1/20° topography

[AndyHoggANU]

It looks like we will begin a second attempt at a higher resolution (1/20°) PanAnt configuration. Last time we attempted this we simply sampled the old ACCESS-OM2-01 bathymetry to give the simplest possible 1/20° configuration. But that is probably not ideal in the longterm. Furthermore, @ChrisC28 is doing the same thing in mom6-eac (see https://github.com/COSIMA/mom6-eac/issues/6), so perhaps we should combine methodologies.

Possible options seem to be:

• The block subsampling that we used last time;
• Interpolating the 0.1° bathymetry?
• Sourcing a new and updated bathymetry and starting from scratch. It would be nice to think that the 3rd option is possible, but I don't know how possible it is.

Any suggestions or comments? Any other pitfalls we need to think about, especially in matching low resolution boundary conditions?

[adele-morrison]

I vote for:

• Sourcing a new and updated bathymetry and starting from scratch.

Given these are regional domains, hopefully it will be only minimally time consuming if we need to manually fix any problem areas.

Possibly @pedrocol and I could work on this next week when he visits. Except I know nothing about what's needed. @russfiedler or @aekiss, do you have scripts / documentation to share for what was done for the ACCESS-OM2 bathymetry and advice on what we need to do differently for C-grid?

[ChrisC28]

I'm somewhat agnostic about the exact approach to generate the new grid and topo. However, as caught by @aidanheerdegen in MOM6-eac the grid has some odd values that looked like round-off/truncation from the interpolation. Not sure if that's a problem with the pan-Ant config but it should probably be checked. As I discussed at length with @russfiedler, ideally the high-res grid should "nest" into the low-res grid, so that the T, u, v and q points of the low-res grid sit on top of certain high-res grid points. I'd be leaning towards starting the topo from scratch. The EAC region has quite highly resolved topography as the various voyages up and down the coast has swathed it to death. This data should make it's way to GEBCO or ETOPO. There are a lot of features, such as submarine canyons, that aren't going to be resolved at 1/10th degrés grid spacing that I'd like to target with my planned higher res runs.

[aekiss]

It would be good to establish a reproducible workflow for the topo generation. For ACCESS-OM2 the 0.25deg and 1deg topographies have repositories that fully document how they were generated, e.g. https://github.com/COSIMA/make_025deg_topo, and the exact commit used to generate them is recorded in the topog.nc history metadata. Hand edits were needed for important sills and straits using https://github.com/COSIMA/topogtools/blob/master/editTopo.py but these edits were recorded in topog_edits.txt and form part of the workflow for reproducibility. This reproducible approach has been very useful when we've needed to tweak the topography. The topo workflows for ACCESS-OM2 contain checks and fixes to ensure that the topo will work properly on a B grid. It should be a bit more straightforward with MOM6 due to the C grid.

[aidanheerdegen]

Given it is a C-grid it probably makes sense to start from scratch rather than just using the ACCESS-OM2 grid. Is there an existing 0.1 degree C-grid bathymetry for MOM6?

As for generating a new bathymetry, a new Bedmap2 product has just been released

https://www.bas.ac.uk/project/bedmap-2/

It extends up to 60S and is 1km resolution.

Or Bedmachine Antarctica v2

https://nsidc.org/data/NSIDC-0756/versions/2

That is 500m resolution, but only extends to 70S. The Bedmachine data is utilised in GEBCO, so that would be the one to use if that was the preferred to Bedmap2. Using GEBCO means you also have a relatively seamless global version that is compatible with the higher resolution Pan-Antarctic.

Because Paul asked about interpolating the Bedmachine data on to the ACCESS-OM2 grid, I ended up writing up a blog post about using proj4 for this

https://climate-cms.org/posts/2021-11-02-pyproj-regrid.html

In case it is useful.

[ChrisC28]

Perhaps a naive question: what are the main challenges with generating a "good" topography? In MITGCM I interpolate ETOPO onto the relevant grid (T-points) and it's done. I can imagine modifying straits/internal seas/sills etc.... however for the generation of the basic topography, what are the issues we need to be aware of, as it doesn't appear to be a straightforward process (when compared with MITGCM, for example).

[AndyHoggANU]

There's no doubt that the C-grid is much more amenable to naive grid production than B-grid. Maybe the best thing to do is to take one of these configurations, produce a basic grid at higher res, ensure the boundaries will be well-behaved and then give it a burl?

[aekiss]

Yep, keep it simple to begin with, and then tweak it via scripts on github to keep it reproducible.

