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<div><span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">Hi Paul,</span></div>
<div class="elementToProof"><span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);"><br>
</span></div>
<div class="elementToProof"><span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">Great if it helps. However, I am not sure why there should have a negative on the RHS
of (A4)?</span></div>
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</span></div>
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</span></div>
<div class="elementToProof"><span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">Sandy<br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>De :</b> MITgcm-support <mitgcm-support-bounces@mitgcm.org> de la part de Burns, Paul <P.Burns2@exeter.ac.uk><br>
<b>Envoyé :</b> mardi 12 décembre 2023 05:51<br>
<b>À :</b> MITgcm-support@mitgcm.org <MITgcm-support@mitgcm.org><br>
<b>Objet :</b> Re: [MITgcm-support] Vertical diffusion for non-hydrostatic ocean model with a stretched grid</font>
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Hi Sandy,</div>
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Yes that is very clear now, many thanks for your help. </div>
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It appears that (A4) should have a negative on the RHS, but otherwise it makes sense to me. </div>
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Cheers,</div>
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Paul</div>
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<div><span style="font-family:Calibri,sans-serif; font-size:14.6667px; color:rgb(12,100,192); background-color:rgb(255,255,255)"><u> </u></span></div>
<div><span style="font-family:Calibri,sans-serif; font-size:14.6667px; color:rgb(23,78,134); background-color:rgb(255,255,255)">Dr Paul Burns MInstP FRMetS</span></div>
<div><span style="font-family:Calibri,sans-serif; font-size:14.6667px; color:rgb(23,78,134)">Associate Research Fellow</span></div>
<div><span style="font-family:Calibri,sans-serif; font-size:14.6667px; color:rgb(23,78,134)">& </span></div>
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<span style="font-size:11pt; color:rgb(23,78,134)">Atmospheric Processes and Parametrisation (APP)</span></div>
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<span style="font-size:11pt; color:rgb(23,78,134)">Met Office</span></div>
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<span style="font-size:11pt; color:rgb(23,78,134)">Exeter</span></div>
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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> MITgcm-support <mitgcm-support-bounces@mitgcm.org> on behalf of Gregorio Sandy <Sandy.Gregorio@uqar.ca><br>
<b>Sent:</b> 11 December 2023 15:31<br>
<b>To:</b> mitgcm-support@mitgcm.org <mitgcm-support@mitgcm.org><br>
<b>Subject:</b> Re: [MITgcm-support] Vertical diffusion for non-hydrostatic ocean model with a stretched grid</font>
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Hi Paul,</div>
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I used the paper of Winters and Seim (2000) to derive the coefficient as a function of N2, their equation A6. By extracting the factor |S| and considering a Prandtl number of order 1, you find an expression of the coefficient as a function of the Richardson
number (you can look at the paper of Kirkpatrick et al. (2006), their equations 18 and 19).</div>
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I hope it clarifies what I did.</div>
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Cheers,</div>
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Sandy<br>
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<div id="x_x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>De :</b> MITgcm-support <mitgcm-support-bounces@mitgcm.org> de la part de Burns, Paul <P.Burns2@exeter.ac.uk><br>
<b>Envoyé :</b> lundi 11 décembre 2023 04:10<br>
<b>À :</b> MITgcm-support@mitgcm.org <MITgcm-support@mitgcm.org><br>
<b>Objet :</b> Re: [MITgcm-support] Vertical diffusion for non-hydrostatic ocean model with a stretched grid</font>
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Hi Sandy,</div>
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No problem and thanks for clarifying. </div>
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It seemed from a first look at your code that you used N^2 rather than a function of the Richardson number and so I wondered if you could provide a reference that explains your approach?</div>
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Many thanks,</div>
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Paul</div>
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<div><span style="font-family:Calibri,sans-serif; font-size:14.6667px; color:rgb(12,100,192); background-color:rgb(255,255,255)"><u> </u></span></div>
<div><span style="font-family:Calibri,sans-serif; font-size:14.6667px; color:rgb(23,78,134); background-color:rgb(255,255,255)">Dr Paul Burns MInstP FRMetS</span></div>
<div><span style="font-family:Calibri,sans-serif; font-size:14.6667px; color:rgb(23,78,134)">Associate Research Fellow</span></div>
