[MITgcm-support] Glue mnc_files with exch2 // MITgcm-support Digest, Vol 125, Issue 16
Alexandre Pohl
Alexandre.Pohl at lsce.ipsl.fr
Mon Nov 25 03:14:11 EST 2013
Hi Martin,
Thank you for your answer. I had not seen the utils/matlab/cs_grid directory , there are indeed a lot of very good scripts (plotcube, cube2latlong-fast and uvcube2latlon allow many useful plots I think).
Actually I am just beginning my PhD about the Ordovician glaciation at the Laboratoire des Sciences du Climat et de l'Environnement (LSCE). My main supervisor is Yannick Donnadieu. We previously worked with the FOAM gcm and we are very interested in using the MITgcm, too. We have to make new grids and paleomaps, determine what packages are to be used and so on. I am very new to the model, and I therefore do not promise that I will not ask for your help in the future ;)
Thank you again,
Regards
Alexandre
Le Jeudi 21 Novembre 2013 18:00 CET, mitgcm-support-request at mitgcm.org a écrit:
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> Today's Topics:
>
> 1. Re: How to glue mnc output files with the cube-sphere exch2
> grid ? (Martin Losch)
> 2. Re: MITgcm-support Digest, Vol 125, Issue 15 (P?r Jansson)
> 3. Re: What is the unit of PH and PNH in the output files?
> (Jody Klymak)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 21 Nov 2013 11:53:49 +0100
> From: Martin Losch <Martin.Losch at awi.de>
> To: <mitgcm-support at mitgcm.org>
> Subject: Re: [MITgcm-support] How to glue mnc output files with the
> cube-sphere exch2 grid ?
> Message-ID: <3ABD0EC2-818D-47D5-9FAF-E03DC6DA9437 at awi.de>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi Alexandre,
>
> this is exactly the expected result. This experiment uses the cubed sphere that does not have the simple connectivity of a regluar lon-lat-grid, so you cannot simply glue the faces together in the same way in that you cannot create a 2D cube.
>
> There are some matlab or python functions in the utils directory that you can use to visualize the output of scalar fields. E.g. in matlab:
>
> t = rdmds('THETA'); % gives you a field 192x32x15 field, right?
> xg=rdmds('XG'); % 192x32
> yg=rdmds('YG'); % 192x32
>
> then
> cs_pcol(xg,yg,theta(:,:,1)) % I am attaching this function, as it does not seem to in the repository
> should give you the surface temperature on a simple cyclindrical map projection.
>
> There is more in the utils/matlab/cs_grid directory that maybe interesting for you.
>
> in python something like (I am using output of global_ocean.cs32x15 here):
> import MITgcmutils as mit
> g=mit.rdmnc('grid.*')
> s=mit.rdmnc('state.*','Temp')
> mit.cs.pcol(g["XG"],g["YG"],s["Temp"][0,0,:,:])
>
> Martin
>
> On Nov 21, 2013, at 11:32 AM, Alexandre Pohl <Alexandre.Pohl at lsce.ipsl.fr> wrote:
>
> > Hi,
> >
> > I ran the verification/cpl_aim+ocn experience and I produced NetCdf files.It uses a cube-sphere Exch2 grid and I got one file per face (6 files).
> >
> > I previously used gluemnc to glue the cartesian output files together, but it does not work with the exch2.
> >
> > I also tested the rdmnc.m script. It extracts the variables from the 6 tiles but the result is not correct. The faces are glued to each other in no particular order. I join the result. We can see Africa on the left and Antarctica on the right.... not the expected result!
> >
> > Is there a way to do that, like gluemnc does for a cartesian grid?
> > I think you probably encountered this problem before?
