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 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 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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Hi Ariadna, How about tomorrow at 10AM PDT? -Matt On Wed, Jul 16, 2014 at 11:43 AM, Ariadna Murguia 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 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 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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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"? Thank you! Ariadna From: doggies012@hotmail.com To: yt-users@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@gmail.com Date: Thu, 17 Jul 2014 07:15:30 -0500 To: yt-users@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 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 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 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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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@gmail.com Date: Mon, 21 Jul 2014 20:36:46 -0500 To: yt-users@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 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@hotmail.com To: yt-users@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@gmail.com Date: Thu, 17 Jul 2014 07:15:30 -0500 To: yt-users@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 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 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 > > 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 > > > > _______________________________________________ > > yt-users mailing list > > yt-users@lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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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@gmail.com Date: Wed, 30 Jul 2014 14:41:06 -0500 To: yt-users@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-parti...

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 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@gmail.com Date: Mon, 21 Jul 2014 20:36:46 -0500

...

To: yt-users@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 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@hotmail.com To: yt-users@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@gmail.com Date: Thu, 17 Jul 2014 07:15:30 -0500 To: yt-users@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 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 > 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 > >> > >> 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 > >> > > >> > _______________________________________________ > >> > yt-users mailing list > >> > yt-users@lists.spacepope.org > >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >> > > >> _______________________________________________ > >> yt-users mailing list > >> yt-users@lists.spacepope.org > >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > _______________________________________________ > > yt-users mailing list > > yt-users@lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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