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<span style="font-size:11pt; color:rgb(23,78,134)">Atmospheric Processes and Parametrisation (APP)</span></div>
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<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="x_x_x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> MITgcm-support <mitgcm-support-bounces@mitgcm.org> on behalf of Gregorio Sandy <Sandy.Gregorio@uqar.ca><br>
<b>Sent:</b> 11 December 2023 02:11<br>
<b>To:</b> mitgcm-support@mitgcm.org <mitgcm-support@mitgcm.org><br>
<b>Subject:</b> Re: [MITgcm-support] Vertical diffusion for non-hydrostatic ocean model with a stretched grid</font>
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Hi Paul,</div>
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<br>
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<div class="x_x_x_x_elementToProof"><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">I tested the 3D scheme with the default values for smag3D_coeff and smag3D_diffCoeff, that
is smag3D_coeff=1.E-2 and smag3D_diffCoeff=0. I also tried smag3D_coeff=5.E-2. In the end, I decided not to use Smagorinsky for my experiments. Thus I cannot guarantee that these values are suitable for your setup.<br>
</span></div>
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</span></div>
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<div id="x_x_x_x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>De :</b> MITgcm-support <mitgcm-support-bounces@mitgcm.org> de la part de Burns, Paul <P.Burns2@exeter.ac.uk><br>
<b>Envoyé :</b> samedi 9 décembre 2023 07:40<br>
<b>À :</b> MITgcm-support@mitgcm.org <MITgcm-support@mitgcm.org><br>
<b>Objet :</b> Re: [MITgcm-support] Vertical diffusion for non-hydrostatic ocean model with a stretched grid</font>
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Hi Sandy,</div>
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Since you've already used the 3D scheme, can I ask if you also determined values for:</div>
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<span style="letter-spacing:normal; font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt; font-weight:400; color:black">smag3Ddiff_coeff</span></div>
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<span style="letter-spacing:normal; font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt; font-weight:400; color:black"><br>
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<span style="letter-spacing:normal; font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt; font-weight:400; color:black">Many thanks,</span></div>
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<span style="letter-spacing:normal; font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt; font-weight:400; color:black">Paul</span></div>
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<div><span style="font-family:Calibri,sans-serif; font-size:14.6667px; color:rgb(12,100,192); background-color:rgb(255,255,255)"><u> </u></span></div>
<div><span style="font-family:Calibri,sans-serif; font-size:14.6667px; color:rgb(23,78,134); background-color:rgb(255,255,255)">Dr Paul Burns MInstP FRMetS</span></div>
<div><span style="font-family:Calibri,sans-serif; font-size:14.6667px; color:rgb(23,78,134)">Associate Research Fellow</span></div>
<div><span style="font-family:Calibri,sans-serif; font-size:14.6667px; color:rgb(23,78,134)">& </span></div>
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<div id="x_x_x_x_x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Burns, Paul <P.Burns2@exeter.ac.uk><br>
<b>Sent:</b> 08 December 2023 13:49<br>
<b>To:</b> mitgcm-support@mitgcm.org <mitgcm-support@mitgcm.org><br>
<b>Subject:</b> Re: [MITgcm-support] Vertical diffusion for non-hydrostatic ocean model with a stretched grid</font>
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Hi Sandy,</div>
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That's a great help! </div>
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I will try your code and should our work get published I'll happily include your contribution. </div>
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Many thanks, </div>
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Paul</div>
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<div><span style="font-family:Calibri,sans-serif; font-size:14.6667px; color:rgb(23,78,134); background-color:rgb(255,255,255)">Dr Paul Burns MInstP FRMetS</span></div>
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<div id="x_x_x_x_x_x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> MITgcm-support <mitgcm-support-bounces@mitgcm.org> on behalf of Gregorio Sandy <Sandy.Gregorio@uqar.ca><br>
<b>Sent:</b> 08 December 2023 13:37<br>
<b>To:</b> mitgcm-support@mitgcm.org <mitgcm-support@mitgcm.org><br>
<b>Subject:</b> Re: [MITgcm-support] Vertical diffusion for non-hydrostatic ocean model with a stretched grid</font>
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<div class="x_x_x_x_x_x_x_elementToProof"><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">Hi Paul,</span></div>
<div><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)"><br>
</span></div>
<div class="x_x_x_x_x_x_x_elementToProof"><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">I computed the 3D Smagorinsky coefficient by accounting for the buoyancy last winter.
