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<p class="MsoNormal"><span style="font-size:11.0pt;mso-fareast-language:EN-US"> Hi all,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;mso-fareast-language:EN-US">Building on Paola’s email, here is a link towards a recent paper explaining in details how Boussinesq models need to be constructed to be traceable to that of the fully compressible
Navier-Stokes equations. It also explain how current Boussinesq models could be modified to energetically much more accurate with only little changes to existing codes, if anybody is interested in trying it out.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;mso-fareast-language:EN-US"><a href="https://doi.org/10.1016/j.ocemod.2024.102339">https://doi.org/10.1016/j.ocemod.2024.102339</a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;mso-fareast-language:EN-US">Best wishes,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;mso-fareast-language:EN-US">Remi.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">Dr. Remi Tailleux<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">Associate Professor in Physical Oceanography<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">Department of Meteorology, University of Reading<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">Whiteknights road, Earley Gate<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">Reading, RG6 6ET, United Kingdom<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black"><br>
</span><span lang="FR" style="font-size:11.0pt;color:black">Phone: +44(0)118 378 8328 / Fax: +44(0)118 378 8316</span><span style="font-size:11.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="FR" style="font-size:11.0pt;color:black">Email: </span><span style="font-size:11.0pt;color:black"><a href="mailto:R.G.J.Tailleux@reading.ac.uk" title="mailto:R.G.J.Tailleux@reading.ac.uk"><span lang="FR" style="color:#0078D4">R.G.J.Tailleux@reading.ac.uk</span></a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">Web: <a href="http://www.met.reading.ac.uk/~sws04rgt" title="http://www.met.reading.ac.uk/~sws04rgt"><span style="color:#954F72">http://www.met.reading.ac.uk/~sws04rgt</span></a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black"><a href="https://research.reading.ac.uk/meteorology/people/remi-tailleux/" title="https://research.reading.ac.uk/meteorology/people/remi-tailleux/"><span style="color:#0563C1">Remi Tailleux - Meteorology
(reading.ac.uk)</span></a><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="FR" style="font-size:11.0pt;color:black">Twitter: @RemiTailleux </span><span style="font-size:11.0pt;color:black"><a href="https://twitter.com/RemiTailleux" title="https://twitter.com/RemiTailleux"><span lang="FR" style="color:#0563C1">Remi
Tailleux (@RemiTailleux) / Twitter</span></a><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="FR" style="font-size:11.0pt;color:black">Orcid: </span><span style="font-size:11.0pt;color:black"><a href="https://orcid.org/0000-0001-8998-9107" title="https://orcid.org/0000-0001-8998-9107"><span lang="FR" style="color:#0563C1">Remi
Tailleux (0000-0001-8998-9107) (orcid.org)</span></a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">Researchgate: <a href="https://researchgate.net/profile/Remi-Tailleux" title="https://researchgate.net/profile/Remi-Tailleux"><span style="color:#954F72">https://researchgate.net/profile/Remi-Tailleux</span></a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">-- <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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</span></b><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">MITgcm-support <mitgcm-support-bounces@mitgcm.org> on behalf of mitgcm-support-request@mitgcm.org <mitgcm-support-request@mitgcm.org><br>
<b>Date: </b>Wednesday, 13 March 2024 at 11:30<br>
<b>To: </b>mitgcm-support@mitgcm.org <mitgcm-support@mitgcm.org><br>
<b>Subject: </b>MITgcm-support Digest, Vol 249, Issue 8<o:p></o:p></span></p>
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Today's Topics:<br>
<br>
1. Re: Nonlinear equations of state (Martin Losch)<br>
2. Re: Closing DIC budget (Wenrui Jiang)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Wed, 13 Mar 2024 12:08:03 +0100<br>
From: Martin Losch <Martin.Losch@awi.de><br>
To: MITgcm Support <mitgcm-support@mitgcm.org><br>
Subject: Re: [MITgcm-support] Nonlinear equations of state<br>
Message-ID: <51862E5B-308B-4A96-916F-002398566AC0@awi.de><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi all,<br>
<br>
I don?t seem to be on top of things here, so thanks to Paola for the clarification.<br>
<br>
But the MITgcm can do more (o:<br>
<br>
there?s the parameter `selectP_inEOS_Zc` that can be set in data&PARM01. Otherwise it defaults to the historical settings associated with the eosType. From `PARAMS.h`:<br>
C selectP_inEOS_Zc :: select which pressure to use in EOS (for z-coords)<br>
C =0: simply: -g*rhoConst*z<br>
C =1: use pRef = integral{-g*rho(Tref,Sref,pRef)*dz}<br>
C =2: use hydrostatic dynamical pressure<br>
C =3: use full (Hyd+NH) dynamical pressure<br>
<br>
So using eosType=?MDJWF? together with selectP_inEOS_Zc = 0 should also work and not violate the energy budget.<br>
<br>
Martin<br>
<br>
> On 12. Mar 2024, at 16:49, Paola Cessi <pcessi@ucsd.edu> wrote:<br>
> <br>
> Hi Dave,<br>
> <br>
> another issue of using a complex EoS such as TEOS-10 in a model which makes the Boussinesq approximation is that proper conservation of total energy (including internal energy) is lost unless some care is taken. For example, with the Boussinesq approximation
the dependence of the EoS on the pressure, p, must be through the term p = -rhoConst*gravity*z, not the in situ pressure. If the actual in situ pressure is used in a Boussinesq model, then there is an inconsistent energy budget.
