Improve topography at 1deg and 025deg?

[aekiss]

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:

There are also gaps in the depth distribution at 1 and 0.25 deg: #141
and other problems at 1deg: mom-ocean/MOM5#172
and non-advective points at 0.25 deg: #210

[aekiss]

The new 0.1 deg grid has removed the smallest cells near the tripoles (#126) and looks like this (note the larger minimum size)

[aekiss]

Here's what the 1 deg topography looks like on a shallow shelf (colourbar from 0-100m). Due to inheriting the 10m quantisation from GFDL50 (#141) the minimum depth is 50m and there's 10m terracing, so we're missing the finesse that KDS50 could give

Here's the 0.25 deg topography - now the minimum depth is ~40m, and there's ~10m terraces to deeper water

...whereas this is the glorious 0.1 deg with none of those issues

[russfiedler]

It looks like the 1 degree and 0.25 degree topographies are still infected by the old dodgy OCCAM bathymetry, the 0.25 bathymetry in particular. The Laptev Sea is particularly bad and closer to home the Gulf of Carpentaria should not be 130m deep.

[aidanheerdegen]

The gift that keeps on giving.

[aekiss]

The East Siberian and Chukchi seas south of Wrangel Island are also bad at 1 and 0.25 deg.
Is this 1deg topog.nc the same as what's used in ACCESS-CM2?

[russfiedler]

Yep, I brought this up several years ago and it never got fixed for some reason.

[aekiss]

@russfiedler and I have generated new 1deg and 0.25deg topography from GEBCO 2014:
1 deg: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/topog.nc
0.25 deg: /g/data/ik11/inputs/access-om2/input_rc/mom_025deg/topog.nc
which might be considered as replacements for the existing ones (perhaps after a bit more tweaking).

They were created using /scratch/v45/aek156/bathymetry/tools/*_deg_test/make_topog.sh.

They use a KDS50 vertical grid and set a minimum full depth of 11.8m (4 levels), with a minimum cell thickness of 1m, and eliminate terracing (fixing #141). And starting from GEBCO eliminates the erroneous pits on shelves (#158 (comment) and mom-ocean/MOM5#172).

The 1deg uses the same land mask as before, but the 0.25deg slightly modifies the previous land mask in ocean_mask.nc, adding 3 land points and 2 ocean points to deal with non-advective cells/edges (#210). So far this is the only hand-editing that has been done (everything else was automatic, via make_topog.sh).

The 1 deg model runs fine but I haven't successfully tested the 0.25deg as I'm still trying to generate remapping weights.

I've made some comparisons to the previous topography halfway down this notebook.
On the whole it doesn't look like there are major differences. These are the differences that jumped out at me:

• The new topo has min depth of 11.8m instead of 40-45m so that accounts for the shallowing near coasts.
• The new topo also has no terracing, e.g. in the Laptev Sea.
• Lombok Str is shallower in new 1deg
• Timor Str is shallower/narrower in new 1deg
• Bering Str is is shallower in new 1deg, deeper in new 0.25deg
• Denmark Str seems to have been hand-deepened in old 1deg and is shallower in new 1deg
• Florida Current has shallower sills in new 1deg and 0.25deg
• shelf pits fixed in Carpentaria, Bass Str, Chukchi Sea, Yellow Sea and between Hainan and Vietnam at 025deg

Of these, I think only Lombok, Timor and Denmark Straits could do with hand-editing at 1deg, I guess to make them match the old topo. Does that sound sensible?

Are there any other straits, pathways etc we should check?

FYI I have a fixed-up version of Alistair's GUI topography editing tool on this fork & branch: https://github.com/aekiss/MOM6-examples/blob/editTopo-update/ice_ocean_SIS2/OM4_025/preprocessing/editTopo.py that makes editing fairly straightforward.

[russfiedler]

Probably have a look at the outflow pathway from the Med. Maybe ask those with an interest in the Southern Ocean to have a look.

[aekiss]

Ah yes, I'd meant to add Gibraltar. It's there now.
It's a bit shallower at the west of the Gibraltar sill and a bit deeper to the east in both the new 1deg and 0.25deg.

