Add files_for_e3sm steps for ocean and sea-ice meshes
#570
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files_for_e3sm steps for ocean and sea-ice meshes
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TestingI tested this on the following 6 meshes:
which I have created and placed in: |
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Based off of #563, so in draft mode until that gets merged. |
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Can't build docs locally until I fix #567 |
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@mark-petersen, I could use your review on this. I'll point out specific things I'd appreciate your feedback on. |
| self.mesh_vars = [ | ||
| 'areaCell', 'cellsOnCell', 'edgesOnCell', 'indexToCellID', | ||
| 'latCell', 'lonCell', 'meshDensity', 'nEdgesOnCell', | ||
| 'verticesOnCell', 'xCell', 'yCell', 'zCell', 'angleEdge', | ||
| 'cellsOnEdge', 'dcEdge', 'dvEdge', 'edgesOnEdge', | ||
| 'indexToEdgeID', 'latEdge', 'lonEdge', 'nEdgesOnCell', | ||
| 'nEdgesOnEdge', 'verticesOnEdge', 'weightsOnEdge', 'xEdge', | ||
| 'yEdge', 'zEdge', 'areaTriangle', 'cellsOnVertex', 'edgesOnVertex', | ||
| 'indexToVertexID', 'kiteAreasOnVertex', 'latVertex', | ||
| 'lonVertex', 'xVertex', 'yVertex', 'zVertex'] |
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@mark-petersen, could you sanity check that I didn't miss any variables that are necessary for defining the horizontal mesh?
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For reference, these are my notes on how to add a mesh for a paraview visualiztion from a netcdf file without a mesh:
set GridVars=latCell,lonCell,maxLevelCell,nEdgesOnCell,xCell,yCell,zCell,dcEdge,dvEdge,indexToEdgeID,latEdge,lonEdge,nEdgesOnEdge,xEdge,yEdge,zEdge,areaTriangle,indexToVertexID,latVertex,lonVertex,xVertex,yVertex,zVertex,edgesOnVertex,cellsOnVertex,indexToCellID,indexToEdgeID,indexToVertexID,cellsOnEdge,edgesOnCell,edgesOnEdge,cellsOnCell,refBottomDepth,verticesOnCell
ncks -d Time,0 -v ${GridVars},temperature file1.nc file2.nc
Yes, your list includes all the horizontal variables from my notes. I agree that you have them all.
| 'refBottomDepth', 'vertCoordMovementWeights', | ||
| 'bottomDepth', 'maxLevelCell', | ||
| 'layerThickness', 'restingThickness' | ||
| ] |
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@mark-petersen, in addition to the horizontal mesh variables, these seem to be the minimum set available for defining the vertical grid. Does that seem right?
| if 'minLevelCell' not in ds: | ||
| ds['minLevelCell'] = xr.ones_like(ds.maxLevelCell) | ||
| ds.minLevelCell.attrs['long_name'] = \ | ||
| 'Index to the first active ocean cell in each column.' | ||
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| ds['refTopDepth'] = ('nVertLevels', interfaces[0:-1]) | ||
| ds.refTopDepth.attrs['units'] = 'm' | ||
| ds.refTopDepth.attrs['long_name'] = \ | ||
| "Reference depth of ocean for each vertical level. Used in " \ | ||
| "'z-level' type runs." | ||
| ds['refZMid'] = ('nVertLevels', | ||
| -0.5 * (interfaces[1:] + interfaces[0:-1])) | ||
| ds.refZMid.attrs['units'] = 'm' | ||
| ds.refZMid.attrs['long_name'] = \ | ||
| 'Reference mid z-coordinate of ocean for each vertical ' \ | ||
| 'level. This has a negative value.' | ||
| ds['refLayerThickness'] = ('nVertLevels', | ||
| interfaces[1:] - interfaces[0:-1]) | ||
| ds.refLayerThickness.attrs['units'] = 'm' | ||
| ds.refLayerThickness.attrs['long_name'] = \ | ||
| 'Reference layer thickness of ocean for each vertical level.' | ||
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| ds['cellMask'] = compute_cell_mask( | ||
| ds.minLevelCell - 1, ds.maxLevelCell - 1, | ||
| ds.sizes['nVertLevels']) | ||
| ds.cellMask.attrs['long_name'] = \ | ||
| 'Mask on cells that determines if computations should be ' \ | ||
| 'done on cells.' | ||
| ds['ssh'] = compute_ssh_from_layer_thickness( | ||
| ds.layerThickness, ds.bottomDepth, ds.cellMask) | ||
| ds.ssh.attrs['units'] = 'm' | ||
| ds.ssh.attrs['long_name'] = 'sea surface height' | ||
| ds['zMid'] = compute_zmid_from_layer_thickness( | ||
| ds.layerThickness, ds.ssh, ds.cellMask) | ||
| ds.zMid.attrs['units'] = 'm' | ||
| ds.zMid.attrs['long_name'] = \ | ||
| 'z-coordinate of the mid-depth of the layer' |
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@mark-petersen, in addition to the "required" vertical grid variables above, I'm also adding these (using the layerThickness variable from the initial condition):
- minLevelCell
- refTopDepth
- refZMid
- refLayerThickness
- cellMask
- ssh
- zMid
Anything in that list seem out of place? Anything important I'm missing?
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Yes, that looks good. The variables edgeMask and vertexMask would match your cellMask, but we probably don't need them.
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I thought about that, too. I don't currently have compass routines for computing those (and I needed cellMask for computing ssh and zMid) so I decided to let them be.
Thanks for taking a look!
These also need to be added to `inputdata` in `shared/meshes/mpas`
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@mark-petersen, this has been rebased. You are also welcome to look at the meshes it generated: Here are the QU240 tests as well, to show it within compass: In particular, look at: |
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@mark-petersen, could you let me know if you want to take some more time to look at the results from this PR? If not, could you approve so I can merge? |
These also need to be added to
inputdatainshared/meshes/mpasThis merge also makes public some functions from the
compass.ocean.verticalmodule that are used to addcellMaskandzMidvariables to the MPAS-Ocean mesh.Checklist
api.rst) has any new or modified class, method and/or functions listedTestingin this PR) any testing that was used to verify the changescloses #569