[yt-users] Extracting a list of star particles, their positions and masses from enzo
Carla Bernhardt
carla.j.bernhardt at gmail.com
Wed Mar 15 02:52:14 PDT 2017
Thank you for the help! I seem to be getting the information I was wanting
out of my simulations now.
Best regards,
Carla Bernhardt
2017-03-14 18:20 GMT+01:00 Ari Maller <AMaller at citytech.cuny.edu>:
> Hi Carla,
>
> You want to do something like the following
>
> import yt.mods as ytm
> from yt.data_objects.particle_filters import add_particle_filter
>
> def enzo_stars(pfilter,data):
> filter = data[('io', 'particle_type')] == 2 # DM = 1, Stars = 2
> return filter
>
> ds=ytm.load(my_snapshot_name))
> add_particle_filter("stars",function=enzo_stars,filtered_
> type='io',requires=["particle_type"])
> ds.add_particle_filter("stars”)
> ad = ds.all_data()
> x=ad[(‘stars’,’particle_position_x’)]
> etc…
>
> using stars will now just return star particles. The fields will have to
> be fields in your file which you can check with ds.field_list.
>
> Ari
>
>
>
> > On Mar 14, 2017, at 11:32 AM, yt-users-request at lists.spacepope.org
> wrote:
> >
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> > Today's Topics:
> >
> > 1. Re: yt-users Digest, Vol 109, Issue 27 (Slavin, Jonathan)
> > 2. Re: Extracting a list of star particles, their positions and
> > masses from enzo (Carla Bernhardt)
> > 3. Re: Extracting a list of star particles, their positions and
> > masses from enzo (Nathan Goldbaum)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Tue, 14 Mar 2017 11:27:18 -0400
> > From: "Slavin, Jonathan" <jslavin at cfa.harvard.edu>
> > To: yt-users at lists.spacepope.org
> > Subject: Re: [yt-users] yt-users Digest, Vol 109, Issue 27
> > Message-ID:
> > <CACcRS=fSRQ=4THnqMR3jCDiup1rRcvfAEFPYaATup_92Df=
> DCQ at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > ?Hi Nathan,
> >
> > I finally uploaded the data file to the curldrop site:
> > ?> curl -T
> > /data/plato/mmsnr/flash_data/run-3f818dc2/sedov_hdf5_plt_cnt_0200
> > http://use.yt/upload/
> > Stream body handler: received 467741048 bytes
> > http://use.yt/upload/147aa558
> >
> > Tell me if you need more information about reproducing my issue.
> >
> > Thanks a lot,
> > Jon
> >
> > On Fri, Mar 10, 2017 at 4:05 PM, <yt-users-request at lists.spacepope.org>
> > wrote:
> >
> >> Date: Fri, 10 Mar 2017 12:14:55 -0800
> >> From: Nathan Goldbaum <nathan12343 at gmail.com>
> >> To: Discussion of the yt analysis package
> >> <yt-users at lists.spacepope.org>
> >> Subject: Re: [yt-users] cutting plane not working or changed behavior
> >> Message-ID:
> >> <CAJXewOmWwY1CU4nrafG5_=GrAScGBnq=VMNxxh3s0OUzDzaGVw@
> >> mail.gmail.com>
> >> Content-Type: text/plain; charset="utf-8"
> >>
> >> Hi Jonathan,
> >>
> >> I'm not able to reproduce the behavior you're seeing with a test dataset
> >> (e.g. see http://paste.yt-project.org/show/7080/, this uses a dataset
> from
> >> yt-project.org/data).
> >>
> >> Is there any chance you can share a dataset that triggers this?
> >> Alternatively, can you reproduce this using one of the test datasets on
> >> yt-project.org/data?
> >>
> >> The yt curldrop might be useful to share a dataset that triggers the
> issue
> >> you're seeing, see docs.hub.yt. If you're not comfortable sharing the
> >> dataset publicly, feel free to share it with me off-list.
> >>
> >> -Nathan
> >>
> >
> >
> >
> >
> > --
> > ________________________________________________________
> > Jonathan D. Slavin Harvard-Smithsonian CfA
> > jslavin at cfa.harvard.edu 60 Garden Street, MS 83
> > phone: (617) 496-7981 Cambridge, MA 02138-1516
> > cell: (781) 363-0035 USA
> > ________________________________________________________
> > -------------- next part --------------
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> >
> > ------------------------------
> >
> > Message: 2
> > Date: Tue, 14 Mar 2017 16:28:17 +0100
> > From: Carla Bernhardt <carla.j.bernhardt at gmail.com>
> > To: Discussion of the yt analysis package
> > <yt-users at lists.spacepope.org>
> > Subject: Re: [yt-users] Extracting a list of star particles, their
> > positions and masses from enzo
> > Message-ID:
> > <CAKQMXAVTzJ9Y2D7xXWHHg+2HXpWY4=7RzSfHoJPwosYGSMsx-g@
> mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Nathan,
> >
> > Yes, of course. Here is what I tried
> > <http://paste.yt-project.org/show/7082/> and here is the error message
> > <http://paste.yt-project.org/show/7084/> I get. What I tried might not
> be
> > the right way to get this list, but I was hoping someone else has done
> this
> > before and has some insight.
> >
> > Best,
> > Carla
> >
> > 2017-03-14 16:00 GMT+01:00 Nathan Goldbaum <nathan12343 at gmail.com>:
> >
> >> Hi Carla,
> >>
> >> Can you share the script you're running and the full error message and
> >> traceback you're seeing? If you can, it helps if you can make your
> script
> >> that triggers your issue as minimal as possible.
