[MITgcm-support] Layers package : nothing but zeros for output?
Dan Jones
dcjones.work at gmail.com
Thu Jun 12 02:22:19 EDT 2014
Thanks, Ryan! It's working well now.
On Wed, Jun 11, 2014 at 5:00 PM, <mitgcm-support-request at mitgcm.org> wrote:
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> 1. Re: Layers package : nothing but zeros for output?
> (Ryan Abernathey)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 11 Jun 2014 10:12:50 -0400
> From: Ryan Abernathey <ryan.abernathey at gmail.com>
> To: "mitgcm-support at mitgcm.org" <mitgcm-support at mitgcm.org>
> Subject: Re: [MITgcm-support] Layers package : nothing but zeros for
> output?
> Message-ID:
> <CAJAZx5BACfbz053JUvVLu33BTjRWhzJHcEUmFwq=
> 31bJKSnQ_w at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Sorry, I skipped the part of your email where you said the version you were
> running. You will definitely have to use the new syntax. Hopefully my
> example is sufficient to get it working.
>
> -Ryan
>
>
> On Wed, Jun 11, 2014 at 10:10 AM, Ryan Abernathey <
> ryan.abernathey at gmail.com
> > wrote:
>
> > Dan,
> > What version of the code are you using? The syntax for data.layers has
> > changed considerably in the past year or so. If you are using a newer
> > version of MITgcm, you will have to change some things. It is perfectly
> > reasonable to be confused by this, since there is zero documentation. We
> > are working on a new version of layers and accompanying documentation,
> > hopefully coming out in the next few months.
> > -Ryan
> >
> > Here is an example of a "modern" data.layers that does averaging in theta
> > layers
> > -----
> > &LAYERS_PARM01
> > layers_taveFreq=0.,
> > layers_diagFreq=0.,
> > layers_name(1) = 'TH',
> > layers_bolus(1) = .TRUE.,
> > layers_bounds(1:17,1)=
> > -1.182, -1.109, -1.012, -0.882, -0.709,
> > -0.478, -0.169, 0.241, 0.789, 1.52,
> > 2.494, 3.793, 5.526, 7.836, 10.917,
> > 15.025, 20.504,
> > &data.layers
> > ---
> >
> > This syntax allows you to have multiple simultaneous layer computations
> > running (e.g. theta and potential density). The number of possible layers
> > coordinates is set in LAYERS_SIZE.h by layers_maxNum
> > ---
> > PARAMETER( Nlayers = 16 )
> > PARAMETER( FineGridFact = 10 )
> > PARAMETER( FineGridMax = Nr * FineGridFact )
> > PARAMETER( layers_maxNum = 1 )
> > ----
> >
> > Also, we now prefer to do the output via the diagnostics package. For
> > example
> > ---
> > &DIAGNOSTICS_LIST
> > filename(1) = 'DiagLAYERS',
> > frequency(1) = 31104000.,
> > fields(1:3,1)= 'LaVH1TH ','LaHs1TH ','LaPs1TH ', '
> > &
> > &DIAG_STATIS_PARMS
> > &
> > ---
> >
> >
> >
> > On Wed, Jun 11, 2014 at 9:04 AM, Dan Jones <dcjones.work at gmail.com>
> wrote:
> >
> >> Hi all,
> >>
> >> I am interested in implementing the layers package in an idealized
> model.
> >> I can get it to compile, run, and produce output files such as Hs, Hw,
> UH,
> >> and VH. However, these output files contain nothing but zeros! I'm
> very
> >> likely making some trivial error somewhere - please take a look at my
> setup
> >> below:
> >>
> >> -------------------- /code/LAYERS_SIZE.h
> >>
> -------------------------------------------------------------------------------
> >>
> >> C $Header: /u/gcmpack/MITgcm/pkg/layers/LAYERS_SIZE.h,v 1.3 2013/01/08
> >> 21:52:34 jmc Exp $
> >> C $Name: checkpoint64t $
> >> C * Compiled-in size options for the LAYERS package *
> >> C
> >> C - Just as you have to define Nr in SIZE.h, you must define the number
> >> C of vertical layers for isopycnal averaging so that the proper array
> >> C sizes can be declared in the LAYERS.h header file.
> >> C
> >> C - Variables -
> >> C NLayers :: the number of isopycnal layers (must match
> >> data.layers)
> >> C FineGridFact :: how many fine-grid cells per dF cell
> >> C FineGridMax :: the number of points in the finer vertical grid
> >> C used for interpolation
> >> C layers_maxNum :: max number of tracer fields used for layer
> >> averaging
> >> INTEGER Nlayers, FineGridFact, FineGridMax, layers_maxNum
> >> PARAMETER( Nlayers = 10 )
> >> PARAMETER( FineGridFact = 10 )
> >> PARAMETER( FineGridMax = Nr * FineGridFact )
> >> PARAMETER( layers_maxNum = 1 )
> >>
> >> -------------------- /input/data.layers
> >>
> -------------------------------------------------------------------------------
> >>
> >> &LAYERS_PARM01
> >> # averaging
> >> layers_taveFreq=45000.,
> >> # no instantaneous output
> >> layers_diagFreq=0.,
> >> layers_G=-0.2,0.6,1.5,2.3,3.2,4.0,4.8,5.7,6.5,7.4,8.2,
> >> &
> >> # Note: Some systems use & as the
> >> # namelist terminator. Other systems
> >> # use a / character.
> >>
> >> As you can see in the header file, I'm running MITgcm c64t. Based on
> the
> >> thread linked below, I assume that I'm using the default layer
> coordinate
> >> (i.e. theta), so as long as I'm picking reasonable values of theta I
> should
> >> have well-defined layers. Is that correct?
> >>
> >> http://mitgcm.org/pipermail/mitgcm-support/2011-December/007569.html
> >>
> >> Thanks in advance for taking a look!
> >> Dan
> >>
> >> ---------------------------------------------------------
> >>
> >> Dr Dan Jones
> >> British Antarctic Survey, NERC
> >> Cambridge, UK
> >>
> >> Phone: +44 (0)1223 221505
> >> Fax: +44 (0)1223 362616
> >> Skype: dcjones.work
> >>
> >> ---------------------------------------------------------
> >>
> >> _______________________________________________
> >> MITgcm-support mailing list
> >> MITgcm-support at mitgcm.org
> >> http://mitgcm.org/mailman/listinfo/mitgcm-support
> >>
> >>
> >
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