[ofa001]

In response to @russfiedler on the southern Ocean Simon added some extra Glacier Tongues to try and create more polynyas, but it does lead to ice build up behind them wich happens as fast ice in the real world at 1 deg back in 2007/8 . I have often wanted them relooked at though they are the source of a limited high salinity water they do have a latent heat signature to the atmosphere (which is realistic). There is also the issue of trapped embayments for ice where it cant move out velocity wise at 1 deg, I haven't checked the 0.25 deg for this but it might be a good time to do it whilst the grids are under discussion.

Shallowing at Bering St can lead to strong a flow depending on width so you might need to look at bottom drag.

[aekiss]

Thanks @ofa001 we are using the previous Antarctic land mask at both resolutions, so if there were glacial tongues in the old topography they'll still be there in the new one.

There are no B-grid non-advective cells, but are you talking about ice trapping by some other process?

[ofa001]

Sometimes it still gets a bit trapped and thick even if there is an adjective point, it depends on the local winds, In very long runs you might get it partially breaking out after 30-40 years if a wind change occurs. Having the glacial tongues and polynyas isn't too much of an issue in there are often icebergs also causing temporary blocks in the flow, and then polynyas behind as well, in observations. Be great to eventually try a fast ice parameterization at 0.1 degree resolution.

[aekiss]

I've put an updated candidate 1 degree topography in /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/topog.nc.
This was created with https://github.com/COSIMA/make_1deg_topo/blob/b13ad6b/make_topog.sh

The bathymetry is mostly new, created from scratch from GEBCO 2014, but has 249 edits at important straits (see https://github.com/COSIMA/make_1deg_topo/blob/b13ad6b/topog_edits.txt) where the automatically generated GEBCO value was replaced by the value from the old topography /g/data/ik11/inputs/access-om2/input_20200530/mom_1deg/topog.nc. These edited cells are marked by red circles in the plots below. They mostly deepened the GEBCO topography, but in the Gibraltar Strait it was a shallowing. Many of these locations appeared to have been hand-edited in the old topography, presumably for a reason, so I thought they should be retained.

How does that look? Is there anything I've missed?

If you want to compare the old and new topography you can get editTopo.py from https://github.com/COSIMA/topogtools and do

module use /g/data/hh5/public/modules
module load conda/analysis3
./editTopo.py --ref /g/data/ik11/inputs/access-om2/input_20200530/mom_1deg/topog.nc --apply /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/topog_edits.txt /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/topog.nc

[aekiss]

An update:

The 1 degree topography is awaiting discussion re. which of Simon's hand-edits in the old topography we should include in the new one. These edits are marked in red:

However I think the 0.25deg topography in /g/data/ik11/inputs/access-om2/input_rc/mom_025deg/topog.nc is ready to use. Its history attribute contains a url showing the exact steps used to create it: https://github.com/COSIMA/make_025deg_topo/tree/37274b2

In addition to what is described here, this new version now fills in the Sulu Sea to the sill depth (~503m), copying what was done in the old topography (this is the only obvious hand-editing I could see in the old topography). This is a 4000-5000m deep enclosed basin with a ~500m sill all around so presumably this was done to avoid issues with the deep water being stagnant.

Here are some plots and stats calculated by https://github.com/COSIMA/topogtools/blob/8b2de2c/bathymetry.ipynb

The mean depth increase in the new topography is 30.6m or 1.9% and the median increases is 11.7m (0.5%).
90% of absolute depth increases are between -125.3m and 224.4m
90% of relative depth increases are between -24.5% and 12.9%
Here are the histograms (log scale):

...and bivariate histograms (log scale; the gaps are due to the 20% minimum partial cell height). Note that the new topography extends to shallower depth (11.81m rather than 40.35m).

Here is the spatial distribution of changes (click to enlarge; see here for closeups on particular regions)

The new bathymetry fixes the gaps in the depth distribution (#141), making better use of the vertical coordinate and partial cells, particularly in shallow water:

closeup:

In the absence of any real provenance as to how the old topography was generated I'm prepared to believe that these differences are improvements in the new topography, since it is generated directly from GEBCO 2014 so it should be more realistic. Whether that will translate into improved simulations is a question to be resolved by test runs, but even if it doesn't, that would seem to indicate error cancellation when using the old topography.

