[yt-users] yt-users Digest, Vol 98, Issue 14

Sushilkumar sushil.sush19us at gmail.com
Fri Apr 15 14:49:38 PDT 2016 

Dear Suoqing JI:

Thank you

On Fri, Apr 15, 2016 at 12:59 PM, <yt-users-request at lists.spacepope.org>
wrote:

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> Today's Topics:
>
>    1. Re: Camera Options (Suoqing Ji)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 15 Apr 2016 10:59:22 -0700
> From: Suoqing Ji <suoqing at physics.ucsb.edu>
> To: Discussion of the yt analysis package
>         <yt-users at lists.spacepope.org>
> Subject: Re: [yt-users] Camera Options
> Message-ID: <B885F215-5F0A-49D5-9712-2D8FCEAA1366 at physics.ucsb.edu>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Sushi,
>
> I think the off-axis slice/projection plot will meet your requirement
> best, where the camera orientation is determined by the normal vector:
>
> http://yt-project.org/doc/visualizing/plots.html#off-axis-slices <
> http://yt-project.org/doc/visualizing/plots.html#off-axis-slices>
> http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots
> <
> http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots
> >
>
> And of course, if you?re interested in the features provided by volume
> rendering, it?s also worth a try. This cookbook gives an example of moving
> a camera; specifically you might want to use the camera.rotation:
>
>
> http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rendering-camera
> <
> http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rendering-camera
> >
>
> Best wishes,
> --
> Suoqing JI
> Ph.D Candidate
> Department of Physics
> University of California, Santa Barbara
> http://web.physics.ucsb.edu/~suoqing
>
> > On Apr 15, 2016, at 8:38 AM, Sushilkumar <sushil.sush19us at gmail.com>
> wrote:
> >
> > Dear yt:
> >
> > I would like to change/customize/rotate my camera angle for my slice
> plots without rotating the axis.
> >
> > What options do I have using yt if I want to move my camera angle by say
> 45 degrees?
> >
> > Can I use the following link or can you suggest me something else
> > http://yt-project.org/doc/visualizing/volume_rendering.html <
> http://yt-project.org/doc/visualizing/volume_rendering.html>
> >
> > Thanks in advance
> >
> >
> >
> > On Thu, Mar 31, 2016 at 10:11 PM, <yt-users-request at lists.spacepope.org
> <mailto:yt-users-request at lists.spacepope.org>> wrote:
> > Send yt-users mailing list submissions to
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> >
> >
> > Today's Topics:
> >
> >    1. Inclination problem (Sushilkumar)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Thu, 31 Mar 2016 22:11:09 -0500
> > From: Sushilkumar <sushil.sush19us at gmail.com <mailto:
> sushil.sush19us at gmail.com>>
> > To: Discussion of the yt analysis package
> >         <yt-users at lists.spacepope.org <mailto:
> yt-users at lists.spacepope.org>>
> > Subject: [yt-users] Inclination problem
> > Message-ID:
> >         <
> CAKARaKXPyQedHNjW0PwFvrO0qyjFGY4FMU6c2O5_PZWt-OxKEg at mail.gmail.com
> <mailto:CAKARaKXPyQedHNjW0PwFvrO0qyjFGY4FMU6c2O5_PZWt-OxKEg at mail.gmail.com
> >>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Dear Nathan:
> >
> > Thank you very much, implementing now
> >
> >
> > On Thu, Mar 31, 2016 at 9:50 AM, <yt-users-request at lists.spacepope.org
> <mailto:yt-users-request at lists.spacepope.org>>
> > wrote:
> >
> > > Send yt-users mailing list submissions to
> > >         yt-users at lists.spacepope.org <mailto:
> yt-users at lists.spacepope.org>
> > >
> > > To subscribe or unsubscribe via the World Wide Web, visit
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> <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
> > > or, via email, send a message with subject or body 'help' to
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> > >
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> > > When replying, please edit your Subject line so it is more specific
> > > than "Re: Contents of yt-users digest..."