I attach the files mom_calc_smag_3d.F, mom_diagnostics_init.F, MOM_COMMON_OPTIONS.h and CPP_OPTIONS.h. In CPP_OPTIONS.h, I defined a flag to include or not the buoyancy in the calculation of the 3D Smagorinsky coefficient.</span></div>
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<div><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">I hope it helps.</span></div>
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<div><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">Cheers,</span></div>
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<div id="x_x_x_x_x_x_x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>De :</b> MITgcm-support <mitgcm-support-bounces@mitgcm.org> de la part de Burns, Paul <P.Burns2@exeter.ac.uk><br>
<b>Envoyé :</b> vendredi 8 décembre 2023 08:34<br>
<b>À :</b> mitgcm-support@mitgcm.org <mitgcm-support@mitgcm.org><br>
<b>Objet :</b> Re: [MITgcm-support] Vertical diffusion for non-hydrostatic ocean model with a stretched grid</font>
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Hi Martin,</div>
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Ok that is great. I'll have a go and get back to you. </div>
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Many thanks,</div>
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Paul</div>
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<div><span style="font-family:Calibri,sans-serif; font-size:14.6667px; color:rgb(23,78,134); background-color:rgb(255,255,255)">Dr Paul Burns MInstP FRMetS</span></div>
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<div id="x_x_x_x_x_x_x_x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> MITgcm-support <mitgcm-support-bounces@mitgcm.org> on behalf of Martin Losch <Martin.Losch@awi.de><br>
<b>Sent:</b> 08 December 2023 12:46<br>
<b>To:</b> MITgcm Support <mitgcm-support@mitgcm.org><br>
<b>Subject:</b> Re: [MITgcm-support] Vertical diffusion for non-hydrostatic ocean model with a stretched grid</font>
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<div>Hi Paul,
<div><br>
</div>
<div>if you need that functionality, it should be relatively easy for you to add:</div>
<div>- in the header file “DYNVARS.h”, there’s already the global sigmaRfield, just need to change/remove the CPP-flags</div>
<div>- velocities are available via DYNVARS.h, too, so that it should be straightforward to compute N2/dVdz from that, similarly to what’s done in pkg/ggl90/ggl90_calc.F</div>
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<div>Martin</div>
<div>
<div><br>
<blockquote type="cite">
<div>On 8. Dec 2023, at 12:55, Burns, Paul <P.Burns2@exeter.ac.uk> wrote:</div>
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<span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt">Ok that's easier then. I believe the Richardson number function could be added to the code where the Smagorinsky viscosity is computed at some
k-level in</span></div>
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<span style="font-family:Menlo; font-size:11px">mom_calc_smag_3d.F</span></div>
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<span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif">Many thanks,</span></div>
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<span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif">Paul</span></div>
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<div><span style="font-family:Calibri,sans-serif; font-size:14.6667px; color:rgb(12,100,192); background-color:rgb(255,255,255)"><u> </u></span></div>
<div><span style="font-family:Calibri,sans-serif; font-size:14.6667px; color:rgb(23,78,134); background-color:rgb(255,255,255)">Dr Paul Burns MInstP FRMetS</span></div>
<div><span style="font-family:Calibri,sans-serif; font-size:14.6667px; color:rgb(23,78,134)">Associate Research Fellow</span></div>
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<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt"><span style="font-size:11pt; color:rgb(23,78,134)">Exeter</span></div>
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<font face="Calibri, sans-serif" style="font-size:11pt"><b>From:</b><span class="x_x_x_x_x_x_x_x_x_Apple-converted-space"> </span>MITgcm-support <<a href="mailto:mitgcm-support-bounces@mitgcm.org">mitgcm-support-bounces@mitgcm.org</a>> on behalf of Martin Losch
<<a href="mailto:Martin.Losch@awi.de">Martin.Losch@awi.de</a>><br>
<b>Sent:</b><span class="x_x_x_x_x_x_x_x_x_Apple-converted-space"> </span>08 December 2023 10:49<br>
<b>To:</b><span class="x_x_x_x_x_x_x_x_x_Apple-converted-space"> </span>MITgcm Support <<a href="mailto:mitgcm-support@mitgcm.org">mitgcm-support@mitgcm.org</a>><br>
<b>Subject:</b><span class="x_x_x_x_x_x_x_x_x_Apple-converted-space"> </span>Re: [MITgcm-support] Vertical diffusion for non-hydrostatic ocean model with a stretched grid</font>
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<div>There are plenty of places, where Ri-numbers are computed, e.g. in pkg/ggl90/ggl90_calc.F, or even full routines, e.g. pkg/pp81/pp81_ri_number.F (although when that was written the vertical gradient of density SigmaRw as not availalbe).
