Hardcoded model config in lfric_xios_setup_mod

[mo-lottieturner]

Are there any linked Issues or Pull Requests?

lfric_apps:#455 adds metadata checks which will make issues like this easier to catch in future

Brief description

In components/lfric-xios/source/lfric_xios_setup_mod.x90, ll184-186 are calls to init_xios_axis for three axes: vert_axis_full_levels, vert_axis_half_levels, and radiation_levels. This means that no other axes (eg, soil_levels) are properly initialised and are therefore missing their coordinate/metadata which is important for eg viewing fields in iris.

Further details of the issue.

No response

[mo-lottieturner]

pinging mo-marqh

[mo-lottieturner]

components/lfric-xios/source/lfric_xios_setup_mod.x90, ll184-186:

    call init_xios_axis( "vert_axis_full_levels", mesh, W0 )
    call init_xios_axis( "vert_axis_half_levels", mesh, W3 )
    call init_xios_axis( "radiation_levels", mesh, W0 )

[mo-lottieturner]

abbreviated ncdump -h -v half_levels,full_levels of the vn3.1 kgo file for lfricinputs_um2lfric-basicgal-N96L70_C12L70_azspice_gnu_full-debug-64bit. Notably, even though multiple axes (including soil_levels) are listed under "dimensions", only half_levels and full_levels have datasets

netcdf checkpoint_um2lfric_000001 {
dimensions:
	axis_nbounds = 2 ;
	Two = 2 ;
	nMesh2d_node = 866 ;
	nMesh2d_edge = 1728 ;
	nMesh2d_face = 864 ;
	nMesh2d_vertex = 4 ;
	half_levels = 70 ;
	full_levels = 71 ;
	land_tiles = 9 ;
	snow_layers_and_tiles = 27 ;
	soil_levels = 4 ;
	time = UNLIMITED ; // (0 currently)
variables:
	int Mesh2d ;
		Mesh2d:cf_role = "mesh_topology" ;
		Mesh2d:long_name = "Topology data of 2D unstructured mesh" ;
		Mesh2d:topology_dimension = 2 ;
		Mesh2d:node_coordinates = "Mesh2d_node_x Mesh2d_node_y" ;
		Mesh2d:edge_coordinates = "Mesh2d_edge_x Mesh2d_edge_y" ;
		Mesh2d:edge_node_connectivity = "Mesh2d_edge_nodes" ;
		Mesh2d:face_edge_connectivity = "Mesh2d_face_edges" ;
		Mesh2d:edge_face_connectivity = "Mesh2d_edge_face_links" ;
		Mesh2d:face_face_connectivity = "Mesh2d_face_links" ;
		Mesh2d:face_coordinates = "Mesh2d_face_x Mesh2d_face_y" ;
		Mesh2d:face_node_connectivity = "Mesh2d_face_nodes" ;
		Mesh2d:geometry = "spherical" ;
	float Mesh2d_node_x(nMesh2d_node) ;
		Mesh2d_node_x:standard_name = "longitude" ;
		Mesh2d_node_x:long_name = "Longitude of mesh nodes." ;
		Mesh2d_node_x:units = "degrees_east" ;
	float Mesh2d_node_y(nMesh2d_node) ;
		Mesh2d_node_y:standard_name = "latitude" ;
		Mesh2d_node_y:long_name = "Latitude of mesh nodes." ;
		Mesh2d_node_y:units = "degrees_north" ;
	float Mesh2d_edge_x(nMesh2d_edge) ;
		Mesh2d_edge_x:standard_name = "longitude" ;
		Mesh2d_edge_x:long_name = "Characteristic longitude of mesh edges." ;
		Mesh2d_edge_x:units = "degrees_east" ;
	float Mesh2d_edge_y(nMesh2d_edge) ;
		Mesh2d_edge_y:standard_name = "latitude" ;
		Mesh2d_edge_y:long_name = "Characteristic latitude of mesh edges." ;
		Mesh2d_edge_y:units = "degrees_north" ;
	int Mesh2d_edge_nodes(nMesh2d_edge, Two) ;
		Mesh2d_edge_nodes:cf_role = "edge_node_connectivity" ;
		Mesh2d_edge_nodes:long_name = "Maps every edge/link to two nodes that it connects." ;
		Mesh2d_edge_nodes:start_index = 0 ;
	float Mesh2d_face_x(nMesh2d_face) ;
		Mesh2d_face_x:standard_name = "longitude" ;
		Mesh2d_face_x:long_name = "Characteristic longitude of mesh faces." ;
		Mesh2d_face_x:units = "degrees_east" ;
	float Mesh2d_face_y(nMesh2d_face) ;
		Mesh2d_face_y:standard_name = "latitude" ;
		Mesh2d_face_y:long_name = "Characteristic latitude of mesh faces." ;
		Mesh2d_face_y:units = "degrees_north" ;
	int Mesh2d_face_nodes(nMesh2d_face, nMesh2d_vertex) ;
		Mesh2d_face_nodes:cf_role = "face_node_connectivity" ;
		Mesh2d_face_nodes:long_name = "Maps every face to its corner nodes." ;
		Mesh2d_face_nodes:start_index = 0 ;
	int Mesh2d_face_edges(nMesh2d_face, nMesh2d_vertex) ;
		Mesh2d_face_edges:cf_role = "face_edge_connectivity" ;
		Mesh2d_face_edges:long_name = "Maps every face to its edges." ;
		Mesh2d_face_edges:start_index = 0 ;
		Mesh2d_face_edges:_FillValue = -999 ;
	int Mesh2d_edge_face_links(nMesh2d_edge, Two) ;
		Mesh2d_edge_face_links:cf_role = "edge_face_connectivity" ;
		Mesh2d_edge_face_links:long_name = "neighbor faces for edges" ;
		Mesh2d_edge_face_links:start_index = 0 ;
		Mesh2d_edge_face_links:_FillValue = -999 ;
		Mesh2d_edge_face_links:comment = "missing neighbor faces are indicated using _FillValue" ;
	int Mesh2d_face_links(nMesh2d_face, nMesh2d_vertex) ;
		Mesh2d_face_links:cf_role = "face_face_connectivity" ;
		Mesh2d_face_links:long_name = "Indicates which other faces neighbor each face" ;
		Mesh2d_face_links:start_index = 0 ;
		Mesh2d_face_links:_FillValue = -999 ;
		Mesh2d_face_links:flag_values = -1 ;
		Mesh2d_face_links:flag_meanings = "out_of_mesh" ;
	float half_levels(half_levels) ;
		half_levels:name = "half_levels" ;
	float full_levels(full_levels) ;
		full_levels:name = "full_levels" ;
	double ew_wind(half_levels, nMesh2d_face) ;
		ew_wind:standard_name = "eastward_wind" ;
		ew_wind:long_name = "eastward_wind" ;
		ew_wind:units = "m s-1" ;
		ew_wind:mesh = "Mesh2d" ;
		ew_wind:location = "face" ;
		ew_wind:online_operation = "once" ;
		ew_wind:coordinates = "Mesh2d_face_y Mesh2d_face_x" ;
	double ns_wind(half_levels, nMesh2d_face) ;
		ns_wind:standard_name = "northward_wind" ;
		ns_wind:long_name = "northward_wind" ;
		ns_wind:units = "m s-1" ;
		ns_wind:mesh = "Mesh2d" ;
		ns_wind:location = "face" ;
		ns_wind:online_operation = "once" ;
		ns_wind:coordinates = "Mesh2d_face_y Mesh2d_face_x" ;
	double upward_wind(full_levels, nMesh2d_face) ;
		upward_wind:standard_name = "upward_air_velocity" ;
		upward_wind:long_name = "upward_air_velocity" ;
		upward_wind:units = "m s-1" ;
		upward_wind:mesh = "Mesh2d" ;
		upward_wind:location = "face" ;
		upward_wind:online_operation = "once" ;
		upward_wind:coordinates = "Mesh2d_face_y Mesh2d_face_x" ;
	double theta(full_levels, nMesh2d_face) ;
		theta:standard_name = "air_potential_temperature" ;
		theta:long_name = "air_potential_temperature" ;
		theta:units = "K" ;
		theta:mesh = "Mesh2d" ;
		theta:location = "face" ;
		theta:online_operation = "once" ;
		theta:coordinates = "Mesh2d_face_y Mesh2d_face_x" ;
	double rho(half_levels, nMesh2d_face) ;
		rho:long_name = "air_density" ;
		rho:units = "1" ;
		rho:mesh = "Mesh2d" ;
		rho:location = "face" ;
		rho:online_operation = "once" ;
		rho:coordinates = "Mesh2d_face_y Mesh2d_face_x" ;
	double m_v(full_levels, nMesh2d_face) ;
		...
	double sea_ice_temperature(nMesh2d_face) ;
		sea_ice_temperature:long_name = "Sea-ice bulk temperature" ;
		sea_ice_temperature:units = "K" ;
		sea_ice_temperature:mesh = "Mesh2d" ;
		sea_ice_temperature:location = "face" ;
		sea_ice_temperature:online_operation = "once" ;
		sea_ice_temperature:coordinates = "Mesh2d_face_y Mesh2d_face_x" ;

