[yt-users] Loading files query

Nathan Goldbaum nathan12343 at gmail.com
Thu Dec 10 08:36:44 PST 2015


On Wed, Dec 9, 2015 at 5:44 PM, Sushilkumar <sushil.sush19us at gmail.com>
wrote:

> Dear yt:
>
> Thank you for your reply .
> Now, my code generates a file which is in matrix market format. I would
> like to plot this file using yt. Is there a way that yt can read this type
> of  file format?
>

yt doesn't have native support for the matrix market format (which I'd
actually never heard of before you mentioned it). It does have the ability
to load data as NumPy arrays. See here:

http://yt-project.org/doc/examining/loading_data.html#generic-amr-data
http://yt-project.org/doc/examining/loading_data.html#generic-array-data
http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-data


> Thanks in advance
>
>
> On Wed, Dec 9, 2015 at 12:50 PM, <yt-users-request at lists.spacepope.org>
> wrote:
>
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>> Today's Topics:
>>
>>    1. yt query (Sushilkumar)
>>    2. Re: yt query (Nathan Goldbaum)
>>    3. Re: code support for ZEUS-MP 2 (Andrea Negri)
>>    4. Re: code support for ZEUS-MP 2 (Matthew Turk)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Tue, 8 Dec 2015 12:56:03 -0600
>> From: Sushilkumar <sushil.sush19us at gmail.com>
>> To: yt-users at lists.spacepope.org
>> Subject: [yt-users] yt query
>> Message-ID:
>>         <CAKARaKXB9FxdXv=_=
>> q2iW7+eCfofsjW0oKsXTYiPh-vMtH6MBA at mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Dear yt:
>>
>> I would like to plot magnetic field lines in 3D using either streamline or
>> 3D quiver plots. Could you suggest me ways for the doing the same?
>>
>> Thanks in advance
>>
>>
>>
>> --
>> *SK2*
>>
>> *"**Claiming that something can move faster than light is a good
>> conversation-stopper in physics. People edge away from you in cocktail
>> parties; friends never return phone calls. You just don?t mess with Albert
>> Einstein.**"*
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>> ------------------------------
>>
>> Message: 2
>> Date: Tue, 8 Dec 2015 13:52:17 -0600
>> From: Nathan Goldbaum <nathan12343 at gmail.com>
>> To: Discussion of the yt analysis package
>>         <yt-users at lists.spacepope.org>
>> Subject: Re: [yt-users] yt query
>> Message-ID:
>>         <CAJXewOnxB9hbTKWwiiJrX+Q7un0fQrqHw99J55P6c=
>> D4bG4vew at mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> If you have data that's loadable by yt, you should be able to create the
>> streamlines following this document:
>>
>> http://yt-project.org/doc/visualizing/streamlines.html
>>
>> yt doesn't natively visualize streamlines, but you can use matplotlib or
>> mayavi to visualize the streamlines in 3d:
>>
>> * http://docs.enthought.com/mayavi/mayavi/mlab.html
>> * http://matplotlib.org/mpl_toolkits/mplot3d/tutorial.html
>>
>> Hope that helps,
>>
>> Nathan
>>
>> On Tue, Dec 8, 2015 at 12:56 PM, Sushilkumar <sushil.sush19us at gmail.com>
>> wrote:
>>
>> > Dear yt:
>> >
>> > I would like to plot magnetic field lines in 3D using either streamline
>> or
>> > 3D quiver plots. Could you suggest me ways for the doing the same?
>> >
>> > Thanks in advance
>> >
>> >
>> >
>> > --
>> > *SK2*
>> >
>> > *"**Claiming that something can move faster than light is a good
>> > conversation-stopper in physics. People edge away from you in cocktail
>> > parties; friends never return phone calls. You just don?t mess with
>> Albert
>> > Einstein.**"*
>> >
>> >
>> > _______________________________________________
>> > yt-users mailing list
>> > yt-users at lists.spacepope.org
>> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> >
>> >
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>> ------------------------------
>>
>> Message: 3
>> Date: Wed, 9 Dec 2015 10:38:43 +0100
>> From: Andrea Negri <negri.andre at gmail.com>
>> To: Discussion of the yt analysis package
>>         <yt-users at lists.spacepope.org>
>> Subject: Re: [yt-users] code support for ZEUS-MP 2
>> Message-ID:
>>         <CAPUxaiQnwSY=FT_e+a0AQi=
>> uu8mx42K9pO3pj6kRwBnTvtJGNg at mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Hi Matthew,
>> sorry for the late reply.
>>
>> I forgot to say that the spacing of the (spherical) radial grid is not
>> constant with the radius,  but it is logarithmically sampled. Is it a
>> problem?
>>
>>
>> Andrea
>>
>> On 2 December 2015 at 18:13, Matthew Turk <matthewturk at gmail.com> wrote:
>> > Hi Andrea,
>> >
>> > It should be straightforward to do this.  You can load it in to yt
>> > using the yt.load_uniform_grid function, and then specify the geometry