<div><br>
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<div>In which routine would you need the Ri-number exactly?</div>
<div><br>
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<div>Martin<br id="x_x_x_x_x_x_x_x_x_x_lineBreakAtBeginningOfMessage">
<div><br>
<blockquote type="cite">
<div>On 8. Dec 2023, at 11:20, Burns, Paul <P.Burns2@exeter.ac.uk> wrote:</div>
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Hi Martin,</div>
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<span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt">A quick message to thank you for your help with this. I've found the fortran file where<span class="x_x_x_x_x_x_x_x_x_x_Apple-converted-space"> </span></span><span style="letter-spacing:normal; font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt; font-weight:400">smag3D_coeff</span></div>
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<span style="letter-spacing:normal; font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt; font-weight:400">(and smag3Ddiff_coeff) are used to compute the viscosity (diffusivity), so hopefully I can work through
the code and compare that with a relevant paper about using the Smagorinsky-Lilly model in the ocean to figure out what the values of<span class="x_x_x_x_x_x_x_x_x_x_Apple-converted-space"> </span></span><span style="letter-spacing:normal; font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:16px; font-weight:400; background-color:rgb(255,255,255)">smag3D_coeff</span><span style="letter-spacing:normal; font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt; font-weight:400"> and<span class="x_x_x_x_x_x_x_x_x_x_Apple-converted-space"> </span></span><span style="letter-spacing:normal; font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:16px; font-weight:400; background-color:rgb(255,255,255)">smag3Ddiff_coeff</span><span style="letter-spacing:normal; font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt; font-weight:400"> should
be in MITgcm. </span></div>
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</span></div>
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<span style="letter-spacing:normal; font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt; font-weight:400">It might be useful to add a Richardson number function to the existing 3D Smagorinsky model in MITgcm
to try and account for buoyancy effects, but not sure how tricky that will be. Mathematically it's straightforward. I'd need to pass relevant variables to calculate a local Richardson number and I'd need to first find a reasonable Richardson number function
for the ocean. Not sure if anyone has tried this already?</span></div>
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</span></div>
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<span style="letter-spacing:normal; font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt; font-weight:400">Cheers,</span></div>
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<span style="letter-spacing:normal; font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt; font-weight:400">Paul</span></div>
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<div><span style="font-family:Calibri,sans-serif; font-size:14.6667px; color:rgb(12,100,192); background-color:rgb(255,255,255)"><u> </u></span></div>
<div><span style="font-family:Calibri,sans-serif; font-size:14.6667px; color:rgb(23,78,134); background-color:rgb(255,255,255)">Dr Paul Burns MInstP FRMetS</span></div>
<div><span style="font-family:Calibri,sans-serif; font-size:14.6667px; color:rgb(23,78,134)">Associate Research Fellow</span></div>
<div><span style="font-family:Calibri,sans-serif; font-size:14.6667px; color:rgb(23,78,134)">& </span></div>
<div><span style="font-family:Calibri,Helvetica,sans-serif; font-size:11pt; color:rgb(23,78,134)">Senior Scientist</span></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt"><span style="font-size:11pt; color:rgb(23,78,134)">Atmospheric Processes and Parametrisation (APP)</span></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt"><span style="font-size:11pt; color:rgb(23,78,134)">Met Office</span></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt"><span style="font-size:11pt; color:rgb(23,78,134)">Exeter</span></div>
</div>