> > >
> > >
> > > Today's Topics:
> > >
> > >    1. Re: Inclination problem (Nathan Goldbaum)
> > >
> > >
> > > ----------------------------------------------------------------------
> > >
> > > Message: 1
> > > Date: Thu, 31 Mar 2016 09:50:31 -0500
> > > From: Nathan Goldbaum <nathan12343 at gmail.com <mailto:
> nathan12343 at gmail.com>>
> > > To: Discussion of the yt analysis package
> > >         <yt-users at lists.spacepope.org <mailto:
> yt-users at lists.spacepope.org>>
> > > Subject: Re: [yt-users] Inclination problem
> > > Message-ID:
> > >         <CAJXewOnvXjZ+shfKG4SPubn_TYTAbLUu8y9ZRvovzBu=
> > > DcFZtQ at mail.gmail.com <mailto:DcFZtQ at mail.gmail.com>>
> > > Content-Type: text/plain; charset="utf-8"
> > >
> > > Hi SK,
> > >
> > > I'm going to reference this example:
> > >
> > >
> > >
> http://yt-project.org/doc/visualizing/streamlines.html?highlight=streamlines
> <
> http://yt-project.org/doc/visualizing/streamlines.html?highlight=streamlines
> >
> > >
> > > specifically this snippet:
> > >
> > > for stream in streamlines.streamlines:
> > >     stream = stream[np.all(stream != 0.0, axis=1)]
> > >     ax.plot3D(stream[:,0], stream[:,1], stream[:,2], alpha=0.1)
> > >
> > > Here, the 'stream' object is just a Nx3 numpy array, where N is the
> number
> > > of points sampled along the streamline. So each row of the numpy array
> is
> > > just the coordinates of the streamline along one direction.
> > >
> > > To answer your question, no, there's nothing in yt that will rotate the
> > > streamlines into a new coordinate system. Fortunately you should be
> able to
> > > do it yourself using e.g. an Euler angle rotation matrix. You will
> need to
> > > identify the new coordinate system you would like to transform to,
> > > calculate a 3D rotation matrix, then apply it using matrix
> multiplication
> > > (e.g. np.dot, which supports broadcasting) to each coordinate along the
> > > streamline.
> > >
> > > Hope that helps,
> > >
> > > Nathan
> > >
> > > On Thu, Mar 31, 2016 at 8:56 AM, Sushilkumar <
> sushil.sush19us at gmail.com <mailto:sushil.sush19us at gmail.com>>
> > > wrote:
> > >
> > > > Dear Matt:
> > > >
> > > > Pleas correct me if I am wrong but "off axis slices" takes slices of
> the
> > > > plot that is already plotted.
> > > >
> > > > However, I would like to plot my data in a new coordinate frame
> > > (x`,y`,z`)
> > > > which is inclined at an angle of say alpha from the default (x,y,z)
> > > frame.
> > > >
> > > > Or I would like to plot my data in a rotated frame (x`,y`,z`), which
> is
> > > > rotated at an angle of alpha from (x,y,z).
> > > >
> > > >
> > > >
> > > >
> > > > On Wed, Mar 30, 2016 at 5:01 PM, <
> yt-users-request at lists.spacepope.org <mailto:
> yt-users-request at lists.spacepope.org>>
> > > > wrote:
> > > >
> > > >> Send yt-users mailing list submissions to
> > > >>         yt-users at lists.spacepope.org <mailto:
> yt-users at lists.spacepope.org>
> > > >>
> > > >> To subscribe or unsubscribe via the World Wide Web, visit
> > > >>
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
> > > >> or, via email, send a message with subject or body 'help' to
> > > >>         yt-users-request at lists.spacepope.org <mailto:
> yt-users-request at lists.spacepope.org>
> > > >>
> > > >> You can reach the person managing the list at
> > > >>         yt-users-owner at lists.spacepope.org <mailto:
> yt-users-owner at lists.spacepope.org>
> > > >>
> > > >> When replying, please edit your Subject line so it is more specific
> > > >> than "Re: Contents of yt-users digest..."
