CICE grid generation from MOM supergrid #6

ezhilsabareesh8 · 2024-02-26T22:36:09Z

This pull request addresses issues COSIMA/access-om3#101 and COSIMA/access-om2#280 by adding a Python script to generate the CICE6 grid from the MOM6 supergrid.

The script facilitates the creation of a CICE grid, resolving a previously encountered longitude mismatch issue by correctly positioning the U points in the NE corner.

anton-seaice · 2024-02-26T23:00:47Z

grid_generation/Gen_CICE_grid.py

+
+    # Constants
+    ULAT = np.deg2rad(in_superGridFile['y'][2::2, 1::2])
+    ULON = np.deg2rad(in_superGridFile['x'][1::2, 2::2])


shouldn't this be

ULAT = np.deg2rad(in_superGridFile['y'][2::2, 2::2]) ULON = np.deg2rad(in_superGridFile['x'][2::2, 2::2])

?

it might be clearer to write:
np.deg2rad(in_superGridFile.y.sel(x=slice(start=2,step=2), y=slice(start=2, step=2)))

?

Agreed, but with isel, not sel

anton-seaice · 2024-02-26T23:02:54Z

I'll mostly defer to Andrew review but we'll want some versioning information added to the output of both the source mom file and the script version used

aekiss · 2024-02-27T01:24:10Z

Yes, versioning info would be good too, e.g. https://github.com/COSIMA/om3-scripts/blob/main/mesh_generation/generate_mesh.py#L397-L413

aekiss · 2024-02-27T01:34:53Z

It would be a good idea to compare the new grid.nc with the old one to check that it differs only in the ways we want it to.

There might be something in here that could be useful:
https://github.com/aekiss/notebooks/blob/master/check_updates.ipynb

grid_generation/Gen_CICE_grid.py

aekiss · 2024-02-27T01:44:21Z

This is missing the following from /g/data/ik11/inputs/access-om2/input_20201102/cice_025deg/grid.nc - are they needed in CICE? I noticed there are even more things in /g/data/ik11/inputs/access-om2/input_20201102/cice_1deg/grid.nc but they apparently aren't needed, so maybe the following are also unnecessary too...?

	double angleT(ny, nx) ;
		angleT:units = "radians" ;
		angleT:title = "Rotation angle of T cells." ;
	double tarea(ny, nx) ;
		tarea:units = "m^2" ;
		tarea:title = "Area of T cells." ;
	double uarea(ny, nx) ;
		uarea:units = "m^2" ;
		uarea:title = "Area of U cells." ;

anton-seaice · 2024-02-27T02:04:52Z

Those three quantities are computer internally in CICE:

https://github.com/CICE-Consortium/CICE/blob/64177e3e5658711f5f19030ddfcc6927f1dbda5d/cicecore/cicedyn/infrastructure/ice_grid.F90#L952

We might want to think a little bit about whether computing the areas in a projection aware way improves accuracy. I guess the first check would be whether the old uarea = HTN* HTE

aekiss · 2024-02-27T03:10:34Z

I wonder whether it would be better to make CICE read the MOM supergrid directly?

anton-seaice · 2024-02-27T05:04:19Z

It looks like code was added to cice5 to read tarea, tlat and tlon from the cice grid file rather than calculate them:

https://github.com/COSIMA/cice5/blob/edcfa6f9c76ed05b63196ce4b5355fa5a8f4fe3a/source/ice_grid.F90#L662

#ifdef AusCOM
! we also let cice read in the following fields to avoid possible mismatch
! between cice and mom4.
! ( 8) TLAT
! ( 9) TLON
! (10) TAREA
! (11) UAREA
! (12) ANGLET
! the following fields are also available in grid.nc but not read in 'cos they
! are not critical 
!  LONT_BONDS
!  LATT_BONDS
!  LONU_BONDS
!  LATU_BONDS
#endif

anton-seaice · 2024-02-27T05:36:38Z

There is something similar in the cmeps driver for CICE:
https://github.com/CICE-Consortium/CICE/blob/64177e3e5658711f5f19030ddfcc6927f1dbda5d/cicecore/drivers/nuopc/cmeps/ice_comp_nuopc.F90#L731