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<font face="Calibri, sans-serif" style="font-size:11pt"><b>From:</b><span class="x_x_x_x_x_x_x_x_x_x_Apple-converted-space"> </span>MITgcm-support <<a href="mailto:mitgcm-support-bounces@mitgcm.org">mitgcm-support-bounces@mitgcm.org</a>> on behalf of Martin
Losch <<a href="mailto:Martin.Losch@awi.de">Martin.Losch@awi.de</a>><br>
<b>Sent:</b><span class="x_x_x_x_x_x_x_x_x_x_Apple-converted-space"> </span>01 December 2023 06:51<br>
<b>To:</b><span class="x_x_x_x_x_x_x_x_x_x_Apple-converted-space"> </span>MITgcm Support <<a href="mailto:mitgcm-support@mitgcm.org">mitgcm-support@mitgcm.org</a>><br>
<b>Subject:</b><span class="x_x_x_x_x_x_x_x_x_x_Apple-converted-space"> </span>Re: [MITgcm-support] Vertical diffusion for non-hydrostatic ocean model with a stretched grid</font>
<div> </div>
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<span style="color:rgb(156,101,0); font-weight:bold">CAUTION:</span><span class="x_x_x_x_x_x_x_x_x_x_Apple-converted-space"> </span>This email originated from outside of the organisation. Do not click links or open attachments unless you recognise the sender
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<div>Hi Paul,
<div><br>
</div>
<div>I have no experience with the Smag3D code and don’t have any suggestions for setting the coefficients, but this is what I do to find code:</div>
<div><br>
</div>
<div>Compile the experiment that uses the code (here: tutorial_deep_convection), in fact, just the genmake2 and make depend steps are enough, then you have all necessary code in the build directory and you can grep for useSmag3D (or ALLOW_SMAG_3D). This gives
me:</div>
<div>
<div style="margin:0px; font-style:normal; font-variant-caps:normal; font-stretch:normal; font-size:11px; line-height:normal; font-family:Menlo; font-size-adjust:none; font-kerning:auto; font-variant-alternates:normal; font-variant-ligatures:normal; font-variant-numeric:normal; font-variant-east-asian:normal; font-feature-settings:normal">
<span style="font-variant-ligatures:no-common-ligatures">>> grep -i useSmag3D *.F</span></div>
<div style="margin:0px; font-style:normal; font-variant-caps:normal; font-stretch:normal; font-size:11px; line-height:normal; font-family:Menlo; font-size-adjust:none; font-kerning:auto; font-variant-alternates:normal; font-variant-ligatures:normal; font-variant-numeric:normal; font-variant-east-asian:normal; font-feature-settings:normal">
<span style="font-variant-ligatures:no-common-ligatures">calc_gw.F: IF ( useSmag3D .AND. k.GT.1 ) THEN</span></div>
<div style="margin:0px; font-style:normal; font-variant-caps:normal; font-stretch:normal; font-size:11px; line-height:normal; font-family:Menlo; font-size-adjust:none; font-kerning:auto; font-variant-alternates:normal; font-variant-ligatures:normal; font-variant-numeric:normal; font-variant-east-asian:normal; font-feature-settings:normal">
<span style="font-variant-ligatures:no-common-ligatures">config_check.F: IF ( useSmag3D ) THEN</span></div>
<div style="margin:0px; font-style:normal; font-variant-caps:normal; font-stretch:normal; font-size:11px; line-height:normal; font-family:Menlo; font-size-adjust:none; font-kerning:auto; font-variant-alternates:normal; font-variant-ligatures:normal; font-variant-numeric:normal; font-variant-east-asian:normal; font-feature-settings:normal">
<span style="font-variant-ligatures:no-common-ligatures">config_check.F: & 'Cannot set useSmag3D=TRUE when compiled with'</span></div>
<div style="margin:0px; font-style:normal; font-variant-caps:normal; font-stretch:normal; font-size:11px; line-height:normal; font-family:Menlo; font-size-adjust:none; font-kerning:auto; font-variant-alternates:normal; font-variant-ligatures:normal; font-variant-numeric:normal; font-variant-east-asian:normal; font-feature-settings:normal">
<span style="font-variant-ligatures:no-common-ligatures">config_check.F: & useSmag3D .AND. useCDscheme ) THEN</span></div>
<div style="margin:0px; font-style:normal; font-variant-caps:normal; font-stretch:normal; font-size:11px; line-height:normal; font-family:Menlo; font-size-adjust:none; font-kerning:auto; font-variant-alternates:normal; font-variant-ligatures:normal; font-variant-numeric:normal; font-variant-east-asian:normal; font-feature-settings:normal">
<span style="font-variant-ligatures:no-common-ligatures">config_check.F: IF ( useSmag3D .AND.</span></div>
