel_id => get_panel_id(mesh%get_id())
+
+    call prognostic_fields%get_field('theta', theta)
+    call prognostic_fields%get_field('u', u)
+    call prognostic_fields%get_field('rho', rho)
+    call prognostic_fields%get_field('exner', exner)
 
     call ls_fields%get_field('ls_theta', ls_theta)
     call ls_fields%get_field('ls_u', ls_u)
@@ -74,6 +175,12 @@ subroutine linear_diagnostics_driver( mesh,    &
     call ls_fields%get_field('ls_exner', ls_exner)
 
     ! Scalar fields
+    call write_scalar_diagnostic('rho', rho, &
+                                 modeldb%clock, mesh, nodal_output_on_w3)
+    call write_scalar_diagnostic('theta', theta, &
+                                 modeldb%clock, mesh, nodal_output_on_w3)
+    call write_scalar_diagnostic('exner', exner, &
+                                 modeldb%clock, mesh, nodal_output_on_w3)
     call write_scalar_diagnostic('ls_rho', ls_rho, &
                                  modeldb%clock, mesh, nodal_output_on_w3)
     call write_scalar_diagnostic('ls_theta', ls_theta, &
@@ -82,6 +189,40 @@ subroutine linear_diagnostics_driver( mesh,    &
                                  modeldb%clock, mesh, nodal_output_on_w3)
 
     ! Vector fields
+    if (use_physics .and. use_xios_io .and. .not. write_fluxes) then
+      ! These have already been calculated, so no need to recalculate them
+      call derived_fields%get_field('u_in_w2h', u_in_w2h)
+      call derived_fields%get_field('v_in_w2h', v_in_w2h)
+      call derived_fields%get_field('w_in_wth', w_in_wth)
+      tmp_write_ptr => write_field_generic
+      call u_in_w2h%set_write_behaviour(tmp_write_ptr)
+      call v_in_w2h%set_write_behaviour(tmp_write_ptr)
+      if (modeldb%clock%is_initialisation()) then
+        if (diagnostic_to_be_sampled("init_u_in_w2h")) then
+          call u_in_w2h%write_field("init_u_in_w2h")
+        end if
+        if (diagnostic_to_be_sampled("init_v_in_w2h")) then
+          call v_in_w2h%write_field("init_v_in_w2h")
+        end if
+        if (diagnostic_to_be_sampled("init_w_in_wth")) then
+          call w_in_wth%write_field("init_w_in_wth")
+        end if
+      else
+        if (diagnostic_to_be_sampled("u_in_w2h")) then
+          call u_in_w2h%write_field("u_in_w2h")
+        end if
+        if (diagnostic_to_be_sampled("v_in_w2h")) then
+          call v_in_w2h%write_field("v_in_w2h")
+        end if
+        if (diagnostic_to_be_sampled("w_in_wth")) then
+          call w_in_wth%write_field("w_in_wth")
+        end if
+      end if
+    else
+      call write_vector_diagnostic('u', u, &
+                                   modeldb%clock, mesh, nodal_output_on_w3)
+    end if
+
     call write_vector_diagnostic('ls_u', ls_u, &
                                  modeldb%clock, mesh, nodal_output_on_w3)
 
@@ -107,6 +248,43 @@ subroutine linear_diagnostics_driver( mesh,    &
       end do
     end if
 
+    ! Derived physics fields (only those on W3 or Wtheta)
+    if (use_physics .and. use_xios_io .and. .not. modeldb%clock%is_initialisation()) then
+      field_ptr => null()
+      call iterator%initialise(derived_fields)
+      do
+        if ( .not.iterator%has_next() ) exit
+        field_ptr => iterator%next()
+        select type(field_ptr)
+          type is (field_type)
+            fs = field_ptr%which_function_space()
+            if ( fs == W3 .or. fs == Wtheta ) then
+              name = trim(adjustl( field_ptr%get_name() ))
+              if (diagnostic_to_be_sampled(trim(name))) &
+                   call field_ptr%write_field(trim(name))
+            end if
+        end select
+      end do
+      field_ptr => null()
+
+      ! Get w_in_wth for WBig calculation
+      call derived_fields%get_field('w_in_wth', w_in_wth)
+      call calc_wbig_diagnostic_alg(w_in_wth, mesh)
+
+      ! Pressure diagnostics
+      call prognostic_fields%get_field('exner', exner)
+      call pressure_diag_alg(exner)
+
+      call derived_fields%get_field('exner_in_wth', exner_in_wth)
+      call pressure_diag_alg(exner_in_wth)
+
+      temp_corr_io_value => get_io_value( modeldb%values, 'temperature_correction_io_value')
+      call column_total_diagnostics_alg(rho, mr, derived_fields, exner, &
+                                        mesh, twod_mesh,                &
+                                        temp_corr_io_value%data(1))
+
+    end if
+
   end subroutine linear_diagnostics_driver
 
 end module linear_diagnostics_driver_mod
diff --git a/science/linear/source/driver/linear_driver_mod.f90 b/science/linear/source/driver/linear_driver_mod.f90
index aac98282d..e4164e273 100644
--- a/science/linear/source/driver/linear_driver_mod.f90
+++ b/science/linear/source/driver/linear_driver_mod.f90
@@ -15,8 +15,6 @@ module linear_driver_mod
   use io_value_mod,               only : io_value_type
   use section_choice_config_mod,  only : stochastic_physics, &
                                          stochastic_physics_um
-  use gungho_diagnostics_driver_mod, &
-                                  only : gungho_diagnostics_driver
   use gungho_model_mod,           only : initialise_infrastructure, &
                                          initialise_model, &
                                          finalise_infrastructure, &
@@ -31,7 +29,6 @@ module linear_driver_mod
   use gungho_time_axes_mod,       only : gungho_time_axes_type, &
                                          get_time_axes_from_collection
   use init_fd_prognostics_mod,    only : init_fd_prognostics_dump
-  use initial_output_mod,         only : write_initial_output
   use initialization_config_mod,  only : init_option_fd_start_dump, &
                                          ls_option_file
   use io_context_mod,             only : io_context_type
@@ -45,7 +42,8 @@ module linear_driver_mod
   use linear_model_mod,           only : initialise_linear_model, &
                                          finalise_linear_model
   use linear_diagnostics_driver_mod, &
-                                  only : linear_diagnostics_driver
+                                  only : linear_diagnostics_driver, &
+                                         linear_write_initial_output
   use linear_step_mod,            only : linear_step
   use linear_data_algorithm_mod,  only : update_ls_file_alg
   use mesh_mod,                   only : mesh_type
@@ -188,8 +186,8 @@ subroutine initialise( program_name, modeldb )
     nodal_output_on_w3 = modeldb%config%io%nodal_output_on_w3()
 
     ! Initial output
-    call write_initial_output( modeldb, mesh, twod_mesh, &
-                               io_context_name, nodal_output_on_w3 )
+    call linear_write_initial_output( modeldb, mesh, twod_mesh, &
+                                      io_context_name, nodal_output_on_w3 )
 
     ! Linear model configuration initialisation
     call initialise_linear_model( mesh,        &
@@ -259,11 +257,10 @@ subroutine step( modeldb )
          .and. ( write_diag ) ) then
 
       ! Calculation and output diagnostics
-      call gungho_diagnostics_driver( modeldb, mesh, twod_mesh, &
-                                      nodal_output_on_w3 )
 
-      call linear_diagnostics_driver( mesh,    &
-                                      modeldb, &
+      call linear_diagnostics_driver( modeldb,   &
+                                      mesh,      &
+                                      twod_mesh, &
                                       nodal_output_on_w3 )
     end if