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Perhaps you can clarify this a bit by adding something indicating the water Depth to your plots? It looks to me like you have set a Gaussian temperature fill, but the topography is actually just a straight cylinder at the edges.</div>
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If that is true, then the fact that the water extends downwards is just convection because you have dense water over lighter (assuming you are using a non-linear equation of state). </div>
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I’m also confused by your Y axis only going from -3400 to -3150, whereas you specify YC from -3400 to +3400. </div>
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In all, I suspect you have gotten your dimensions confused, and have not set the bathymetry up the way you intended. </div>
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Cheers, Jody</div>
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<b>From: </b>MITgcm-support <mitgcm-support-bounces@mitgcm.org> on behalf of Fateme Sharifi <fateme.sharifi1391@gmail.com><br>
<b>Date: </b>Sunday, August 31, 2025 at 10:49 PM<br>
<b>To: </b>MITgcm-support@mitgcm.org <MITgcm-support@mitgcm.org><br>
<b>Subject: </b>[MITgcm-support] RBCS extending to bottom & shelf dry points in lake setup<br>
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<p dir="ltr" class="ms-outlook-mobile-reference-message skipProofing">Dear MITgcm users,</p>
<p dir="ltr" class="ms-outlook-mobile-reference-message skipProofing">I am setting up a small lake experiment with
<b>Gaussian bathymetry, a dry shelf band, and a shallow “moat” region (within 400 m of shoreline, depth ≤ 5 m) where I apply RBCS restoring toward 4 °C</b>.</p>
<p dir="ltr" class="ms-outlook-mobile-reference-message skipProofing">My input files are generated with a MATLAB script (attached) that writes:</p>
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<code>Depth.bin</code> (outside/shelf = 0 m),</p>
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<code>hFacC.bin</code> with proper partial cells,</p>
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<p dir="ltr" class="ms-outlook-mobile-reference-message skipProofing" role="presentation">
<code>rbcs_mask.bin</code> limited to shallow moat layers only (z_mid ≤ moat_depth, hFacC > 0),</p>
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<p dir="ltr" class="ms-outlook-mobile-reference-message skipProofing" role="presentation">
<code>rbcs_Tr1_fld.bin</code> set to 4 °C inside the mask.</p>
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<p dir="ltr" class="ms-outlook-mobile-reference-message skipProofing">At model start (<code>t=1</code>), the RBCS mask behaves correctly (restricted to the top ~5 m near the boundary). However, after just 2–3 timesteps, the RBCS influence appears to extend
vertically to the bottom (see attached figure with Y–Z sections at t=1 and t=3). This was unexpected because the written
<code>rbcs_mask.bin</code> only has ones in shallow moat layers.</p>
<p dir="ltr" class="ms-outlook-mobile-reference-message skipProofing">I also noticed some sensitivity to shelf dry points: despite setting
<code>Depth=0</code> and checking that <code>hFacC=0</code> in the shelf region, I worry that something in RBCS or partial cells may be activating those points during runtime.</p>
<p dir="ltr" class="ms-outlook-mobile-reference-message skipProofing"><b>My questions:</b></p>
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Has anyone seen RBCS restoring “leak” into deeper layers, even if the input mask is strictly shallow?</p>
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Is there an additional runtime parameter (e.g. in <code>data.rbcs</code> or <code>
data</code>) needed to prevent the restoring from being applied throughout the column?</p>
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<p dir="ltr" class="ms-outlook-mobile-reference-message skipProofing" role="presentation">
What is the recommended way to guarantee that RBCS remains limited to the intended top layers throughout the run (not just in the input mask)?</p>
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<p dir="ltr" class="ms-outlook-mobile-reference-message skipProofing" role="presentation">
Any best practices for handling dry shelf points with RBCS in lakes or enclosed basins?</p>
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<p dir="ltr" class="ms-outlook-mobile-reference-message skipProofing">I have attached both my MATLAB setup script (<code>setup_gaussian_lake_rbcs_revised_v2.m</code>) and the figure (<code>vertical_section_temperature.jpg</code>).</p>
<p dir="ltr" class="ms-outlook-mobile-reference-message skipProofing">Best regards,</p>
<div dir="ltr" class="gmail_signature">Fatemeh Sadat Sharifi<br>
Ph.D. Candidate at<br>
The Leibniz Institute of Freshwater</div>
<div dir="ltr" class="gmail_signature"> Ecology and Inland Fisheries (IGB)</div>
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