@ChrisC28 https://github.com/COSIMA/make_025deg_topo/blob/master/make_topog.sh will give you an idea of what things needed to be done for that model, including

• float_vgrid ensures the vertical grid consists of double-precision values that also exist at single precision
• deseas removes lakes and unwanted seas
• do_partial_cells
• min_max_depth
• apply_mask etc

[pedrocol]

I would just add a smoothing prior to masking (it could be a Shapiro filter, I have a fortran code for this) and probably the coast will need hand editing (for extra smoothing and specific topographic features). Also, perhaps it is a good opportunity to extend the horizontal grid further to the south in order to fully include the cavities in a near future.

[micaeljtoliveira]

I would be happy to help with this, in particular with the scripts and making sure everything is reproducible.

[adele-morrison]

Fantastic @micaeljtoliveira! Sounds like we have enough info here to get us progressing with this. Let's work on it together next week when @pedrocol is in town.

[aidanheerdegen]

Also worth bearing in mind what your optimal dimensions (in cells) should be. Maybe it isn't such an issue in MOM6, but MOM5 grids were generally chosen to be divisible by as many factors as possible, to make decomposition as straightforward and flexible as possible.

[adele-morrison]

Here's a summary of the work flow needed for the new bathymetry:

0. Create horizontal grid.
1. Interpolate most recent GEBCO data onto new model grid. Existing script: gen_topo.f90
2. Remove isolated seas. Existing script: deseas.f90
3. Apply minimum and maximum allowed ocean depths. Existing script: min_max_depth.f90
4. Remove potholes. Existing scripts (but can remove code for fixing non-advective coastal cells): fix_nonadvective_mosaic.f90 and check_nonadvective_mosaic.f90
5. Generate the land mask from the topography. Existing script: topog2mask.py
6. Possibly optional: Smooth regional boundary to match forcing model grid.

Some notes on choices that need to be made in this process:

• Which bathymetry data product to use. GEBCO.
• Size of domain. For PanAntarctic we want to extend far enough south to include ice shelves later. Also consider the optimal dimensions for different decompositions of core layouts here.
• Minimum ocean depth. We'll be running z* initially, so aim for ~10 m.

Compared with the work flow for MOM5 bathymetry, we no longer need to do: coastal editing of non-advective cells, editing to ensure minimum thickness of partial cells, calculating single/double precision vertical grids.

[micaeljtoliveira]

As discussed during the meeting, here is the new git repository to collect the pieces and bits of code used for these tasks:

https://github.com/COSIMA/domain-tools

I will start by adding the Fortran tools mentioned in the work flow.

[micaeljtoliveira]

I've now added the Fortran tools (plus a simple CMake based build` system) to the new repository.

[aekiss]

The ACCESS-OM2 topography was based on GEBCO2014, but the latest is GEBCO2021 https://www.gebco.net/data_and_products/gridded_bathymetry_data/gebco_2021/ so if we use GEBCO I think we should use that version as there has been quite a bit of progress in mapping bathymetry since 2014: https://seabed2030.org/mapping-progress

[dpath2o]

Has anyone had a good and thorough look at GEBCO 2021? Others that I work with won't touch it for high resolution (less than a 1/10 of a degree) 3D ocean dynamic modelling. I have correspondence on a secure network that highlights these issues and it is something that I'd like to investigate myself, but it's down there on the priority list at the moment.

[aekiss]

Hm, thanks for the heads up - I haven't looked into it, and was naively assuming newer=better. Can you be more specific about the flaws?

[dpath2o]

Yes, of course. I'll get into my work email tomorrow and bring it into this conversation.

[yuhang559]

Hi, I am Yuhang, a UTAS Honours student. In my Honours project, we compare two high-resolution models (MITgcm) configured with two bathymetry data ( BedMachine Antarctica and SRTM15_PLUS) in the Denman region, East Antarctica. BedMachine is smoother and maybe lacks some small-scale features, whereas SRTM15 is rougher with more small-scale features. In the current stage, we can only see the two bathymetry datasets are different and make a significant impact on ocean circulation. As we haven't compared the two datasets with the observations (seal data), so we can't give a definite answer on which bathymetry data is better. COSIMA_Yuhang Liu.pdf

[aekiss]

Thanks @yuhang559!

[aekiss]

Following Alex Fraser's talk at COSIMA meeting today, we could also put in grounded icebergs as land in order to get fast ice in the right places (if we have tensile strength in the sea ice).

[adele-morrison]

@adfraser maybe you can check if SIS2 has the required dynamics for us?

[adfraser]

Hi @aekiss and @adele157 -- it looks like Kate Hedstrom has investigated Arctic fast ice with SIS2: https://twitter.com/UAFOceans/status/1417624387008696320. It makes me think it supports fast ice out of the box, but I can't confirm quickly sorry.

