[yt-users] Unstructured grid yt support‏‏ -question

Ariadna Murguia doggies012 at hotmail.com
Thu Jul 31 10:17:06 PDT 2014


Hi!
Thank you, it's working!
I'll e-mail you if I have other questions, but for the time it worked :)
Ari

> From: matthewturk at gmail.com
> Date: Wed, 30 Jul 2014 14:41:06 -0500
> To: yt-users at lists.spacepope.org
> Subject: Re: [yt-users] Unstructured grid yt support‏‏ -question
> 
> Hi Ari,
> 
> Sorry for the delay!  Have had a crazy couple days.
> 
> Basically, yes, you are right.  xdmf_points_000*.dat gives the "x" and
> "y" coordinates.  But, for the most part, that's not the important
> part -- in fact, I apologize for having given such a complex example.
> 
> The basics you want are identical to "loading particle data" here:
> 
> http://yt-project.org/docs/dev-3.0/examining/loading_data.html#generic-particle-data
> 
> That's all that the script I was doing did, up until the point where
> it has the "ds" object.  At that point, you can and should be able to
> do whatever you need to.  I would recommend doing it like so:
> 
>  * Either decide on loading in vertex or centered data
>  * Add in scalar fields for volume, if you have them, for the FEM mesh
>  * Use IDW weighting (also in the script) for visualization
> 
> As a note, there are places where yt will build its own mesh and
> indexing system; these may give incorrect results.  So once you have
> it loaded in and have made a few projections, let's figure out what
> the next steps are, and how we can make sure your results are
> high-fidelity.
> 
> -Matt
> 
> On Wed, Jul 23, 2014 at 7:12 PM, Ariadna Murguia <doggies012 at hotmail.com> wrote:
> > Hi!
> > I have some other questions: I'm guessing that in the xdmf_points_0000.dat
> > and xdmf_points_0001.dat the number 0 or 1 refers to the x coordinate and y
> > coordinate, but what about the other variables, do they refer to the
> > component x and y of the variable? If so, what happens when dealing with a
> > scalar?
> >
> > Thank you!
> > Ari
> >
> >> From: matthewturk at gmail.com
> >> Date: Mon, 21 Jul 2014 20:36:46 -0500
> >
> >> To: yt-users at lists.spacepope.org
> >> Subject: Re: [yt-users] Unstructured grid yt support‏‏ -question
> >>
> >> Hi Ariadna,
> >>
> >> On Mon, Jul 21, 2014 at 8:30 PM, Ariadna Murguia <doggies012 at hotmail.com>
> >> wrote:
> >> > Hi!
> >> > I was looking at the unstructured grid script and the data, and I had a
> >> > question. What is the field "abs", "z", and "s"?
> >>
> >> abs was my data field -- in this case, the absolute value of the
> >> displacement. s was my radius, and z the cylindrical axis coordinate.
> >>
> >> > Thank you!
> >> > Ariadna
> >> >
> >> > ________________________________
> >> > From: doggies012 at hotmail.com
> >> > To: yt-users at lists.spacepope.org
> >> > Date: Thu, 17 Jul 2014 11:39:11 -0500
> >> >
> >> > Subject: Re: [yt-users] Unstructured grid yt support‏‏ -question
> >> >
> >> > Hi!
> >> > Ok, tomorrow at 10AM PDT :)
> >> > Ariadna
> >> >
> >> >> From: matthewturk at gmail.com
> >> >> Date: Thu, 17 Jul 2014 07:15:30 -0500
> >> >> To: yt-users at lists.spacepope.org
> >> >> Subject: Re: [yt-users] Unstructured grid yt support‏‏ -question
> >> >>
> >> >> Hi Ariadna,
> >> >>
> >> >> How about tomorrow at 10AM PDT?
> >> >>
> >> >> -Matt
> >> >>
> >> >> On Wed, Jul 16, 2014 at 11:43 AM, Ariadna Murguia
> >> >> <doggies012 at hotmail.com> wrote:
> >> >> >
> >> >> > Hi!
> >> >> > Don't worry, I'm thankful for your help. My data is a vtk legacy file
> >> >> > for
> >> >> > unstructured grid. The coordinates are of the vertex, but the values
> >> >> > of
> >> >> > the