> > > >>
> > > >>
> > > >> Today's Topics:
> > > >>
> > > >>    1. Re: load spherical polar coordinate data with mesh refinement
> > > >>       in HDF5 (Jiang, Yanfei)
> > > >>    2. Re: load spherical polar coordinate data with mesh refinement
> > > >>       in HDF5 (Matthew Turk)
> > > >>    3. Re: Inclination problem (Matthew Turk)
> > > >>    4. Re: load spherical polar coordinate data with mesh refinement
> > > >>       in HDF5 (Jonah Miller)
> > > >>
> > > >>
> > > >>
> ----------------------------------------------------------------------
> > > >>
> > > >> Message: 1
> > > >> Date: Wed, 30 Mar 2016 15:49:26 -0400
> > > >> From: "Jiang, Yanfei" <yanfei.jiang at cfa.harvard.edu <mailto:
> yanfei.jiang at cfa.harvard.edu>>
> > > >> To: Discussion of the yt analysis package
> > > >>         <yt-users at lists.spacepope.org <mailto:
> yt-users at lists.spacepope.org>>
> > > >> Subject: Re: [yt-users] load spherical polar coordinate data with
> mesh
> > > >>         refinement in HDF5
> > > >> Message-ID:
> > > >>         <
> > > >> CANixPav-VmbXfhNvmA5wb5gj19mF+-Ryq5YD-LrYrByDe3Ne7A at mail.gmail.com
> <mailto:
> CANixPav-VmbXfhNvmA5wb5gj19mF%2B-Ryq5YD-LrYrByDe3Ne7A at mail.gmail.com>>
> > > >> Content-Type: text/plain; charset="utf-8"
> > > >>
> > > >> Hi Jonah,
> > > >>
> > > >>    I am able to load the data to yt now using load_amr_grids(). I
> notice
> > > >> that it can also set geometry to spherical. This is great. But to
> make
> > > >> life
> > > >> more complicate. Is it possible to let yt know that the grid is
> > > >> logarithmic? Currently, load_amr_grids() just take left and right
> edges
> > > of
> > > >> each block. I guess yt assumes the grid is uniform between left and
> > > right
> > > >> edges. Is it possible to provide arrays of coordinate values for
> each
> > > cell
> > > >> in each block?
> > > >>
> > > >> Thanks.
> > > >>
> > > >> On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller <
> > > >> jonah.maxwell.miller at gmail.com <mailto:
> jonah.maxwell.miller at gmail.com>> wrote:
> > > >>
> > > >> > Hi Yan-Feng,
> > > >> >
> > > >> > I haven't tried it, but I think there is functionality for this.
> You
> > > can
> > > >> > use the load_amr_grids() function which can load amr data in
> > > Cartesian,
> > > >> > spherical, or polar coordinates. Here's the documentation:
> > > >> >
> > > >> >
> > > >>
> > >
> http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-array
> <
> http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-array
> >
> > > >> >
> > > >> >
> > > >> >
> > > >>
> > >
> http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_structures.load_amr_grids.html#yt.frontends.stream.data_structures.load_amr_grids
> <
> http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_structures.load_amr_grids.html#yt.frontends.stream.data_structures.load_amr_grids
> >
> > > >> >
> > > >> > Best,
> > > >> > Jonah
> > > >> >
> > > >> > On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei <
> > > >> yanfei.jiang at cfa.harvard.edu <mailto:yanfei.jiang at cfa.harvard.edu>>
> > > >> > wrote:
> > > >> >
> > > >> >> Hi,
> > > >> >>          I have some data from a new version of Athena
> simulations.
> > > It
> > > >> is
> > > >> >> in spherical polar coordinate with mesh refinement written in
> HDF5.
> > > The
> > > >> >> data structure is similar to flash data but not the same. Does
> anyone
> > > >> have
> > > >> >> suggestions to load such data to yt directly?
> > > >> >>
> > > >> >> Thank you.
> > > >> >> --
> > > >> >> Yan-Fei Jiang
> > > >> >>
> > > >> >> Einstein Fellow
> > > >> >> Harvard-Smithsonian Center for Astrophysics
> > > >> >> 60 Garden Street, Cambridge MA USA 02138
> > > >> >> _______________________________________________
> > > >> >> yt-users mailing list
> > > >> >> yt-users at lists.spacepope.org <mailto:
> yt-users at lists.spacepope.org>
> > > >> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
> > > >> >>
> > > >> >
> > > >> > _______________________________________________
> > > >> > yt-users mailing list
> > > >> > yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org
> >
> > > >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
> > > >> >
> > > >> >
> > > >>
> > > >>
> > > >> --
> > > >> Yan-Fei Jiang
> > > >>
> > > >> Einstein Fellow
> > > >> Harvard-Smithsonian Center for Astrophysics
> > > >> 60 Garden Street, Cambridge MA USA 02138
> > > >> -------------- next part --------------
> > > >> An HTML attachment was scrubbed...
