[MITgcm-support] MITgcm-support: python (smaeilpour)
Josué Martínez Moreno
josue_pingu at ciencias.unam.mx
Fri Dec 16 11:57:26 EST 2016
Hi Saeid,
Before plotting the MITgcm outputs in python, you need to install the
package MITgcmutils located in
"/Path2MITgcm/MITgcm/utils/python/MITgcmutils/" by running:
*python setup.py install*
or just copy and paste the mds.py located in
"/Path2MITgcm/MITgcm/utils/python/MITgcmutils/MITgcmutils/" to your output
folder.
After this, you can write a script or in a python console write:
from pylab import *
from mds import *
temp=rdmds('U.0000000100')
pcolor(temp[:,50,:])
show()
Maybe if you plot a section of your interest like
http://mitgcm.org/public/pelican/online_documents/node9.html, you can find
an evidence of internal waves.
Otherwise you can set up your simulation to get the density anomaly (Check:
http://mitgcm.org/pipermail/mitgcm-support/2005-July/003250.html) like this
article:
http://nonlin-processes-geophys.net/17/575/2010/npg-17-575-2010.pdf
I hope this help you.
Thanks,
Josué.
On Fri, Dec 16, 2016 at 9:51 AM, <mitgcm-support-request at mitgcm.org> wrote:
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> Today's Topics:
>
> 1. python (smaeilpour)
> 2. weird temperature signal using 3D floats with the FLT package
> (Steffie Ypma - CITG)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 16 Dec 2016 15:16:05 +0000 (UTC)
> From: smaeilpour <saeid_gal at yahoo.com>
> To: <mitgcm-support at mitgcm.org>
> Subject: [MITgcm-support] python
> Message-ID: <259517693.6254643.1481901365343 at mail.yahoo.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
> would you please tell me, how can i show data results below in python as
> plot or graph that they are internal wave outputs?
> what are commands for that?
>
> CVS DXG.data generateGifs.txt maskInW.meta
> __pycache__ RF.meta T.init W.0000000000.data
> data DXG.meta GIF_MOVIES mitgcmuv
> RAC.data RhoRef.data topog.concave W.0000000000.meta
> data.obcs DYC.data hFacC.data PH.0000000100.data
> RAC.meta RhoRef.meta topog.convex W.0000000100.data
> data.pkg DYC.meta hFacC.meta PH.0000000100.meta
> RAS.data S.0000000000.data topog.slope W.0000000100.meta
> delXvar DYG.data hFacS.data PHL.0000000100.data
> RAS.meta S.0000000000.meta U.0000000000.data XC.data
> Depth.data DYG.meta hFacS.meta PHL.0000000100.meta
> RAW.data S.0000000100.data U.0000000000.meta XC.meta
> Depth.meta eedata hFacW.data PHrefC.data
> RAW.meta S.0000000100.meta U.0000000100.data XG.data
> DRC.data eedata.mth hFacW.meta PHrefC.meta
> RAZ.data STDERR.0000 U.0000000100.meta XG.meta
> DRC.meta Eta.0000000000.data maskInC.data PHrefF.data
> RAZ.meta STDOUT.0000 V.0000000000.data YC.data
> DRF.data Eta.0000000000.meta maskInC.meta PHrefF.meta
> RC.data T.0000000000.data V.0000000000.meta YC.meta
> DRF.meta Eta.0000000100.data maskInS.data pickup.ckptA.data
> RC.meta T.0000000000.meta V.0000000100.data YG.data
> DXC.data Eta.0000000100.meta maskInS.meta pickup.ckptA.meta
> results T.0000000100.data V.0000000100.meta YG.meta
> DXC.meta gendata.m maskInW.data PNG_IMAGES
> RF.data T.0000000100.meta variables.py
>
> thanks in advance
> saeid
>
>
> --------------------------------------------
> On Thu, 11/10/16, Matthew Mazloff <mmazloff at ucsd.edu> wrote:
>
> Subject: Re: [MITgcm-support] Hello
> To: mitgcm-support at mitgcm.org
> Date: Thursday, November 10, 2016, 2:11 PM
>
> if you don?t want to
> compile multicore just don?t add
> -mpi
>
> to your compile command.
