[MITgcm-support] MITgcm-support Digest, Vol 124, Issue 25

李志远 oceanlizy at 163.com
Tue Oct 29 00:12:29 EDT 2013



first, thanks for your advice ,but I tried "../../../tools/genmake2 -mods=../code -of=../../../OPTFILE" 
something is still wrong:   
    Warning: ROOTDIR was not specified; try using a local copy of MITgcm found at "../../.. "
   getting OPTFILE information:
Error : can't read OPTFILE="../../../OPTFILE"




I don't know what does it mean .


many thanks!






At 2013-10-29 11:45:57,mitgcm-support-request at mitgcm.org wrote:
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>Today's Topics:
>
>   1. diagnosing numerical diffusion (Ryan Abernathey)
>   2. diagnosing gmredi fluxes for tracers (Christoph Voelker)
>   3. problems with specifying optfile (???)
>   4. Re: problems with specifying optfile (Alexander Slavin)
>   5. Re: problems with specifying optfile (Jody Klymak)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Mon, 28 Oct 2013 12:01:11 -0400
>From: Ryan Abernathey <ryan.abernathey at gmail.com>
>To: mitgcm-support at mitgcm.org
>Subject: [MITgcm-support] diagnosing numerical diffusion
>Message-ID:
>	<CAJAZx5DbR2ue_KiQQJOCyxEOEmNbS6+Aa-bbUXtomqatLd1Lag at mail.gmail.com>
>Content-Type: text/plain; charset="iso-8859-1"
>
>Hello,
>
>We are working on closing the tracer variance budget in a way that is
>consistent with MITgcm numerics. In the variance budget, the distinction
>between advection and diffusion is crucial, because diffusion leads to
>dissipation, while advection does not. The biggest challenge is that the
>nonlinear advection schemes introduce numerical diffusion even with
>explicit diffusion set to zero, resulting in a dissipation of variance. We
>would like to quantify this effect locally at each grid point.
>
>The idea we have come up with is to define a residual advective flux as the
>difference between the advective flux estimated via naive centered
>differences (i.e the way the diagnostics such as UVELTH are computed in
>pkg/diagnostics/diagnostics_fill_state.F) and the "true" advective flux
>calculated by the GAD package (i.e. the diagnostics such as ADVx_TH as
>calculated in pkg/generic_advdiff/gad_calc_rhs.F). Our thinking is that
>this will tell us something about the "extra" flux introduced by the
>nonlinear scheme.
>
>I know that variance is not conserved exactly. We just want to do the best
>we can. I am emailing the list to find whether you think this idea is sane
>or not. If any of you numerical gurus has a better idea about how this can
>be done, I would love to hear your suggestions.
>
>Best,
>Ryan
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>------------------------------
>
>Message: 2
>Date: Mon, 28 Oct 2013 23:34:05 +0100
>From: Christoph Voelker <christoph.voelker at awi.de>
>To: <mitgcm-support at mitgcm.org>
>Subject: [MITgcm-support] diagnosing gmredi fluxes for tracers
>Message-ID: <526EE65D.2000206 at awi.de>
>Content-Type: text/plain; charset="ISO-8859-1"
>
>Dear MITgcm'ers,
>
>I have a run of a biogeochemical model (i.e. with several additional
>passive tracers) and I am trying to diagnose (and hopefully understand)
>what the GMREDI eddy parameterization contributes to my tracer fluxes.
>In doing so I got somewhat confused my the many options and parameter
>settings that are possible in that package; I found it hard to follow
>how the advective and diffusive fluxes are really calculated.
>
>My settings include
>#define GM_VISBECK_VARIABLE_K
>#define GM_BOLUS_ADVEC
>in GMREDI_OPTIONS.h.
>so, I am using the bolus velocity form, not the skew flux form, with
>variable kappa_GM, a la Visbeck et al. '97. In addition I am using the
>Large, Danabasoglu, Doney tapering scheme. 
>
>My questions concern the diagnostics associated with the tracer fluxes.
>
>- Firstly, I assume that the explicit diffusive terms like DFrETr01
>contain the Redi isopycnal diffusion, perhaps plus the additional
>diffusion induced e.g. by the KPP sheme that I am using. Is this right?
>
>- Secondly, is the bolus advective flux part of the advective flux
>diagnostics, like ADVrTr01? Or is this only the non-bolus advection?
>
>- And finally, is there a way to diagnose the advective tracer fluxes
>from the bolus velocity alone, i.e. separate it from the background
>velocity advection, in a diagnostic variable, or does one have to write
>out the bolus stream function terms GM_PsiX and GM_PsiY, and then
>compute the induced additional advection offline?
>
>Sorry if my questions are daft, but I really first tried to understand
>all this from the code,
>