> > > >> URL: <
> > > >>
> > >
> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160330/aedc3b19/attachment-0001.htm
> <
> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160330/aedc3b19/attachment-0001.htm
> >
> > > >> >
> > > >>
> > > >> ------------------------------
> > > >>
> > > >> Message: 2
> > > >> Date: Wed, 30 Mar 2016 16:15:30 -0500
> > > >> From: Matthew Turk <matthewturk at gmail.com <mailto:
> matthewturk at gmail.com>>
> > > >> To: Discussion of the yt analysis package
> > > >>         <yt-users at lists.spacepope.org <mailto:
> yt-users at lists.spacepope.org>>
> > > >> Subject: Re: [yt-users] load spherical polar coordinate data with
> mesh
> > > >>         refinement in HDF5
> > > >> Message-ID:
> > > >>         <CALO3=
> > > >> 5F1-_9V5XHS4vF_eXvKoPerz3Zo20X8uPtcFjQSAQS1MA at mail.gmail.com
> <mailto:5F1-_9V5XHS4vF_eXvKoPerz3Zo20X8uPtcFjQSAQS1MA at mail.gmail.com>>
> > > >> Content-Type: text/plain; charset=UTF-8
> > > >>
> > > >> Hi Yanfei,
> > > >>
> > > >> This is possible -- but it will also slow some things down.  You can
> > > >> use the load_hexahedral_mesh function, and there're examples of
> this.
> > > >> This takes away some of the optimizations that regular grids can do,
> > > >> but we're hoping to add them back in shortly.  Like the other
> > > >> functions it too takes a geometry argument.
> > > >>
> > > >> -Matt
> > > >>
> > > >> On Wed, Mar 30, 2016 at 2:49 PM, Jiang, Yanfei
> > > >> <yanfei.jiang at cfa.harvard.edu <mailto:yanfei.jiang at cfa.harvard.edu>>
> wrote:
> > > >> > Hi Jonah,
> > > >> >
> > > >> >    I am able to load the data to yt now using load_amr_grids(). I
> > > notice
> > > >> > that it can also set geometry to spherical. This is great. But to
> make
> > > >> life
> > > >> > more complicate. Is it possible to let yt know that the grid is
> > > >> logarithmic?
> > > >> > Currently, load_amr_grids() just take left and right edges of each
> > > >> block. I
> > > >> > guess yt assumes the grid is uniform between left and right
> edges. Is
> > > it
> > > >> > possible to provide arrays of coordinate values for each cell in
> each
> > > >> block?
> > > >> >
> > > >> > Thanks.
> > > >> >
> > > >> > On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller
> > > >> > <jonah.maxwell.miller at gmail.com <mailto:
> jonah.maxwell.miller at gmail.com>> wrote:
> > > >> >>
> > > >> >> Hi Yan-Feng,
> > > >> >>
> > > >> >> I haven't tried it, but I think there is functionality for this.
> You
> > > >> can
> > > >> >> use the load_amr_grids() function which can load amr data in
> > > Cartesian,
> > > >> >> spherical, or polar coordinates. Here's the documentation:
> > > >> >>
> > > >> >>
> > > >> >>
> > > >>
> > >
> http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-array
> <
> http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-array
> >
> > > >> >>
> > > >> >>
> > > >> >>
> > > >>
> > >
> http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_structures.load_amr_grids.html#yt.frontends.stream.data_structures.load_amr_grids
> <
> http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_structures.load_amr_grids.html#yt.frontends.stream.data_structures.load_amr_grids
> >
> > > >> >>
> > > >> >> Best,
> > > >> >> Jonah
> > > >> >>
> > > >> >> On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei <
> > > >> yanfei.jiang at cfa.harvard.edu <mailto:yanfei.jiang at cfa.harvard.edu>>
> > > >> >> wrote:
> > > >> >>>
> > > >> >>> Hi,
> > > >> >>>          I have some data from a new version of Athena
> simulations.
