[MITgcm-support] more questions

Wed Nov 1 04:14:58 EST 2006

hi,...
first of all...i'd like to say thanks to martin for answering my question...
but i still have problem..i have done something wrong but i dont remember what i have done untill i got long error message :
In program 'main' :
main.f : 438
        if (eebooterror) then
invalid declaration of or reference to symbol 'eebooterror' at (^) [Initially seen at (^)] 
main.f : 439

       fatalerror=.true.

invalid declaration of or reference to symbol '  fatalerror' at (^) [Initially seen at (^)] 
main.f : 443

          if (useSETRLSTK) then

invalid declaration of or reference to symbol 'usesetrlstk' at (^) [Initially seen at (^)]
main.f : 447
    if (useSIGREG) then

invalid declaration of or reference to symbol 'usesigreg' at (^) [Initially seen at (^)]
main.f : 448

   i_got_signal=0

invalid declaration of or reference to symbol ' i_got_signal' at (^) [Initially seen at (^)]
main.f : 498

 Do I=1, nthreads

invalid declaration of or reference to symbol ' nthreads' at (^) [Initially seen at (^)].
main.f : 512
threadIsComplete(myThid)=.true.

invalid declaration of or reference to symbol ' threadIsComplete' at (^) [Initially seen at (^)]
make : ***(main.o) error 1

what should i do??

for martin : about z coordinate....as seen on fig.1.15 at page 22 (MITgcm manual's )..there are variation of delZ, for several grid there are 5 layers, but there also 6 layers for another grid, how to determine the layers in program?? maximum layers (6) or variation of layers??

and i have problem when my topography found sill or seamount, how to apply the z coordinate?? can you give me some example for this kind of case?? 

i'll hardly wait for your reply...
thank you

regards,
rima

 ----- Original Message ----
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Today's Topics:

   1. questions (Riema Rachmayani)
   2. Re: questions (Martin Losch)

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Message: 1
Date: Sun, 29 Oct 2006 22:00:28 -0800 (PST)
From: Riema Rachmayani <imoth_22 at yahoo.com>
Subject: [MITgcm-support] questions
To: mitgcm-support at mitgcm.org
Message-ID: <20061030060029.97958.qmail at web53803.mail.yahoo.com>
Content-Type: text/plain; charset="us-ascii"

hi all..

Is MITGCM using sigma coordinate?? how to treat if there is slope for vertical grid without sigma coordinate??

what the different between T.init and tref in internal_wave verification??

thx
rima

----- Original Message ----
From: "mitgcm-support-request at mitgcm.org" <mitgcm-support-request at mitgcm.org>
To: mitgcm-support at mitgcm.org
Sent: Friday, October 27, 2006 11:00:06 PM
Subject: MITgcm-support Digest, Vol 40, Issue 16

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Today's Topics:

   1. KPP and KPP_ghatUseTotalDiffus (David Ferreira)
   2. Re: KPP and KPP_ghatUseTotalDiffus (Martin Losch)

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

Message: 1
Date: Thu, 26 Oct 2006 20:40:08 -0400
From: David Ferreira <dfer at ocean.mit.edu>
Subject: [MITgcm-support] KPP and KPP_ghatUseTotalDiffus
To: mitgcm-support <mitgcm-support at mitgcm.org>
Message-ID: <45415568.9000800 at ocean.mit.edu>
Content-Type: text/plain; charset=us-ascii; format=flowed

Hi,

I just run into the "KPP_ghatUseTotalDiffus" flag in KPP.
It seems to be adding some contribution coming from
GM Redi to the KPP diffusivity, but it's not quite to clear to me.

Could someone explain me what this flag exactly does
and what's the reason for it ?
Thanks,
david

-- 

Ferreira David               Tel : 617 253 7967 
EAPS Room 54-1515,
Massachusetts Institute of Technology,
77 Massachusetts Avenue
Cambridge, MA, 02139

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

Message: 2
Date: Fri, 27 Oct 2006 08:38:26 +0200
From: Martin Losch <mlosch at awi-bremerhaven.de>
Subject: Re: [MITgcm-support] KPP and KPP_ghatUseTotalDiffus
To: mitgcm-support at mitgcm.org
Message-ID: <BA52AD18-38D9-4876-BB03-C92FDADC5F42 at awi-bremerhaven.de>
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed

Hi David,
as far as I can see, the flag is used in kpp_transport_t/s/ptr where  
the counter-gradient flux (or non-local term) of KPP is applied (the  
second term in the following expression):
kappa1*dtracer/dz - kappa2*ghat*surfaceFlux

In pure KPP kappa1=kappa2, but GM has a vertical component of kappa  
as well and I guess here you can decide whether this contribution is  
included in kappa2 (it's part of kappa1) as well. I don't know the  
reason/"physics" behind this.

