[MITgcm-support] more questions

Riema Rachmayani imoth_22 at yahoo.com
Mon Oct 2 04:40:50 EDT 2006


dear all,

the output of our simulation is in .data and .meta (mdsio output) which could read and draw the output in matlab right?? or mnc output which utilize netcdf to read and to draw the output, but we have how to convert .mnc to .nc first right?? how to convert .mnc to .nc??  

for now my output is in  .data and .meta, and i've try to draw the output in matlab, but it wasnt work well. To make it simple to read, i've try to save  .data and .meta in ascii file, but it wasnt work well too, any clue?? 

thank you..thank you...

regards, 
rima 




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Today's Topics:

   1. thanks martin (Riema Rachmayani)


----------------------------------------------------------------------

Message: 1
Date: Mon, 2 Oct 2006 08:40:54 +0100 (BST)
From: Riema Rachmayani 
Subject: [MITgcm-support] thanks martin
To: mitgcm-support at mitgcm.org
Message-ID: <20061002074054.66605.qmail at web53815.mail.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"

dear martin,
you were right about lines in data:
implicSurfPress=0.5,
implicDiv2DFlow=0.5,
i change them become 1.0 respectively....is that correct??
thanks martin

regards,
rima, indonesia

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Today's Topics:

   1. question... (Riema Rachmayani)
   2. Re: question... (Martin Losch)
   3. Numerical diffusion (Lars Inge Enstad)
   4. Re: Numerical diffusion (chris hill)
   5. Re: Numerical diffusion (Martin Losch)
   6. Re: Numerical diffusion (Baylor Fox-Kemper)


----------------------------------------------------------------------

Message: 1
Date: Fri, 29 Sep 2006 05:09:34 +0100 (BST)
From: Riema Rachmayani 
Subject: [MITgcm-support] question...
To: mitgcm-support at mitgcm.org
Message-ID: <20060929040934.71651.qmail at web53801.mail.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"

dear all,

i've already run verification of internal wave, i'm not change the input...i just run it!!....when i check the input, Tref is various to the vertical layer (20 layer), and Sref is uniform to the vertical layer (20 layer), nonhydrostatic=.false....(it mean the equation still hydrostatic right?)...and then i change nonhydrostatic=.true. , when i run it again...there was a message : 

config_check : nonhydrostatic  NOT SAFE with non fully implicit barotopic                         solver
config_check : to by-pass this STOP, comment this test and re-compile                           config_check
STOP ABNORMAL END : S/R Confid_check statement executed

i thought that it happen because Sref uniform, so i change Sref became various like Tref, but when i run it again, there was appears the same message...

what should i do??

thx mitgcm

best regard, 
rima, indonesia


mitgcm-support-request at mitgcm.org wrote: Send MITgcm-support mailing list submissions to
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Today's Topics:

   1. Specifying the tile size in curvilinear grids (Ian G. Fenty)
   2. Re: OBC problem: spurious boundary jets with C-D coupling
      (Mark Hadfield)
   3. Exf depends on cal? (Mark Hadfield)
   4. Re: Exf depends on cal? (Dimitris Menemenlis)


----------------------------------------------------------------------

Message: 1
Date: Wed, 27 Sep 2006 15:13:47 -0400
From: "Ian G. Fenty" 
Subject: [MITgcm-support] Specifying the tile size in curvilinear
 grids
To: mitgcm-support at mitgcm.org
Message-ID: <451ACD6B.9020108 at mit.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hello,
Is there a way to pre-specify exactly the x,y size of each tile at run 
time even if this means they have non-uniform sizes?  If so, would each 
tile then be known by a unique thread-id which could be known, or 
assigned, beforehand? 

