[MITgcm-support] Diagnostics package codes:: where are vertical flux and velocity fields?

[Jean-Michel Campin]

Hi Ian,

I am replying to support for now, but we will probably have to open an issue regarding
some of this confusing 9th character code.

1) You are right (and the documentation is not wrong here) that 3-D diagnostics with
 label "L" in 9th position are supposed to be at the vertical interface between 2 levels
 such as diagnostic level k would be between tracer level k-1 and level k ; describing 
 it's vertical position as "k -1/2" is not that wrong.
 The main problem here is that the letter "L" has been inherited from atmospheric set-up
 in pressure coordinate where, in this case, k -1/2 is physically "lower" than level k.

2) Regarding 2-D diagnostics, I think this label "U" is not right (and mis-leading), and 
  we should either use nothing (blank) or a specific code (other than current L/M/U) if 
  it's physically located at model domain top or bottom.
  Personally, I don't have any problem with some 2-D diagnostics with label "M1"
  (e.g., MXLDEPTH) when they are associated with some column/domain interior property.

Cheers,
Jean-Michel

On Wed, Jan 13, 2021 at 10:49:34AM +0000, Fenty, Ian G (US 329C) wrote:
> Hi JM,
> 
> I???m producing another set of ECCO NetCDF files for distribution and am hoping you can quickly help clarify something that came up between Ryan and I in his xmitgcm Python code.
> 
> As you know, the MITgcm diagnostics package uses several character ???codes??? to describe where variables are with respect to the C-grid.
> https://mitgcm.readthedocs.io/en/latest/outp_pkgs/outp_pkgs.html?highlight=wvelmass#diagnostic-parsing-array
> 
> All 3D vertical velocity and flux variables such as WVELMASS and ADVr_TH have the ???LR??? code in the 9 and 10 positions.
> 
> WVELMASS| 50 |       |WM      LR|m/s             |Vertical Mass-Weighted Comp of Velocity
> 
> According to the documentation, ???L??? means ???model level -1/2??? and ???R??? means Nr levels.  The confusion comes with the meaning of ???model level ???1/2???.  I interpret that these variable should start counting DOWN from the TOP face of the tracer cells, which should make the first value of WVELMASS the vertical velocity of the ocean surface, wvel(k=1).  Since k increases DOWN, model level ??? 1/2 should mean that the variable is located ABOVE the center of the tracer cell, UP towards to the surface.
> 
> It appears that at least superficially Ryan???s xmitgcm interprets the ???LR??? code to mean ???lower??? face, meaning that the first wvel is the vertical velocity of the BOTTOM of the tracer cell at k=1.
> 
> Adding confusion is the ???U??? code in the 9 position for several 2D surface flux fields (e.g., oceTAUX), with ???U??? meaning ???model level + 1/2 ???.  Since these are 2D surface fields, the ???model level + 1 /2 ??? strongly suggests that one should be counting UP by 1/2 from the tracer cell center to get to the surface. It kind of makes sense, but contradicts the interpretation of ???L???.
> 
> I examined the DIAGNOSTICS_FILL call for WVELMASS:     CALL DIAGNOSTICS_FILL(wVel, 'WVELMASS',0,Nr,0,1,1,myThid)
> 
> To me, this looks like the entire wVel field is passed, all 50 levels. None of the arguments suggest that WVELMASS starts from the BOTTOM of the tracer grid cell, wvel(k=2).
> 
>       SUBROUTINE DIAGNOSTICS_FILL(
>      I               inpFld, chardiag,
>      I               kLev, nLevs, bibjFlg, biArg, bjArg, myThid )
> 
> kLev = 0 : fill-in in the same order as the input array
> NLevs = Nr
> 
> Finally, I looked at the budget document that you put together with Abhishek.  Consider the equation for temperature tendency from advection:
> 
> Adv_tend = - [ {ADVr_TH(ix,iy,iz) ??? ADVr_TH(ix,iy,iz+1)}/CellVol + {ADVx_TH(ix+1,iy,iz) ??? ADVx_TH(ix,iy,iz)}/CellVol + {ADVy_TH(ix,iy+1,iz) ??? ADVy_TH(ix,iy,iz)}/CellVol ]
> 
> The vertical flux divergence term is ADVr_TH(iz) ??? ADVr_TH(iz+1) and the horizontal flux divergence terms are on ???iz???.  Again, this suggests that for a tracer cell at vertical level k=iz, ADVr_TH(iz) is the TOP of the grid cell and ADVr_TH(iz+1) is at the BOTTOM of the grid cell.
> 
> Please help shed some light!  Where is the first value in WVELMASS, ADVr_TH, etc?  The top or bottom of the tracer grid cells? Does the first value correspond to the top or bottom of the uppermost grid cell?  Is there an inconsistency between the ???L??? and ???U??? codes?
> 
> Thank you in advance.
> 
> -Ian
> 
> 
>