Hi yt-users, I was able to get the arbitrary grid working by updating yt to the newest version. I am quite confused, however, by the output. If I extract my arbitrary grid: obj = ds.arbitrary_grid(left_edge, right_edge, dims=[256, 256, 256]) and extract the desired fields: temp = obj["temperature"] HIdens = obj["HI_Density"] (which all works successfully), I then want to write this to a file and would expect that such a file would have 256^3 = 16777216 lines, but I not only don't get this number of lines for my outputs, I even get different number of lines for different fields. Here is the part of my code https://pastebin.com/REcRd2u0 that writes the file. Ideas? Thanks in advance. Cheers, Carla 2017-07-12 12:35 GMT+02:00 Carla Bernhardt :

Hi Matthew,

Thank you for your reply. I was using yt Version 3.2.3 and am working out some installation issues on our server with version 3.3.5. As for the type of data, I have an enzo simulation with static nested grids as well as up to 6 levels AMR grids. I will have to get back to you once I get past the issues with the newest installation of yt.... Thanks for the initial pointers.

Cheers, Carla

2017-07-11 14:15 GMT+02:00 Matthew Turk :

...

Hi Carla,

Interesting. It's possible, for the call to "temperature" (which raises NotImplementedError) that the version of yt you're on doesn't yet support mesh fields in arbitrary grids; that was added reasonably recently. For the others, I'm not totally sure why it's breaking -- which version of yt are you using, and what type of data? It may just be that they aren't deposit fields. In that case, try explicitly stating obj["gas","temperature"] or obj["gas","HI_Density"]. It may also be that the aliasing is getting in the way, in which case instead of "HI_Density" you might need to try "Hp0_density".

...

Dear yt-users,

I am trying to extract a unigrid data cube within a specific region and specified dimensions, thus I am using arbitrary_grid(), however, beyond

On Tue, Jul 11, 2017 at 5:42 AM, Carla Bernhardt wrote: the

...

example given in the docs, my field extractions all fail. I would like to extract temperature, HI_Density and HII_Density. Here is a snippet from my code:

obj = ds.arbitrary_grid(left_edge, right_edge, dims=[256, 256, 256]) print(obj["deposit", "all_density"]) print(obj["temperature"]) print(obj["HI_Density"])

The line print(obj["deposit", "all_density"]) works, but the two lines after both fail. Here is the traceback from the temperature, and I even tried out deposited temperature and deposited HI_Density. Am I formatting this incorrectly, or is there a different way to extract the fields?

Kind regards, Carla Bernhardt PhD Student ZAH Institut für Theoretische Astrophysik Universität Heidelberg

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Hi Matthew, Thank you for the suggestion. That works much better for the temperature field. I also need, however, HI_Density and HII_Density and these do not seem to be within the "gas" (here is the Traceback https://pastebin.com/CKHsXDd5 from when I try that). This is the field list https://pastebin.com/44ZtK8JU from my data, do you have any suggestions for how I could also extract the HI_Density and HII_Density successfully? Thanks, Carla 2017-07-20 16:38 GMT+02:00 Matthew Turk :

Hi Carla,

It's possible that it's writing out the particle values. If you explicitly ask for ["gas", "temperature"] it may write that value out. You can control how the values are deposited on the grid by specifying smoothed, deposited, etc fields.

...

Hi yt-users,

I was able to get the arbitrary grid working by updating yt to the newest version. I am quite confused, however, by the output. If I extract my arbitrary grid:

obj = ds.arbitrary_grid(left_edge, right_edge, dims=[256, 256, 256])

and extract the desired fields:

temp = obj["temperature"] HIdens = obj["HI_Density"]

(which all works successfully), I then want to write this to a file and would expect that such a file would have 256^3 = 16777216 lines, but I not only don't get this number of lines for my outputs, I even get different number of lines for different fields. Here is the part of my code that writes the file. Ideas? Thanks in advance.

Cheers, Carla

2017-07-12 12:35 GMT+02:00 Carla Bernhardt

...

Hi Matthew,

Thank you for your reply. I was using yt Version 3.2.3 and am working

out

...

some installation issues on our server with version 3.3.5. As for the type of data, I have an enzo simulation with static nested grids as well as up to 6 levels AMR grids. I will have to get back to you once I get past the issues with the newest installation of yt.... Thanks for the initial pointers.

Cheers, Carla

2017-07-11 14:15 GMT+02:00 Matthew Turk :

...

Hi Carla,

Interesting. It's possible, for the call to "temperature" (which raises NotImplementedError) that the version of yt you're on doesn't yet support mesh fields in arbitrary grids; that was added reasonably recently. For the others, I'm not totally sure why it's breaking -- which version of yt are you using, and what type of data? It may just be that they aren't deposit fields. In that case, try explicitly stating obj["gas","temperature"] or obj["gas","HI_Density"]. It may also be that the aliasing is getting in the way, in which case instead of "HI_Density" you might need to try "Hp0_density".

On Tue, Jul 11, 2017 at 5:42 AM, Carla Bernhardt wrote:

...

Dear yt-users,

I am trying to extract a unigrid data cube within a specific region

and

...

...

specified dimensions, thus I am using arbitrary_grid(), however, beyond the example given in the docs, my field extractions all fail. I would

...

