10km mesh x1.5898242 grid.nc missing R3 dimension for MPAS v8.4.1 init_atmosphere

[ljjxgg1]

I'm trying to run init_atmosphere_model (MPAS v8.4.1) with the 10km quasi-uniform mesh x1.5898242 downloaded from the official mesh page. The model is compiled with Intel MPI (intel-mpi target, ifort 17.0.5). When running init_atmosphere_model, the bootstrap phase fails with:

ERROR: At least one fields to be read from the 'input' stream is dimensioned
ERROR: by 'R3', but the 'R3' dimension is not defined
ERROR: in the file x1.5898242.grid.nc

The grid.nc file does not contain the R3 dimension or variables like edgeNormalVectors, localVerticalUnitVectors, cellTangentPlane,
and coeffs_reconstruct. However, the static.nc file for the same mesh DOES contain these R3 fields with correct geometric values. I noticed that core_atmosphere/Registry.xml
(lines 535-537 and 566) declares these as persistent fields without package qualifiers, and init_atmosphere/Registry.xml (lines 444-447) declares them with packages="gwd_stage_in;vertical_stage_in;met_stage_in".
My questions:
1. Is there a way to make init_atmosphere read the R3 fields from static.nc
instead of grid.nc?
2. Is there an updated version of the 10km grid.nc that includes R3?
3. Is there a standalone tool to compute and add coeffs_reconstruct and edgeNormalVectors to an existing grid.nc?

 

[Ming Chen]

Hi,

R3 is used to define the dimensionality of vectors. At the stage to create grid.nc, R3 is not used and grid.nc doesn't contain this variable.

Would you please confirm that these error messages related to R3 occurred when you run nit_atmosphere_model to generate initial condition? If so, please upload your streams.init_atmosphere for me to take a look.

Please see my answers below to your other questions.

My questions:
1. Is there a way to make init_atmosphere read the R3 fields from static.nc
instead of grid.nc?

when we run init_atmosphere to produce initial condition, the model does read R3 from static input data.

2. Is there an updated version of the 10km grid.nc that includes R3?

I don't think it is necessary to include R3 in grid.nc file.

3. Is there a standalone tool to compute and add coeffs_reconstruct and edgeNormalVectors to an existing grid.nc?

No, MPAS doesn't have this utility.

 

[mgduda]

@ljjxgg1 The x1.5898242.grid.nc file should work without problem as long as you've set config_static_interp = true in the &preproc_stages namelist group in your namelist.init_atmosphere file. Can you confirm that you have this namelist option set?