<div style="margin:0px; font-style:normal; font-variant-caps:normal; font-stretch:normal; font-size:11px; line-height:normal; font-family:Menlo; font-size-adjust:none; font-kerning:auto; font-variant-alternates:normal; font-variant-ligatures:normal; font-variant-numeric:normal; font-variant-east-asian:normal; font-feature-settings:normal">
<span style="font-variant-ligatures:no-common-ligatures">config_summary.F: CALL WRITE_0D_L( useSmag3D, INDEX_NONE,</span></div>
<div style="margin:0px; font-style:normal; font-variant-caps:normal; font-stretch:normal; font-size:11px; line-height:normal; font-family:Menlo; font-size-adjust:none; font-kerning:auto; font-variant-alternates:normal; font-variant-ligatures:normal; font-variant-numeric:normal; font-variant-east-asian:normal; font-feature-settings:normal">
<span style="font-variant-ligatures:no-common-ligatures">config_summary.F: & 'useSmag3D =', ' /* Use isotropic 3-D Smagorinsky viscosity */')</span></div>
<div style="margin:0px; font-style:normal; font-variant-caps:normal; font-stretch:normal; font-size:11px; line-height:normal; font-family:Menlo; font-size-adjust:none; font-kerning:auto; font-variant-alternates:normal; font-variant-ligatures:normal; font-variant-numeric:normal; font-variant-east-asian:normal; font-feature-settings:normal">
<span style="font-variant-ligatures:no-common-ligatures">config_summary.F: IF ( useSmag3D )</span></div>
<div style="margin:0px; font-style:normal; font-variant-caps:normal; font-stretch:normal; font-size:11px; line-height:normal; font-family:Menlo; font-size-adjust:none; font-kerning:auto; font-variant-alternates:normal; font-variant-ligatures:normal; font-variant-numeric:normal; font-variant-east-asian:normal; font-feature-settings:normal">
<span style="font-variant-ligatures:no-common-ligatures">dynamics.F: IF ( useSmag3D ) THEN</span></div>
<div style="margin:0px; font-style:normal; font-variant-caps:normal; font-stretch:normal; font-size:11px; line-height:normal; font-family:Menlo; font-size-adjust:none; font-kerning:auto; font-variant-alternates:normal; font-variant-ligatures:normal; font-variant-numeric:normal; font-variant-east-asian:normal; font-feature-settings:normal">
<span style="font-variant-ligatures:no-common-ligatures">dynamics.F: IF ( useSmag3D ) THEN</span></div>
<div style="margin:0px; font-style:normal; font-variant-caps:normal; font-stretch:normal; font-size:11px; line-height:normal; font-family:Menlo; font-size-adjust:none; font-kerning:auto; font-variant-alternates:normal; font-variant-ligatures:normal; font-variant-numeric:normal; font-variant-east-asian:normal; font-feature-settings:normal">
<span style="font-variant-ligatures:no-common-ligatures">ini_parms.F: & viscC2leith, viscC4leith, smag3D_coeff, useSmag3D,</span></div>
<div style="margin:0px; font-style:normal; font-variant-caps:normal; font-stretch:normal; font-size:11px; line-height:normal; font-family:Menlo; font-size-adjust:none; font-kerning:auto; font-variant-alternates:normal; font-variant-ligatures:normal; font-variant-numeric:normal; font-variant-east-asian:normal; font-feature-settings:normal">
<span style="font-variant-ligatures:no-common-ligatures">ini_parms.F: IF ( smag3D_diffCoeff.NE.zeroRL .AND. .NOT.useSmag3D ) THEN</span></div>
<div style="margin:0px; font-style:normal; font-variant-caps:normal; font-stretch:normal; font-size:11px; line-height:normal; font-family:Menlo; font-size-adjust:none; font-kerning:auto; font-variant-alternates:normal; font-variant-ligatures:normal; font-variant-numeric:normal; font-variant-east-asian:normal; font-feature-settings:normal">
<span style="font-variant-ligatures:no-common-ligatures">ini_parms.F: & 'will not use "smag3D_diffCoeff" without useSmag3D'</span></div>
<div style="margin:0px; font-style:normal; font-variant-caps:normal; font-stretch:normal; font-size:11px; line-height:normal; font-family:Menlo; font-size-adjust:none; font-kerning:auto; font-variant-alternates:normal; font-variant-ligatures:normal; font-variant-numeric:normal; font-variant-east-asian:normal; font-feature-settings:normal">
<span style="font-variant-ligatures:no-common-ligatures">set_defaults.F: useSmag3D = .FALSE.</span></div>
