[MITgcm-support] nonlinear equation of state
Remi Tailleux
r.g.j.tailleux at reading.ac.uk
Wed Mar 13 11:33:51 EDT 2024
Hi all,
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.
https://doi.org/10.1016/j.ocemod.2024.102339
Best wishes,
Remi.
Dr. Remi Tailleux
Associate Professor in Physical Oceanography
Department of Meteorology, University of Reading
Whiteknights road, Earley Gate
Reading, RG6 6ET, United Kingdom
Phone: +44(0)118 378 8328 / Fax: +44(0)118 378 8316
Email: R.G.J.Tailleux at reading.ac.uk<mailto:R.G.J.Tailleux at reading.ac.uk>
Web: http://www.met.reading.ac.uk/~sws04rgt
Remi Tailleux - Meteorology (reading.ac.uk)<https://research.reading.ac.uk/meteorology/people/remi-tailleux/>
Twitter: @RemiTailleux Remi Tailleux (@RemiTailleux) / Twitter<https://twitter.com/RemiTailleux>
Orcid: Remi Tailleux (0000-0001-8998-9107) (orcid.org)<https://orcid.org/0000-0001-8998-9107>
Researchgate: https://researchgate.net/profile/Remi-Tailleux
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From: MITgcm-support <mitgcm-support-bounces at mitgcm.org> on behalf of mitgcm-support-request at mitgcm.org <mitgcm-support-request at mitgcm.org>
Date: Wednesday, 13 March 2024 at 11:30
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Today's Topics:
1. Re: Nonlinear equations of state (Martin Losch)
2. Re: Closing DIC budget (Wenrui Jiang)
----------------------------------------------------------------------
Message: 1
Date: Wed, 13 Mar 2024 12:08:03 +0100
From: Martin Losch <Martin.Losch at awi.de>
To: MITgcm Support <mitgcm-support at mitgcm.org>
Subject: Re: [MITgcm-support] Nonlinear equations of state
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Hi all,
I don?t seem to be on top of things here, so thanks to Paola for the clarification.
But the MITgcm can do more (o:
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`:
C selectP_inEOS_Zc :: select which pressure to use in EOS (for z-coords)
C =0: simply: -g*rhoConst*z
C =1: use pRef = integral{-g*rho(Tref,Sref,pRef)*dz}
C =2: use hydrostatic dynamical pressure
C =3: use full (Hyd+NH) dynamical pressure
So using eosType=?MDJWF? together with selectP_inEOS_Zc = 0 should also work and not violate the energy budget.
Martin
> On 12. Mar 2024, at 16:49, Paola Cessi <pcessi at ucsd.edu> wrote:
>
> Hi Dave,
>
> 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.
>
> This is explained in detail in the attached paper. If you are using an incompressible, Boussinesq model use JMD95Z, not JMD95P.
>
> Cheers,
> Paola
>
>
>> On Mar 12, 2024, at 4:44 AM, Dave Munday - BAS <danday at bas.ac.uk <mailto:danday at bas.ac.uk>> wrote:
>>
>> 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.
>>
>> D
>>
>>> On 12 Mar 2024, at 09:16, Martin Losch <Martin.Losch at awi.de <mailto:Martin.Losch at awi.de>> wrote:
>>>
>>> Hi Dave,
>>>
>>> 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.
>>> JMD95Z uses the actual hydrostatic pressure (lagged by one timestep), and hence requires a little more computation
>>> 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
>>>
>>> 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?.
>>>
>>> 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: https://github.com/MITgcm/MITgcm/pull/812 <https://urldefense.com/v3/__https://github.com/MITgcm/MITgcm/pull/812__;!!Mih3wA!DjhCnEwPZhyprmcYr_89m6KqNgmJNB21EC-PMgNe0EpUy6Vm-BFs2jS5snW4uYL1HBOPG_wQVFB303U$<https://urldefense.com/v3/__https:/github.com/MITgcm/MITgcm/pull/812__;!!Mih3wA!DjhCnEwPZhyprmcYr_89m6KqNgmJNB21EC-PMgNe0EpUy6Vm-BFs2jS5snW4uYL1HBOPG_wQVFB303U$>>
>>>
>>> Martin
>>>
>>>> On 11. Mar 2024, at 18:35, Dave Munday - BAS <danday at bas.ac.uk <mailto:danday at bas.ac.uk>> wrote:
>>>>
>>>> Dear MITgcm-ers,
>>>>
>>>> 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?
>>>>
>>>> Many thanks,
>>>>
>>>> Dave
>>>>
>>>>
>>>> This email and any attachments are intended solely for the use of the named recipients. If you are not the intended recipient you must not use, disclose, copy or distribute this email or any of its attachments and should notify the sender immediately and delete this email from your system. UK Research and Innovation (UKRI) has taken every reasonable precaution to minimise risk of this email or any attachments containing viruses or malware but the recipient should carry out its own virus and malware checks before opening the attachments. UKRI does not accept any liability for any losses or damages which the recipient may sustain due to presence of any viruses.