<br>
> <br>
> This is explained in detail in the attached paper. If you are using an incompressible, Boussinesq model use JMD95Z, not JMD95P.<br>
> <br>
> Cheers,<br>
> Paola<br>
> <br>
> <br>
>> On Mar 12, 2024, at 4:44 AM, Dave Munday - BAS <danday@bas.ac.uk <<a href="mailto:danday@bas.ac.uk">mailto:danday@bas.ac.uk</a>>> wrote:<br>
>> <br>
>> Thanks Martin. That?s quite reassuring that I haven?t made a daft choice with at least trying out MDJWF. TEOS-10 would have been nice, but I?m quite happy to do without for now.<br>
>> <br>
>> D<br>
>> <br>
>>> On 12 Mar 2024, at 09:16, Martin Losch <Martin.Losch@awi.de <<a href="mailto:Martin.Losch@awi.de">mailto:Martin.Losch@awi.de</a>>> wrote:<br>
>>> <br>
>>> Hi Dave,<br>
>>> <br>
>>> JMD95Z (based on Jackett and McDougall 1995) is basically a ?re-tuned? UNESCO formula (UNESCO for in-situ temperature and JMD95Z for potential temperature), both use p = -rhoConst*gravity*z as an approximation for pressure.<br>
>>> JMD95Z uses the actual hydrostatic pressure (lagged by one timestep), and hence requires a little more computation<br>
>>> MDJWF implements McDougall, et al (2003). The EOS is based on a different fromula and principles and contains fewer terms, so that the authors (?) claim that there fewer computations involved, hence it should be faster. This EOS also uses the hydrostatic
pressure of the previous time step<br>
>>> <br>
>>> In practice, the EOS is not the bottleneck of any simulation, so that I would not expect any significant speed differences. For potential temperature I wouild use MDJWF, just because it is ?newer?.
<br>
>>> <br>
>>> There?s also TEOS10, which requires that ?THETA? and ?SALT? are interpreted as conservative temperature and absolute salinity. This implementation is not quite complete yet, see PR #812:
<a href="https://github.com/MITgcm/MITgcm/pull/812">https://github.com/MITgcm/MITgcm/pull/812</a> <<a href="https://urldefense.com/v3/__https:/github.com/MITgcm/MITgcm/pull/812__;!!Mih3wA!DjhCnEwPZhyprmcYr_89m6KqNgmJNB21EC-PMgNe0EpUy6Vm-BFs2jS5snW4uYL1HBOPG_wQVFB303U$">https://urldefense.com/v3/__https://github.com/MITgcm/MITgcm/pull/812__;!!Mih3wA!DjhCnEwPZhyprmcYr_89m6KqNgmJNB21EC-PMgNe0EpUy6Vm-BFs2jS5snW4uYL1HBOPG_wQVFB303U$</a>><br>
>>> <br>
>>> Martin<br>
>>> <br>
>>>> On 11. Mar 2024, at 18:35, Dave Munday - BAS <danday@bas.ac.uk <<a href="mailto:danday@bas.ac.uk">mailto:danday@bas.ac.uk</a>>> wrote:<br>
>>>> <br>
>>>> Dear MITgcm-ers,<br>
>>>> <br>
>>>> I?ve just been trying to make a decision about which particular nonlinear EOS to use for a very long-running two basin sector model with biogeochemistry. In reading the docs the MDJWF EOS is described as ?more accurate and less expensive?, which is appealing
when running models for 10-20 000 years. A lot of the verification experiments are set to use JMD95Z or JMD95P. Is there a reason to prefer them over MDJWF?<br>
>>>> <br>
>>>> Many thanks,<br>
>>>> <br>
>>>> Dave<br>
>>>> <br>
>>>> <br>
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> <br>
> <SeawaterBoussinesq.pdf><br>
<br>
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<br>
Message: 2<br>
Date: Tue, 12 Mar 2024 16:31:56 +0000<br>
