[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:
>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. 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
>-------------- next part --------------
>An HTML attachment was scrubbed...
>URL: <http://mitgcm.org/pipermail/mitgcm-support/attachments/20131028/b119ede9/attachment-0001.htm>
>
>------------------------------
>
>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 !
>-------------- next part --------------
>An HTML attachment was scrubbed...
>URL: <http://mitgcm.org/pipermail/mitgcm-support/attachments/20131029/1c74f2f3/attachment-0001.htm>
>
>------------------------------
>
>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
>-------------- next part --------------
>An HTML attachment was scrubbed...
>URL: <http://mitgcm.org/pipermail/mitgcm-support/attachments/20131028/38297e97/attachment-0001.htm>
>
>------------------------------
>
>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/
>
>
>
>
>-------------- next part --------------
>An HTML attachment was scrubbed...
>URL: <http://mitgcm.org/pipermail/mitgcm-support/attachments/20131028/019b9086/attachment.htm>
>
>------------------------------
>
>_______________________________________________
>MITgcm-support mailing list
>MITgcm-support at mitgcm.org
>http://mitgcm.org/mailman/listinfo/mitgcm-support
>
>
>End of MITgcm-support Digest, Vol 124, Issue 25
>***********************************************
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mitgcm.org/pipermail/mitgcm-support/attachments/20131029/11757ce8/attachment-0001.htm>
More information about the MITgcm-support
mailing list