Will new sigma formulation give problems?

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lanerolle
Posts: 157
Joined: Mon Apr 28, 2003 5:12 pm
Location: NOAA

Will new sigma formulation give problems?

#1 Post by lanerolle » Tue Dec 13, 2005 9:41 pm

Hi Everybody,

I have coded up a new sigma formulation in to ROMS where theta_b is no longer a constant (but theta_s, Tcline, hC are all constant as before) but is a function of depth (h): theta_b=A*tanh(c_cut*(h-h_cut))+B where A, B, h_cut, c_cut are all constants. This means that over the grid, if the bottom bathymetry (h) is varying then so will the sigma parameter Cs_r (and Cs_w). I like this formulation because in the deep, it refines the grid both at the surface and the bottom but in the shallow regions, it refines mainly at the bottom thereby resolving the bottom boundary layer; furthermore, this formulation also prevents excessive heating (due to heat fluxes) of the shallow regions of the model domain.

A colleague of mine who put a similar sigma formulation in to his ocean model informed me that when Cs_r (and Cs_w) is no longer constant in x-y (or i-j) space, the flow equations coded up in the model also need to be modified accordingly. Is this true - in particular for ROMS? Do theta_s, theta_b, Tcline in ROMS need to be global constants?

Thank you.

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shchepet
Posts: 185
Joined: Fri Nov 14, 2003 4:57 pm

RE: Will new sigma formulation give problems?

#2 Post by shchepet » Sun Dec 18, 2005 6:50 pm

No, changes of this kind will not cause any conflict.

All ROMS codes are written in such a way that any physical code interacts only with arrays z_r and z_w and makes no assumption about where these arrays are coming from. In fact, the only places in the code which are aware of the S-coordinate are set_scoord and set_depth, which compute z_r and z_w. In principle, these two subroutines can be modified to be virtually anything, and the rest of the code is still OK with it.

THE ONLY DELICATE issue here is distrurbance of vertical coordinate system due to free-surface elevation. In ROMS codes (unlike SCRUM, this is different) it is done in two stages: first set "unperturbed" coordinate, which corresponds to zero free surface; then the whole column is perturbed in a very specific way, see set_depth:

Code: Select all

z_w0= .......      <--- whatever coordinate transformation
z_w(i,j,k)=z_w0+Zt_avg1(i,j)*(1.0_r8+z_w0/h(i,j))
the second line must be exactly as above.

Inconsistency here results in wrong computation of vertical velocity, and loss of constancy preservation for tracers.

ilicakme
Posts: 14
Joined: Mon Jun 27, 2005 4:38 pm
Location: University of Bergen

Re: Will new sigma formulation give problems?

#3 Post by ilicakme » Tue Jun 26, 2007 4:53 pm

Hi,

I want to change my theta_b with depth just as "lanerolle" did it in the past,
by chance could you send me your code or explain how you did it?

Thanks,
Mehmet

lanerolle wrote:Hi Everybody,

I have coded up a new sigma formulation in to ROMS where theta_b is no longer a constant (but theta_s, Tcline, hC are all constant as before) but is a function of depth (h): theta_b=A*tanh(c_cut*(h-h_cut))+B where A, B, h_cut, c_cut are all constants. This means that over the grid, if the bottom bathymetry (h) is varying then so will the sigma parameter Cs_r (and Cs_w). I like this formulation because in the deep, it refines the grid both at the surface and the bottom but in the shallow regions, it refines mainly at the bottom thereby resolving the bottom boundary layer; furthermore, this formulation also prevents excessive heating (due to heat fluxes) of the shallow regions of the model domain.

A colleague of mine who put a similar sigma formulation in to his ocean model informed me that when Cs_r (and Cs_w) is no longer constant in x-y (or i-j) space, the flow equations coded up in the model also need to be modified accordingly. Is this true - in particular for ROMS? Do theta_s, theta_b, Tcline in ROMS need to be global constants?

Thank you.
MI

User avatar
shchepet
Posts: 185
Joined: Fri Nov 14, 2003 4:57 pm

identification standard for vertical coordinates

#4 Post by shchepet » Tue Jun 26, 2007 11:03 pm

It reminds me that we, as a community, should come up with an
identification standard for different types of vertical coordinates
in order for pre- and post-processing software to recognize it
correctly and automatically.


I personally no longer use the original S-coordinate for quite
a while, more than one year, and consider that obsolete because
of inherent limitation of "hc < hmin", where "hc" is intended
to be thermocline depth, "hmin" is minimum topographic depth.
Instead I use

Code: Select all

       z^{(0)} = h * [s*hc + Cs(s)*h] / [h + hc]
which is subsequently perturbed by free surface in a standard way

Code: Select all

            z =  z^{(0)} + zeta * [1 + z^{(0)}/h].
Above: h = h(x,y) is bottom topography (positive); z^{(0)} is
unperturbed depth (negative) as function of (x,y,s); "s" is
sigma-coordinate, -1 < s < 0, where, as usual s=0 means surface,
and s=-1 bottom; "C_s(s)" is nonlinear stretching function,
typically Cs(s) = sinh(theta_s*s)/sinh(theta_s), but consider
others as well; "hc" is expected thermocline depth, typically
chosen as 100 to 250 meters. Note that the minimum depth
limitation no longer applies, and it is OK to have hmin = 25
meters, while hc = 250 meters in Pacific grid.


The above results in nearly uniform grid spacing above "hc" with
mild topographic dependency of top-most grid boxes in deep areas.


Since we want to keep the vertical transformation open,
I introduced the following set of rules for netCDF files:

1. Introduce global attribute called "VertCoordType" to identify
transformation (implying that a 3-letter code is assigned to
each transform), so that post processing software can read it
and interpret the data correctly.

2. Keep only minimal information sufficient to identify
transformation, for example, ncdump on history file reads

Code: Select all

global attributes:
         ...
                :VertCoordType = "NEW" ;
                :hc = 250.f ;
                :Cs_w = -1.f, -0.8290268f, ...., 0.f ;
                :Cs_r = -0.9105092f, ....,  -0.00046545f ;
         ....
where:

(i) it is my preference to store things like "Cs_w" and "Cs_r" as
global attributes rather than variables because it requires
fewer netCDF calls to accomplish (AGRIF/RomsTools by Pierrick
follow the same convention, and it is all dated back to 2001,
but Rutgers ROMS stores "Cs_r,w" as variables);

(ii) Non-stretched coordinates "s_r" and "s_w" are no longer
stored because it silly;

(iii) "hc" is stored because it is necessary for transformation
above.

(iv) "theta_s" and "theta_b" which are used to construct "Cs_w"
and "Cs_r" may be, or may not be stored for human information
purposes only: but the post-processing software MUST NOT RELY
on them. Instead, it must read "Cs_w" and "Cs_r" as arrays
of 0:N and N values and use them [NOT "theta_s,b"(!)] to
reconstruct the transformation. The reason for this is that
the particular functional form of "Cs_r,w" may be changed
without notice at any moment, but if post-processing software
reads them, rather than trying to reproduce via "theta_s,b"
(hence relying on specific formulas), the transformation
can still be correctly interpreted.

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