Martin

On 27 Oct 2006, at 02:40, David Ferreira wrote:

> Hi,
>
> I just run into the "KPP_ghatUseTotalDiffus" flag in KPP.
> It seems to be adding some contribution coming from
> GM Redi to the KPP diffusivity, but it's not quite to clear to me.
>
> Could someone explain me what this flag exactly does
> and what's the reason for it ?
> Thanks,
> david
>
>
>
> -- 
>
> Ferreira David               Tel : 617 253 7967 EAPS Room 54-1515,
> Massachusetts Institute of Technology,
> 77 Massachusetts Avenue
> Cambridge, MA, 02139
>
> _______________________________________________
> MITgcm-support mailing list
> MITgcm-support at mitgcm.org
> http://mitgcm.org/mailman/listinfo/mitgcm-support

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

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Message: 2
Date: Mon, 30 Oct 2006 09:48:49 +0100
From: Martin Losch <mlosch at awi-bremerhaven.de>
Subject: Re: [MITgcm-support] questions
To: mitgcm-support at mitgcm.org
Message-ID: <971293D7-88C7-441E-B1C4-C449CA52E49D at awi-bremerhaven.de>
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed

Riema,

the MITgcm is z-coordinate model (that is, layers are approximately  
geopotential surfaces). Theres is no bottom-following sigma  
coordinate. Slopes are represented as a step wise stair case as in  
all z-coordinates models. As you may know this approach leads to  
problems with flow down the slope, when the resolution is poor, that  
is, when you don't resolve the slope properly.

tRef/hydrogThetaFile: please have a look at ini_theta.F, where you  
will see, that theta is first initialized with tRef, then overwritten  
with whatever is in the file that you specify for hydrogThetaFile  
(T.init in your case). If hydrogThetaFile = ' ' (default), tRef is  
the initial profiles (everywhere in your domain).
if EOStype = 'LINEAR', tRef/sRef play a second role: they are the  
reference temperaure/salinity in the linear eos: rho = rho0*(1-talpha* 
(theta-tref) + sbeta*(salt-sref)).

Martin

On 30 Oct 2006, at 07:00, Riema Rachmayani wrote:

> hi all..
>
> Is MITGCM using sigma coordinate?? how to treat if there is slope  
> for vertical grid without sigma coordinate??
>
> what the different between T.init and tref in internal_wave  
> verification??
>
> thx
> rima
>
> ----- Original Message ----
> From: "mitgcm-support-request at mitgcm.org" <mitgcm-support- 
> request at mitgcm.org>
> To: mitgcm-support at mitgcm.org
> Sent: Friday, October 27, 2006 11:00:06 PM
> Subject: MITgcm-support Digest, Vol 40, Issue 16
>
> Send MITgcm-support mailing list submissions to
>     mitgcm-support at mitgcm.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>     http://mitgcm.org/mailman/listinfo/mitgcm-support
> or, via email, send a message with subject or body 'help' to
>     mitgcm-support-request at mitgcm.org
>
> You can reach the person managing the list at
>     mitgcm-support-owner at mitgcm.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of MITgcm-support digest..."
>
>
> Today's Topics:
>
>    1. KPP and KPP_ghatUseTotalDiffus (David Ferreira)
>    2. Re: KPP and KPP_ghatUseTotalDiffus (Martin Losch)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 26 Oct 2006 20:40:08 -0400
> From: David Ferreira <dfer at ocean.mit.edu>
> Subject: [MITgcm-support] KPP and KPP_ghatUseTotalDiffus
> To: mitgcm-support <mitgcm-support at mitgcm.org>
> Message-ID: <45415568.9000800 at ocean.mit.edu>
> Content-Type: text/plain; charset=us-ascii; format=flowed
>
> Hi,
>
> I just run into the "KPP_ghatUseTotalDiffus" flag in KPP.
> It seems to be adding some contribution coming from
> GM Redi to the KPP diffusivity, but it's not quite to clear to me.
>
> Could someone explain me what this flag exactly does
> and what's the reason for it ?
> Thanks,
> david
>
>
>
> -- 
>
> Ferreira David               Tel : 617 253 7967
> EAPS Room 54-1515,
> Massachusetts Institute of Technology,
> 77 Massachusetts Avenue
> Cambridge, MA, 02139
>
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 27 Oct 2006 08:38:26 +0200
> From: Martin Losch <mlosch at awi-bremerhaven.de>
> Subject: Re: [MITgcm-support] KPP and KPP_ghatUseTotalDiffus
> To: mitgcm-support at mitgcm.org
> Message-ID: <BA52AD18-38D9-4876-BB03-C92FDADC5F42 at awi-bremerhaven.de>
> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
>
> Hi David,
> as far as I can see, the flag is used in kpp_transport_t/s/ptr where
> the counter-gradient flux (or non-local term) of KPP is applied (the
> second term in the following expression):
> kappa1*dtracer/dz - kappa2*ghat*surfaceFlux
>
> In pure KPP kappa1=kappa2, but GM has a vertical component of kappa
> as well and I guess here you can decide whether this contribution is
> included in kappa2 (it's part of kappa1) as well. I don't know the
> reason/"physics" behind this.
>
> Martin
>
> On 27 Oct 2006, at 02:40, David Ferreira wrote:
>
> > Hi,
> >
> > I just run into the "KPP_ghatUseTotalDiffus" flag in KPP.
> > It seems to be adding some contribution coming from
> > GM Redi to the KPP diffusivity, but it's not quite to clear to me.
> >
> > Could someone explain me what this flag exactly does
> > and what's the reason for it ?
> > Thanks,
> > david
> >
> >
> >
> > --
> >
> > Ferreira David               Tel : 617 253 7967 EAPS Room 54-1515,
> > Massachusetts Institute of Technology,
> > 77 Massachusetts Avenue
> > Cambridge, MA, 02139
> >
> > _______________________________________________
> > MITgcm-support mailing list
> > MITgcm-support at mitgcm.org
> > http://mitgcm.org/mailman/listinfo/mitgcm-support
>
>
>
> ------------------------------
>
> _______________________________________________
> MITgcm-support mailing list
> MITgcm-support at mitgcm.org
> http://mitgcm.org/mailman/listinfo/mitgcm-support
>
>
> End of MITgcm-support Digest, Vol 40, Issue 16
> **********************************************
>
>
> Send instant messages to your online friends http:// 
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