[StephenGriffies]

Beautiful work @aekiss !

[aekiss]

I think the new 1 degree topography in /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/ is ready to use.
Its history attribute contains a url showing the exact steps used to create it: https://github.com/COSIMA/make_1deg_topo/tree/db7b546

It is based on GEBCO_2014 v20150318 but with these edits https://github.com/COSIMA/make_1deg_topo/blob/db7b546/topog_edits.txt marked in red, which are mostly where the old topography was copied to the new:

This latest iteration has additional edits in the Red Sea, Indonesian Throughflow, Caribbean, Gibraltar Strait and Northwest Passage suggested by Simon Marsland.

It uses a KDS50 vertical grid and a minimum full depth of 11.8m (4 levels), with a minimum cell thickness of 1m, and eliminates terracing (fixing #141). And starting from GEBCO eliminates the erroneous pits on shelves (#158 (comment) and mom-ocean/MOM5#172).

It uses the same land mask as before.

Here are some plots and stats calculated by https://github.com/COSIMA/topogtools/blob/b2f5ff3/bathymetry.ipynb

The mean depth increase in the new topography is 79.9m or 10.1% and the median increases is 31.2m (1.2%).
90% of absolute depth increases are between -130.8m and 443.6m
90% of relative depth increases are between -16.6% and 35.8%
Here are the histograms (log scale):

...and bivariate histograms (log scale; the gaps are due to the 20% minimum partial cell height). Note that the new topography extends to shallower depth (11.81m rather than 45.1m).

Here is the spatial distribution of changes (click to enlarge; see here for closeups on particular regions)

The new bathymetry fixes the gaps in the depth distribution (#141), making better use of the vertical coordinate and partial cells, particularly in shallow water:

closeup:

As for the 0.25deg topography, I'm prepared to believe that these differences are improvements in the new topography, since it is generated directly from GEBCO 2014 so it should be more realistic. Whether that will translate into improved simulations is a question to be resolved by test runs. It is possible that some more tweaking around critical straits will be required.

[rmholmes]

Thanks for all the work @aekiss, looks great!

[aidanheerdegen]

Agreed, fantastic work, including the meticulous documentation

[StephenGriffies]

Impressive work!

[aekiss]

Thanks - credit is shared with @russfiedler, Simon Marsland, @ofa001 and @adcroft for their advice and software.

We'll need to see if these new topog files have any unwanted effects on the circulation or water masses etc at 1 deg or 0.25 deg.

Most grid cell depths are set as the average of GEBCO data over that cell, which will underestimate the depth of poorly-resolved sills. At 1 deg we reused some of the key sill depths from the previous topography that were carefully chosen to allow the appropriate water masses to exchange. We didn't make these sill adjustments in the 0.25deg so that's worth keeping an eye on. This is an incomplete list of examples:

At 1 deg we also applied a 160m sill depth to the Red Sea outlet but retained the ~600m deep basin behind it, so hopefully that won't fill up with hypersaline water in a long run (in the old topography the Red Sea was set to 50m to avoid this, increasing to 80m at the mouth).

We also didn't do any hand-edits at the outlet of the Baltic, which is now 11.8m deep instead of 50m.

The GEBCO average also underestimates the height of sharp features like Macquarie Ridge, which is deeper in the new 1 deg topography.

Also Simon had deepened the previous 1 deg topography on parts of the Antarctic shelf in order to reduce a bias of excessive ice thickness. We haven't done that in the new topography because we don't seem to be having this problem. (We were getting excessive Antarctic ice until we changed to a turning angle of zero (rather than 16.26°) which I think is more justifiable since we resolve the Ekman layer better with a surface vertical resolution of 2.3m instead of 10m.)

It will also be interesting to see how well the EAC behaves at 1 deg without these shallow points sticking out from the coast:

[aidanheerdegen]

Positive means new bathymetry is deeper than old?

