<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body style="overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">Hi,<div><br></div><div>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><div><br></div><div>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><div><br></div><div>Martin</div><div><br><div><blockquote type="cite"><div>On 6. Mar 2024, at 17:41, Wenrui Jiang <wjiang33@jhu.edu> wrote:</div><br class="Apple-interchange-newline"><div><meta charset="UTF-8"><div class="elementToProof" style="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; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt;">Hi Sandy,</div><div class="elementToProof" style="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; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt;"><br></div><div class="elementToProof" style="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; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt;">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></div><div class="elementToProof" style="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; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt;"><br></div><div class="elementToProof" style="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; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt;">Best,<div>Wenrui</div><br></div><div id="appendonsend" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; -webkit-text-stroke-width: 0px; text-decoration: none;"></div><hr tabindex="-1" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; display: inline-block; width: 1025.078125px;"><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;"></span><div id="divRplyFwdMsg" dir="ltr" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; -webkit-text-stroke-width: 0px; text-decoration: none;"><font face="Calibri, sans-serif" style="font-size: 11pt;"><b>From:</b><span class="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="Apple-converted-space"> </span>Tuesday, March 5, 2024 11:13 AM<br><b>To:</b><span class="Apple-converted-space"> </span><a href="mailto:mitgcm-support@mitgcm.org">mitgcm-support@mitgcm.org</a><span class="Apple-converted-space"> </span><<a href="mailto:mitgcm-support@mitgcm.org">mitgcm-support@mitgcm.org</a>><br><b>Subject:</b><span class="Apple-converted-space"> </span>Re: [MITgcm-support] Closing DIC budget</font><div> </div></div><div dir="ltr" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; -webkit-text-stroke-width: 0px; text-decoration: none;"><div style="margin-top: 0px; margin-bottom: 0px;"><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></div><div style="margin-top: 0px; margin-bottom: 0px;"><strong><span style="background: red; color: white; font-family: "Times New Roman", serif; font-size: 12pt;"><br></span></strong></div><div style="margin-top: 0px; margin-bottom: 0px;"><strong><span style="background: red; color: white; font-family: "Times New Roman", serif; font-size: 12pt;"><br></span></strong></div><div><div class="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;">Hi Wenrui,</span></div><div class="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></span></div><div class="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><div class="x_elementToProof"><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;"><br></span></div><div class="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_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_elementToProof"><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;">Good luck,</span></div><div class="x_elementToProof"><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;"><br></span></div><div class="x_elementToProof"><span style="font-family: Arial, Helvetica, sans-serif; font-size: 12pt;">Sandy</span></div><div id="x_appendonsend"></div><hr tabindex="-1" style="display: inline-block; width: 1025.078125px;"><div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size: 11pt;"><b>De :</b><span class="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="Apple-converted-space"> </span>lundi 4 mars 2024 13:18<br><b>À :</b><span class="Apple-converted-space"> </span>mitgcm-support@mitgcm.org <mitgcm-support@mitgcm.org><br><b>Objet :</b><span class="Apple-converted-space"> </span>[MITgcm-support] Closing DIC budget</font><div> </div></div><div dir="ltr"><table border="0" cellspacing="0" cellpadding="0" align="left" width="100%"><tbody><tr><td style="background: rgb(255, 0, 0); padding: 5pt 2pt;"></td><td width="100%" cellpadding="7px 6px 7px 15px" style="background: rgb(255, 224, 224); padding: 5pt 4pt 5pt 12pt; overflow-wrap: break-word;"><div style=""><span style="font-weight: bold;">ATTENTION :</span><span class="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 sur un lien. Dans le doute, signalez le message.</span></div></td></tr></tbody></table><br><div><div class="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="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><div class="x_x_elementToProof"><span style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 11pt;"><br></span></div><div class="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><div class="x_x_elementToProof" style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt;"><br></div><div class="x_x_elementToProof" style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt;">Sincerely,<div>Wenrui</div><br></div><div id="x_x_Signature"><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><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"><br></div></div></div></div></div></div><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; -webkit-text-stroke-width: 0px; text-decoration: none;"><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;">MITgcm-support mailing list</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; -webkit-text-stroke-width: 0px; text-decoration: none;"><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;">MITgcm-support@mitgcm.org</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; -webkit-text-stroke-width: 0px; text-decoration: none;"><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;">http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support</span></div></blockquote></div><br></div></body></html>