[MITgcm-support] advective and diffusive diagnostics

[Stefano Querin]

Hi Dimitris, hi everybody,

I also use KPP (with implicit vertical diffusion) but NOT GMRedi and I can close the heat and salt budget, without considering explicit vertical diffusion.
In fact, I usually comment that term in my data.diagnostics:

#  frequency(112) =  86400,
#   fields(1,112) = 'DFrE_TH',
#   filename(112) = 'DFrE_TH',

#  frequency(120) =  86400,
#   fields(1,120) = 'DFrE_SLT',
#   filename(120) = 'DFrE_SLT',

If I enable the diagnostics for explicit vertical diffusion, I get this warning in my STDERR file:

(PID.TID 0189.0001) - WARNING - from DIAGNOSTICS_OUT at iter=       432
(PID.TID 0189.0001) - WARNING -   diag.#   111 : DFrE_TH  (#   1 ) in outp.Stream: DFrE_TH
(PID.TID 0189.0001) - WARNING -   has not been filled (ndiag=  0 )
(PID.TID 0189.0001) WARNING DIAGNOSTICS_OUT  => write ZEROS instead
(PID.TID 0189.0001) - WARNING - from DIAGNOSTICS_OUT at iter=       432
(PID.TID 0189.0001) - WARNING -   diag.#   128 : DFrE_SLT (#   1 ) in outp.Stream: DFrE_SLT
(PID.TID 0189.0001) - WARNING -   has not been filled (ndiag=  0 )
(PID.TID 0189.0001) WARNING DIAGNOSTICS_OUT  => write ZEROS instead

So, things seem to be consistent in my configuration (I am using the checkpoint64v version of the code): only implicit vertical diffusion, no explicit term, heat and salt budget OK. Most likely the problem is in GMRedi, but I never used that package...
To whom it might concern, here is also a link to a very nice and clear technical report on heat and salt budget in MITgcm by Abhisek Chakraborty and Jean-Michel Campin:

http://wwwcvs.mitgcm.org/viewvc/MITgcm/MITgcm/doc/Heat_Salt_Budget_MITgcm.pdf?revision=1.1&view=co

Hope this helps somehow...

Cheers,

SQ


On 25 Jan 2017, at 23:59:35, Dimitris Menemenlis wrote:

> Hi Martin, Zhan Su and I were puzzled by exactly the same question
> and came across your MITgcm question, but no answer :-(
> 
> Ou points out that DFrE_TH contains the GM contribution to vertical
> diffusivity computed “explicitly” in gmredi_rtransport.F, even when
> implicitDiffusion=.TRUE.
> 
> Dimitris Menemenlis
> 
>> On Mar 2, 2007, at 12:45 AM, Martin Losch <Martin.Losch at awi.de> wrote:
>> 
>> Hi,
>> let me add a related question:
>> 
>> for vertical diffusive flux there are two fields:
>> 1. DFrI_TH, implicit diffusive flux of theta
>> 2. DFrE_TH, explicit diffusive flux of theta
>> 
>> when I use a vertical mixing scheme that require implicit vertical diffusion such as KPP (in conjunction with GMredi), I expect that all diffusive flux is in DFrI_TH. But I still get a small contribution in DFrE_TH (explicit diffusive flux). Why is that so?
>> 
>> (Actually I have tried this only with passive tracers, so DFrITR01 and DFrETR01, but from looking a the code I don't see, why it should be different for theta).
>> 
>> Martin
>> 
>> On 1 Mar 2007, at 20:29, Patrick Heimbach wrote:
>> 
>>> 
>>> To add to Baylor's description at the thread
>>> http://forge.csail.mit.edu/pipermail/mitgcm-support/2007-February/004605.html
>>> 
>>> Quoting:
>>> 1) UVELTH is just the correlation between U and T.
>>> 2) UTHMASS is the correlation between U and T, weighted by 'mass', or
>>> HFac, which gives free-surface corrections.
>>> 3) ADVx_TH is the 'effect of advection'.  It includes flux-limiting
>>> and diffusion from the numerical scheme.
>>> 
>>> there is a fourth diagnostic
>>> 4) DFxE_TH
>>> which could be termed "diffusive", i.e. it contains all
>>> non-advective components in the dT/dt sum, such as diffusion due to
>>> Laplacian or biharmonic diffusion (diffKh, diffK4) and due to GM/Redi.
>>> 
>>> The fields 3) and 4) (ADVx_TH, DFxE_TH) are mass-weighted as well
>>> (yes, it's the mass of water in the grid cell),
>>> so you don't have to worry about cell area, thickness or surface corrections
>>> when computing sums or budgets.
>>> 
>>> 
>>> -p.
>>> 
>>> 
>>> 
>>> On Mar 1, 2007, at 1:54 PM, Valerie Benesh wrote:
>>> 
>>>> I am currently trying to understand the units of the advective and diffusive fluxes in the available diagnostics.  What is the difference between mass-weighted transport of a tracer and the advective flux of the tracer?  Does the mass transport include diffusion? I take it mass-weighting involves the mass of water in the grid cell?   How exactly are the units (kg/kg)*(m/s) come by for mass-weighted transport?  How are the units (kg/kg)*(m^3/s) achieved for fluxes of the tracer?  Are these the fluxes themselves at each cell boundary?  Any help understanding these units is appreciated.  Thanks,
>>>> 
>>>> Val
>>>> 
>>>> 
>>>> 
>>>> ***************************************************
>>>> Val Bennington
>>>> Graduate Student
>>>> Atmospheric and Oceanic Sciences
>>>> University of Wisconsin-Madison
>>>> benesh at wisc.edu
>>>> ***************************************************
>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> MITgcm-support mailing list
>>>> MITgcm-support at mitgcm.org
>>>> http://mitgcm.org/mailman/listinfo/mitgcm-support
>>> 
>>> ---
>>> Dr Patrick Heimbach | heimbach at mit.edu | http://www.mit.edu/~heimbach
>>> MIT | EAPS, 54-1518 | 77 Massachusetts Ave | Cambridge, MA 02139, USA
>>> FON: +1-617-253-5259 | FAX: +1-617-253-4464 | SKYPE: patrick.heimbach
>>> 
>>> 
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>> 
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