[aekiss]

yes

[aekiss]

Closing - apart from the differing land masks between resolution (which we decided not to fix), all these issues have been addressed in /g/data/ik11/inputs/access-om2/input_20201022/

[aekiss]

Summary from /g/data/ik11/inputs/access-om2/input_20201022/README.txt:

• new topography for 1 deg and 0.25 deg based on GEBCO_2014 v20150318 30 arc-second topography
  • see Improve topography at 1deg and 025deg? #158 (comment)
  • mom_1deg/topog.nc, mom_1deg/ocean_vgrid.nc, mom_1deg/ocean_mask.nc and cice_1deg/kmt.nc created by https://github.com/COSIMA/make_1deg_topo/tree/db7b546
  • mom_025deg/topog.nc, mom_025deg/ocean_vgrid.nc, mom_025deg/ocean_mask.nc and cice_025deg/kmt.nc created by https://github.com/COSIMA/make_025deg_topo/tree/37274b2
  • set minimum full depth of 11.8m (4 levels), and minimum cell thickness of 1m: Improve topography at 1deg and 025deg? #158
  • fixed erroneous pits on shelves: Problems identified with bathymetry file used by several experiments mom-ocean/MOM5#172
  • fixed terracing: 1deg and 0.25deg KDS50 bathymetry inherits terraces from GFDL50 #141
  • mom_1deg has the same land mask as previously, e.g. /g/data/ik11/inputs/access-om2/input_20200530
  • mom_025deg has 5 land mask changes (adding 3 and removing 2 land points), eliminating non-advective cells/edges: Non-advective points in 0.25deg topography #210
    • this required new remapping files generated by https://github.com/COSIMA/access-om2/blob/master/tools/make_remap_weights.sh
      using Russ' tripole bug fix to ESMF_RegridWeightGen https://github.com/COSIMA/esmf/tree/f536c3e (see ESMF_RegridWeightGen not working for conservative fields #216)
      • common_025deg_jra55/rmp_jra55_cice_patch.nc
      • common_025deg_jra55/rmp_jra55_cice_1st_conserve.nc
      • common_025deg_jra55/rmp_jra55_cice_2nd_conserve.nc
    • also needed initial condition interpolated into land points in cice_025deg/o2i.nc (as for 1 deg and 0.1 deg)
      • done with https://github.com/COSIMA/topogtools/blob/master/unmask.py

[aekiss]

@rmholmes @AndyHoggANU I've had a closer look at some of the key North Atlantic straits and it seems they were hand-edited in the old (GFDL) 0.25deg topography. This might explain the different AMOC you are getting with the new topography in the OMIP 0.25deg runs.

I could edit the 0.25 topography to copy the old GFDL depths in those key straits - let me know.

The Denmark Strait sill was apparently hand-deepened in the old (GFDL) topography to 619.9m and widened slightly at that depth. In the new topography the sill depth is 540m and more constricted. These 3 figures show (respectively) the new topog, old topog and difference. They were obtained by /g/data/ik11/inputs/access-om2/bin/editTopo.py --ref /g/data/ik11/inputs/access-om2/input_20200530/mom_025deg/topog.nc /g/data/ik11/inputs/access-om2/input_20201022/mom_025deg/topog.nc

The Faroe Bank channel was also deepened (sill depth increased from 540m to 837.7m) and widened at that depth in the old topography.

Nares Strait was also deepened to at least 397.5m thoughout the channel, whereas it is much more constricted in the new topography and has a sill depth of about 160m.

There don't appear to be any hand edits in Fram Strait.

There were also some edits for the Florida Current that I could copy while we're at it

[AndyHoggANU]

OK, so I think we can agree that we need to do a little more digging in the Baltic -- Andrew can take care of that one relatively quickly, and I can re-run the test. Sound OK?

Once we have that, then I think we have enough for Martin to slot the new topography into CM2. That still leaves the Antarctic problem ... which I would love to solve but I don't think we have the bandwidth to do it right now. If we have a volunteer, that would be great? Otherwise, let's document option 2 above as our ideal solution, and get to it when we have the spare capacity...

[aekiss]

@AndyHoggANU I've updated the topography
/g/data/ik11/inputs/access-om2/input_20211123_025deg_topog/mom_025deg/topog.nc
with https://github.com/COSIMA/make_025deg_topo/tree/7b801dc which has these edits
to make channels 40m deep and >3 cells wide (where land mask permits) between all Baltic basins.

