[MITgcm-support] Adding 3D diffusivity field to model input

Robert Nazarian rn2 at Princeton.EDU
Sat Oct 7 12:37:20 EDT 2017

Hi Jody,

It is indeed a CFL issue. Thanks so much for the advice!


From: MITgcm-support [mitgcm-support-bounces at mitgcm.org] on behalf of Jody Klymak [jklymak at uvic.ca]
Sent: Friday, October 06, 2017 3:26 PM
To: mitgcm-support at mitgcm.org
Subject: Re: [MITgcm-support] Adding 3D diffusivity field to model input

Hi Robert,

I’m pretty sure there is a CFL criterion for vertical diffusivity; basically dt < dz^2/K .  Are you sure that is being satisfied everywhere, in particular in any partial near-bottom cells you have?  Its unusual for it to be violated, but if dz is very small or your imposed K very large.

Have you tried inputting a constant low K to make sure its being input properly?

Cheers,   Jody

On 6 Oct 2017, at  11:47 AM, Robert Nazarian <rn2 at Princeton.EDU<mailto:rn2 at Princeton.EDU>> wrote:


I'm attempting to insert a 3D matrix of vertical diapycnal diffusivities that are constant in time (with no wave forcing) and comparing it with a simulation where the diapycnal diffusivities are not included (but the wave forcing is included). To modify the existing simulation, I've turned off the wave forcing and, based on documentation, made two changes to account for a 3D difussivity input. First, I’ve added #define ALLOW_3D_DIFFKR in CPP_OPTIONS.h. Second, I’ve added diffKrFile=‘FileName’ under &PARM05 in data. This file is formatted in the same manner as my initial T and S fields, so I know that the formatting is not the issue. The values of vertical diapycnal diffusivities in this 3D matrix are all greater than or equal to 0. I've run the model for just a few time steps and time 0 is fine, however, the first time step yields NaN velocity and temperature values, so something is clearly wrong. Any advice on what I’m missing in my setup would be much appreciated.

Thanks so much,
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Jody Klymak

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