<div dir="ltr"><div><div>Dear yt:<br><br></div>Thank you for your reply . <br>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?<br><br></div>Thanks in advance<br><div><div><br><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Dec 9, 2015 at 12:50 PM, <span dir="ltr"><<a href="mailto:yt-users-request@lists.spacepope.org" target="_blank">yt-users-request@lists.spacepope.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send yt-users mailing list submissions to<br>
<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
<br>
To subscribe or unsubscribe via the World Wide Web, visit<br>
<a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
or, via email, send a message with subject or body 'help' to<br>
<a href="mailto:yt-users-request@lists.spacepope.org">yt-users-request@lists.spacepope.org</a><br>
<br>
You can reach the person managing the list at<br>
<a href="mailto:yt-users-owner@lists.spacepope.org">yt-users-owner@lists.spacepope.org</a><br>
<br>
When replying, please edit your Subject line so it is more specific<br>
than "Re: Contents of yt-users digest..."<br>
<br>
<br>
Today's Topics:<br>
<br>
1. yt query (Sushilkumar)<br>
2. Re: yt query (Nathan Goldbaum)<br>
3. Re: code support for ZEUS-MP 2 (Andrea Negri)<br>
4. Re: code support for ZEUS-MP 2 (Matthew Turk)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Tue, 8 Dec 2015 12:56:03 -0600<br>
From: Sushilkumar <<a href="mailto:sushil.sush19us@gmail.com">sushil.sush19us@gmail.com</a>><br>
To: <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
Subject: [yt-users] yt query<br>
Message-ID:<br>
<CAKARaKXB9FxdXv=_=<a href="mailto:q2iW7%2BeCfofsjW0oKsXTYiPh-vMtH6MBA@mail.gmail.com">q2iW7+eCfofsjW0oKsXTYiPh-vMtH6MBA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear yt:<br>
<br>
I would like to plot magnetic field lines in 3D using either streamline or<br>
3D quiver plots. Could you suggest me ways for the doing the same?<br>
<br>
Thanks in advance<br>
<br>
<br>
<br>
--<br>
*SK2*<br>
<br>
*"**Claiming that something can move faster than light is a good<br>
conversation-stopper in physics. People edge away from you in cocktail<br>
parties; friends never return phone calls. You just don?t mess with Albert<br>
Einstein.**"*<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <<a href="http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20151208/89b7f4f3/attachment.html" rel="noreferrer" target="_blank">http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20151208/89b7f4f3/attachment.html</a>><br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Tue, 8 Dec 2015 13:52:17 -0600<br>
From: Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com">nathan12343@gmail.com</a>><br>
To: Discussion of the yt analysis package<br>
<<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a>><br>
Subject: Re: [yt-users] yt query<br>
Message-ID:<br>
<CAJXewOnxB9hbTKWwiiJrX+Q7un0fQrqHw99J55P6c=<a href="mailto:D4bG4vew@mail.gmail.com">D4bG4vew@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
If you have data that's loadable by yt, you should be able to create the<br>
streamlines following this document:<br>
<br>
<a href="http://yt-project.org/doc/visualizing/streamlines.html" rel="noreferrer" target="_blank">http://yt-project.org/doc/visualizing/streamlines.html</a><br>
<br>
yt doesn't natively visualize streamlines, but you can use matplotlib or<br>
mayavi to visualize the streamlines in 3d:<br>
<br>
* <a href="http://docs.enthought.com/mayavi/mayavi/mlab.html" rel="noreferrer" target="_blank">http://docs.enthought.com/mayavi/mayavi/mlab.html</a><br>
* <a href="http://matplotlib.org/mpl_toolkits/mplot3d/tutorial.html" rel="noreferrer" target="_blank">http://matplotlib.org/mpl_toolkits/mplot3d/tutorial.html</a><br>
<br>
Hope that helps,<br>
<br>
Nathan<br>
<br>
On Tue, Dec 8, 2015 at 12:56 PM, Sushilkumar <<a href="mailto:sushil.sush19us@gmail.com">sushil.sush19us@gmail.com</a>><br>
wrote:<br>
<br>
> Dear yt:<br>
><br>
> I would like to plot magnetic field lines in 3D using either streamline or<br>
> 3D quiver plots. Could you suggest me ways for the doing the same?<br>
><br>
> Thanks in advance<br>
><br>