<div style="margin:0px; font-style:normal; font-variant-caps:normal; font-stretch:normal; font-size:11px; line-height:normal; font-family:Menlo; font-size-adjust:none; font-kerning:auto; font-variant-alternates:normal; font-variant-ligatures:normal; font-variant-numeric:normal; font-variant-east-asian:normal; font-feature-settings:normal">
<span style="font-variant-ligatures:no-common-ligatures">set_parms.F: useSmag3D = momViscosity .AND. useSmag3D</span></div>
<div><br>
</div>
<div>You can probably figure out yourself, that the files starting with “ini_” or “config_”, “set_defaults/params.F” are only initialisation, and that calc_gw.F and dynamics.F are more interesting to you. In these files you’ll see that with this flag=Ture,
specific routines (e.g., MOM_W_SMAG_3D, MOM_CALC_3D_STRAIN, ...) are called which (probably) contain most of the code. Most of the time in MITgcm, a routine lives in a file with the same name (e.g., mom_w_smag_3d.F, if not you’d have to grep for it again).
This routine is linked from the source directory (pkg/mom_common).</div>
<div><br>
</div>
<div>Martin</div>
<div><br>
<blockquote type="cite">
<div>On 30. Nov 2023, at 20:07, Burns, Paul <P.Burns2@exeter.ac.uk> wrote:</div>
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Hi,</div>
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I've only recently come back to some work I started about a year ago about regional modelling in the Arctic ocean, having been distracted by a change of jobs. I received some useful advice from Jean-Michel about the two types of Smagorinsky scheme available
in MITgcm. I was advised to look at tutorial_deep_convection for details of the parameters that need setting when using the 3D Smagorinsky scheme (i.e., required with useSmag3D=.TRUE.), however, the documentation in that tutorial is very limited and it isn't
clear what values should be chosen for: </div>
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smag3D_coeff</div>
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smag3Ddiff_coeff</div>
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I would be grateful is someone could give some advice about how to choose values for these parameters. </div>
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<span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt">Also, it might be useful to look at the source code for the 3D Smagorinsky scheme (</span><span style="letter-spacing:normal; font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:16px; font-weight:400; background-color:rgb(255,255,255)">useSmag3D=.TRUE.)</span><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt">,
but I am not sure where it is located?</span></div>
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Many thanks,</div>
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Paul</div>
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<div><span style="font-family:Calibri,sans-serif; font-size:14.6667px; color:rgb(23,78,134); background-color:rgb(255,255,255)">Dr Paul Burns MInstP FRMetS</span></div>
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<font face="Calibri, sans-serif" style="font-size:11pt"><b>From:</b><span class="x_x_x_x_x_x_x_x_x_x_x_Apple-converted-space"> </span>Burns, Paul <<a href="mailto:P.Burns2@exeter.ac.uk">P.Burns2@exeter.ac.uk</a>><br>
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<b>Subject:</b><span class="x_x_x_x_x_x_x_x_x_x_x_Apple-converted-space"> </span>Re: [MITgcm-support] Vertical diffusion for non-hydrostatic ocean model with a stretched grid</font>
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Hi Jean-Michel,</div>
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Many thanks for your quick and clear response.</div>
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I agree that I should try option 2), which appears to calculate both the viscosity and diffusivity for the tracers (simply by using a constant Prandtl number)? Yes, the Smagorinsky model essentially parameterises subgrid mixing by using the resolved shear
and grid resolution, and so does not explicitly account for stratification. I hope that my very fine vertical grid resolves most buoyancy-driven (and mechanical) mixing. </div>
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MITgcm does have a TKE 1.5-order closure scheme (i.e., package ggl90), however, it seems only suitable for hydrostatic simulations, when the mixing length in the scheme doesn't need to be limited to the grid resolution. This at least is my understanding from