>Thanks, Christoph
>
>-- 
>Christoph Voelker
>Alfred Wegener Institute for Polar and Marine Research
>Am Handelshafen 12
>27570 Bremerhaven, Germany
>e: Christoph.Voelker at awi.de
>t: +49 471 4831 1848
>
>
>
>
>------------------------------
>
>Message: 3
>Date: Tue, 29 Oct 2013 09:58:19 +0800 (CST)
>From: ??? <oceanlizy at 163.com>
>To: MITgcm <mitgcm-support at mitgcm.org>
>Subject: [MITgcm-support] problems with specifying optfile
>Message-ID: <739dc92.2e93.14201eed88c.Coremail.oceanlizy at 163.com>
>Content-Type: text/plain; charset="utf-8"
>
> Dear all;
>     I started running  with MITgcm recently, so I?m pretty new to the model . However,when I start with the Barotropic Gyre tutorial ,something goes wrong.  I do it as follows: 
>                                                 
>                                             cd MITgcm/verification/tutorial-barotropic_gyre/build
>                                             ../../../tools/genmake2 -mods=../code
>then it appeared warning:  NO OPTFILE  specified 
>                                           searching for possible setting for optfile
>
>
>
>
>I don't know how to specify  optfile   ,  someone can  help me  ?
>
>
>
>
>                   many  thanks ! 
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>------------------------------
>
>Message: 4
>Date: Mon, 28 Oct 2013 20:05:55 -0700
>From: Alexander Slavin <aslavin at mun.ca>
>To: mitgcm-support at mitgcm.org
>Subject: Re: [MITgcm-support] problems with specifying optfile
>Message-ID: <526F2613.20707 at mun.ca>
>Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>
>Hello,
>
>You need to specify OPTFILE manually, for example like this:
>../../../tools/genmake2 -mods=../code -of=../../../OPTFILE
>You can find example OPT files here:
>\MITgcm\tools\build_options
>
>Good luck!
>
>Alexander
>
>On 28/10/2013 6:58 PM, ??? wrote:
>>  Dear all;
>> I started running  with MITgcm recently, so I?m pretty new to the 
>> model . However,when I start with the Barotropic Gyre tutorial 
>> ,something goes wrong.  I do it as follows:
>>                      cd MITgcm/verification/tutorial-barotropic_gyre/build
>>                      ../../../tools/genmake2 -mods=../code
>> then it appeared warning:  NO OPTFILE  specified
>>                    searching for possible setting for optfile
>>
>>
>> I don't know how to specify  optfile   ,  someone can  help me  ?
>>
>>
>>                    many  thanks !
>>
>>
>>
>>
>> _______________________________________________
>> MITgcm-support mailing list
>> MITgcm-support at mitgcm.org
>> http://mitgcm.org/mailman/listinfo/mitgcm-support
>
>
>This electronic communication is governed by the terms and conditions at
>http://www.mun.ca/cc/policies/electronic_communications_disclaimer_2012.php
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>------------------------------
>
>Message: 5
>Date: Mon, 28 Oct 2013 20:45:42 -0700
>From: Jody Klymak <jklymak at uvic.ca>
>To: mitgcm-support at mitgcm.org
>Subject: Re: [MITgcm-support] problems with specifying optfile
>Message-ID: <96942482-B229-47A5-84A3-EBCE96604778 at uvic.ca>
>Content-Type: text/plain; charset="utf-8"
>
>Hi,
>
>Have a look at Sec 3.5 of the manual, but you probably want to add "-opt=../../../tools/build_options/YourMachine" to your "genmake2"
>
>Where YourMachine is modified from one of the files already in that directory.  
>
>Cheers,   Jody
>
>
>On Oct 28, 2013, at  18:58 PM, ??? <oceanlizy at 163.com> wrote:
>
>>  Dear all;
>>      I started running  with MITgcm recently, so I?m pretty new to the model . However,when I start with the Barotropic Gyre tutorial ,something goes wrong.  I do it as follows: 
>>                                                  
>>                                              cd MITgcm/verification/tutorial-barotropic_gyre/build
>>                                              ../../../tools/genmake2 -mods=../code
>> then it appeared warning:  NO OPTFILE  specified 
>>                                            searching for possible setting for optfile
>> 
>> 
>> I don't know how to specify  optfile   ,  someone can  help me  ?
>> 
>> 
>>                    many  thanks ! 
>> 
>> 
>> _______________________________________________
>> MITgcm-support mailing list
>> MITgcm-support at mitgcm.org
>> http://mitgcm.org/mailman/listinfo/mitgcm-support
>
>--
>Jody Klymak    
>http://web.uvic.ca/~jklymak/
>
>
>
>
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>End of MITgcm-support Digest, Vol 124, Issue 25
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