> >
> > Thanks a lot and with kind regards,
> > Alexandre<Assemblage-cube_sphere_avec_rdmnc.eps>_______________________________________________
> > MITgcm-support mailing list
> > MITgcm-support at mitgcm.org
> > http://mitgcm.org/mailman/listinfo/mitgcm-support
> -------------- next part --------------
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> ------------------------------
>
> Message: 2
> Date: Thu, 21 Nov 2013 13:32:28 +0100
> From: P?r Jansson <jansson.par at telia.com>
> To: mitgcm-support at mitgcm.org
> Subject: Re: [MITgcm-support] MITgcm-support Digest, Vol 125, Issue 15
> Message-ID: <683B68D5-EE42-416B-8C9C-4FE7FB0009AF at telia.com>
> Content-Type: text/plain; charset=windows-1252
>
> Thank you both. It all falls into place then...;)
> The diagnostics package seem useful too. should look into that?
> Best regards!
> P?r
>
>
> 21 nov 2013 kl. 11:32 skrev mitgcm-support-request at mitgcm.org:
>
> > 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. What is the unit of PH and PNH in the output files? (P?r Jansson)
> > 2. Re: What is the unit of PH and PNH in the output files?
> > (Jody Klymak)
> > 3. Re: What is the unit of PH and PNH in the output files?
> > (Martin Losch)
> > 4. How to glue mnc output files with the cube-sphere exch2 grid
> > ? (Alexandre Pohl)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Wed, 20 Nov 2013 22:01:44 +0100
> > From: P?r Jansson <jansson.par at telia.com>
> > To: mitgcm-support at mitgcm.org
> > Subject: [MITgcm-support] What is the unit of PH and PNH in the output
> > files?
> > Message-ID: <BDE5D665-5DF9-4848-ADA6-1CF273C6E0E2 at telia.com>
> > Content-Type: text/plain; charset=iso-8859-1
> >
> > Hi there!
> > Sorry for asking such a trivial question, but I've scoured the manual, the online documentation and the support mails.
> > Nowhere did i find the answer to my question;
> >
> > What are the units of the pressure (PH and PNH) in the output fields from the model?
> > I'm trying to evaluate the energy flux contents in internal waves etc. for my masters' thesis and
> > was assuming the output would be SI-units. That would mean Pascal (N/m^2), but they seem too small.
> > In the variable list, some variables has the pressure in db and some are in Pascal. So I'm still confused...
> >
> >
> > Best regards!
> > /P?r Jansson
> > University of Gothenburg
> >
> >
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Wed, 20 Nov 2013 16:08:43 -0800
> > From: Jody Klymak <jklymak at uvic.ca>
> > To: mitgcm-support at mitgcm.org
> > Subject: Re: [MITgcm-support] What is the unit of PH and PNH in the
> > output files?
> > Message-ID: <F69C7C14-6ED7-47A0-9951-2E52FFABCA03 at uvic.ca>
> > Content-Type: text/plain; charset=iso-8859-1
> >
> > Hi Par,
> >
> > Its P/rhoconst, to the units are m^2/s^2.
> >
> > Cheers, Jody
> >
> >
> >
> >
> > On Nov 20, 2013, at 13:01 PM, P?r Jansson <jansson.par at telia.com> wrote:
> >
> >> Hi there!
> >> Sorry for asking such a trivial question, but I've scoured the manual, the online documentation and the support mails.
> >> Nowhere did i find the answer to my question;
> >>
> >> What are the units of the pressure (PH and PNH) in the output fields from the model?
> >> I'm trying to evaluate the energy flux contents in internal waves etc. for my masters' thesis and
> >> was assuming the output would be SI-units. That would mean Pascal (N/m^2), but they seem too small.
> >> In the variable list, some variables has the pressure in db and some are in Pascal. So I'm still confused...
> >>
> >>
> >> Best regards!
> >> /P?r Jansson
> >> University of Gothenburg
> >>
> >>
> >> _______________________________________________
> >> MITgcm-support mailing list
> >> MITgcm-support at mitgcm.org
> >> http://mitgcm.org/mailman/listinfo/mitgcm-support
> >
> > --
> > Jody Klymak
> > http://web.uvic.ca/~jklymak/
> >
> >
> >
> >
> >
> >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Thu, 21 Nov 2013 08:44:40 +0100
> > From: Martin Losch <Martin.Losch at awi.de>
> > To: <mitgcm-support at mitgcm.org>
> > Subject: Re: [MITgcm-support] What is the unit of PH and PNH in the
> > output files?
