[MITgcm-support] Closing DIC budget

Wed Mar 13 19:32:51 EDT 2024

Hi Jonathan,

Thank you very much for your help! I am now able to close the budget.

Thanks,
Wenrui

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From: MITgcm-support <mitgcm-support-bounces at mitgcm.org> on behalf of Jonathan Lauderdale <jml1 at mit.edu>
Sent: Wednesday, March 13, 2024 10:36 AM
To: mitgcm-support at mitgcm.org <mitgcm-support at mitgcm.org>
Subject: Re: [MITgcm-support] Closing DIC budget

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Hi Wenrui,

I have a DIC budget calculation in Jupyter Notebook format<https://nbviewer.org/github/seamanticscience/Lauderdale_etal_2016_GBC/blob/master/CO2_Flux_Drivers_Online.ipynb>. My 3° configuration differs from the tutorial slightly (I used KPP mixing, the virtual flux, and rigid lid), but it should give you something to compare to.

You can see that the biological tendency is more than just DICBIOA, which only represents uptake of phosphate due to net biological production, and DICCARB, which is net change in carbon due to calcite production/remin:

# Calculate biological activity terms (mol/m2/s)
dic_bio_flux  = (Rcp*(-dicdiag.DICBIOA+dicdiag.DICPFLUX+dicdiag.DICRDOP)*grid.drF).sel(ZC=slice(0,-kave)).sum("ZC")*grid.cmask.isel(ZC=0)
dic_carb_flux = ((dicdiag.DICCARB)*grid.drF).sel(ZC=slice(0,-kave)).sum("ZC")*grid.cmask.isel(ZC=0)

See also the code for S/R dic_biotic_forcing.F<https://github.com/MITgcm/MITgcm/blob/7456fbd729aef084d56996e0e389c63422447ab9/pkg/dic/dic_biotic_forcing.F#L276>.

So, first, you need to multiply DICBIOA by the Redfield ratio (R_cp=117), which will get you two orders of magnitude. Then, you may need to include the additional diagnostics for DICPFLUX, which is the remineralization of sinking particulate organic phosphate, and DICRDOP, which is the remineralization of dissolved organic phosphate, again multiplied by R_cp.

You might need to modify the code to get all the diagnostics you need: PFLUX should appear in your dic_tave file, but doesn’t have a diagnostic package output, DICRDOP might appear as the gchem tendency for tracer 4? Let me know if you need further help with this.

DICTFLX is probably the right diagnostic for CO2 fluxes in your case, but you might consider comparing DICTFLX and DICCFLX

If you use r* coordinates, then you have to take into account the changing volume of the upper cell (see the example for salt/salinity budgets <https://ecco-v4-python-tutorial.readthedocs.io/ECCO_v4_Salt_and_salinity_budget.html> in that case)

Hope this helps, and sorry if I suggested things you already tried.

Cheers,

Jonathan

On Mar 12, 2024, at 12:31, Wenrui Jiang <wjiang33 at jhu.edu<mailto:wjiang33 at jhu.edu>> wrote:

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<mailto:mitgcm-support-bounces at mitgcm.org>> on behalf of Martin Losch <Martin.Losch at awi.de<mailto:Martin.Losch at awi.de>>
Sent: Tuesday, March 12, 2024 5:03 AM
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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<mailto: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<mailto: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<mailto: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>>
Sent: Tuesday, March 5, 2024 11:13 AM
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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<mailto:mitgcm-support-bounces at mitgcm.org>> de la part de Wenrui Jiang <wjiang33 at jhu.edu<mailto: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<mailto:wjiang33 at jh.edu>

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