This brings up an intersting possibility. If you have an easy way to get fast ice happening, there's a chance @dpath2o 's PhD could pivot to using this (rather than CICE6) to do at least some of his PhD work. Getting CICE6 running correctly is proving to be tricky and many of Dan's aims could be accomplished without waves. @willrhobbs @PaulSpence any thoughts?

[adele-morrison]

Great that SIS2 looks good for fast ice.

Sounds like a nice option for @dpath2o to use this model - shall we chat offline about what simulations / diagnostics are needed and if it would be suitable? If so, we could perhaps do a 5 year test of the model with a) the new bathymetry, and b) new bathymetry plus grounded icebergs?

[adfraser]

Thanks @adele157 - I'll have a chat just with @dpath2o, @willrhobbs and @PaulSpence too - could be really good!

BTW -- speaking of bathymetry, I note that IBCSO 2 was just released. I know that IBCSO 2 has the new multibeam near Cape Darnley from the Japanese program (and I'm not sure if the new GEBCO does or not). Could be another one to throw in the mix when thinking about new bathymetry products. https://ibcso.org/ibcso-version-2-released/ @aekiss

[aekiss]

Thanks @adfraser. I'm not an expert on bathymetric datasets, but IBCSO 2 seems definitely worth considering. They describe it as "the most authoritative seafloor map of the area south of 50°S" and it also includes sub-ice shelf bathymetry. Hopefully it can be smoothly combined with some other dataset to cover north of 50°S.

[adfraser]

@aekiss Jodie Smith from Geoscience Australia will know more if you need - she's a contributor to IBCSO2. I've always preferred IBCSO (1) on the continental shelf but I haven't done any comparisons in the last few years.

[aekiss]

GEBCO2022 has just been released, and includes sub-ice shelf data https://www.gebco.net/data_and_products/gridded_bathymetry_data/gebco_2022/ The GEBCO2022 resolution is 15 arc-second (ie 1/240 deg = 460m at equator and finer zonally nearer the poles), whereas IBCSO is coarser (500m x 500m). They're both GEBCO projects but I don't know how GEBCO2022 is related to IBCSO 2 south of 50S (maybe they are the same, apart from resolution?) I've contacted Jodie Smith for advice.

[aekiss]

Boris Dorschel (lead author of the IBCSO2 release paper) has confirmed that IBCSO2 has been merged into GEBCO2022. So GEBCO2022 sounds like a good choice, unless there are issues with it that @dpath2o knows about.

[dpath2o]

I've downloaded the full GEBCO2022 and I will incorporate into the CICE6 stand-alone that I'm currently standing up locally as I'll be using a cubic spline to reduce to the ACCESS-OM2 CICE tri-polar grid as a first step. However, with my other hat, I'm currently working with USN (FNMOC/NRL) and I'll see if they have any prickly bits that are cautionary for operational oceanography and advise as required.

[aekiss]

Great, thanks @dpath2o

[AndyHoggANU]

Hi All -- just touching base on this one. It seems that the current blocker is that we need to decide absolutely on the data source for the topo. @aekiss -- do we take it from your latest post that we have decided on GEBCO2022? In which case we could download and see if @micaeljtoliveira can have a crack at using the domain tools to generate a smoothed topography and land mask?

[aekiss]

I don't know a lot about the pros and cons of different topographic datasets, but GEBCO2022 looks good to me unless @dpath2o has a good reason not to use it.

I've downloaded it to /g/data/ik11/inputs/GEBCO_2022. There are 3 data files:

• GEBCO_2022.nc which gives the ice-atmosphere interface height at ice shelves
• GEBCO_2022_sub_ice_topo.nc which gives the seabed in ice shelf cavities but also the ice-rock interface under ice sheets; I imagine this matches GEBCO_2022.nc in ocean areas that aren't in cavities
• GEBCO_2022_TID.nc, which has flag value of 0 for land and ice shelves and could be useful for land mask generation

We would still need ice sheet draft (i.e. cavity ceiling) and grounding line data to do ice cavities - @pedrocol can you suggest a source for these? I guess if we have the ceiling and floor we can work out the grounding line.

Here's what the 3 files look like:

[pedrocol]

The cavities data comes from Bedmachine (https://nsidc.org/data/nsidc-0756), which uses the bathymetry from IBCSO (see user guide, page 6). What I did is to interpolate the data coming from Bedmachine (both the draft and bathymetry) and combine it with GEBCO2021 (I didn't have the 2022 version at that point). The tools I used come from the NEMO community (NEMOBAT), but is a simple 2D extrapolation as done with the bathymetry. Happy to discuss this in detail or provide scripts.