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>
> <SeawaterBoussinesq.pdf>
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Message: 2
Date: Tue, 12 Mar 2024 16:31:56 +0000
From: Wenrui Jiang <wjiang33 at jhu.edu>
To: MITgcm Support <mitgcm-support at mitgcm.org>
Subject: Re: [MITgcm-support] Closing DIC budget
Message-ID:
<BL0PR01MB406746F05B1899E554602E8DCB2B2 at BL0PR01MB4067.prod.exchangelabs.com>
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Hi,
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.
Thanks,
Wenrui
________________________________
From: MITgcm-support <mitgcm-support-bounces at mitgcm.org> on behalf of Martin Losch <Martin.Losch at awi.de>
Sent: Tuesday, March 12, 2024 5:03 AM
To: MITgcm Support <mitgcm-support at mitgcm.org>
Subject: Re: [MITgcm-support] Closing DIC budget
External Email - Use Caution
Hi Dave,
thanks for the clarification and sorry for my inaccurate post.
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).
Martin
On 11. Mar 2024, at 18:54, Dave Munday - BAS <danday at bas.ac.uk> wrote:
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.
Dave
On 11 Mar 2024, at 07:50, Martin Losch <Martin.Losch at awi.de> wrote:
Hi,
you can also try to set exactConserv = .TRUE., in data (but I am not sure if there?s an effect on the passive tracers).
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.
Martin
On 6. Mar 2024, at 17:41, Wenrui Jiang <wjiang33 at jhu.edu> wrote:
Hi Sandy,
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!
Best,
Wenrui
________________________________
From: MITgcm-support <mitgcm-support-bounces at mitgcm.org<mailto:mitgcm-support-bounces at mitgcm.org>> on behalf of Gregorio Sandy <Sandy.Gregorio at uqar.ca<mailto:Sandy.Gregorio at uqar.ca>>
Sent: Tuesday, March 5, 2024 11:13 AM
To: mitgcm-support at mitgcm.org<mailto:mitgcm-support at mitgcm.org> <mitgcm-support at mitgcm.org<mailto:mitgcm-support at mitgcm.org>>
Subject: Re: [MITgcm-support] Closing DIC budget
External Email - Use Caution
Hi Wenrui,
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):
PTRACERS_linFSConserve(1)=.TRUE.,
PTRACERS_linFSConserve applies mean Free-Surf source/sink at surface.
Good luck,
Sandy
________________________________
De : MITgcm-support <mitgcm-support-bounces at mitgcm.org> de la part de Wenrui Jiang <wjiang33 at jhu.edu>
Envoy? : lundi 4 mars 2024 13:18
? : mitgcm-support at mitgcm.org <mitgcm-support at mitgcm.org>
Objet : [MITgcm-support] Closing DIC budget
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.
Dear MITgcm support group,
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.
I am trying to close the DIC budget on the biogeochemical tutorial example (https://mitgcm.readthedocs.io/en/latest/examples/global_oce_biogeo/global_oce_biogeo.html). The diagnostics that I include are:
TRAC01 |SMR MR|mol/m^3 |Dissolved Inorganic Carbon (DIC) [mol C/m^3] concentration
ForcTr01|SMR MR|mol/m^3/s |DIC forcing tendency
AB_gTr01|SMR MR|mol/m^3/s |DIC tendency from Adams-Bashforth
Tp_gTr01|SMR MR|mol/m^3/s |DIC total transport tendency (before gchem_forcing_sep)
ADVrTr01|WM LR|mol/m^3.m^3/s |Vertical Advective Flux of DIC
ADVxTr01|UU MR|mol/m^3.m^3/s |Zonal Advective Flux of DIC
ADVyTr01|VV MR|mol/m^3.m^3/s |Meridional Advective Flux of DIC
DFrETr01|WM LR|mol/m^3.m^3/s |Vertical Diffusive Flux of DIC (Explicit part)
DFxETr01|UU MR|mol/m^3.m^3/s |Zonal Diffusive Flux of DIC
DFyETr01|VV MR|mol/m^3.m^3/s |Meridional Diffusive Flux of DIC
DFrITr01|WM LR|mol/m^3.m^3/s |Vertical Diffusive Flux of DIC (Implicit part)
DICBIOA | 15 |SM P MR |mol/m3/sec |Biological Productivity (mol/m3/s)
DICCARB | 15 |SM P MR |mol eq/m3/sec |Carbonate chg-biol prod and remin (mol eq/m3/s)
DICTFLX | 1 |SM P L1 |mol/m3/sec |Tendency of DIC due to air-sea exch (mol/m3/s
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.
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.
I would really appreciate it if you could tell me whether:
1. I am using the correct diagnostics in the correct way;
2.there are any model setups that prevent a tracer closure.
Thank you very much!
Sincerely,
Wenrui
Wenrui Jiang
Ph.D. Student,
Department of Earth & Planetary Sciences,
Johns Hopkins University.
Email: wjiang33 at jh.edu
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