Thanks,
Ian Fenty


------------------------------

Message: 2
Date: Thu, 28 Sep 2006 09:49:14 +1200
From: Mark Hadfield 
Subject: Re: [MITgcm-support] OBC problem: spurious boundary jets with
 C-D coupling
To: mitgcm-support at mitgcm.org
Message-ID: <451AF1DA.3060708 at niwa.co.nz>
Content-Type: text/plain; charset="iso-8859-1"

Thanks, Martin and Chris.

chris hill wrote:
> As Martin notes the code for CD with OBCS has not been written.
>  What resolution are you working at? Mostly CD is used for situations 
> where the deformation radius is not resolved i.e. resolutions > 25km. 
> For a limited area run it may not be needed. For resolutions where 
> eddy scale is resolved or at least things are eddy permitting then 
> sub-grid dissipation is more cleanly (although its still a dirty 
> business) handled by either fixed laplacian and biharmonic viscosities 
> or by the flow dependent smag/leith form (described in the online docs).
The simulation I am doing right now is at fairly coarse resolution (25 
km) and is diagnostic & linear, ie

      saltStepping = .FALSE.
      tempStepping = .FALSE.
      momStepping = .TRUE.
      momAdvection = .FALSE.

Simulations of this sort are prone to developing grid-scale noise, as I 
have found with ROMS, but biharmonic viscosity controls that nicely, 
thanks. Future, more realistic (I hope) simulations will use finer 
resolution and full dynamics.

The decision to start with the CD scheme enabled wasn't a decision, 
really, just inertia: I started with one of the verification experiments 
and started hacking.

-- 
Mark Hadfield          "Kei puwaha te tai nei, Hoea tahi tatou"
m.hadfield at niwa.co.nz
National Institute for Water and Atmospheric Research (NIWA)


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Message: 3
Date: Thu, 28 Sep 2006 13:00:22 +1200
From: Mark Hadfield 
Subject: [MITgcm-support] Exf depends on cal?
To: MITgcm Support 
Message-ID: <451B1EA6.8050804 at niwa.co.nz>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

When I tried to build MItgcm with the exf package, but without the cal 
package, it failed during preprocessing with messages about missing 
headers that obviously belong to the cal package. (Or was it during 
linking? Whatever. It failed, the messages clearly implicated cal, and 
when I "cal" to packages.conf, it worked.)

I presume, therefore, that pkg/pkg_depend should have an entry like

exf             +cal

-- 
Mark Hadfield          "Kei puwaha te tai nei, Hoea tahi tatou"
m.hadfield at niwa.co.nz
National Institute for Water and Atmospheric Research (NIWA)





------------------------------

Message: 4
Date: Wed, 27 Sep 2006 21:23:11 -0700
From: Dimitris Menemenlis 
Subject: Re: [MITgcm-support] Exf depends on cal?
To: mitgcm-support at mitgcm.org
Message-ID: <451B4E2F.4010608 at sbcglobal.net>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Mark, you are right.  pkg/exf requires pkg/cal.
I have modified pkg/pkg_depend as suggested and checked it into CVS.
Cheers, Dimitris


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Message: 2
Date: Fri, 29 Sep 2006 08:48:09 +0200
From: Martin Losch 
Subject: Re: [MITgcm-support] question...
To: MITgcm Support 
Message-ID: 
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed

Dear Rima,

this check doesn't have anything to do with Tref or Sref.
S/R (=subroutine) config_check.F tests the consistency of a few  
things. In this case the message is quite clear, isn't it:  
"nonhydrostatic  NOT SAFE with non fully implicit barotopic solver".

As far as I can see, this message is related to these lines in data:
implicSurfPress=0.5,
implicDiv2DFlow=0.5,
which make the solver semi-implicit (I am guessing, I have never used  
these flags myself), they make the model use a Crank-Nickelson time  
stepping scheme (according to model/inc/PARAMS.h, where most  
parameters are briefly described).

You have two options:
1. comment out these lines to go back to full implicit solver (which  
i would do, maybe someone can comment on WHY the solver is not fully  
implicit in this experiment)
2. Ignore the warning and comment out the corresponding STOP  
statement in model/src/check_config.F (as suggested in the second  
line of the warning, but it's probably not safe.)

Martin, Germany

PS. there is also a flag "implicitIntGravWave" (default=false), which  
you may want to try in conjunction with internal gravity wave .