[aekiss]

great, thanks @pedrocol

[adele-morrison]

At this stage I think all we need from the ice cavity bathymetry is the most southerly latitude of any of the grounding lines, so we know how far south to extend the grid. Could you find that out for us @pedrocol ?

[aekiss]

In case it's useful, the current 0.1deg topog is /g/data/ik11/inputs/access-om2/input_20200530/mom_01deg/topog.nc and some of the working for it used tools in https://github.com/COSIMA/topogtools as recorded in the history attribute:

// global attributes:
        :original_file = "topog_190717_deseas_m7_par_nonadv.nc" ;
        :history = "2018-10-23T22:00:44.500081: /home/nic/anaconda3/bin/python cut_and_fill.py 3218 2611 topog_05_09_2018_1m_partial.nc a_topog.nc (Git URL: git@github.com:OceansAus/topogtools.git, Git hash: f8b8bc9) \n 2018-10-23T22:01:00.437933: /home/nic/anaconda3/bin/python cut_and_fill.py 3226 2626 --cut_or_fill_depth 400 a_topog.nc b_topog.nc (Git URL: git@github.com:OceansAus/topogtools.git, Git hash: f8b8bc9) \n 2018-10-23T22:02:20.861163: /home/nic/anaconda3/bin/python cut_and_fill.py 3222 2623 --cut_or_fill_depth 400 b_topog.nc c_topog.nc (Git URL: git@github.com:OceansAus/topogtools.git, Git hash: f8b8bc9) \n 2018-10-23T22:02:44.414990: /home/nic/anaconda3/bin/python cut_and_fill.py 3216 2618 --cut_or_fill_depth 300 c_topog.nc d_topog.nc (Git URL: git@github.com:OceansAus/topogtools.git, Git hash: f8b8bc9) \n 2018-10-23T22:03:00.394537: /home/nic/anaconda3/bin/python cut_and_fill.py 3216 2618 --cut_or_fill_depth 350 d_topog.nc e_topog.nc (Git URL: git@github.com:OceansAus/topogtools.git, Git hash: f8b8bc9)" ;
        :creation_date = "Thu Dec 13 17:49:32 AEDT 2018" ;

There have been several versions (see /g/data/hh5/tmp/cosima/bathymetry) to deal with issues such as https://github.com/COSIMA/access-om2/issues/99 and https://github.com/COSIMA/access-om2/issues/126.

@russfiedler and @nichannah did a lot of this and might recall more details if we need them.

[pedrocol]

@adele157 The most southerly latitude is -86, I would use a slightly southern latitude to avoid being too close to the edge of the cavity (in case the dataset changes), -87 should do it

[schmidt-christina]

I created the bathymetry and land mask for the Southern Hemisphere at 1/20° resolution for 75 z* levels with the help from @micaeljtoliveira . Overall, it looks pretty good to me!

The bathymetry on the Antarctic shelf looks very similar to the original GEBCO 2022 data:

The land mask for South America and Africa does not seem to be “blocky”:

I haven't smoothed the northern boundary yet to match the bathymetry with the 1/10° forcing. Does that need to be done manually? Any other thoughts on this bathymetry or can I go ahead and use this for test runs with the panan-005?

[PaulSpence]

would be good to get Russ Fiedler to take a look https://github.com/russfiedler

P

On Wed, Oct 5, 2022 at 2:19 PM Christina Schmidt @.***> wrote:

I created the bathymetry and land mask for the Southern Hemisphere at 1/20° resolution for 75 z* levels with the help from @micaeljtoliveira https://github.com/micaeljtoliveira . Overall, it looks pretty good to me!

[image: image] https://user-images.githubusercontent.com/38216156/193973100-a802ef88-9fb8-40ae-abdd-f42a51fc1921.png

The bathymetry on the Antarctic shelf looks very similar to the original GEBCO 2022 data:

[image: image] https://user-images.githubusercontent.com/38216156/193973139-2913d1c1-e47e-4d4a-918b-66406b259f39.png

The land mask for South America and Africa does not seem to be “blocky”:

[image: image] https://user-images.githubusercontent.com/38216156/193973307-5a42566b-7d85-4198-b4ad-ec5683689966.png

I haven't smoothed the northern boundary yet to match the bathymetry with the 1/10° forcing. Does that need to be done manually? Any other thoughts on this bathymetry or can I go ahead and use this for test runs with the panan-005?