> > > >> It is
> > > >> >>> in spherical polar coordinate with mesh refinement written in
> HDF5.
> > > >> The data
> > > >> >>> structure is similar to flash data but not the same. Does anyone
> > > have
> > > >> >>> suggestions to load such data to yt directly?
> > > >> >>>
> > > >> >>> Thank you.
> > > >> >>> --
> > > >> >>> Yan-Fei Jiang
> > > >> >>>
> > > >> >>> Einstein Fellow
> > > >> >>> Harvard-Smithsonian Center for Astrophysics
> > > >> >>> 60 Garden Street, Cambridge MA USA 02138
> > > >> >>> _______________________________________________
> > > >> >>> yt-users mailing list
> > > >> >>> yt-users at lists.spacepope.org <mailto:
> yt-users at lists.spacepope.org>
> > > >> >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
> > > >> >>
> > > >> >>
> > > >> >> _______________________________________________
> > > >> >> yt-users mailing list
> > > >> >> yt-users at lists.spacepope.org <mailto:
> yt-users at lists.spacepope.org>
> > > >> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
> > > >> >>
> > > >> >
> > > >> >
> > > >> >
> > > >> > --
> > > >> > Yan-Fei Jiang
> > > >> >
> > > >> > Einstein Fellow
> > > >> > Harvard-Smithsonian Center for Astrophysics
> > > >> > 60 Garden Street, Cambridge MA USA 02138
> > > >> >
> > > >> > _______________________________________________
> > > >> > yt-users mailing list
> > > >> > yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org
> >
> > > >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
> > > >> >
> > > >>
> > > >>
> > > >> ------------------------------
> > > >>
> > > >> Message: 3
> > > >> Date: Wed, 30 Mar 2016 16:16:22 -0500
> > > >> From: Matthew Turk <matthewturk at gmail.com <mailto:
> matthewturk at gmail.com>>
> > > >> To: Discussion of the yt analysis package
> > > >>         <yt-users at lists.spacepope.org <mailto:
> yt-users at lists.spacepope.org>>
> > > >> Subject: Re: [yt-users] Inclination problem
> > > >> Message-ID:
> > > >>         <CALO3=5HMB=
> > > >> joejr6BBh+zdxkwGzJS2NPrkK9tvMJnbch5-7BgQ at mail.gmail.com <mailto:
> joejr6BBh%2BzdxkwGzJS2NPrkK9tvMJnbch5-7BgQ at mail.gmail.com>>
> > > >> Content-Type: text/plain; charset=UTF-8
> > > >>
> > > >> Hi SK,
> > > >>
> > > >> I'm not sure I totally understand, but if you have an inclination
> > > >> angle you can use this directly in yt in the off axis slices and so
> > > >> on.  They typically take a vector, but you should be able to convert
> > > >> one to the other.
> > > >>
> > > >> -Matt
> > > >>
> > > >> On Tue, Mar 29, 2016 at 1:37 PM, Sushilkumar <
> sushil.sush19us at gmail.com <mailto:sushil.sush19us at gmail.com>
> > > >
> > > >> wrote:
> > > >> > Dear yt:
> > > >> >
> > > >> > I am trying to numerically solve the region around a pulsar. Now
> since
> > > >> > pulsar is an inclined rotator with inclination angle between
> rotation
> > > >> axis
> > > >> > and dipole axis I would like to include in my yt script.
> > > >> >
> > > >> > My original code written in FORTRAN incorporated this inclination
> but
> > > >> how
> > > >> > would I incorporate it into my visualization using yt without
> changing
> > > >> my
> > > >> > data.
> > > >> >
> > > >> > Could you suggest ways for the same?