>
> Matt
>
>
> > On Nov 10, 2016, at 11:04
> AM, smaeilpour <saeid_gal at yahoo.com>
> wrote:
> >
> > Hi
> again
> >
> > Please if
> it's possible for you, check my error upon my pics
> sending you, and other idea you have ...
> >
> > Best
> > saeid
> >
> >
> >
> >
> >
> ----------------------------
> > On Thu,
> 11/10/16, Matthew Mazloff <mmazloff at ucsd.edu>
> wrote:
> >
> > Subject:
> Re: [MITgcm-support] Hello
> > To: mitgcm-support at mitgcm.org
> > Date: Thursday, November 10, 2016, 9:28
> PM
> >
> > This is likely
> a platform
> > issue. Most likely your path
> to your ifort compiler is
> > wrong.?
> >
> > You need to
> > change your optfile to point to the
> correct path. If all was
> > working fine
> and now it is not then it is likely that
> > someone updated the fortran compilers on
> your machine and
> > the paths have
> changed.
> >
> > Clean
> out your build folder. Fix your paths.
> >
> Try again
> >
> > Hope
> this
> > helps
> >
> > -Matt
> >
> >
> >
> >> On Nov 10, 2016, at 9:39 AM,
> smaeilpour
> > <saeid_gal at yahoo.com>
> > wrote:
> >>
> >> Hi,
> >>
> >> I have been having
> > some problem compiling my code today,
> after doing
> >>
> >>> make depend
> >>
> >> I get the
> following
> > error
> >>
> >>
> >
> ../../../tools/cyrus-imapd-makedepend/makedepend: warning
> > :
> >>
> mdsio_readfield.F (reading SUPPORT.h,
> >
> line 179): cannot find include
> >>
> file
> > "mpif.h"?
> >>
> >>? ? ? ?
> ? ? not in mpif.h
> >>? ? ? ? ?
> ? not in mpif.h
> >>? ? ? ? ? ?
> not in???
> >
> opt/ifort/8.0.044/include/mpif.h
> >>
>
> >
> ../../../tools/f90makedepend>>makefile
> >>
> >>
> >> and as a result I cannot compile
> the
> > code.
> >> I am
> sure i have overlooked
> > something quite
> simple.
> >>
> >>
> any Idea
> >>
> >>
> thanks a lot in advance
> >> saeid
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >
> --------------------------------------------
> >>
> >>
> >>
> >
> ------------------------------------------------------------
> ----------------------------
> >> On Thu, 11/10/16, Jean-Michel
> Campin
> > <jmc at mit.edu> wrote:
> >>
> >> Subject:
> Re:
> > [MITgcm-support] river runoff
> >> To: mitgcm-support at mitgcm.org
> >> Date: Thursday, November 10, 2016,
> 10:42
> > AM
> >>
> >> Hi,
> >>
> >> There are few
> >
> available options for including
> >>
> > run-off:
> >>
> >> 1) the
> > most
> >> commonly used is to include just
> > in the surface level,
> >>???as part of
> > surface forcing (substracted to EmP
> >>
> > into EmPmR).
> >>???Obviously this
> approach
> > is not
> >> great for deep estuary with
> > high
> >>???vertical
> >>
> > resolution
> (small dz).
> >>???And the
> effect
> > on
> >>
> sea-level is accounted for with
> >>
> useRealFreshWaterFlux=.TRUE.,
> >>???and in a
> >> consistent
> > way
> for any tracers when Non-Lin Freee-surface
> >> is
> >>???used.
