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<p style="margin-top:0;margin-bottom:0">Hi Martin,</p>
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<p style="margin-top:0;margin-bottom:0">No, I never figured this out. For now I've settled on using hFacMinDr=20 even though that means the partial cells don't do very much in the cavity.</p>
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<p style="margin-top:0;margin-bottom:0">Cheers,</p>
<p style="margin-top:0;margin-bottom:0">Kaitlin</p>
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<div>Dr Kaitlin Naughten</div>
<div>British Antarctic Survey</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> MITgcm-support <mitgcm-support-bounces@mitgcm.org> on behalf of Martin Losch <Martin.Losch@awi.de><br>
<b>Sent:</b> 18 December 2018 12:42:05<br>
<b>To:</b> MITgcm Support<br>
<b>Subject:</b> Re: [MITgcm-support] Tracer instabilities when I reduce hFacMinDr</font>
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<div class="PlainText">Did you get anywhere with this?<br>
<br>
Martin<br>
<br>
> On 30. Oct 2018, at 17:15, Naughten, Kaitlin A. <kaight@bas.ac.uk> wrote:<br>
> <br>
> Hi Spencer,<br>
> <br>
> Thanks for your email. It's good to know that instabilities can result from too-deep bathymetry. However, I did actually check for that at the grid generation stage - and also, the bathymetry in this region is nowhere near the deepest in the domain. Thanks
anyway!<br>
> <br>
> All the best,<br>
> Kaitlin<br>
> From: MITgcm-support <mitgcm-support-bounces@mitgcm.org> on behalf of C Spencer Jones <csjones@ucsd.edu><br>
> Sent: 30 October 2018 15:51:08<br>
> To: mitgcm-support@mitgcm.org<br>
> Subject: Re: [MITgcm-support] Tracer instabilities when I reduce hFacMinDr<br>
> <br>
> Hi Kaitlin, <br>
> I had a similar problem, but with the Prather advection scheme, when the maximum bathymetry depth exceeded the sum of the cell depths (these often have pretty similar values). I found that reducing the maximum depth of my bathymetry by a couple of meters
solved the problem. Maybe that is worth a try?<br>
> Thanks, <br>
> Spencer<br>
> <br>
> On Tue, 30 Oct 2018 at 11:20, Naughten, Kaitlin A. <kaight@bas.ac.uk> wrote:<br>
> Hi again,<br>
> <br>
> The three simulations I tried yesterday (decrease timestep even more, increase vertical viscosity, increase vertical diffusivity) all showed similar instabilities as before. Also, increasing the (horizontal) Leith viscosity doesn't fix the problem. I can't
easily increase the horizontal diffusivities as these are set by GM. <br>
> <br>
> Could GM be part of the problem here? Or Leith? Clearly it's something to do with the thinner partial cells, but I think I've ruled out a simple CFL error...<br>
> <br>
> Please let me know if you can think of anything else!<br>
> <br>
> Many thanks,<br>
> Kaitlin<br>
> From: MITgcm-support <mitgcm-support-bounces@mitgcm.org> on behalf of Naughten, Kaitlin A. <kaight@bas.ac.uk><br>
> Sent: 29 October 2018 11:34:26<br>
> To: MITgcm Support<br>
> Subject: Re: [MITgcm-support] Tracer instabilities when I reduce hFacMinDr<br>
> <br>
> Hi Martin,<br>
> <br>
> Thanks so much for your ideas. I'm waiting on the results of some simulations, but I'll respond to what I can now:<br>
> <br>
> • advcfl_W_hf_max and advcfl_wvel_max are the same for every monitor output. Is this normal/okay? For my simulations with hFacMinDr=20, they are usually very slightly different.<br>
> • The instabilities mostly happen on the side of a trough. It's not the steepest side of the trough, and not as steep as many other parts of the domain. So, I don't think there is any correlation with steep or rough bathymetry. But, this trough is
a region of strong sea ice formation, so maybe that's causing strong downslope flows.<br>
> • I also see no correlation with the transition from minimum 5m to minimum >5m. The instability is well within the region with vertical resolution 25m, so 5m is the smallest allowable partial cell.<br>
> • I looked at the vertical structure and the instabilities seem to be coming from the bottom partial cells, especially water columns where that cell is 5m. They spread 1-2 cells in each direction (both vertical and horizontal) but the worst values