 ! Initialize the cice mesh and the cice mask
       if (trim(grid_format) == 'meshnc') then
          ! In this case cap code determines the mask file
          call ice_mesh_setmask_from_maskfile(ice_maskfile, ice_mesh, rc=rc)
          if (ChkErr(rc,__LINE__,u_FILE_u)) return
          call ice_mesh_init_tlon_tlat_area_hm()
          if (ChkErr(rc,__LINE__,u_FILE_u)) return
       else
          ! In this case init_grid2 will initialize tlon, tlat, area and hm
          call init_grid2()
          call ice_mesh_check(gcomp,ice_mesh, rc=rc)
          if (ChkErr(rc,__LINE__,u_FILE_u)) return
       end if

Which looks like it will get the area from the mesh file.

Co-authored-by: Andrew Kiss <[email protected]>

grid_generation/Gen_CICE_grid.py

micaeljtoliveira · 2024-02-28T01:14:11Z

@ezhilsabareesh8 Thanks for the changes! I think generate_cice_grid.py. was a better name, but the most important is that it's consistent.

anton-seaice · 2024-02-28T02:19:13Z

@ezhilsabareesh8 - Can you test the new grid with OM2?

I think you will need to add:

! ( 8) TLAT
! ( 9) TLON
! (10) TAREA
! (11) UAREA
! (12) ANGLET

for it to work in OM2.

Should we have two versions of this grid? One for OM2 and one for OM3 (with less variables?)

I wonder whether it would be better to make CICE read the MOM supergrid directly?

Shall we split this into a different issue? Current OM3 implementation has CICE calculating area internally, which is problematic.

ezhilsabareesh8 · 2024-02-28T03:40:47Z

@anton-seaice I can test OM2 with the new grid.nc. It seems we don't need two versions of grid.nc, as the additional data will likely be ignored by CICE.

The newly generated grid.nc contains the following data:

- `ulat`: Latitude of U points (radians)
- `ulon`: Longitude of U points (radians)
- `tlat`: Latitude of T points (radians)
- `tlon`: Longitude of T points (radians)
- `htn`: Width of T cells on the N side (cm)
- `hte`: Width of T cells on the E side (cm)
- `angle`: Rotation angle of U cells (radians) 
'''

Additionally, we may need to include `TAREA` and `UREA` for OM2.

anton-seaice · 2024-02-28T03:45:03Z

Oh yes - I was just thinking of two versions because its confusing if we have a grid.nc file loaded by OM3 that is then only using some of the variables.

ezhilsabareesh8 · 2024-03-01T03:05:13Z

@aekiss, I've incorporated the TAREA and UAREA variables in the latest commit (09be9fb). However, I've noticed a discrepancy between the output of the newly generated grid.nc and the old OM2 grid.nc for a 1degree grid. I'm uncertain whether the issue lies with the CICE grid or if the wrapping is not implemented correctly in the new grid. Could you please have a look at the following output?

(grid_ds['uarea'] - grid_old_ds['uarea']).plot()

anton-seaice · 2024-03-01T03:24:01Z

It looks like we need to something different at the ~~fold~~ join. (Calculated from mom supergrid on top, old one below)

aekiss · 2024-03-04T03:53:11Z

re. the differences at the fold - not sure if this helps, but FYI we are using grid_type = "tripole" rather than tripoleT, so the northern poles and the fold between them all lie on U points rather than T points (see here). This is to match the alignment in MOM5 - see Elements of MOM sec 9.3 and fig 9.9 (copied below)

aekiss · 2024-03-04T04:00:49Z

Sec 9.4.3 of Elements of MOM describes the special treatment of grid cell areas long the fold.

aekiss · 2024-03-04T06:11:30Z

Re. the area mismatch, I guess the original 1deg areas in the supergrid were calculated using update_cell_area. Is the new code calculating areas the same way?

navidcy · 2024-03-04T11:24:27Z

Sorry to intrude in the discussion, somehow I get notifications for this.