> >>???In this case, the
> >>
> > run-off can be
> provide as part of EmPmR or
> >>
> >> separately (e.g.,
> >
> using pkg/exf), but only the run-off that
> >> fall
> >>???on ocean grid
> > cell (wet-cell) will be
> >> considered.
> >>
>
> >> 2) If you want
> >> to address the issue of deep
> estuaries,
> > you can
> >>? ? try to prescribe
> > a 3-D run-off input (file:
> >> addMassFile
> >
> loaded into
> >>? ? model 2-D
> > array
> >>
> "addMass") using
> >
> selectAddFluid=1.
> >>? ? This
> > requires to compile with #define
> >>
> >
> ALLOW_ADDFLUID
> >>
> >>? ? Note that
> >> the current code does not provide
> an
> > option to prescribe
> >>? ? time
> >
> dependent "addMass" inflow
> >>
> > (but should not
> be difficult to add).
> >>
> >
> >> 3) And the last
> option, as described
> > by Andrea,
> >> is to use OBCS. This enable
> >
> >>? ? to
> account,
> >> in the momentum budget,
> for the speed of
> > the incoming
> >> run-off.
> >>? ?
> Probably useful at very high
> > to
> >> high resolution (bot horizontal and
> > vertical)
> >>? ?
> but may be not
> > so important at lower
> >> resolution.
> >>
>
> >> Cheers,
> >>
> Jean-Michel
> >>
> >> On
> >> Wed, Nov
> 09, 2016
> > at 08:31:34AM +0100, Andrea
> Cimatoribus
> >>
> >
> wrote:
> >>> Certainly not the
> most
> > expert
> >>
> around here, but I have been
> > dealing
> >>>
> >> with
> > this lately, so I can try an answer.
> >>>
> >>> The
> neatest
> > way to
> >>
> do it is with obcs package, that
> > is,
> the open
> >>> boundary package.
> In
> > data.obcs you can
> >> define the (vertical)
> > grid
> >>> faces
> >>
> > through which
> you want to apply the discharge (see
> >> manual).
> >>>
> Using
> > the correct grid metric,
> >> you can set
> > the
> discharge velocity to
> >>>
> >> match the total volume discharge (and
> you
> > can easily check
> >> if you
> >>>
> are doing it right using the
> >>
> diagnostic output). The simplest way to
> >>>
> >> impose
> a
> > time-variable discharge and
> temperature is via the
> >> exf
> >>> package, in a
> >
> new namelist which is
> >> provided by
> the
> > OBCS package,
> >>> something
> >>
> along these lines:
> >>>???
> >>
> >
> &EXF_NML_OBCS
> >>> # OBCS
> > prescribe
> >>>?
> ? obcsEstartdate1???=
> >>
> 20080101,
> >>>???
> >> obcsEstartdate2???=
> 010000,
> >>>? ?
> obcsEperiod???
> >? ? =
> >> 3600.,
> >>>?
> ? obcsWstartdate1???=
> >>
> 20080101,
> >>>???
> >> obcsWstartdate2???=
> 010000,
> >>>? ?
> obcsWperiod???
> >? ? =
> >> 3600.,
> >>>?
> ? &
> >>> As
> >> far as I
> >
> understand, the temperature of the discharge must
> >> span
> >>>
> exactly the
> > same time interval and
> >> have the same
> >
> periodicity as the
> >>>
> >> velocity.
> >>>
> The
> > file names containing the
> >> data are
> > defined
> in the data.obcs
> >>>
> >> (again, see manual).
> >>>
> >>> Hope
> this
> > helps, best,
> >>>
> >>>
> Andrea
> >>
> >
> Cimatoribus
> >>> postdoctoral
> > researcher
> >>>
> EPFL ENAC IIE ECOL
> >>> https://people.epfl.ch/andrea.cimatoribus
> >>>
> >>> On
> 09/11/16
> > 03:26,
> >> ????????? wrote:
> >>>> Hi
> >>>>
> >
> >>>> I am using
> >> mitgcm to simulate SST variation in
> > coastal area with
> >>
> large
> >>>> runoff. Does anyone
> tell me
> >> how to set up the river?
