# Bathymetry for ocean model at any resolution **URL:** \ **Category:** COSIMA\ **Tags:** inputs\ **Created:** [23 February 2023 19:50 UTC](https://forum.access-hive.org.au/t/bathymetry-for-ocean-model-at-any-resolution/462 "2023-02-23T19:50:32Z")\ **Posts on this page:** 1\ **Showing post:** 8
**Author:** ![aekiss](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/aekiss/32/46_2.png) [@aekiss](https://forum.access-hive.org.au/u/aekiss)\ **Post date:** [27 February 2023 00:01 UTC](https://forum.access-hive.org.au/t/bathymetry-for-ocean-model-at-any-resolution/462/8 "2023-02-27T00:01:10Z")
The ACCESS-OM2 1deg and 0.25deg topography were created with these scripts > **[GitHub - COSIMA/make\_1deg\_topo: Make 1 degree topog.nc](https://github.com/COSIMA/make_1deg_topo)** > > Make 1 degree topog.nc. Contribute to COSIMA/make\_1deg\_topo development by creating an account on GitHub. > **[GitHub - COSIMA/make\_025deg\_topo: Make 0.25 degree topog.nc](https://github.com/COSIMA/make_025deg_topo)** > > Make 0.25 degree topog.nc. Contribute to COSIMA/make\_025deg\_topo development by creating an account on GitHub. but some of this processing is only needed for a B grid and unnecessary for a C grid- see [1/20° topography · Issue #12 · COSIMA/mom6-panan · GitHub](https://github.com/COSIMA/mom6-panan/issues/12) There is a lot of ACCESS-OM2 (B-grid) topography-related discussion here > > > This issue was first discussed \[here\](https://github.com/COSIMA/access-om2/issue…s/158). More details in this \[comment\](https://github.com/COSIMA/access-om2/issues/158#issuecomment-971064268) and comments following. > > The proposed solution is: > > \> We decided that the way forward is to change the land mask for the Antarctic coast (and nowhere else) to match GEBCO 2014, which will convert some ocean regions to land, but also convert some land to ocean, which will change the number of active tiles and may require tweaks to remove non-advective cells. > > > We went to a lot of effort to eliminate problematic non-advective points in the …0.1deg \`topog.nc\` (https://github.com/COSIMA/access-om2/issues/99) but we still need to do the same for the other resolutions. > > From https://arccss.slack.com/archives/C6PP0GU9Y/p1592289744341700?thread\_ts=1592285883.339600&cid=C6PP0GU9Y > @russfiedler finds 21 non-advective columns in the grid at \`/g/data/ik11/inputs/access-om2/input\_20200530/mom\_025deg/topog.nc\`: > \`\`\` > \[raf599@gadi-login-02 topog\]$ ./check\_nonadvective\_mosaic topog.nc > depth dimensions 1440 1080 > Zeta dimensions 101 50 > 816 651 0.0000000E+00 ! nonadvective > 819 1080 Surface North south nonadvective > 889 49 nonadvective, Deep 25 24 > 1018 192 nonadvective, Deep 49 48 > 1328 455 nonadvective, Deep 46 45 > 1328 456 nonadvective, Deep 46 45 > 1329 467 nonadvective, Deep 46 45 > 196 494 nonadvective, Deep 26 25 > 197 494 nonadvective, Deep 26 25 > 176 554 nonadvective, Deep 9 0 > 816 651 nonadvective, Deep 9 0 > 246 742 nonadvective, Deep 11 0 > 932 801 nonadvective, Deep 30 29 > 1003 854 nonadvective, Deep 22 21 > 1094 864 nonadvective, Deep 38 37 > 1090 886 nonadvective, Deep 35 34 > 1099 906 nonadvective, Deep 35 34 > 169 1080 East west nonadvective, Deep 11 12 > 11 > 387 1080 East west nonadvective, Deep 40 41 > 40 > 862 1080 East west nonadvective, Deep 21 22 > 21 > 1153 1080 East west nonadvective, Deep 43 44 > 43 > \`\`\` > Results and check program at \`/scratch/v45/raf599/bathymetry\` > > > It could also be worthwhile looking for choked estuaries with this tool https://github.com/aekiss/notebooks/blob/master/non-advective.ipynb > > Other issues with this topography: https://github.com/mom-ocean/MOM5/issues/172, https://github.com/COSIMA/access-om2/issues/141, https://github.com/COSIMA/access-om2/issues/158 > > > At some point should we consider creating new topography for 1 and 0.25deg which… is more consistent with the 0.1 deg topo? > > The minimum depth is probably too large at 1deg and 025deg, now that we have finer surface resolution with KDS50: > 45.11m (10 levels) in ACCESS-OM2, > 40.36m (9 levels) in ACCESS-OM2-025, and > 10.43m (7 levels) in ACCESS-OM2-01 > > The land masks are inconsistent, particularly near the tripoles: > !\[Screen Shot 2019-08-15 at Thu 15-8 1 58pm\](https://user-images.githubusercontent.com/31054815/63071981-d1436300-bf64-11e9-9493-d1a34e12d266.png) > > There are also gaps in the depth distribution at 1 and 0.25 deg: https://github.com/COSIMA/access-om2/issues/141 > and other problems at 1deg: https://github.com/mom-ocean/MOM5/issues/172 > and non-advective points at 0.25 deg: https://github.com/COSIMA/access-om2/issues/210 > > > See below for a scatter plot of partial cell thickness versus full cell thicknes…s in the three configurations used in the paper. The upper and lower lines have slopes of 1 and 0.2, respectively. > The scatter shows how model bottom cell thickness ranges between the full cell thickness and 20% of that (with a 10m minimum at 0.1deg discussed \[here\](https://github.com/OceansAus/access-om2/issues/99#issuecomment-414922491)). > > I'm posting this issue to note the gaps in the 1deg and 0.25deg distributions. > > The 1deg and 0.25deg topog.nc files use the KDS50 vertical grid but were based on files generated for the GFDL50 grid, which already had a (presumably 20%) minimum partial cell thickness. When adapted to KDS50 the GFDL50 minimum cell thickness produces gaps in the thickness distribution, i.e. the small terraces produced by the GFDL minimum partial cell thickness are inherited by the topography on the KDS50 vertical grid. At least, that's what I think is going on. > > If we wanted to fix this we'd need to go back to a more raw topography file, before the minimum-thickness threshold was applied. > > !