><br>
><br>
> --<br>
> *SK2*<br>
><br>
> *"**Claiming that something can move faster than light is a good<br>
> conversation-stopper in physics. People edge away from you in cocktail<br>
> parties; friends never return phone calls. You just don?t mess with Albert<br>
> Einstein.**"*<br>
><br>
><br>
> _______________________________________________<br>
> yt-users mailing list<br>
> <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
> <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
><br>
><br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <<a href="http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20151208/64610d27/attachment-0001.htm" rel="noreferrer" target="_blank">http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20151208/64610d27/attachment-0001.htm</a>><br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Wed, 9 Dec 2015 10:38:43 +0100<br>
From: Andrea Negri <<a href="mailto:negri.andre@gmail.com">negri.andre@gmail.com</a>><br>
To: Discussion of the yt analysis package<br>
<<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a>><br>
Subject: Re: [yt-users] code support for ZEUS-MP 2<br>
Message-ID:<br>
<CAPUxaiQnwSY=FT_e+a0AQi=<a href="mailto:uu8mx42K9pO3pj6kRwBnTvtJGNg@mail.gmail.com">uu8mx42K9pO3pj6kRwBnTvtJGNg@mail.gmail.com</a>><br>
Content-Type: text/plain; charset=UTF-8<br>
<br>
Hi Matthew,<br>
sorry for the late reply.<br>
<br>
I forgot to say that the spacing of the (spherical) radial grid is not<br>
constant with the radius, but it is logarithmically sampled. Is it a<br>
problem?<br>
<br>
<br>
Andrea<br>
<br>
On 2 December 2015 at 18:13, Matthew Turk <<a href="mailto:matthewturk@gmail.com">matthewturk@gmail.com</a>> wrote:<br>
> Hi Andrea,<br>
><br>
> It should be straightforward to do this. You can load it in to yt<br>
> using the yt.load_uniform_grid function, and then specify the geometry<br>
> as spherical. In the docs we have some examples:<br>
><br>
> <a href="http://yt-project.org/docs/3.2/examining/loading_data.html#generic-array-data" rel="noreferrer" target="_blank">http://yt-project.org/docs/3.2/examining/loading_data.html#generic-array-data</a><br>
><br>
> Specifying geometry="spherical" works here, and if your data is not in<br>
> r,theta,phi, you can specify the axis ordering with<br>
> geometry=("spherical", ("theta", "phi", "r")) (or whatever).<br>
><br>
> -Matt<br>
><br>
> On Wed, Dec 2, 2015 at 10:43 AM, Andrea Negri <<a href="mailto:negri@iap.fr">negri@iap.fr</a>> wrote:<br>
>> Hello,<br>
>><br>
>> I'm a ZEUS-MP 2 user, and I was wondering if is it possible to add the<br>
>> support to ZEUS-MP 2 data, which are stored in HDF5 files.<br>
>><br>
>> The data are nothing special or fancy, forget about particles or multiple<br>
>> levels of refinement. The code has a fixed grid in spherical coordinates,<br>
>> and all my simulations are axially symmetric, i.e. all the variables depends<br>
>> only on the spherical radius and co-latitude.<br>
>><br>
>> It would be great to benefits of all the yt features!<br>
>><br>
>> Thanks in advance,<br>
>> Andrea Negri<br>
>> _______________________________________________<br>
>> yt-users mailing list<br>
>> <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
>> <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
> _______________________________________________<br>
> yt-users mailing list<br>
> <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
> <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
<br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Wed, 9 Dec 2015 05:56:05 -0600<br>
From: Matthew Turk <<a href="mailto:matthewturk@gmail.com">matthewturk@gmail.com</a>><br>
To: Discussion of the yt analysis package<br>
<<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a>><br>
Subject: Re: [yt-users] code support for ZEUS-MP 2<br>
Message-ID:<br>
<CALO3=5HPm=HoxuXwJnSXjuU=<a href="mailto:NX26pDHNGqCC%2BRy-aLVwETfXEw@mail.gmail.com">NX26pDHNGqCC+Ry-aLVwETfXEw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi Andrea,<br>
<br>
For that, you can use the load_hexahedral_mesh function. There's an example<br>
in the docs as well.<br>
<br>
Matt<br>