The area of a quadrilateral on the sphere is uniquely defined given the lon-lat coords of its four vertices. It doesn’t need to be approximated. So, regardless how it was done in the past, it’s a good idea to drop any unnecessary approximations. The sum of all grid areas should be precisely 4πR^2 (up to machine precision).

navidcy · 2024-03-04T11:39:56Z

See eg

https://github.com/COSIMA/regional-mom6/blob/b0e13c5f6a45eec9451ea2165f19ae0fe9176aed/regional_mom6/utils.py#L42

navidcy · 2024-03-04T11:44:04Z

There a way to avoid needing to ensure you give the vertices in counter-clockwise order. I can put more details when I am in front of a computer.

anton-seaice · 2024-03-04T23:06:29Z

Sorry to intrude in the discussion, somehow I get notifications for this.

The area of a quadrilateral on the sphere is uniquely defined given the lon-lat coords of its four vertices. It doesn’t need to be approximated. So, regardless how it was done in the past, it’s a good idea to drop any unnecessary approximations. The sum of all grid areas should be precisely 4πR^2 (up to machine precision).

Thanks. We are trying to calculate the area of each cice grid cell by using the mom supergrid file. The areas in the mom supergrid seem to be calculated consistently with the way you are saying (https://github.com/ESMG/gridtools/blob/de0a18c1ce0807748aa70023300dfc415277bd4c/gridtools/spherical.py#L36).

This is a good thing for us to try though, if the areas calculated based on the lat/lons only are the same as the ones derived from the mom supergrid, that would be a good validation of the method.

anton-seaice · 2024-03-04T23:13:49Z

Re. the area mismatch, I guess the original 1deg areas in the supergrid were calculated using update_cell_area. Is the new code calculating areas the same way?

All we are doing is summing the area of the four relevant cells from the supergrid to make the cice grid, I can't see anything inconsistent with the update_cell_area in that?

This is similar to what Navid is saving I think - we could use this method to calculate area based on lat/lon only, and not from the supergrid.

anton-seaice · 2024-03-04T23:25:24Z

The 1deg grid has meridional grid refinement near the equator, and coarsening elsewhere

(figure from here)

This may play a role in these differences at mid-latitudes.

Does this mean the coordinates move away from regular 1 degree spacing?

p.s. Its also odd that the patterning below 65N is there in the uarea calc and not the tarea calc.

anton-seaice · 2024-03-06T05:40:14Z

The patterning found above in t-area seems to only be there in the 1-degree grid, so it might be an artifact of the Meridional refinement and the grids getting out of sync at some point. Its not there in the 0.25 degree grid, so maybe we can ignore it.

The difference in u-area, is still strange. In our current grid at the join:

and in the calculating from the mom supergrid at the join:

I think the second one is correct. (Amusingly the files in '/g/data/ik11/grids/' also have one of each option)

This figure kind of demonstrates it (viewed straight down on the north pole):

u-area is the sum of the areas of a quarter of each grid cell which surrounds each u-point (i.e. NE corner point). The areas north of the join (The thick line) are smaller than those south of the join with a notable change. So the u-areas at the join are the average of the smaller and larger cell areas which exist either side of the join, and therefore create the 'step' shown in the second figure.

As an aside, I stumbled across this code which Nic wrote and does what we want:

https://github.com/COSIMA/esmgrids/blob/130c8d00774c624c196fc2ca15f5cad78c4cdbc1/esmgrids/mom_grid.py

aekiss · 2024-03-06T06:10:36Z

Does this mean the coordinates move away from regular 1 degree spacing?

yes, the meridional (y) spacing is refined to 1/3° near the equator on the 1° grid.