\[partialcells\](https://user-images.githubusercontent.com/31054815/55699711-724a6c00-5a0f-11e9-8fbd-97e9180253d4.png) > (plot script is \[here\](https://github.com/OceansAus/ACCESS-OM2-1-025-010deg-report/blob/master/figures/bathymetry/bathymetry.ipynb)) > > > We currently have a relatively small number of very small cells (\<1km), which li…mits the timestep, primarily in CICE, necessitating shortening the ice dynamic timestep by the factor ndtd=3 relative to MOM, which in turn messes up the CICE-MOM load balance. It could therefore give a significant speed boost and cost reduction if we convert these into land points. > > The small dimension is dy, close to the tripoles at 65N,100W and 65N,80E. It looks like the ocean cells were filled in at 0.25 deg so that the global minimum dy equals the minimum dx (6km). This hasn't been done at 0.1 deg, giving very small (down to 880m) y-sizes near the tripole. The minimum x-size is 2500m so we get large aspect ratios (dx/dy up to 5.1). > !\[screen shot 2018-12-10 at mon 10-12 9 10am\](https://user-images.githubusercontent.com/31054815/49703649-982b5400-fc5b-11e8-882d-33a31708e50a.png) > > A cumulative histogram shows a steep dropoff at very small sizes, with \<1% of cells smaller than 2000m and \<0.2% smaller than about 1200m > !\[screen shot 2018-12-10 at mon 10-12 9 28am 2\](https://user-images.githubusercontent.com/31054815/49703816-083ad980-fc5e-11e8-91fb-d385343db076.png) > > The small cells are in the Canadian Archipelago (along the southern coasts of the passages south of Victoria Island and King William Island and the passage and estuary east of Southampton Island in northern Hudson Bay), and in the Ob River in Siberia: > !\[screen shot 2018-12-10 at mon 10-12 10 37am\](https://user-images.githubusercontent.com/31054815/49704487-cf076700-fc67-11e8-9736-e4f82455c0d5.png) > > In grid coords (heavily distorted as we are close to tripoles) these regions look like this (click to enlarge): > !\[grid\_tripole\_dyt01deg\](https://user-images.githubusercontent.com/31054815/49704726-b3519000-fc6a-11e8-966e-2c9dde7e3e10.png) > > If we were to take the same approach as at 0.25deg and set a minimum y-size of 2500m this would join Victoria, Prince of Wales and Baffin islands onto North America and eliminate the Ob estuary, which seems quite drastic but is what is done at 0.25deg: > !\[screen shot 2018-12-10 at mon 10-12 9 52am\](https://user-images.githubusercontent.com/31054815/49704596-0d515600-fc69-11e8-9cfe-5c27a09347dc.png) > > "bad departure points" errors in CICE with ndtd=2 and RYF occurred mostly with dyt\<1100m. So a less-drastic alternative would be to limit the y-size to (say) \>1150m to keep Victoria, Prince of Wales and Baffin as islands, retaining passages for ice flow (but probably still joining Southampton Island onto North America). However using ndtd=2 with this topography could still risk "bad departure points" errors due to increased variability with IAF, and maybe retaining constricting versions of these passages could lead to ice congestion there. > > Any thoughts/suggestions? > > > I'm getting crashes like this from time to time: > \`\`\` > FATAL from PE 3457: Err…or: temperature out of range with value 3.081776472849E+02 at (i,j,k) = (2153,2093, 2), (lon,lat,dpt) = ( -64.7500, 64.3310, 1.7294 m) > \`\`\` > always at the same i,j=2153,2093 but with k=2 or 3. This is at the coast on the southern side of the mouth of Cumberland Sound on the east coast of Baffin Island, Canada. This is marked by the red circle in the figures below. It looks like \`/g/data3/hh5/tmp/cosima/bathymetry/topog\_latest.nc\` has a large shallow estuary with a 1-cell mouth on Hall Peninsula, whereas in \`/g/data3/hh5/tmp/cosima/bathymetry/gebco.nc\` this is a series of islands and fjords. > > I think we could just close off the "estuary". @russfiedler what do you think? Would you have a chance to look at this sometime soon? > > !\[screen shot 2018-06-12 at tue 12-6 9 08am\](https://user-images.githubusercontent.com/31054815/41261682-2e1fc8b2-6e20-11e8-945e-e830057fc378.png) > > !\[screen shot 2018-06-12 at tue 12-6 8 57am\](https://user-images.githubusercontent.com/31054815/41261410-e98c679c-6e1e-11e8-9978-32e5aa7e48d9.png) > > !\[screen shot 2018-06-12 at tue 12-6 8 58am 1\](https://user-images.githubusercontent.com/31054815/41261403-dfd87010-6e1e-11e8-82a5-10949e348ba0.png) --- _[View the full topic](https://forum.access-hive.org.au/t/bathymetry-for-ocean-model-at-any-resolution/462)._