// global attributes:
		:name = "checkpoint_um2lfric_000001" ;
		:title = "Created by xios" ;
		:timeStamp = "2026-Mar-02 14:35:10 GMT" ;
		:uuid = "e4754189-ee5e-4f08-98b9-135e94733b19" ;
		:description = "LFRic file format v0.2.0" ;
		:Conventions = "UGRID-1.0" ;
data:

 half_levels = 0.5, 1.5, 2.5, 3.5, 4.5, 5.5, 6.5, 7.5, 8.5, 9.5, 10.5, 11.5, 
    12.5, 13.5, 14.5, 15.5, 16.5, 17.5, 18.5, 19.5, 20.5, 21.5, 22.5, 23.5, 
    24.5, 25.5, 26.5, 27.5, 28.5, 29.5, 30.5, 31.5, 32.5, 33.5, 34.5, 35.5, 
    36.5, 37.5, 38.5, 39.5, 40.5, 41.5, 42.5, 43.5, 44.5, 45.5, 46.5, 47.5, 
    48.5, 49.5, 50.5, 51.5, 52.5, 53.5, 54.5, 55.5, 56.5, 57.5, 58.5, 59.5, 
    60.5, 61.5, 62.5, 63.5, 64.5, 65.5, 66.5, 67.5, 68.5, 69.5 ;

 full_levels = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 
    18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 
    36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 
    54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70 ;

}