Here are the edits. Quite a bit more extensive than last time. Hopefully it will have an impact!

[MartinDix]

@aekiss Baltic average freshwater inputs (units 1e3 m^3/s) from the CM2 PD runs and obs are all remarkably close.

	River	P-E
Obs	15.0	1.7
O025	14.5	2.5
O1	15.0	2.0

Obs from Omstedt & Nohr (2004) Calculating the water and heat
balances of the Baltic Sea using ocean modelling and available meteorological, hydrological and ocean data, https://doi.org/10.3402/tellusa.v56i4.14428

However in O1 the Baltic average SSS is stable after the first couple of hundred years (not sure why it starts out higher than the 025 run).

The gradient along 55N looks like there's saltier water mixing in? The MOM namelist differences between CM2 and OM2 are summarised at https://accessdev.nci.org.au/trac/ticket/415#comment:5 (use NCI login). Could there be something that makes CM2 mix more?

[AndyHoggANU]

So, the Baltic saga continues. We are now adding two more topographies to the mix (TOPO3 and TOPO4). Both are slightly wider than the original. TOPO4 is down to 40m depth (so, similar to the OCCAM topography) while TOPO3 is 31m depth (noting that this is only one gridpoint).

You can see that TOPO3 becomes too saline, while TOPO4 is only marginally saltier than the topography we used in OMIP and CM2:

Timeseries confirm this:

So, it would seem that the extra gridpoint in the vertical flicks the switch between over-exchange and under-exchange at the mouth of the Baltic. Not sure what more we can do here ... half a grid cell??

[aekiss]

We could try half a grid cell, say 35m - they are partial cells after all.

[aekiss]

For the record, here's TOPO4, which decreased edited depths in the Baltic from 40m to 31m (or GEBCO depth if >31m) but retains the widened channels of the previous attempt (TOPO3)
/g/data/ik11/inputs/access-om2/input_20211124_025deg_topog/mom_025deg/topog.nc

[aekiss]

Thanks @MartinDix - I'm unable to log into accessdev, so could you post the namelist diff here please?

[MartinDix]

@aekiss This comparison uses the namelists printed by MOM so excludes spurious differences in default values. Here CMIP6 means the CM2-O1 configuration.

auscom_ice_nml	CMIP6	O025
do_sfix_at_start	True	False
dt_cpl	1800	1200
ire2	335	331
kmxice	15	5
redsea_gulfbay_sfix	True	False
sfix_hours	24	12

ocean_adv_vel_diag_nml	CMIP6	O025
verbose_cfl	False	True

ocean_barotropic_nml	CMIP6	O025
barotropic_halo	1	10
smooth_eta_t_biharmonic	True	False
smooth_eta_t_laplacian	False	True
smooth_pbot_t_biharmonic	True	False
smooth_pbot_t_laplacian	False	True
use_legacy_barotropic_halos	True	False

ocean_bbc_nml	CMIP6	O025
bmf_implicit	False	True
cdbot	0.001	0.0025
cdbot_hi	0.003	0.007
cdbot_roughness_uamp	False	True

ocean_bbc_ofam_nml	CMIP6	O025
uresidual2_max	1.0	0.05

ocean_bihgen_friction_nml	CMIP6	O025
bottom_5point	True	False
ncar_boundary_scaling	True	False

ocean_convect_nml	CMIP6	O025
convect_full_scalar	True	False

ocean_density_nml	CMIP6	O025
neutralrho_max	1030.0	1038.0
neutralrho_min	1020.0	1028.0

ocean_domains_nml	CMIP6	O025
max_tracers	20	5

ocean_form_drag_nml	CMIP6	O025
cprime_aiki	0.6	0.3

ocean_frazil_nml	CMIP6	O025
frazil_only_in_surface	True	False
freezing_temp_preteos10	False	True
freezing_temp_simple	True	False

ocean_grids_nml	CMIP6	O025
debug_this_module	True	False

ocean_increment_eta_nml	CMIP6	O025
days_to_increment	0	1
secs_to_increment	3600	0