> >> >> > variables are cell-center. I'm available on thursday and on friday
> >> >> > before
> >> >> > noon (PDT). Are you available?
> >> >> > Ariadna
> >> >> >
> >> >> >
> >> >> >> Hi Ariadna,
> >> >> >>
> >> >> >> Sorry for the delay in my reply. I think that there might need to be
> >> >> >> a slight modification to the script I sent to get it working for
> >> >> >> your
> >> >> >> data. Ultimately, none of the reshaping/loading/etc matter -- the
> >> >> >> end
> >> >> >> result, where you supply particle_position_x, particle_position_y,
> >> >> >> and
> >> >> >> particle_position_z is the important part. Do you think that it
> >> >> >> would
> >> >> >> be feasible to do that with your data? And, are your data values
> >> >> >> vertex defined or cell-center defined? If the former, the technique
> >> >> >> I
> >> >> >> showed should work, but if the latter, there is likely a much easier
> >> >> >> technique to use.
> >> >> >>
> >> >> >> Today I'm going to have limited availability, but perhaps we could
> >> >> >> set
> >> >> >> up a time on Thursday or Friday to go over this in our IRC channel,
> >> >> >> with lower latency responses?
> >> >> >>
> >> >> >> -Matt
> >> >> >>
> >> >> >> On Tue, Jul 15, 2014 at 12:58 PM, Ariadna Murguia
> >> >> >> <doggies012 at hotmail.com> wrote:
> >> >> >> > Hi!
> >> >> >> > My data has 3 coordinates (cylindrical), although the angle is
> >> >> >> > cero
> >> >> >> > (so
> >> >> >> > it
> >> >> >> > is a 2D simulation). I changed it to 3, but still vals.size/3 is
> >> >> >> > not
> >> >> >> > an
> >> >> >> > integer. Can you tell me the order of your data? In the
> >> >> >> > simulations
> >> >> >> > I'm
> >> >> >> > using the first numbers correspond to the 3 coordinates of each of
> >> >> >> > the
> >> >> >> > cells
> >> >> >> > vertex. Then, there is a number for the shape of the mesh (4 in
> >> >> >> > the
> >> >> >> > case
> >> >> >> > of
> >> >> >> > squares), followed by the list of vertex. After that, it has the
> >> >> >> > values
> >> >> >> > of
> >> >> >> > the variables inside the square.
> >> >> >> > Thank you for your help,
> >> >> >> > Ariadna
> >> >> >> >
> >> >> >> >
> >> >> >> >> Are you doing 3D visualization? The simulation I was using when I
> >> >> >> >> wrote that script was 2D -- if yours is 3D, you will likely need
> >> >> >> >> to
> >> >> >> >> change it to 3, rather than 2, in that line. If you give a bit
> >> >> >> >> more
> >> >> >> >> info about the data (shape for instance) I can try replicating it
> >> >> >> >> here.
> >> >> >> >>
> >> >> >> >> -Matt
> >> >> >> >>
> >> >> >> >> On Mon, Jul 14, 2014 at 2:51 PM, Ariadna Murguia
> >> >> >> >> <doggies012 at hotmail.com>
> >> >> >> >> wrote:
> >> >> >> >> > Hi!
> >> >> >> >> > I wrote a while back asking to visualize a dataset in an
> >> >> >> >> > unstructured
> >> >> >> >> > grid
> >> >> >> >> > with AMR and a vtk output file. I was given a script that could
> >> >> >> >> > do
> >> >> >> >> > simple
> >> >> >> >> > visualizations: http://paste.yt-project.org/show/4879/ .
> >> >> >> >> > I tried altering it in order to visualize my data but (line
> >> >> >> >> > 39),
> >> >> >> >> > the
> >> >> >> >> > number
> >> >> >> >> > of elements in my vals array is odd, making the reshape become
> >> >> >> >> > an
> >> >> >> >> > error.
> >> >> >> >> > Is
> >> >> >> >> > there a way around it?
> >> >> >> >> > Thank you very much
> >> >> >> >> > Ariadna Murguia Berthier
> >> >> >> >> >
> >> >> >> >> > _______________________________________________
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> >> >> >> >> >
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