On Dec 9, 2015 3:39 AM, "Andrea Negri" <<a href="mailto:negri.andre@gmail.com">negri.andre@gmail.com</a>> wrote:<br>
<br>
> Hi Matthew,<br>
> sorry for the late reply.<br>
><br>
> I forgot to say that the spacing of the (spherical) radial grid is not<br>
> constant with the radius, but it is logarithmically sampled. Is it a<br>
> problem?<br>
><br>
><br>
> Andrea<br>
><br>
> On 2 December 2015 at 18:13, Matthew Turk <<a href="mailto:matthewturk@gmail.com">matthewturk@gmail.com</a>> wrote:<br>
> > Hi Andrea,<br>
> ><br>
> > It should be straightforward to do this. You can load it in to yt<br>
> > using the yt.load_uniform_grid function, and then specify the geometry<br>
> > as spherical. In the docs we have some examples:<br>
> ><br>
> ><br>
> <a href="http://yt-project.org/docs/3.2/examining/loading_data.html#generic-array-data" rel="noreferrer" target="_blank">http://yt-project.org/docs/3.2/examining/loading_data.html#generic-array-data</a><br>
> ><br>
> > Specifying geometry="spherical" works here, and if your data is not in<br>
> > r,theta,phi, you can specify the axis ordering with<br>
> > geometry=("spherical", ("theta", "phi", "r")) (or whatever).<br>
> ><br>
> > -Matt<br>
> ><br>
> > On Wed, Dec 2, 2015 at 10:43 AM, Andrea Negri <<a href="mailto:negri@iap.fr">negri@iap.fr</a>> wrote:<br>
> >> Hello,<br>
> >><br>
> >> I'm a ZEUS-MP 2 user, and I was wondering if is it possible to add the<br>
> >> support to ZEUS-MP 2 data, which are stored in HDF5 files.<br>
> >><br>
> >> The data are nothing special or fancy, forget about particles or<br>
> multiple<br>
> >> levels of refinement. The code has a fixed grid in spherical<br>
> coordinates,<br>
> >> and all my simulations are axially symmetric, i.e. all the variables<br>
> depends<br>
> >> only on the spherical radius and co-latitude.<br>
> >><br>
> >> It would be great to benefits of all the yt features!<br>
> >><br>
> >> Thanks in advance,<br>
> >> Andrea Negri<br>
> >> _______________________________________________<br>
> >> yt-users mailing list<br>
> >> <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
> >> <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
> > _______________________________________________<br>
> > yt-users mailing list<br>
> > <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
> > <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
> _______________________________________________<br>
> yt-users mailing list<br>
> <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
> <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
><br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <<a href="http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20151209/247f39d9/attachment-0001.htm" rel="noreferrer" target="_blank">http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20151209/247f39d9/attachment-0001.htm</a>><br>
<br>
------------------------------<br>
<br>
Subject: Digest Footer<br>
<br>
_______________________________________________<br>
yt-users mailing list<br>
<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
<a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
<br>
<br>
------------------------------<br>
<br>
End of yt-users Digest, Vol 94, Issue 5<br>
***************************************<br>
</blockquote></div><br><br clear="all"><br>-- <br><div class="gmail_signature"><span style="border-collapse:collapse"><div style="color:rgb(80,0,80);font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px;border-collapse:collapse"><b><i>SK<sup>2</sup></i></b></span></div><div style="color:rgb(80,0,80);font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px;border-collapse:collapse"><b><i><sup><br></sup></i></b></span></div><div><span style="color:rgb(80,0,80);font-family:arial,sans-serif;border-collapse:collapse"><b><sup>"</sup></b></span><font face="arial, sans-serif" color="#500050"><b>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.</b></font><b style="color:rgb(80,0,80);font-family:arial,sans-serif"><sup>"</sup></b></div><div style="color:rgb(80,0,80);font-family:arial,sans-serif;font-size:13px"><br></div></span></div>
</div></div></div></div></div></div>