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 http://yt-project.org/doc/analyzing/objects.html#arbitrary-grid, 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 https://pastebin.com/BusfAeKh, and I even tried out deposited temperature https://pastebin.com/me9uKMHP and deposited HI_Density https://pastebin.com/BxPJj7B0. 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
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 carla.j.bernhardt@gmail.com 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 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
yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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 matthewturk@gmail.com:
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 carla.j.bernhardt@gmail.com 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 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
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
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 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 matthewturk@gmail.com:
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 carla.j.bernhardt@gmail.com 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 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
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
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.
On Thu, Jul 20, 2017 at 5:03 AM, Carla Bernhardt carla.j.bernhardt@gmail.com wrote:
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 matthewturk@gmail.com:
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 carla.j.bernhardt@gmail.com 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 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
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
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 matthewturk@gmail.com:
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.
On Thu, Jul 20, 2017 at 5:03 AM, Carla Bernhardt carla.j.bernhardt@gmail.com wrote:
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 matthewturk@gmail.com:
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 carla.j.bernhardt@gmail.com 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
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
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
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 matthewturk@gmail.com:
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.
On Thu, Jul 20, 2017 at 5:03 AM, Carla Bernhardt carla.j.bernhardt@gmail.com wrote:
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 matthewturk@gmail.com:
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 carla.j.bernhardt@gmail.com 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
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
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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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 nathan12343@gmail.com:
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 matthewturk@gmail.com:
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.
On Thu, Jul 20, 2017 at 5:03 AM, Carla Bernhardt carla.j.bernhardt@gmail.com wrote:
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 matthewturk@gmail.com:
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 carla.j.bernhardt@gmail.com 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
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 > > _______________________________________________ > 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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-
Carla Bernhardt -
Matthew Turk -
Nathan Goldbaum