...

...

...

to extract temperature, HI_Density and HII_Density. Here is a snippet from my code:

obj = ds.arbitrary_grid(left_edge, right_edge, dims=[256, 256, 256]) print(obj["deposit", "all_density"]) print(obj["temperature"]) print(obj["HI_Density"])

The line print(obj["deposit", "all_density"]) works, but the two

...

...

...

...

after both fail. Here is the traceback from the temperature, and I even

On Thu, Jul 20, 2017 at 5:03 AM, Carla Bernhardt wrote: like lines tried

...

...

...

...

out deposited temperature and deposited HI_Density. Am I formatting this incorrectly, or is there a different way to extract the fields?

Kind regards, Carla Bernhardt PhD Student ZAH Institut für Theoretische Astrophysik Universität Heidelberg

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Hi Nathan, Now that you mention it, it seems so obvious! Thank you for helping me out. That seems to work just fine. Cheers, Carla 2017-07-21 16:13 GMT+02:00 Nathan Goldbaum :

Hi Carla,

You could use the ('enzo', 'HI_Density') and ('enzo', 'HII_Density') fields.

The reasons there aren't 'gas' fields for those field names is that yt has a different internal naming convention for species fields. If you take a look at ds.derived_field_list, I bet you have ('gas', 'H_p0_density') and ('gas', 'H_p1_density') fields. These are the "universal" alias fields for the Enzo fields you are looking for.

-Nathan

On Fri, Jul 21, 2017 at 6:13 AM Carla Bernhardt < carla.j.bernhardt@gmail.com> wrote:

...

Hi Matthew,

Thank you for the suggestion. That works much better for the temperature field. I also need, however, HI_Density and HII_Density and these do not seem to be within the "gas" (here is the Traceback https://pastebin.com/CKHsXDd5 from when I try that). This is the field list https://pastebin.com/44ZtK8JU from my data, do you have any suggestions for how I could also extract the HI_Density and HII_Density successfully?

Thanks, Carla

2017-07-20 16:38 GMT+02:00 Matthew Turk :

...

Hi Carla,

It's possible that it's writing out the particle values. If you explicitly ask for ["gas", "temperature"] it may write that value out. You can control how the values are deposited on the grid by specifying smoothed, deposited, etc fields.

...

Hi yt-users,

I was able to get the arbitrary grid working by updating yt to the newest version. I am quite confused, however, by the output. If I extract my arbitrary grid:

obj = ds.arbitrary_grid(left_edge, right_edge, dims=[256, 256, 256])

and extract the desired fields:

temp = obj["temperature"] HIdens = obj["HI_Density"]

(which all works successfully), I then want to write this to a file and would expect that such a file would have 256^3 = 16777216 lines, but I not only don't get this number of lines for my outputs, I even get different number of lines for different fields. Here is the part of my code that writes the file. Ideas? Thanks in advance.

Cheers, Carla

2017-07-12 12:35 GMT+02:00 Carla Bernhardt < carla.j.bernhardt@gmail.com>:

...

Hi Matthew,

Thank you for your reply. I was using yt Version 3.2.3 and am working

out

...

some installation issues on our server with version 3.3.5. As for the type of data, I have an enzo simulation with static nested grids as well as up to 6 levels AMR grids. I will have to get back to you once I get past the issues with the newest installation of yt.... Thanks for the initial pointers.

Cheers, Carla

2017-07-11 14:15 GMT+02:00 Matthew Turk :

...

Hi Carla,

Interesting. It's possible, for the call to "temperature" (which raises NotImplementedError) that the version of yt you're on doesn't yet support mesh fields in arbitrary grids; that was added reasonably recently. For the others, I'm not totally sure why it's breaking -- which version of yt are you using, and what type of data? It may

just

...

be that they aren't deposit fields. In that case, try explicitly stating obj["gas","temperature"] or obj["gas","HI_Density"]. It may also be that the aliasing is getting in the way, in which case instead of "HI_Density" you might need to try "Hp0_density".

On Tue, Jul 11, 2017 at 5:42 AM, Carla Bernhardt wrote: > Dear yt-users, > > I am trying to extract a unigrid data cube within a specific region and > specified dimensions, thus I am using arbitrary_grid(), however, beyond > the > example given in the docs, my field extractions all fail. I would

...

...

...

> to > extract temperature, HI_Density and HII_Density. Here is a snippet from > my > code: > > obj = ds.arbitrary_grid(left_edge, right_edge, dims=[256, 256, 256]) > print(obj["deposit", "all_density"]) > print(obj["temperature"]) > print(obj["HI_Density"]) > > The line print(obj["deposit", "all_density"]) works, but the two

...

...

...

> after > both fail. Here is the traceback from the temperature, and I even

...

...

...

> out > deposited temperature and deposited HI_Density. Am I formatting

On Thu, Jul 20, 2017 at 5:03 AM, Carla Bernhardt wrote: like lines tried this

...

...

...

> incorrectly, or is there a different way to extract the fields? > > Kind regards, > Carla Bernhardt > PhD Student > ZAH Institut für Theoretische Astrophysik > Universität Heidelberg > > _______________________________________________ > 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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