> > Message-ID: <CBD969E3-C52C-48ED-8E4E-4D9C62CAA3E2 at awi.de>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > May I add that according to "available_diagnostics.log" (a useful list that you get when you turn on the diagnostics package):
> > XX |PHIHYD | XX | |SMR MR|m^2/s^2 |Hydrostatic Pressure Pot.(p/rho) Anomaly
> >
> > Here, "Anomaly" means that the constant contribution of gravity*abs(RC) is missing from PH and PHL (diagnostics names are PHIHYD and PHIBOT). That's another reason, why the values of PH may appear low. So to get the full pressure you need to do this:
> >
> > P = (PHIHYD + gravity*abs(RC))*rho_const
> >
> > although the second contribution is dynamically not relevant.
> >
> > Martin
> >
> > On Nov 21, 2013, at 1:08 AM, Jody Klymak <jklymak at uvic.ca> wrote:
> >
> >> Hi Par,
> >>
> >> Its P/rhoconst, to the units are m^2/s^2.
> >>
> >> Cheers, Jody
> >>
> >>
> >>
> >>
> >> On Nov 20, 2013, at 13:01 PM, P?r Jansson <jansson.par at telia.com> wrote:
> >>
> >>> Hi there!
> >>> Sorry for asking such a trivial question, but I've scoured the manual, the online documentation and the support mails.
> >>> Nowhere did i find the answer to my question;
> >>>
> >>> What are the units of the pressure (PH and PNH) in the output fields from the model?
> >>> I'm trying to evaluate the energy flux contents in internal waves etc. for my masters' thesis and
> >>> was assuming the output would be SI-units. That would mean Pascal (N/m^2), but they seem too small.
> >>> In the variable list, some variables has the pressure in db and some are in Pascal. So I'm still confused...
> >>>
> >>>
> >>> Best regards!
> >>> /P?r Jansson
> >>> University of Gothenburg
> >>>
> >>>
> >>> _______________________________________________
> >>> MITgcm-support mailing list
> >>> MITgcm-support at mitgcm.org
> >>> http://mitgcm.org/mailman/listinfo/mitgcm-support
> >>
> >> --
> >> Jody Klymak
> >> http://web.uvic.ca/~jklymak/
> >>
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> MITgcm-support mailing list
> >> MITgcm-support at mitgcm.org
> >> http://mitgcm.org/mailman/listinfo/mitgcm-support
> >
> >
> >
> >
> > ------------------------------
> >
> > Message: 4
> > Date: Thu, 21 Nov 2013 11:32:00 +0100
> > From: "Alexandre Pohl" <Alexandre.Pohl at lsce.ipsl.fr>
> > To: <mitgcm-support at mitgcm.org>
> > Subject: [MITgcm-support] How to glue mnc output files with the
> > cube-sphere exch2 grid ?
> > Message-ID: <997-528de100-19-2c496900 at 43585670>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hi,
> >
> > I ran the verification/cpl_aim+ocn experience and I produced NetCdf files.It uses a cube-sphere Exch2 grid and I got one file per face (6 files).
> >
> > I previously used gluemnc to glue the cartesian output files together, but it does not work with the exch2.
> >
> > I also tested the rdmnc.m script. It extracts the variables from the 6 tiles but the result is not correct. The faces are glued to each other in no particular order. I join the result. We can see Africa on the left and Antarctica on the right.... not the expected result!
> >
> > Is there a way to do that, like gluemnc does for a cartesian grid?
> > I think you probably encountered this problem before?
> >
> > Thanks a lot and with kind regards,
> > Alexandre
> > -------------- next part --------------
> > A non-text attachment was scrubbed...