On Sep 29, 2006, at 6:09 AM, Riema Rachmayani wrote:

> dear all,
>
> i've already run verification of internal wave, i'm not change the  
> input...i just run it!!....when i check the input, Tref is various  
> to the vertical layer (20 layer), and Sref is uniform to the  
> vertical layer (20 layer), nonhydrostatic=.false....(it mean the  
> equation still hydrostatic right?)...and then i change  
> nonhydrostatic=.true. , when i run it again...there was a message :
>
> config_check : nonhydrostatic  NOT SAFE with non fully implicit  
> barotopic                         solver
> config_check : to by-pass this STOP, comment this test and re- 
> compile                           config_check
> STOP ABNORMAL END : S/R Confid_check statement executed
>
> i thought that it happen because Sref uniform, so i change Sref  
> became various like Tref, but when i run it again, there was  
> appears the same message...
>
> what should i do??
>
> thx mitgcm
>
> best regard,
> rima, indonesia


------------------------------

Message: 3
Date: Fri, 29 Sep 2006 10:51:30 +0200
From: Lars Inge Enstad 
Subject: [MITgcm-support] Numerical diffusion
To: mitgcm-support at mitgcm.org
Message-ID: <1159519890.3396.3.camel at fikentre.ii.uib.no>
Content-Type: text/plain; charset=ISO-8859-15

Hello

I am currently trying to implement an alternative vertical turbulence
model in MITgcm (GOTM (General Ocean Turbulence Model Burchard et
al.), has this been tried before?). My question is about the numerical
diffusion in the momentum advection scheme in MITgcm. How does this
depend on the spatial and temporal discretisation? What is the momentum
advection scheme with the lowest possible numerical diffusion in
MITgcm?  

One of the test cases I want to verify the code with is channel
flow. In previous models I have used for channel flow, I have used a
constant pressure gradient to force the flow. Is there some easy way
to set up MITgcm this way?

Best Regards
Lars Inge Enstad

-- 
Lars Inge Enstad
Post Doc
Computational Mathematics Unit
Bergen Center for Computational Science
UNIFOB/University of Bergen
Thormøhlensgt. 55
N-5008 Bergen, Norway




------------------------------

Message: 4
Date: Fri, 29 Sep 2006 07:32:49 -0400
From: chris hill 
Subject: Re: [MITgcm-support] Numerical diffusion
To: mitgcm-support at mitgcm.org
Message-ID: <451D0461.5000909 at mit.edu>
Content-Type: text/plain; charset=ISO-8859-15; format=flowed

Lars,

  The centered second order scheme is not diffusive, but it is dispersive!

  There is a section in the online reference manual

http://mitgcm.org/r2_web_testing/latest/online_documents/node85.html

on how ( mostly horizontal ) viscosity is calculated. For vertical 
mixing there is Large et al KPP code incorporated into the dynamics.

  Martin Losch at AWI was recently thinking about whether to connect to 
the GOTM suite of schemes. He may have some thoughts on this. Martin 
also has a nice channel setup that he may be willing to share? He is on 
this list.

Chris


Lars Inge Enstad wrote:
> Hello
> 
> I am currently trying to implement an alternative vertical turbulence
> model in MITgcm (GOTM (General Ocean Turbulence Model Burchard et
> al.), has this been tried before?). My question is about the numerical
> diffusion in the momentum advection scheme in MITgcm. How does this
> depend on the spatial and temporal discretisation? What is the momentum
> advection scheme with the lowest possible numerical diffusion in
> MITgcm?  
> 
> One of the test cases I want to verify the code with is channel
> flow. In previous models I have used for channel flow, I have used a
> constant pressure gradient to force the flow. Is there some easy way
> to set up MITgcm this way?
> 
> Best Regards
> Lars Inge Enstad
> 



------------------------------

Message: 5
Date: Fri, 29 Sep 2006 15:16:40 +0200
From: Martin Losch 
Subject: Re: [MITgcm-support] Numerical diffusion
To: mitgcm-support at mitgcm.org
Message-ID: <9636ED5C-87E3-400C-8BD2-83D387AAB75A at awi-bremerhaven.de>
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed

Please wait until Monday,

M.
On 29 Sep 2006, at 13:32, chris hill wrote:

> Lars,
>
>  The centered second order scheme is not diffusive, but it is  
> dispersive!
>
>  There is a section in the online reference manual
>
> http://mitgcm.org/r2_web_testing/latest/online_documents/node85.html
>
> on how ( mostly horizontal ) viscosity is calculated. For vertical  
> mixing there is Large et al KPP code incorporated into the dynamics.
>
>  Martin Losch at AWI was recently thinking about whether to connect  
> to the GOTM suite of schemes. He may have some thoughts on this.  
> Martin also has a nice channel setup that he may be willing to  
> share? He is on this list.
>
> Chris
>
>
> Lars Inge Enstad wrote:
>> Hello
>> I am currently trying to implement an alternative vertical turbulence
>> model in MITgcm (GOTM (General Ocean Turbulence Model Burchard et
>> al.), has this been tried before?). My question is about the  
>> numerical
>> diffusion in the momentum advection scheme in MITgcm. How does this
>> depend on the spatial and temporal discretisation? What is the  
>> momentum
>> advection scheme with the lowest possible numerical diffusion in
>> MITgcm?  One of the test cases I want to verify the code with is  
>> channel
>> flow. In previous models I have used for channel flow, I have used a
>> constant pressure gradient to force the flow. Is there some easy way
>> to set up MITgcm this way?
>> Best Regards
>> Lars Inge Enstad
>
> _______________________________________________
> MITgcm-support mailing list
> MITgcm-support at mitgcm.org
> http://mitgcm.org/mailman/listinfo/mitgcm-support



------------------------------

Message: 6
Date: Fri, 29 Sep 2006 09:29:22 -0400
From: Baylor Fox-Kemper 
Subject: Re: [MITgcm-support] Numerical diffusion
To: mitgcm-support at mitgcm.org
Message-ID: 
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed

Lars,
   If you are serious about including the GOTM, you should take a  
look at how KPP is implemented, MITgcm/pkg/kpp
   You may have significant difficulties in incorporating GOTM, as it  
seems that GOTM prescribes fluxes and changes to the mean flow not  
diffusivities/viscosities (which is how the MITgcm receives all  
current parameterizations).  However, I would LOVE to see it  
implemented!
    -Baylor

On Sep 29, 2006, at 7:32 AM, chris hill wrote:

> Lars,
>
>  The centered second order scheme is not diffusive, but it is  
> dispersive!
>
>  There is a section in the online reference manual
>
> http://mitgcm.org/r2_web_testing/latest/online_documents/node85.html
>
> on how ( mostly horizontal ) viscosity is calculated. For vertical  
> mixing there is Large et al KPP code incorporated into the dynamics.
>
>  Martin Losch at AWI was recently thinking about whether to connect  
> to the GOTM suite of schemes. He may have some thoughts on this.  
> Martin also has a nice channel setup that he may be willing to  
> share? He is on this list.
>
> Chris
>
>
> Lars Inge Enstad wrote:
>> Hello
>> I am currently trying to implement an alternative vertical turbulence
>> model in MITgcm (GOTM (General Ocean Turbulence Model Burchard et
>> al.), has this been tried before?). My question is about the  
>> numerical
>> diffusion in the momentum advection scheme in MITgcm. How does this
>> depend on the spatial and temporal discretisation? What is the  
>> momentum
>> advection scheme with the lowest possible numerical diffusion in
>> MITgcm?  One of the test cases I want to verify the code with is  
>> channel
>> flow. In previous models I have used for channel flow, I have used a
>> constant pressure gradient to force the flow. Is there some easy way
>> to set up MITgcm this way?
>> Best Regards
>> Lars Inge Enstad
>
> _______________________________________________
> MITgcm-support mailing list
> MITgcm-support at mitgcm.org
> http://mitgcm.org/mailman/listinfo/mitgcm-support



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