> >>
> >> We have the yt pastebin set up for sharing snippets of code and text:
> >> paste.yt-project.org.
> >>
> >> -Nathan
> >>
> >> On Tue, Mar 14, 2017 at 2:30 AM, Carla Bernhardt <
> >> carla.j.bernhardt at gmail.com> wrote:
> >>
> >>> Dear yt users,
> >>>
> >>> I am trying to extract a list of star particles and their positions and
> >>> masses from enzo. This seems to be right along the lines of this
> tutorial
> >>> <http://yt-project.org/doc/analyzing/fields.html>, but I am still
> stuck.
> >>> If I try
> >>>
> >>> print(ad["dark_matter", "particle_position"])
> >>> print(ad["stars", "particle_position"])
> >>> print(ad["black_holes", "particle_position"])
> >>>
> >>> I get that none of these fields are available in my provided data. I am
> >>> using Stochastic Star Formation with a MBH inserted (i.e.
> >>> StarParticleCreation=514).
> >>>
> >>> Thanks in advance,
> >>> Carla Bernhardt
> >>> PhD Student
> >>> Universit?t Heidelberg
> >>> ZAH Institut f?r Theoretische Astrophysik
> >>>
> >>>
> >>> _______________________________________________
> >>> yt-users mailing list
> >>> yt-users at lists.spacepope.org
> >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>>
> >>>
> >>
> >> _______________________________________________
> >> yt-users mailing list
> >> yt-users at lists.spacepope.org
> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>
> >>
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> >
> > ------------------------------
> >
> > Message: 3
> > Date: Tue, 14 Mar 2017 10:32:00 -0500
> > From: Nathan Goldbaum <nathan12343 at gmail.com>
> > To: Discussion of the yt analysis package
> > <yt-users at lists.spacepope.org>
> > Subject: Re: [yt-users] Extracting a list of star particles, their
> > positions and masses from enzo
> > Message-ID:
> > <CAJXewO=sCXCpFn1bpsSL3vK9AjiA7OMwPy5SRAmb8Lp09XDhzQ at mail.
> gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > You need to define some particle filters. Enzo only has one on-disk
> > particle type. Particle filters let you define new particle types based
> on
> > some filtering criterion. For Enzo it's usually sufficient to filter on
> the
> > ('io', 'particle_type') field.
> >
> > There is an example of adding a particle filter with enzo data in the
> docs
> > here:
> >
> > http://yt-project.org/docs/dev/cookbook/calculating_
> information.html#using-particle-filters-to-calculate-star-formation-rates
> >
> > And more information on particle filters here:
> >
> > http://yt-project.org/docs/dev/analyzing/filtering.html?
> highlight=filter#filtering-particle-fields
> >
> > The Enzo frontend does not predefine any particle fields since we don't
> > want to accidentally cause users to generate anaylsis or visualization
> > results based on a particle filter definition that does not apply to all
> > data types.
> >
> > -Nathan
> >
> > On Tue, Mar 14, 2017 at 10:28 AM, Carla Bernhardt <
> > carla.j.bernhardt at gmail.com> wrote:
> >
> >> Nathan,
> >>
> >> Yes, of course. Here is what I tried
> >> <http://paste.yt-project.org/show/7082/> and here is the error message
> >> <http://paste.yt-project.org/show/7084/> I get. What I tried might not
> be
> >> the right way to get this list, but I was hoping someone else has done
> this
> >> before and has some insight.
> >>
> >> Best,
> >> Carla
> >>
> >> 2017-03-14 16:00 GMT+01:00 Nathan Goldbaum <nathan12343 at gmail.com>:
> >>
> >>> Hi Carla,
> >>>
> >>> Can you share the script you're running and the full error message and
> >>> traceback you're seeing? If you can, it helps if you can make your
> script
> >>> that triggers your issue as minimal as possible.
> >>>
> >>> We have the yt pastebin set up for sharing snippets of code and text:
> >>> paste.yt-project.org.
> >>>
> >>> -Nathan
> >>>
> >>> On Tue, Mar 14, 2017 at 2:30 AM, Carla Bernhardt <
> >>> carla.j.bernhardt at gmail.com> wrote:
> >>>
> >>>> Dear yt users,
> >>>>
> >>>> I am trying to extract a list of star particles and their positions
> and
> >>>> masses from enzo. This seems to be right along the lines of this
> >>>> tutorial <http://yt-project.org/doc/analyzing/fields.html>, but I am
> >>>> still stuck. If I try
> >>>>
> >>>> print(ad["dark_matter", "particle_position"])
> >>>> print(ad["stars", "particle_position"])
> >>>> print(ad["black_holes", "particle_position"])
> >>>>
> >>>> I get that none of these fields are available in my provided data. I
> am
> >>>> using Stochastic Star Formation with a MBH inserted (i.e.
> >>>> StarParticleCreation=514).
> >>>>
> >>>> Thanks in advance,
> >>>> Carla Bernhardt
> >>>> PhD Student
> >>>> Universit?t Heidelberg
> >>>> ZAH Institut f?r Theoretische Astrophysik
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> yt-users mailing list
> >>>> yt-users at lists.spacepope.org
> >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>>>
> >>>>
> >>>
> >>> _______________________________________________
> >>> yt-users mailing list
> >>> yt-users at lists.spacepope.org
> >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>>
> >>>
> >>
> >> _______________________________________________
> >> yt-users mailing list
> >> yt-users at lists.spacepope.org
> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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