ocean_increment_tracer_nml	CMIP6	O025
days_to_increment	0	1
secs_to_increment	3600	0

ocean_increment_velocity_nml	CMIP6	O025
days_to_increment	0	1
secs_to_increment	3600	0

ocean_lapgen_friction_nml	CMIP6	O025
ncar_only_equatorial	True	False
use_this_module	True	False
vconst_1	8000000.0	10000000.0
vconst_3	0.8	0.16
vconst_4	5e-09	2e-08
vconst_6	300000000.0	10000000.0
viscosity_ncar	True	False
viscosity_ncar_2000	False	True
viscosity_ncar_2007	True	False

ocean_mixdownslope_nml	CMIP6	O025
use_this_module	True	False

ocean_model_nml	CMIP6	O025
barotropic_split	100	80
dt_ocean	1800	1200
io_layout	[0, 0]	[8, 6]
layout	[8, 10]	[32, 24]

ocean_nphysics_util_nml	CMIP6	O025
agm	600.0	1000.0
agm_closure_eden_gamma	0.0	200.0
agm_closure_length	50000.0	20000.0
agm_closure_max	1200.0	200.0
agm_closure_min	100.0	50.0
agm_damping_time	45.0	10.0
aredi	300.0	200.0
aredi_diffusivity_grid_scaling	False	True
smax	0.002	0.01
swidth	0.0002	0.0005

ocean_overexchange_nml	CMIP6	O025
overexch_npts	4	1
overflow_umax	5.0	1.0

ocean_sbc_nml	CMIP6	O025
do_bitwise_exact_sum	True	False
do_langmuir	True	False
ice_salt_concentration	0.004	0.005
max_delta_salinity_restore	0.5	-0.5
max_ice_thickness	8.0	0.0

ocean_shortwave_gfdl_nml	CMIP6	O025
zmax_pen	7000.0	1000000.0

ocean_sigma_transport_nml	CMIP6	O025
sigma_advection_sgs_only	False	True
sigma_umax	0.01	0.1
thickness_sigma_layer	100.0	50.0
thickness_sigma_min	100.0	10.0
tracer_mix_micom	True	False
use_this_module	True	False
vel_micom	0.05	0.5

ocean_solo_nml	CMIP6	O025
dt_cpld	1800	1200

ocean_submesoscale_nml	CMIP6	O025
coefficient_ce	0.07	0.05
smooth_advect_transport_num	2	4
smooth_psi_num	2	3
submeso_advect_limit	False	True
submeso_advect_zero_bdy	False	True
submeso_diffusion_biharmonic	False	True
submeso_diffusion_scale	1.0	10.0

ocean_tempsalt_nml	CMIP6	O025
s_max	55.0	70.0
s_min	-1.0	0.0
s_min_limit	0.0	2.0
t_min	-5.0	-20.0
t_min_limit	-2.0	-5.0

ocean_thickness_nml	CMIP6	O025
rescale_rho0_basin_label	7.0	-1.0
rescale_rho0_value	0.75	1.0
thickness_dzt_min_init	2.0	5.0

ocean_topog_nml	CMIP6	O025
min_thickness	25.0	0.001

ocean_tracer_advect_nml	CMIP6	O025
advect_sweby_all	True	False

ocean_tracer_nml	CMIP6	O025
use_tempsalt_check_range	False	True

ocean_vert_kpp_mom4p1_nml	CMIP6	O025
do_langmuir	True	False
do_langmuir_cvmix	True	False
smooth_blmc	True	False
smooth_ri_kmax_eq_kmu	False	True

ocean_vert_mix_nml	CMIP6	O025
afkph_00	0.65	0.55
afkph_90	0.75	0.55
bryan_lewis_lat_depend	True	False
dfkph_00	1.15	1.05
dfkph_90	0.95	1.05
j09_diffusivity	True	False
vert_diff_back_via_max	False	True

ocean_vert_tidal_nml	CMIP6	O025
decay_scale	300.0	500.0
drag_dissipation_use_cdbot	False	True
drhodz_min	1e-12	1e-10
roughness_scale	20000.0	12000.0
shelf_depth_cutoff	160.0	-1000.0

[aekiss]

Here's TOPO5 - this increases edited depths in Baltic from 31 to 35.3634m and removes any shallower sills in the outlet channel. I was going for 35m but the script adjusted it, I guess due to constraints on how partial a partial cell can be.
/g/data/ik11/inputs/access-om2/input_20211125_025deg_topog/mom_025deg/topog.nc

[AndyHoggANU]

It seems that we have finally managed to walk the tightrope successfully at the 5th attempt of Baltic bulldozing ...