>> > as spherical.  In the docs we have some examples:
>> >
>> >
>> http://yt-project.org/docs/3.2/examining/loading_data.html#generic-array-data
>> >
>> > Specifying geometry="spherical" works here, and if your data is not in
>> > r,theta,phi, you can specify the axis ordering with
>> > geometry=("spherical", ("theta", "phi", "r")) (or whatever).
>> >
>> > -Matt
>> >
>> > On Wed, Dec 2, 2015 at 10:43 AM, Andrea Negri <negri at iap.fr> wrote:
>> >> Hello,
>> >>
>> >> I'm a ZEUS-MP 2 user, and I was wondering if is it possible to add the
>> >> support to ZEUS-MP 2 data, which are stored in HDF5 files.
>> >>
>> >> The data are nothing special or fancy, forget about particles or
>> multiple
>> >> levels of refinement. The code has a fixed grid in spherical
>> coordinates,
>> >> and all my simulations are axially symmetric, i.e. all the variables
>> depends
>> >> only on the spherical radius and co-latitude.
>> >>
>> >> It would be great to benefits of all the yt features!
>> >>
>> >> Thanks in advance,
>> >> Andrea Negri
>> >> _______________________________________________
>> >> yt-users mailing list
>> >> yt-users at lists.spacepope.org
>> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> > _______________________________________________
>> > yt-users mailing list
>> > yt-users at lists.spacepope.org
>> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>>
>> ------------------------------
>>
>> Message: 4
>> Date: Wed, 9 Dec 2015 05:56:05 -0600
>> From: Matthew Turk <matthewturk at gmail.com>
>> To: Discussion of the yt analysis package
>>         <yt-users at lists.spacepope.org>
>> Subject: Re: [yt-users] code support for ZEUS-MP 2
>> Message-ID:
>>         <CALO3=5HPm=HoxuXwJnSXjuU=
>> NX26pDHNGqCC+Ry-aLVwETfXEw at mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Hi Andrea,
>>
>> For that, you can use the load_hexahedral_mesh function. There's an
>> example
>> in the docs as well.
>>
>> Matt
>> On Dec 9, 2015 3:39 AM, "Andrea Negri" <negri.andre at gmail.com> wrote:
>>
>> > Hi Matthew,
>> > sorry for the late reply.
>> >
>> > I forgot to say that the spacing of the (spherical) radial grid is not
>> > constant with the radius,  but it is logarithmically sampled. Is it a
>> > problem?
>> >
>> >
>> > Andrea
>> >
>> > On 2 December 2015 at 18:13, Matthew Turk <matthewturk at gmail.com>
>> wrote:
>> > > Hi Andrea,
>> > >
>> > > It should be straightforward to do this.  You can load it in to yt
>> > > using the yt.load_uniform_grid function, and then specify the geometry
>> > > as spherical.  In the docs we have some examples:
>> > >
>> > >
>> >
>> http://yt-project.org/docs/3.2/examining/loading_data.html#generic-array-data
>> > >
>> > > Specifying geometry="spherical" works here, and if your data is not in
>> > > r,theta,phi, you can specify the axis ordering with
>> > > geometry=("spherical", ("theta", "phi", "r")) (or whatever).
>> > >
>> > > -Matt
>> > >
>> > > On Wed, Dec 2, 2015 at 10:43 AM, Andrea Negri <negri at iap.fr> wrote:
>> > >> Hello,
>> > >>
>> > >> I'm a ZEUS-MP 2 user, and I was wondering if is it possible to add
>> the
>> > >> support to ZEUS-MP 2 data, which are stored in HDF5 files.
>> > >>
>> > >> The data are nothing special or fancy, forget about particles or
>> > multiple
>> > >> levels of refinement. The code has a fixed grid in spherical
>> > coordinates,
>> > >> and all my simulations are axially symmetric, i.e. all the variables
>> > depends
>> > >> only on the spherical radius and co-latitude.
>> > >>
>> > >> It would be great to benefits of all the yt features!
>> > >>
>> > >> Thanks in advance,
>> > >> Andrea Negri
>> > >> _______________________________________________
>> > >> yt-users mailing list
>> > >> yt-users at lists.spacepope.org
>> > >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> > > _______________________________________________
>> > > yt-users mailing list
>> > > yt-users at lists.spacepope.org
>> > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> > _______________________________________________
>> > yt-users mailing list
>> > yt-users at lists.spacepope.org
>> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> >
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>
>
>
> --
> *SK2*
>
> *"**Claiming that something can move faster than light is a good
> conversation-stopper in physics. People edge away from you in cocktail
> parties; friends never return phone calls. You just don’t mess with Albert
> Einstein.**"*
>
>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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