> > Name: Assemblage-cube_sphere_avec_rdmnc.eps
> > Type: image/x-eps
> > Size: 121849 bytes
> > Desc: not available
> > URL: <http://mitgcm.org/pipermail/mitgcm-support/attachments/20131121/53ba8530/attachment.bin>
> >
> > ------------------------------
> >
> > _______________________________________________
> > MITgcm-support mailing list
> > MITgcm-support at mitgcm.org
> > http://mitgcm.org/mailman/listinfo/mitgcm-support
> >
> >
> > End of MITgcm-support Digest, Vol 125, Issue 15
> > ***********************************************
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 21 Nov 2013 08:09:46 -0800
> From: Jody Klymak <jklymak at uvic.ca>
> To: mitgcm-support at mitgcm.org
> Subject: Re: [MITgcm-support] What is the unit of PH and PNH in the
> output files?
> Message-ID: <B697E226-A526-4F3E-A817-DE70562B64DF at uvic.ca>
> Content-Type: text/plain; charset=iso-8859-1
>
> And, to make things confusing, for the linear equation of state:
>
> P_k = (PhiHyd*rhoconst + sum(rho0*dc*g))
> where rho0 is rhoconst+rhoRef(k), and rhoRef(k) is set by Tref and Sref. This doesn't seem consistent with the other equations fo state, but a lot of internal wave folks use linear equation of state, so its something to bear in mind. However, this term has no physical dynamics either, so, can be dropped.
>
> See the thread "difference between PH and PHL" from Aug 2013.
>
> Cheers, Jody
>
> On Nov 20, 2013, at 23:44 PM, Martin Losch <Martin.Losch at awi.de> wrote:
>
> > May I add that according to "available_diagnostics.log" (a useful list that you get when you turn on the diagnostics package):
> > XX |PHIHYD | XX | |SMR MR|m^2/s^2 |Hydrostatic Pressure Pot.(p/rho) Anomaly
> >
> > Here, "Anomaly" means that the constant contribution of gravity*abs(RC) is missing from PH and PHL (diagnostics names are PHIHYD and PHIBOT). That's another reason, why the values of PH may appear low. So to get the full pressure you need to do this:
> >
> > P = (PHIHYD + gravity*abs(RC))*rho_const
> >
> > although the second contribution is dynamically not relevant.
> >
> > Martin
> >
> > On Nov 21, 2013, at 1:08 AM, Jody Klymak <jklymak at uvic.ca> wrote:
> >
> >> Hi Par,
> >>
> >> Its P/rhoconst, to the units are m^2/s^2.
> >>
> >> Cheers, Jody
> >>
> >>
> >>
> >>
> >> On Nov 20, 2013, at 13:01 PM, P?r Jansson <jansson.par at telia.com> wrote:
> >>
> >>> Hi there!
> >>> Sorry for asking such a trivial question, but I've scoured the manual, the online documentation and the support mails.
> >>> Nowhere did i find the answer to my question;
> >>>
> >>> What are the units of the pressure (PH and PNH) in the output fields from the model?
> >>> I'm trying to evaluate the energy flux contents in internal waves etc. for my masters' thesis and
> >>> was assuming the output would be SI-units. That would mean Pascal (N/m^2), but they seem too small.
> >>> In the variable list, some variables has the pressure in db and some are in Pascal. So I'm still confused...
> >>>
> >>>
> >>> Best regards!
> >>> /P?r Jansson
> >>> University of Gothenburg
> >>>
> >>>
> >>> _______________________________________________
> >>> MITgcm-support mailing list
> >>> MITgcm-support at mitgcm.org
> >>> http://mitgcm.org/mailman/listinfo/mitgcm-support
> >>
> >> --
> >> Jody Klymak
> >> http://web.uvic.ca/~jklymak/
> >>
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> 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
>
> --
> Jody Klymak
> http://web.uvic.ca/~jklymak/
>
>
>
>
>
>
>
> ------------------------------
>
> _______________________________________________
> MITgcm-support mailing list
> MITgcm-support at mitgcm.org
> http://mitgcm.org/mailman/listinfo/mitgcm-support
>
>
> End of MITgcm-support Digest, Vol 125, Issue 16
> ***********************************************
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