[MITgcm-support] Closing DIC budget

Tue Mar 12 12:31:56 EDT 2024

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
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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

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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

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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>>
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Subject: Re: [MITgcm-support] Closing DIC budget

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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
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De : MITgcm-support <mitgcm-support-bounces at mitgcm.org> de la part de Wenrui Jiang <wjiang33 at jhu.edu>
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Objet : [MITgcm-support] Closing DIC budget

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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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