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Hi,</div>
<div class="elementToProof" style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
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<div class="elementToProof"><span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">Thank you all for your help. Thanks to your advice, I can now close the budget when
I turn the gchem package off. However, I am having some difficulties adding in the chemistry and atmospheric flux. Could you tell me what diagnostics are needed? It seems like the diagnostics I am using (DICTFLUX, DICBIOA, DICCARB) are off by some factor,
but I could not figure them out.</span></div>
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</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);">Thanks,</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);">Wenrui</span></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> Tuesday, March 12, 2024 5:03 AM<br>
<b>To:</b> MITgcm Support <mitgcm-support@mitgcm.org><br>
<b>Subject:</b> Re: [MITgcm-support] Closing DIC budget</font>
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<p><strong><br>
</strong><strong><span style="background:red; color:white; font-family:"Times New Roman",serif; font-size:12pt"> External Email - Use Caution </span></strong></p>
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<div>Hi Dave,
<div><br>
</div>
<div>thanks for the clarification and sorry for my inaccurate post.</div>
<div>In fact, nonlinFreeSurf=4, select_rStar=2, turns on the r-start coordinates (sorry for not saying that in my previous post), and with r-star, the conservation should be most accurate (better than “just” non-linear free surface).
<div><br>
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<div>Martin<br id="x_lineBreakAtBeginningOfMessage">
<div><br>
<blockquote type="cite">
<div>On 11. Mar 2024, at 18:54, Dave Munday - BAS <danday@bas.ac.uk> wrote:</div>
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<div>
<div style="line-break:after-white-space"><span style="">I’ve been using the DIC pkg with r* coordinates and get extremely good conservation of all the tracers. I’d expect it to be almost as good with the non-linear free surface, as Martin says.</span>
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<div style="">Dave</div>
<div><br>
<blockquote type="cite">
<div>On 11 Mar 2024, at 07:50, Martin Losch <Martin.Losch@awi.de> wrote:</div>
<br class="x_Apple-interchange-newline">
<div><span style="font-family:Helvetica; font-size:14px; font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">Hi,</span>
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you can also try to set exactConserv = .TRUE., in data (but I am not sure if there’s an effect on the passive tracers).</div>
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I am not sure, but I think that the tracer conservation will improve very much with the nonlinear free surface. verification/tutorial_global_oce_biogeo does not use a nonlinear free surface. To turn it on, you’d need to define NONLIN_FRSURF (in CPP_OPTIONS.h),
recompile (“make”) and use the appropriate runtime flags: nonlinFreeSurf=4, select_rStar=2, and maybe hFacInf, hFacSup.</div>
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Martin</div>
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<blockquote type="cite">
<div>On 6. Mar 2024, at 17:41, Wenrui Jiang <wjiang33@jhu.edu> wrote:</div>
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Hi Sandy,</div>
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Thank you very much for the suggestion. Although I have not figured out everything yet, but it is now much closer to a closure. Thank you!<br>
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Best,
<div>Wenrui</div>
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<font face="Calibri, sans-serif" style="font-size:11pt"><b>From:</b><span class="x_Apple-converted-space"> </span>MITgcm-support <<a href="mailto:mitgcm-support-bounces@mitgcm.org">mitgcm-support-bounces@mitgcm.org</a>> on behalf of Gregorio Sandy <<a href="mailto:Sandy.Gregorio@uqar.ca">Sandy.Gregorio@uqar.ca</a>><br>
<b>Sent:</b><span class="x_Apple-converted-space"> </span>Tuesday, March 5, 2024 11:13 AM<br>
<b>To:</b><span class="x_Apple-converted-space"> </span><a href="mailto:mitgcm-support@mitgcm.org">mitgcm-support@mitgcm.org</a><span class="x_Apple-converted-space"> </span><<a href="mailto:mitgcm-support@mitgcm.org">mitgcm-support@mitgcm.org</a>><br>
<b>Subject:</b><span class="x_Apple-converted-space"> </span>Re: [MITgcm-support] Closing DIC budget</font>
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</strong><strong><span style="background:red; color:white; font-family:"Times New Roman",serif; font-size:12pt"> External Email - Use Caution </span></strong></div>
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<span style="font-family:Arial,Helvetica,sans-serif">Hi Wenrui,</span></div>
<div class="x_x_elementToProof" style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt">
<span style="font-family:Arial,Helvetica,sans-serif"><br>
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<div class="x_x_elementToProof"><span style="font-family:Arial,Helvetica,sans-serif; font-size:12pt">I had a problem as well in closing my tracers budget (by just looking at timeseries of my tracers integrated over my domain, I could see a drift). I don't know
if it can help you but I added the following line in data.ptracers for all my tracers (1 to 5):</span></div>
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</span></div>
