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Hi You-Kun,
<div class=""><br class="">
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<div class="">I’ve actually never used the offline code, so I’m not certain. I believe that deltaToffline is the time step used by the model to select the correct velocity file, while delaTtracer is the time step used to advect the tracer in the flow field.</div>
<div class=""><br class="">
</div>
<div class="">But, you might find the answers you’re looking for here: <a href="http://mitgcm.org/public/r2_manual/final/online_documents/node170.html" class="">http://mitgcm.org/public/r2_manual/final/online_documents/node170.html</a></div>
<div class=""><br class="">
</div>
<div class="">These are the example experiments using the offline code. They haven’t been translated from the old documentation yet, so if you only looked at read the docs, you might have missed them.</div>
<div class=""><br class="">
</div>
<div class="">Cheers,</div>
<div class="">Ed</div>
<div class=""><br class="">
<div class="">
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Doddridge</b><br class="">
<i class="">Postdoctoral researcher</i></font></span></font></span></font></span></span></div>
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<div><br class="">
<blockquote type="cite" class="">
<div class="">On 30 May 2019, at 12:38, 钱钰坤 <<a href="mailto:qianyk@mail3.sysu.edu.cn" class="">qianyk@mail3.sysu.edu.cn</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="">Hi Edward,</div>
<div class=""><br class="">
</div>
<div class="">Thanks very much for your reminding. After searching for the 'cfl' stuff in STDOUT, I found indeed</div>
<div class="">that the CFL condition is violated by using deltaTtracer=86400. So I need to reduce this parameter.</div>
<div class=""><br class="">
</div>
<div class="">I am now confused that how does this parameter (and deltaTClock) in data file relate to my daily</div>
<div class="">velocity data and deltaToffline=3600 set in data.off? Can this parameter be adjusted at will without</div>
<div class="">any constraint in my OffLine Run?</div>
<div class=""><sign signid="0" class="">
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------------------</div>
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<div class=""><font size="2" class="">Best regards <br class="">
<br class="">
Yu-Kun Qian (钱钰坤) <br class="">
Center for Monsoon and Environment Research</font> </div>
<font size="2" class="">Department of Atmospheric Sciences<br class="">
School of Environmental Science and Engineering<font size="2" class=""> <br class="">
</font>Sun Yat-sen University <br class="">
No. 135 Xingang West Road, Haizhu District <br class="">
Guangzhou, 510275, P.R. China <br class="">
Tel; 020-84115227 <br class="">
Email: <a href="mailto:qianyk@mail2.sysu.edu.cn" class="">qianyk@mail3.sysu.edu.cn</a>
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<div id="menu_sender" class=""><b class="">发件人:</b> "Edward W Doddridge"<<a href="mailto:ewd@mit.edu" class="">ewd@mit.edu</a>>;</div>
<div class=""><b class="">发送时间:</b> 2019年5月30日(星期四) 晚上10:06</div>
<div class=""><b class="">收件人:</b> "<a href="mailto:mitgcm-support@mitgcm.org" class="">mitgcm-support@mitgcm.org</a>"<<a href="mailto:mitgcm-support@mitgcm.org" class="">mitgcm-support@mitgcm.org</a>>;
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<div class=""><b class="">主题:</b> Re: [MITgcm-support] nondivergent flow advecting a tracer</div>
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Hi Yu-Kun,
<div class=""><br class="">
</div>
<div class="">I suspect that your timestep violates the cfl stability criterion. You should check that deltaTtracer*velocity/grid_spacing is less than 1. Ideally you’d like it to be much less than 1.</div>
<div class=""><br class="">
</div>
<div class="">Cheers,</div>
<div class="">Ed</div>
<div class=""><br class="">
<div class="">
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<span class="Apple-style-span" style="font-family: Tahoma; font-size: 13px;"><font face="Tahoma" size="2" class=""><span dir="ltr" style="font-size: 10pt;" class=""><font size="1" class=""><span style="font-size: 13px;" class=""><font size="2" class=""><b class="">Edward
Doddridge</b><br class="">