From: Wenrui Jiang <wjiang33@jhu.edu><br>
To: MITgcm Support <mitgcm-support@mitgcm.org><br>
Subject: Re: [MITgcm-support] Closing DIC budget<br>
Message-ID:<br>
<BL0PR01MB406746F05B1899E554602E8DCB2B2@BL0PR01MB4067.prod.exchangelabs.com><br>
<br>
Content-Type: text/plain; charset="windows-1252"<br>
<br>
Hi,<br>
<br>
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.<br>
<br>
Thanks,<br>
Wenrui<br>
________________________________<br>
From: MITgcm-support <mitgcm-support-bounces@mitgcm.org> on behalf of Martin Losch <Martin.Losch@awi.de><br>
Sent: Tuesday, March 12, 2024 5:03 AM<br>
To: MITgcm Support <mitgcm-support@mitgcm.org><br>
Subject: Re: [MITgcm-support] Closing DIC budget<br>
<br>
<br>
External Email - Use Caution<br>
<br>
<br>
<br>
Hi Dave,<br>
<br>
thanks for the clarification and sorry for my inaccurate post.<br>
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).<br>
<br>
Martin<br>
<br>
On 11. Mar 2024, at 18:54, Dave Munday - BAS <danday@bas.ac.uk> wrote:<br>
<br>
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.<br>
<br>
Dave<br>
<br>
On 11 Mar 2024, at 07:50, Martin Losch <Martin.Losch@awi.de> wrote:<br>
<br>
Hi,<br>
<br>
you can also try to set exactConserv = .TRUE., in data (but I am not sure if there?s an effect on the passive tracers).<br>
<br>
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.<br>
<br>
Martin<br>
<br>
On 6. Mar 2024, at 17:41, Wenrui Jiang <wjiang33@jhu.edu> wrote:<br>
<br>
Hi Sandy,<br>
<br>
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>
<br>
Best,<br>
Wenrui<br>
<br>
________________________________<br>
From: MITgcm-support <mitgcm-support-bounces@mitgcm.org<mailto:mitgcm-support-bounces@mitgcm.org>> on behalf of Gregorio Sandy <Sandy.Gregorio@uqar.ca<mailto:Sandy.Gregorio@uqar.ca>><br>
Sent: Tuesday, March 5, 2024 11:13 AM<br>
To: mitgcm-support@mitgcm.org<mailto:mitgcm-support@mitgcm.org> <mitgcm-support@mitgcm.org<mailto:mitgcm-support@mitgcm.org>><br>
Subject: Re: [MITgcm-support] Closing DIC budget<br>
<br>
<br>
External Email - Use Caution<br>
<br>
<br>
Hi Wenrui,<br>
<br>
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):<br>
<br>
PTRACERS_linFSConserve(1)=.TRUE.,<br>
<br>
PTRACERS_linFSConserve applies mean Free-Surf source/sink at surface.<br>
<br>
Good luck,<br>
<br>
Sandy<br>
________________________________<br>
De : MITgcm-support <mitgcm-support-bounces@mitgcm.org> de la part de Wenrui Jiang <wjiang33@jhu.edu><br>
Envoy? : lundi 4 mars 2024 13:18<br>
? : mitgcm-support@mitgcm.org <mitgcm-support@mitgcm.org><br>
Objet : [MITgcm-support] Closing DIC budget<br>
<br>
ATTENTION : Ce courriel provient d'une source externe. Assurez-vous que cette derni?re est s?re avant d'ouvrir une pi?ce jointe ou de cliquer sur un lien. Dans le doute, signalez le message.<br>
<br>
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">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>
<br>
Thank you very much!<br>
<br>
Sincerely,<br>
Wenrui<br>
<br>
Wenrui Jiang<br>
<br>
Ph.D. Student,<br>
Department of Earth & Planetary Sciences,<br>
Johns Hopkins University.<br>
<br>
Email: wjiang33@jh.edu<br>
<br>
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