Note that the y spacing is not regular at most latitudes at 0.25° or 0.1° either, because a Mercator grid is used between 65S and 65N to keep the cell aspect ratio equal to 1. See https://github.com/COSIMA/ACCESS-OM2-1-025-010deg-report/blob/master/figures/grid/grid.ipynb

p.s. Its also odd that the patterning below 65N is there in the uarea calc and not the tarea calc.

yes, indeed

aekiss · 2024-03-06T06:14:49Z

I think I agree with your analysis @anton-seaice, so long as the 65°N junction between the Mercator and tripolar grids falls on U points - is that the case?

anton-seaice · 2024-03-06T22:47:10Z

I think I agree with your analysis @anton-seaice, so long as the 65°N junction between the Mercator and tripolar grids falls on U points - is that the case?

Good point - I checked - all three resolutions have the join at u-points

ezhilsabareesh8 · 2024-03-07T00:31:57Z

The angle ANGLET in the current implementation is calculated directly from the super grid as Refer here

ANGLE = np.deg2rad(in_superGridFile['angle_dx'][2::2, 2::2]) ; ANGLET= np.deg2rad(in_superGridFile['angle_dx'][1::2, 1::2])

which is consistent with the OM2 grid.nc file. However, it appears that this differs from the weighted average approach employed in CICE6 here.

Should we consider adapting the angleT calculation method to utilize the weighted average approach used in CICE6?

anton-seaice · 2024-03-07T05:17:34Z

grid_generation/Gen_CICE_grid.py

+    TLON = np.deg2rad(in_superGridFile['x'][1::2, 1::2])
+
+    HTN = in_superGridFile['dx'] * 100.0  # convert to cm
+    HTN = HTN[1::2, ::2] + HTN[1::2, 1::2]


In the mom_grid, dx has units ('nyp','nx'). These correspond to the edges in y and the middle in x. So, the y coordinate (i.e. rows) should be 2::2

…t edge respectively. Therefore for cice we want the index to start from 2.

anton-seaice · 2024-03-07T05:32:02Z

grid_generation/Gen_CICE_grid.py

+    # add an extra column at the end. Also u-cells cross the
+    # tri-polar fold so add an extra row at the top.
+    area_ext = np.append(AREA[:], AREA[:, 0:1], axis=1)
+    area_ext = np.append(area_ext[:], area_ext[-1:, :], axis=0)


I think this line only works because the top row is symmetrical? It doesn't actual seem to fold it... ?

anton-seaice · 2024-03-07T06:11:06Z

I did a plot with every var and every resolution (left to right: 1deg, 0.25deg, 0.1deg). I masked difference which were less than 2e-6

Need to investigate: Angle, 0.1 ULAT/ULON
UAREA doesn't match well at any resolution, which is problematic.

I think we should merge this PR soon. We still have to add CF metadata and test with OM2, but these could be new issues to stop this PR totally blowing out? We also need to decide if we are sticking with np syntax (e.g. [2::2,1::2] or moving to written xarray style (e.g. ds.coarsen and ds.isel(x=slice(...)))

anton-seaice · 2024-03-07T23:55:47Z

I turned on compression:

Before

-rw-r--r-- 1 as2285 tm70 742M Mar  7 16:27 grid_01deg.nc
-rw-r--r-- 1 as2285 tm70 119M Mar  7 16:27 grid_025deg.nc
-rw-r--r-- 1 as2285 tm70 8.3M Mar  7 16:27 grid_1deg.nc

After:

-rw-r--r-- 1 as2285 tm70  123M Mar  8 10:47 grid_01deg.nc
-rw-r--r-- 1 as2285 tm70   15M Mar  8 10:46 grid_025deg.nc
-rw-r--r-- 1 as2285 tm70 1019K Mar  8 10:46 grid_1deg.nc

I left chunking at the default sizes, which gives 0.1 deg chunks of 900, 1200 (y,x) but the other resolutions are full size

anton-seaice · 2024-03-08T02:59:40Z

grid_generation/Gen_CICE_grid.py

+    else:
+        nc.inputfile = f"{in_superGridPath}"
+        nc.timeGenerated = f"{datetime.now()}"
+        nc.created_by = f"{os.environ.get('USER')}"


nc.inputfile = f"{in_superGridPath}" nc.timeGenerated = f"{datetime.now()}" nc.created_by = f"{os.environ.get('USER')}"

These three lines can go outside the if/else as they are the same in both cases.