<i class="">Postdoctoral researcher</i></font></span></font></span></font></span></span></div>
<div style="font-family: Palatino; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
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<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On 30 May 2019, at 09:48, 钱钰坤 <<a href="mailto:qianyk@mail3.sysu.edu.cn" class="">qianyk@mail3.sysu.edu.cn</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="">Hi all,</div>
<div class=""><br class="">
</div>
<div class="">I am using a series of geostrophic velocity data (derived from AVISO sea surface height)</div>
<div class="">to advect a passive tracer in an offline mode. Following the paper by Abernathey and Marshall</div>
<div class="">(2013, JGR), first I made a nondivergent correction to the original geostrophic velocity data</div>
<div class="">through Helmholtz Decomposition. Then I used the nondivergent velocity to advect a tracer.</div>
<div class="">However, after a few timesteps the tracer field is unstable and generates very large values and</div>
<div class="">eventually contaminated the results.</div>
<div class=""><br class="">
</div>
<div class="">I think there are two things need to be verified.</div>
<div class=""><br class="">
</div>
<div class="">First, the correction is done correctly. Actually</div>
<div class="">I followed the guidance by Ryan Abernathey at:</div>
<div class=""> <a href="https://github.com/rabernat/mitgcm_2D_global/blob/master/notebooks/correction.ipynb" class="">
https://github.com/rabernat/mitgcm_2D_global/blob/master/notebooks/correction.ipynb</a></div>
<div class="">I run the offline model first using original geostrophic velocity to dump the diagnostics of streamfunction</div>
<div class="">(psi) and velocity potential (phi). Then I use the xmitgcm utility to calculate the nondivergent velocity as:</div>
<div class="">
<div class=""> u_psi = -(numpy.roll(psi, -1, axis=-2) - psi) / dyG / drF</div>
<div class=""> v_psi = (numpy.roll(psi, -1, axis=-1) - psi) / dxG / drF</div>
</div>
<div class="">This code above should be modified somewhat if one uses the latest xmitgcm released a few days ago.</div>
<div class="">I did not do any mask since I think the MITgcm model will mask the velocity when run in offline mode (</div>
<div class="">I provided a bathymetry data to the model generated based on AVISO SSH land-sea mask).</div>
<div class=""><br class="">
</div>
<div class="">Second, the offline model parameters (delta-t related) are correctly set. Although I've read some emails</div>
<div class="">on this issue, I'm still not so sure how to set these parameters. The following are my choices:</div>
<div class=""> data: deltaTtracer = 86400,</div>
<div class=""> deltaTClock = 86400,</div>
<div class=""> data.off: deltaToffline = 3600, (smaller dt for accuracy)</div>
<div class=""> offlineForcingPeriod = 86400, (AVISO data is daily mean)</div>
<div class=""> offlineForcingCycle = 0, (no need to reuse the velocity)</div>
<div class="">When using the above params, the offline model asks for velocity data whose names are: u.0.data, u.24.data,</div>
<div class="">u.48.data... So I rename the velocity data into this convention.</div>
<div class=""><br class="">
</div>
<div class="">Now I am really confused why the tracer overflows after only 4-5 timesteps (days). Is there anything wrong</div>
<div class="">with the above two procedures?</div>
<div class="">
<div style="color:#909090;font-family:Arial Narrow;font-size:12px" class=""><br class="">
<br class="">
------------------</div>
<div style="font-size: 14px; font-family: Verdana;" class="">
<div class=""><font size="2" class="">Best regards <br class="">
<br class="">
Yu-Kun Qian (钱钰坤) <br class="">
Center for Monsoon and Environment Research</font> </div>
<font size="2" class="">Department of Atmospheric Sciences<br class="">
School of Environmental Science and Engineering<font size="2" class=""> <br class="">
</font>Sun Yat-sen University <br class="">
No. 135 Xingang West Road, Haizhu District <br class="">
Guangzhou, 510275, P.R. China <br class="">
Tel; 020-84115227 <br class="">
Email: <a href="mailto:qianyk@mail2.sysu.edu.cn" class="">qianyk@mail3.sysu.edu.cn</a>
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