[MITgcm-support] Closing DIC budget

Tue Mar 12 05:03:31 EDT 2024

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>
>>> Envoyé : lundi 4 mars 2024 13:18
>>> À : 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 dernière est sûre avant d'ouvrir une pièce 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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