Can we add a hash for the input file? Similar to the payu manifests md5 hash?

anton-seaice · 2024-03-08T04:41:24Z

I compared every resolution & every var between the version from this script, and the version in '/g/data/ik11/inputs/access-om2/input_20200530/'

ulat/ulon/angle for 0.25 degree resolution has been updated to be referencing the correct corner now
angleT in 0.01 degree looks wrong, as Ezhil noted
as discussed, uarea has changed at 1deg/0/25 deg resolution

(SRC: https://github.com/anton-seaice/sandbox/blob/743147926a9f7afabefc90276e45e8e02bcfa3e5/cice_grid_valiation.ipynb)

anton-seaice · 2024-03-12T00:47:09Z

I suggest - to remove duplication in code and make the result more extendable we close this PR and re-write this using https://github.com/COSIMA/esmgrids.

The script can be based on https://github.com/COSIMA/access-om2/blob/master/tools/make_cice_grid.py but we need add version control, fix AngleT in esmgrids and add CF metadata.

Using esmgrids makes this easier to extend in the future (e.g. to make the ocean_grid file for analysis).

anton-seaice · 2024-03-15T00:30:05Z

I suggest - to remove duplication in code and make the result more extendable we close this PR and re-write this using https://github.com/COSIMA/esmgrids.

The script can be based on https://github.com/COSIMA/access-om2/blob/master/tools/make_cice_grid.py but we need add version control, fix AngleT in esmgrids and add CF metadata.

Using esmgrids makes this easier to extend in the future (e.g. to make the ocean_grid file for analysis).

@aekiss thoughts ?

anton-seaice · 2024-03-20T06:02:14Z

Thanks for all your work on this Ezhil. I've taken our lessons and re-worked using esmgrids in a new PR :)

ezhilsabareesh8 and others added 3 commits February 26, 2024 15:34

Added Gen_CICE_grid.py to generate CICE grid from mom supergrid

39277fe

Use np.deg2rad instead of constants

b7d84fa

x index shifted to NE corner from cell centre

0213e6e

ezhilsabareesh8 requested review from aekiss and anton-seaice February 26, 2024 22:36

ezhilsabareesh8 mentioned this pull request Feb 26, 2024

0.25deg configuration COSIMA/access-om3#101

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anton-seaice reviewed Feb 26, 2024

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Updated ULAT and ULON indices

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ezhilsabareesh8 and others added 2 commits February 28, 2024 10:04

Update attributes to match grid.nc

47a0014

Co-authored-by: Andrew Kiss <[email protected]>

update attributes to match grid.nc

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Co-authored-by: Andrew Kiss <[email protected]>

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Updated script filenames

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Added TAREA and UAREA variables

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UAREA wrapping changed similar to esmgrids

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anton-seaice reviewed Mar 7, 2024

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dx and dy are defined on the edges in mom, and include the bottom/lef…

aa89836

…t edge respectively. Therefore for cice we want the index to start from 2.

anton-seaice reviewed Mar 7, 2024

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turn on compression

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anton-seaice reviewed Mar 8, 2024

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anton-seaice mentioned this pull request Mar 20, 2024

make cice grid #8

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ezhilsabareesh8 mentioned this pull request Apr 2, 2024

Upgrade 1-Degree to 025-Degree RYF Configuration ACCESS-NRI/access-om3-configs#48

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anton-seaice mentioned this pull request Apr 4, 2024

Cice grid COSIMA/om3-utils#5

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CICE grid generation from MOM supergrid #6

CICE grid generation from MOM supergrid #6

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