— Reply to this email directly, view it on GitHub https://github.com/COSIMA/mom6-panan/issues/12#issuecomment-1267871358, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABSWJXHKDTIP5D4PA3CM3X3WBTXVNANCNFSM5WYGZDWQ . You are receiving this because you were mentioned.Message ID: @.***>

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Paul Spence, Assoc. Prof. ARC Future Fellow Institute for Marine and Antarctic Studies https://www.imas.utas.edu.au/ University of Tasmania, Hobart, Australia https://paulspence.github.io/

[russfiedler]

Looks to be quite a few problems remaining. e.g. New Zealand's North Island, inland seas in South America. Also, have a good think about what you are trying to model in areas like Patagonia. What detail is needed? In addition, check that you've got deeper channels/canyons/sills well represented. It would be useful to put the topography file somewhere public so others can comment.

[schmidt-christina]

Thanks, for the comment @russfiedler . Here is a zoom into South America and NZ (top: land mask, bottom: bathymetry) and I don't see inland seas/other problems there, but correct me if I am wrong:

This will be the bathymetry for the PanAntarctic configuration at 1/20° resolution with a northern boundary at 37°S or the equator (still needs to be decided), so the main focus should be modelling Antarctic shelf processes and possibly ACC dynamics.

Can you provide me with a list of the deeper channels that you have in mind and which might be a problem?

Is there a public folder on gadi where I should put the file? Otherwise it is now here /g/data/e14/cs6673/shared/panan-005_bathy/ (Coordinates and attributes are still missing in the files and it's on our list to fix that)

[russfiedler]

I think that some of the problems that I thought might be there are just artifacts of the plotting software. You'll need to chat with some real oceanographers(!) with respect to resolving important pathways.

[aekiss]

Great work @schmidt-christina!

I'm not sure whether sills will be a problem at 1/20°. Sills are more of an issue at coarser resolution, where the mean depth doesn't capture the maximum at sills.

We did a lot of tweaking at 0.25°, but not in the southern hemisphere as far as I recall. https://github.com/COSIMA/make_025deg_topo/blob/master/topog_edits.txt

At 1° there were also some edits in Patagonia and the ITF, but they're very unlikely to be needed at 1/20° https://github.com/COSIMA/access-om2/issues/158#issuecomment-708979129

[aekiss]

It might be worth plotting the difference between your new topo and the one used in ACCESS-OM2-01 (with your topo regridded to the ACCESS-OM2-01 grid). Plot both the absolute and relative depth changes to see if anything looks weird.

[AndyHoggANU]

Hi @schmidt-christina - this looks good. I do have some slight worries about the number of channels and fjords, but we should remember that MOM6 is a very robust code. I think it may be worth just giving this a go and seeing what happens?

As it’s running, be sure to monitor sea level — if you have any enclosed lakes then they will show up as their level evolves.

I think the only outstanding question is whether you need to degrade the resolution on the northern boundary to match the original. I think not, but I would defer to @angus-g here …

[schmidt-christina]

I now compared the new topo with ACCESS-OM2-01 (using ht) @aekiss . There are some big differences between them with the new topo being often deeper (red shadings, unit is meter). It seems that often the differences are in regions of gradients in the topography. I am surprised by how big the differences are but I wouldn't think there is anything systematically wrong.

[adfraser]

That Western Weddell Sea difference is probably due to better observations in a newer bathymetry product. It must be very data-sparse there - often multiyear sea ice cover so hard to get a multibeam in there. But wow 400m of difference is wild.

[aekiss]

Hm, interesting. Those differences don't look too concerning to me - I guess the interpolation between the bathymetric observations is least accurate where the gradients are large, so the differences between successive versions of GEBCO are biggest there? That doesn't explain why the new topo is usually a bit deeper though.

Do they both have the same maximum depth, and do they use the same vertical grid and minimum partial cell height?

What do the relative depth differences look like?

2d histogram of old vs new topo can be useful to look for systematic differences, and a plot of partial vs full thickness can catch issues with partial cells - see https://github.com/COSIMA/access-om2/issues/158#issuecomment-698758041 and https://github.com/COSIMA/topogtools/blob/master/bathymetry.ipynb

[adfraser]

The large differences on the Antarctic continental shelf slope in general aren't surprising, given the attention paid to improving/getting better data in these areas (e.g., for better understanding of warm water access) - e.g. I was involved in this one which got new multibeam data offshore of the Totten in 2015: https://agupubs.onlinelibrary.wiley.com/doi/10.1002/2017GL074433 - Fig 3b gives a few transects across the shelf showing huge (400 m+) differences between products (Bedmap2 looks particularly bad in this region). I assume the new multibeam from our cruise is in the gebco2022 product.