[MITgcm-support] nondivergent flow advecting a tracer

[Edward W Doddridge]

Hi You-Kun,

I’ve actually never used the offline code, so I’m not certain. I believe that deltaToffline is the time step used by the model to select the correct velocity file, while delaTtracer is the time step used to advect the tracer in the flow field.

But, you might find the answers you’re looking for here: http://mitgcm.org/public/r2_manual/final/online_documents/node170.html

These are the example experiments using the offline code. They haven’t been translated from the old documentation yet, so if you only looked at read the docs, you might have missed them.

Cheers,
Ed


________________________________
Edward Doddridge
Postdoctoral researcher
Earth, Atmospheric and Planetary Sciences
Massachusetts Institute of Technology

www.doddridge.me<http://www.doddridge.me>

On 30 May 2019, at 12:38, 钱钰坤 <qianyk at mail3.sysu.edu.cn<mailto:qianyk at mail3.sysu.edu.cn>> wrote:

Hi Edward,

Thanks very much for your reminding.  After searching for the 'cfl' stuff in STDOUT, I found indeed
that the CFL condition is violated by using deltaTtracer=86400.  So I need to reduce this parameter.

I am now confused that how does this parameter (and deltaTClock) in data file relate to my daily
velocity data and deltaToffline=3600 set in data.off?  Can this parameter be adjusted at will without
any constraint in my OffLine Run?

------------------
Best regards

Yu-Kun Qian (钱钰坤)
Center for Monsoon and Environment Research
Department of Atmospheric Sciences
School of Environmental Science and Engineering
Sun Yat-sen University
No. 135 Xingang West Road, Haizhu District
Guangzhou, 510275, P.R. China
Tel; 020-84115227
Email: qianyk at mail3.sysu.edu.cn<mailto:qianyk at mail2.sysu.edu.cn>




------------------ 原始邮件 ------------------
发件人: "Edward W Doddridge"<ewd at mit.edu<mailto:ewd at mit.edu>>;
发送时间: 2019年5月30日(星期四) 晚上10:06
收件人: "mitgcm-support at mitgcm.org<mailto:mitgcm-support at mitgcm.org>"<mitgcm-support at mitgcm.org<mailto:mitgcm-support at mitgcm.org>>;
主题: Re: [MITgcm-support] nondivergent flow advecting a tracer

Hi Yu-Kun,

I suspect that your timestep violates the cfl stability criterion. You should check that deltaTtracer*velocity/grid_spacing is less than 1. Ideally you’d like it to be much less than 1.

Cheers,
Ed


________________________________
Edward Doddridge
Postdoctoral researcher
Earth, Atmospheric and Planetary Sciences
Massachusetts Institute of Technology

www.doddridge.me<http://www.doddridge.me/>

On 30 May 2019, at 09:48, 钱钰坤 <qianyk at mail3.sysu.edu.cn<mailto:qianyk at mail3.sysu.edu.cn>> wrote:

Hi all,

I am using a series of geostrophic velocity data (derived from AVISO sea surface height)
to advect a passive tracer in an offline mode.  Following the paper by Abernathey and Marshall
(2013, JGR), first I made a nondivergent correction to the original geostrophic velocity data
through Helmholtz Decomposition.  Then I used the nondivergent velocity to advect a tracer.
However, after a few timesteps the tracer field is unstable and generates very large values and
eventually contaminated the results.

I think there are two things need to be verified.

First, the correction is done correctly.  Actually
I followed the guidance by Ryan Abernathey at:
    https://github.com/rabernat/mitgcm_2D_global/blob/master/notebooks/correction.ipynb
I run the offline model first using original geostrophic velocity to dump the diagnostics of streamfunction
(psi) and velocity potential (phi).  Then I use the xmitgcm utility to calculate the nondivergent velocity as:
    u_psi = -(numpy.roll(psi, -1, axis=-2) - psi) / dyG / drF
    v_psi =  (numpy.roll(psi, -1, axis=-1) - psi) / dxG / drF
This code above should be modified somewhat if one uses the latest xmitgcm released a few days ago.
I did not do any mask since I think the MITgcm model will mask the velocity when run in offline mode (
I provided a bathymetry data to the model generated based on AVISO SSH land-sea mask).

Second, the offline model parameters (delta-t related) are correctly set.  Although I've read some emails
on this issue, I'm still not so sure how to set these parameters.  The following are my choices:
    data:      deltaTtracer = 86400,
                  deltaTClock = 86400,
    data.off:  deltaToffline = 3600,      (smaller dt for accuracy)
                  offlineForcingPeriod = 86400,    (AVISO data is daily mean)
                  offlineForcingCycle = 0,     (no need to reuse the velocity)
When using the above params, the offline model asks for velocity data whose names are: u.0.data, u.24.data,
u.48.data...  So I rename the velocity data into this convention.

Now I am really confused why the tracer overflows after only 4-5 timesteps (days).  Is there anything wrong
with the above two procedures?


------------------
Best regards

Yu-Kun Qian (钱钰坤)
Center for Monsoon and Environment Research
Department of Atmospheric Sciences
School of Environmental Science and Engineering
Sun Yat-sen University
No. 135 Xingang West Road, Haizhu District
Guangzhou, 510275, P.R. China
Tel; 020-84115227
Email: qianyk at mail3.sysu.edu.cn<mailto:qianyk at mail2.sysu.edu.cn>


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