> How mitgcm
> > deal
> >>>> with river mouth?
> >>>
> >>>
> >>>> I've known that the
> runoff
> >> should be added to the
> freshwater flux
> > EmPmR,
> >>>> but how to represent the
> > effect of a
> >> river
> by gridded runoff
> > data is not
> >>>
> >>>
> clear to me (should the river grid
> >
> point be contacted
> >> with ocean
> >>>> interior or
> >>
> > boundary?).
> >>>>
> >>>
>
> >>> It seems
> >
> that the test cases in mitgcm do not provide
> >> enough river
> >>>>
> >
> information.
> >>>>
> >>>> I'd
> >>
> > appreciate any
> help.
> >>>>
> >>>>
> >>>
>
> >>> ------------------
> >>>> Best
> >>
>
> > regards
> >>>>
> >>>
>
> >>> Yu-Kun Qian
> > (?????????)
> >>>> Center
> >> for Monsoon and Environment
> Research
> >>>
> >>> Department
> > of
> Atmospheric Sciences
> >>>
> >>> School of Environmental Science
> and
> > Engineering
> >>>> Sun Yat-sen
> > University
> >>>> No. 135 Xingang West
> > Road, Haizhu
> >>
> District
> >>>> Guangzhou, 510275,
> P.R.
> >> China
> >>>> Tel;
> >
> 020-84115227
> >>>> Email: qianyk at mail3.sysu.edu.cn
> >> <mailto:qianyk at mail2.sysu.edu.cn>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>
>
> >>>
> >
> _______________________________________________
> >>>> 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
> >>
> >
> >>
> >
> _______________________________________________
> >> 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
> >
> >
> >
> _______________________________________________
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> > MITgcm-support at mitgcm.org
> > http://mitgcm.org/mailman/listinfo/mitgcm-support<1.jpg>
> _______________________________________________
> >
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>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 16 Dec 2016 15:51:09 +0000
> From: Steffie Ypma - CITG <S.L.Ypma at tudelft.nl>
> To: "mitgcm-support at mitgcm.org" <mitgcm-support at mitgcm.org>
> Subject: [MITgcm-support] weird temperature signal using 3D floats
> with the FLT package
> Message-ID:
> <4DE6720049273548B7623438093E21BC0C042AAD at SRV361.tudelft.net>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi all,
>
> I have released 3D floats using the FLT package in a very easy set up of
> the MITgcm. I have a 7.5km horizontal resolution in the horizontal, and 20
> levels in the vertical till a depth of 3000m. The basin is closed and a
> cyclonic, warm boundary current is created by restoring temperature in the
> south-east corner between the island and the coast. There is no surface
> forcing. Density is calculated using the linear equation of state and is
> only dependent on temperature.
> The particles are released using the online mode, just after the restoring
> area at y = 40, x = 140:160 and at all depth levels, integrated for the
> duration of 6 months. The figures show:
>
> - temperature.png: surface temperature after 6 months
> - velocity.png: absolute velocity (speed) at surface after 6 months
> - trajectories.png: the path of all particles
> - T_change.png: the temperature change over time of the particles that
> show cooling or warming > 0.5 degrees (24 out of the 181 particles).
>
> I am wondering what could be the cause of the particles jumps in the
> temperature. I have so far not found a correlation between this subset and
> other fields like change in depth, location etc.
> Any ideas are welcome.
>
> Cheers,
> Steffie
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> ------------------------------
>
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>
> End of MITgcm-support Digest, Vol 162, Issue 12
> ***********************************************
>
--
Muchas gracias
Josué
http://faraday.fciencias.unam.mx/josue/
<http://faraday.fciencias.unam.mx/~josue/>
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