[yt-users] Unstructured grid yt support‏‏ -question

Matthew Turk matthewturk at gmail.com
Wed Jul 30 12:41:06 PDT 2014


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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