> > > >> >
> > > >> > The google drive link to my script (streamline.py) and streamline
> plot
> > > >> > (streamline_t000.png) is included
> > > >> >
> > > >> > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc <
> https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc>
> > > >> >
> > > >> > Thanks in advance
> > > >> >
> > > >> > On Tue, Mar 29, 2016 at 12:54 PM, <
> > > yt-users-request at lists.spacepope.org <mailto:
> yt-users-request at lists.spacepope.org>
> > > >> >
> > > >> > wrote:
> > > >> >>
> > > >> >> Send yt-users mailing list submissions to
> > > >> >>         yt-users at lists.spacepope.org <mailto:
> yt-users at lists.spacepope.org>
> > > >> >>
> > > >> >> To subscribe or unsubscribe via the World Wide Web, visit
> > > >> >>
> > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
> > > >> >> or, via email, send a message with subject or body 'help' to
> > > >> >>         yt-users-request at lists.spacepope.org <mailto:
> yt-users-request at lists.spacepope.org>
> > > >> >>
> > > >> >> You can reach the person managing the list at
> > > >> >>         yt-users-owner at lists.spacepope.org <mailto:
> yt-users-owner at lists.spacepope.org>
> > > >> >>
> > > >> >> When replying, please edit your Subject line so it is more
> specific
> > > >> >> than "Re: Contents of yt-users digest..."
> > > >> >>
> > > >> >>
> > > >> >> Today's Topics:
> > > >> >>
> > > >> >>    1. Re: gadget onto unigrid (Carla Bernhardt)
> > > >> >>    2. Re: gadget onto unigrid (Matthew Turk)
> > > >> >>
> > > >> >>
> > > >> >>
> > > ----------------------------------------------------------------------
> > > >> >>
> > > >> >> Message: 1
> > > >> >> Date: Tue, 29 Mar 2016 15:55:27 +0200
> > > >> >> From: Carla Bernhardt <carla.j.bernhardt at gmail.com <mailto:
> carla.j.bernhardt at gmail.com>>
> > > >> >> To: Discussion of the yt analysis package
> > > >> >>         <yt-users at lists.spacepope.org <mailto:
> yt-users at lists.spacepope.org>>
> > > >> >> Subject: Re: [yt-users] gadget onto unigrid
> > > >> >> Message-ID:
> > > >> >>
> > > >> >> <CAFK0O=2vH24ViqeZ5QS3DY3uido0kEaF=
> UhyGS_beuiUMbw7Ag at mail.gmail.com <mailto:UhyGS_beuiUMbw7Ag at mail.gmail.com
> >>
> > > >> >> Content-Type: text/plain; charset="utf-8"
> > > >> >>
> > > >> >> Hi All,
> > > >> >>
> > > >> >> A follow-up question: In using arbitrary_grid (but with enzo
> data),
> > > how
> > > >> >> does one then extract a field of an arbitrary_grid? I tried
> > > >> >> arbgrid["density"] as I have done with a smoothed_covering_grid
> > > object,
> > > >> >> but
> > > >> >> it does not work (here is the traceback <
> > > http://pastebin.com/afgcgpp0 <http://pastebin.com/afgcgpp0>>
> > > >> I
> > > >> >> got).
> > > >> >>
> > > >> >> Thanks,
> > > >> >> Carla
> > > >> >>
> > > >> >> 2016-02-23 17:21 GMT+01:00 Matthew Turk <matthewturk at gmail.com
> <mailto:matthewturk at gmail.com>>:
> > > >> >>
> > > >> >> > Hi Desika,
> > > >> >> >
> > > >> >> > Yup, this can be done reasonably easily using either the
> > > >> >> > .arbitrary_grid object (which was designed for this) or the
> > > interface
> > > >> >> > to the arbitrary grid that's in the development version, which
> is
> > > >> >> > ds.r[ ... ] where the ... is some combination of bounds and
> steps.
> > > >> >> >
> > > >> >> >
> > > http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid <
> http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid>
> > > >> >> >
> > > >> >> >
> > > >> >> >
> > > >>
> > >
> http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-selecting-data
> <
> http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-selecting-data
> >
> > > >> >> >
> > > >> >> > On Tue, Feb 23, 2016 at 10:18 AM, Desika Narayanan
> > > >> >> > <desika.narayanan at gmail.com <mailto:desika.narayanan at gmail.com>>
> wrote:
> > > >> >> > > Hi All,
> > > >> >> > >
> > > >> >> > > Is it possible to deposit the particles from a gadget data
> set
> > > >> onto a
> > > >> >> > > uniform grid in yt?  Or, could it be possible to trick the
> octree
> > > >> >> > deposition
> > > >> >> > > into doing it by forcing no refinements, but some sort of
> native
> > > >> grid
> > > >> >> > > resolution?