<div class="x_x_elementToProof"><span style="font-family:Arial,Helvetica,sans-serif; font-size:12pt"><b>PTRACERS_linFSConserve(1)=.TRUE.,</b></span></div>
<pre><div class="x_x_elementToProof"><span style="font-family:Arial,Helvetica,sans-serif; font-size:12pt">PTRACERS_linFSConserve applies mean Free-Surf source/sink at surface.</span></div></pre>
<div class="x_x_elementToProof"><span style="font-family:Arial,Helvetica,sans-serif; font-size:12pt">Good luck,</span></div>
<div class="x_x_elementToProof"><span style="font-family:Arial,Helvetica,sans-serif; font-size:12pt"><br>
</span></div>
<div class="x_x_elementToProof"><span style="font-family:Arial,Helvetica,sans-serif; font-size:12pt">Sandy</span></div>
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<div id="x_x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt"><b>De :</b><span class="x_Apple-converted-space"> </span>MITgcm-support <mitgcm-support-bounces@mitgcm.org> de la part de Wenrui Jiang <wjiang33@jhu.edu><br>
<b>Envoyé :</b><span class="x_Apple-converted-space"> </span>lundi 4 mars 2024 13:18<br>
<b>À :</b><span class="x_Apple-converted-space"> </span>mitgcm-support@mitgcm.org <mitgcm-support@mitgcm.org><br>
<b>Objet :</b><span class="x_Apple-converted-space"> </span>[MITgcm-support] Closing DIC budget</font>
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<div><span style="font-weight:bold">ATTENTION :</span><span class="x_Apple-converted-space"> </span><span style="font-size:10pt">Ce courriel provient d'une source externe. Assurez-vous que cette dernière est sûre avant d'ouvrir une pièce jointe ou de cliquer
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<div class="x_x_x_elementToProof"><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:11pt">Dear MITgcm support group,<br>
<br>
Thanks for reading this. My name is Wenrui Jiang, and I am a PhD student from Johns Hopkins. I want to apologize in advance for my inexperience.<br>
<br>
I am trying to close the DIC budget on the biogeochemical tutorial example (<a href="https://mitgcm.readthedocs.io/en/latest/examples/global_oce_biogeo/global_oce_biogeo.html" originalsrc="https://mitgcm.readthedocs.io/en/latest/examples/global_oce_biogeo/global_oce_biogeo.html" shash="RxEm2QucUKJCMLfTS5on5cxdtUR/WuqLKFGon/C4iObeSrfrFZkqkHGQzTD/AToSFmRMil18ktIZ4puy3TgMa1RUkIFZ51S4c9JKHRmvhcwx9kWa6YBRYCoBQ5Z7w7BHvt51Koe18n4mDUQwmCN5H4SXu/pfAaKQTZSO0JTyXbE=" originalsrc="https://mitgcm.readthedocs.io/en/latest/examples/global_oce_biogeo/global_oce_biogeo.html" shash="LJLkw2k7DT3JyUOzDRbN0rEq87HhroTztBJekzUviVCKkRAN8+ZI2S7Wv8n0gQydYdKwaoxeos5Mb7Q4tjII7tUc3CtSXKMyOfumix21mWQfDIFrFp4zQXoaCpHsUFwbEKtbbw8pXb6ecegGrkpOd8Bmts8i/gRCEJneDQXHiBc=" id="LPlnk840669">https://mitgcm.readthedocs.io/en/latest/examples/global_oce_biogeo/global_oce_biogeo.html</a>).
The diagnostics that I include are:<br>
<br>
TRAC01 |SMR MR|mol/m^3 |Dissolved Inorganic Carbon (DIC) [mol C/m^3] concentration<br>
ForcTr01|SMR MR|mol/m^3/s |DIC forcing tendency<br>
AB_gTr01|SMR MR|mol/m^3/s |DIC tendency from Adams-Bashforth<br>
Tp_gTr01|SMR MR|mol/m^3/s |DIC total transport tendency (before gchem_forcing_sep)<br>
ADVrTr01|WM LR|mol/m^3.m^3/s |Vertical Advective Flux of DIC<br>
ADVxTr01|UU MR|mol/m^3.m^3/s |Zonal Advective Flux of DIC<br>
ADVyTr01|VV MR|mol/m^3.m^3/s |Meridional Advective Flux of DIC<br>
DFrETr01|WM LR|mol/m^3.m^3/s |Vertical Diffusive Flux of DIC (Explicit part)<br>
DFxETr01|UU MR|mol/m^3.m^3/s |Zonal Diffusive Flux of DIC<br>
DFyETr01|VV MR|mol/m^3.m^3/s |Meridional Diffusive Flux of DIC<br>
DFrITr01|WM LR|mol/m^3.m^3/s |Vertical Diffusive Flux of DIC (Implicit part)<br>
<br>
DICBIOA | 15 |SM P MR |mol/m3/sec |Biological Productivity (mol/m3/s)<br>
DICCARB | 15 |SM P MR |mol eq/m3/sec |Carbonate chg-biol prod and remin (mol eq/m3/s)<br>
DICTFLX | 1 |SM P L1 |mol/m3/sec |Tendency of DIC due to air-sea exch (mol/m3/s<br>
<br>
So far, I managed to close the Tp_gTr01 term with the advective and diffusive flux in the interior to machine precision. However, at the surface there is a large residual, which I am not able to close with ForcTR01. I am wondering if this is a dilution effect
from PTRACER_ref.<br>
<br>
I am also having a hard time matching Tp_gTr01 and the tendency diagnosed from DIC and Eta snapshots using the GCHEM diagnostics. The GCHEM diagnostics seems to have very small value (10^-10 mol/m^3/s) which is much smalller than the difference.<br>
<br>
I would really appreciate it if you could tell me whether:<br>
<br>
1. I am using the correct diagnostics in the correct way;<br>
2.there are any model setups that prevent a tracer closure.<br>
</span></div>
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<div class="x_x_x_elementToProof"><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:11pt">Thank you very much!<br>
</span></div>
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Sincerely,
<div>Wenrui</div>
<br>
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<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt"><span style="font-size:16pt; color:rgb(12,136,42)">Wenrui Jiang</span></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt"><br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">Ph.D. Student,</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">Department of Earth & Planetary Sciences,</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">Johns Hopkins University.</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt"><br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">Email: wjiang33@jh.edu</div>
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