The figure below shows Baltic salinity (noting that I have switched to showing the surface salinity for comparison with CM2 diagnostics) and Baltic salinity restoring for all the cases we have tried so far. Restoring is close to balanced and salinity matches the initial condition pretty well -- certainly better than all previous attempts.

@MartinDix -- I think this is worth a try in ACCESS-CM2-025. What do you think?

---

AK edit: for reference, this was the run
/g/data/ik11/outputs/access-om2-025/025deg_jra55_iaf_omip_straits_topo5_cycle1
which used
/g/data/ik11/inputs/access-om2/input_20211125_025deg_topog/mom_025deg/topog.nc
created by
https://github.com/COSIMA/make_025deg_topo/tree/b646df8
with these edits in the Baltic.

[MartinDix]

@AndyHoggANU Looks good!

Can I start from the same initial state as before? Was using /g/data/ik11/inputs/access-om2/input_20201102/mom_025deg/ocean_temp_salt.res.nc

[AndyHoggANU]

Yep - we still want to start from the same state. I believe that the restart file you used before is filled to the bottom with the deepest value of T/S. @aekiss - can you confirm that?

[MartinDix]

Plotting it shows no missing values at the bottom.

[AndyHoggANU]

In that case -- I would go for it with that initial condition.

[micaeljtoliveira]

I'm currently looking into the issue with the land mask around the Antarctic coast (@aekiss thought this could be a good exercise to get more familiar with the way how the topography is generated).

If I understand correctly, it seems there are three things that can/should be fixed:

1. some cells should be land according to the new topography, but are currently marked as water
2. some cells should be water according to the new topography, but are currently marked as land
3. the grid does not extends South enough to include all the water.

Issues 1. and 2. should be relatively easy to fix, but 3. is more complicated. Furthermore, @aekiss suggested that fixing 1. might be enough. Any comments?

[ofa001]

Yes @micaeljtoliveira item 1 is causing instabilities in the coupled model so is the highest priority, as ice shelves have been labelled as shallow water in the current topography.

3 has probably been occurred as a choice has been made to the southernmost latitude in the grid and a cut off of the large (Ross and Ronnie Filchner) ice shelves has been made at those latitudes it may also have had been due to time stepping constraints.

Future changes in the grid will then involve changes to the land mask in the coupled ACCESS-CM2-025 versions that would use the updated topography, but @MartinDix has said they are relative easy to implement.

[micaeljtoliveira]

@ofa001 Thanks for the comments.

Last week I created a separate issue #265 to track the progress on fixing the land mask. This issue here is getting quite long, so I suggest we move the discussion to the new issue.

[ofa001]

@micaeljtoliveira Yes I spotted it so I was surprised you were back in this thread.

[access-hive-bot]

This issue has been mentioned on ACCESS Hive Community Forum. There might be relevant details there:

https://forum.access-hive.org.au/t/bathymetry-for-ocean-model-at-any-resolution/462/8

[access-hive-bot]

This issue has been mentioned on ACCESS Hive Community Forum. There might be relevant details there:

https://forum.access-hive.org.au/t/bathymetry-for-ocean-model-at-any-resolution/462/11

[aekiss]

There are a couple of other points causing occasional problems in ACCESS-CM2-025 in the Shelekhov Gulf (high salinity) and Weddell Sea (excessive ice thickness)
COSIMA/access-om3#139 (comment)
COSIMA/access-om3#139 (comment)
COSIMA/access-om3#139 (comment)

[access-hive-bot]

This issue has been mentioned on ACCESS Hive Community Forum. There might be relevant details there:

https://forum.access-hive.org.au/t/g-data-ik11-cleanup/2153/14