the paper by Blanke and Delecluse (1993).</div>
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My grid is certainly not isotropic, but I have no bottom topography so the grid cells are at least aligned with the horizontal. I am not sure what errors my grid may introduce when using the Smagorinsky scheme? I guess I can test the results using the Smagorinsky
scheme against simply specifying a profile of viscosity and diffusivity using the relevant Reynolds number (i.e. setting <span class="x_x_x_x_x_x_x_x_x_x_x_x_ContentPasted0" style="font-size:12pt; background-color:rgb(255,255,255); display:inline!important">viscArNr).</span></div>
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Cheers,</div>
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Paul</div>
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<div style="margin:0px; font-size:11pt; font-family:Calibri,sans-serif"><span style="margin:0px; color:rgb(31,78,121)">Dr Paul Burns MInstP FRMetS</span></div>
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<div id="x_x_x_x_x_x_x_x_x_x_x_x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt"><b>From:</b><span class="x_x_x_x_x_x_x_x_x_x_x_Apple-converted-space"> </span>MITgcm-support <<a href="mailto:mitgcm-support-bounces@mitgcm.org">mitgcm-support-bounces@mitgcm.org</a>>
on behalf of Jean-Michel Campin <<a href="mailto:jmc@mit.edu">jmc@mit.edu</a>><br>
<b>Sent:</b><span class="x_x_x_x_x_x_x_x_x_x_x_Apple-converted-space"> </span>01 February 2023 15:25<br>
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<b>Subject:</b><span class="x_x_x_x_x_x_x_x_x_x_x_Apple-converted-space"> </span>Re: [MITgcm-support] Vertical diffusion for non-hydrostatic ocean model with a stretched grid</font>
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<div class="x_x_x_x_x_x_x_x_x_x_x_x_PlainText">CAUTION: This email originated from outside of the organisation. Do not click links or open attachments unless you recognise the sender and know the content is safe.<br>
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<br>
Hi Paul,<br>
<br>
There is some confusion about Smagorinsky in MITgcm since we have 2 implementations:<br>
1) a Smagorinsky like horizontal viscosity that is function of horizontal shear,<br>
with the choice of harmonic (viscC2smag) or bi-harmonic (viscC4smag) viscosity.<br>
2) a simple 3-D Smagorinsky harmonic viscosity that work best when the grid is<br>
near isotropic (mostly for Non-Hydrostatic simulation) and does not acount for<br>
stratification.<br>
Need ALLOW_SMAG_3D_DIFFUSIVITY to be defined and uses run-time parameter:<br>
useSmag3D = .TRUE., with smag3D_coeff,<br>
see experiment: tutorial_deep_convection, with input.smag3d/data<br>
<br>
You may want to try this second implementation.<br>
Alternatively, you could always set a vertical profile of (background)<br>
vertical viscosity using Nr values to set vector "viscArNr" in main parameter<br>
input file "data" (note that the fist value corresponds to the very top,<br>
i.e., surface, vertical index k=1, and has no effect).<br>
<br>
Cheers,<br>
Jean-Michel<br>
<br>
On Wed, Feb 01, 2023 at 12:55:22PM +0000, Burns, Paul wrote:<br>
> Hi,<br>
><br>
> I was hoping that someone could give me some advice about the best way to define the vertical viscosity (and diffusivity) in MITgcm for a non-hydrostatic model using a stretched vertical grid. I've used a stretched vertical grid to resolve very small features
of interest (~0.2 m) in the upper ocean and to keep the simulation practical.<br>
><br>
> The viscosity should vary with the grid resolution (e.g., Smagorinsky, 1993), however, the MITgcm documentation says that the Smagorinsky scheme isn't implemented in the vertical. So would a reasonable approach be to compute a vertical profile of viscosities
using a vertical Reynolds number and use that to set viscArNr?<br>
><br>
><br>
> Many thanks,<br>
> Paul<br>
><br>
><br>
><br>
><br>
> Dr Paul Burns MInstP FRMetS<br>
><br>
> Research Fellow<br>
><br>
> Geophysical and Astrophysical Fluid Dynamics Group<br>
><br>
> Department of Mathematics<br>
><br>
> Harrison Building<br>
><br>
> University of Exeter<br>
><br>
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