are clearly in the bottom. So, that seems to suggest vertical CFL errors.<br>
> <br>
> I've started a few simulations as tests:<br>
> • Decrease timestep by a factor of 10 compared to my original simulations with hFacMinDr=20 (rather than a factor of 4)<br>
> • Increase vertical viscosity (viscAr) by a factor of 10<br>
> • Increase vertical diffusivities (diffKrT and diffKrS) by a factor of 10<br>
> <br>
> Hopefully I will have some results tomorrow.<br>
> <br>
> All the best,<br>
> Kaitlin<br>
> From: MITgcm-support <mitgcm-support-bounces@mitgcm.org> on behalf of Martin Losch <Martin.Losch@awi.de><br>
> Sent: 28 October 2018 10:32:04<br>
> To: MITgcm Support<br>
> Subject: Re: [MITgcm-support] Tracer instabilities when I reduce hFacMinDr<br>
> <br>
> Hi Kailin,<br>
> <br>
> this looks like a difficult problem to solve. Here are my ad-hoc ideas:<br>
> <br>
> The unphysically negative temperatures are most likely just the consequence of your instability and then the flux-limiters (which are never perfect) can’t help. They end to mask problems in the initial state, which is not helpful either. Maybe you want to
try a non-flux-limited scheme to see where the problem starts.<br>
> <br>
> When you checked the clf-numbers, did you also check advcfl_W_hf_max? In contrast to advcfl_wvel_max, this number takes into account the hFacC (so it will be larger for smaller hFacC, i.e. hFacMinDr)?<br>
> Also are your instabilities correlated (in space) with rough or steep topography?<br>
> <br>
> The minimum cell thickness is computed like this (as you probably already know):<br>
> MAX( hFacMin, MIN(hFacMinDr*recip_drF(k),oneRL) )<br>
> so that for thin cells (10m) you’ll have a minimum thickness of 5m, but for thicker cells you’ll have drF*hFacMin, which is larger than 5m for drF>50m. Does this tansition have anything to do with your instability pattern?<br>
> <br>
> Did you have look at the vertical structure of your instabilities. Often not only the horizontal but also the vertical viscosity/diffusivity can cause cfl-like problems.<br>
> <br>
> What happens if you decrease your time step even further? Does the problem go away?<br>
> Try larger viscosities (for momentum) …<br>
> <br>
> Martin<br>
> <br>
> <br>
> > On 24. Oct 2018, at 12:47, Naughten, Kaitlin A. <kaight@bas.ac.uk> wrote:<br>
> > <br>
> > Hi everyone,<br>
> > <br>
> > I'm currently running an ice shelf configuration with hFacMin=0.1, hFacMinDr=20, and vertical resolution ranging from 10 m (top few layers) to 25 m (in the cavity) to 100+ m (deep ocean). I'm trying to decrease hFacMinDr so I can get a better representation
of the ice shelf base, as the current value of 20 m combined with the 25 m resolution in the cavity doesn't allow the partial cells to do very much.<br>
> > <br>
> > I'm trying to get hFacMinDr=5 working. I expected to have to reduce the timestep to prevent vertical CFL errors, and at this point I have reduced the timestep by a factor of 4 (which should exactly compensate for the thinner cells, given the CFL criterion
is linear, correct?) However, the simulation still looks very strange, in particular the bottom water temperature and salinity in a few patches on the continental shelf (not in the cavity): it looks like checkerboard instabilities or false extrema, even though
I'm using a flux-limited advection scheme (33). In some cells, the temperature goes down to -7 C.<br>
> > <br>
> > I checked the CFL terms in the monitor output, and the vertical terms are on the order of 1e-2. This is similar to my previous simulations with hFacMinDr=20. and timestep 4 times larger. So, why am I still seeing these instabilities? Are they still CFL
errors (despite what the monitor terms seem to suggest) or could they be something else?<br>
> > <br>
> > I am using the linear free surface until I find a stable timestep for hFacMinDr=5, so we can rule out any problems related to nonlinear free surface or r*.<br>
> > <br>
> > Many thanks,<br>
> > Kaitlin Naughten<br>
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