> > > >> >> > >
> > > >> >> > > thanks,
> > > >> >> > > desika
> > > >> >> > >
> > > >> >> > >
> > > >> >> > > _______________________________________________
> > > >> >> > > yt-users mailing list
> > > >> >> > > yt-users at lists.spacepope.org <mailto:
> yt-users at lists.spacepope.org>
> > > >> >> > >
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
> > > >> >> > >
> > > >> >> > _______________________________________________
> > > >> >> > yt-users mailing list
> > > >> >> > yt-users at lists.spacepope.org <mailto:
> yt-users at lists.spacepope.org>
> > > >> >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
> > > >> >> >
> > > >> >> -------------- next part --------------
> > > >> >> An HTML attachment was scrubbed...
> > > >> >> URL:
> > > >> >> <
> > > >>
> > >
> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160329/e29a03a1/attachment.html
> <
> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160329/e29a03a1/attachment.html
> >
> > > >> >
> > > >> >>
> > > >> >> ------------------------------
> > > >> >>
> > > >> >> Message: 2
> > > >> >> Date: Tue, 29 Mar 2016 08:57:08 -0500
> > > >> >> From: Matthew Turk <matthewturk at gmail.com <mailto:
> matthewturk at gmail.com>>
> > > >> >> To: Discussion of the yt analysis package
> > > >> >>         <yt-users at lists.spacepope.org <mailto:
> yt-users at lists.spacepope.org>>
> > > >> >> Subject: Re: [yt-users] gadget onto unigrid
> > > >> >> Message-ID:
> > > >> >>
> > > >> >> <CALO3=5HR=zLHujWKgLpqwei_98vBOjpYvQ4m8nnUFR=
> P098utA at mail.gmail.com <mailto:P098utA at mail.gmail.com>>
> > > >> >> Content-Type: text/plain; charset=UTF-8
> > > >> >>
> > > >> >> Hi Carla,
> > > >> >>
> > > >> >> This functionality was recently implemented and is in the
> development
> > > >> >> version, but not yet in the stable.  We're hoping for a release
> very
> > > >> >> shortly, but you can also try the dev version if you'd like!
> > > >> >>
> > > >> >> -Matt
> > > >> >>
> > > >> >> On Tue, Mar 29, 2016 at 8:55 AM, Carla Bernhardt
> > > >> >> <carla.j.bernhardt at gmail.com <mailto:carla.j.bernhardt at gmail.com>>
> wrote:
> > > >> >> > Hi All,
> > > >> >> >
> > > >> >> > A follow-up question: In using arbitrary_grid (but with enzo
> data),
> > > >> how
> > > >> >> > does
> > > >> >> > one then extract a field of an arbitrary_grid? I tried
> > > >> >> > arbgrid["density"] as
> > > >> >> > I have done with a smoothed_covering_grid object, but it does
> not
> > > >> work
> > > >> >> > (here
> > > >> >> > is the traceback I got).
> > > >> >> >
> > > >> >> > Thanks,
> > > >> >> > Carla
> > > >> >> >
> > > >> >> > 2016-02-23 17:21 GMT+01:00 Matthew Turk <matthewturk at gmail.com
> <mailto:matthewturk at gmail.com>>:
> > > >> >> >>
> > > >> >> >> Hi Desika,
> > > >> >> >>
> > > >> >> >> Yup, this can be done reasonably easily using either the
> > > >> >> >> .arbitrary_grid object (which was designed for this) or the
> > > >> interface
> > > >> >> >> to the arbitrary grid that's in the development version,
> which is
> > > >> >> >> ds.r[ ... ] where the ... is some combination of bounds and
> steps.
> > > >> >> >>
> > > >> >> >>
> > > >>
> http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid <
> http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid>
> > > >> >> >>
> > > >> >> >>
> > > >> >> >>
> > > >>
> > >
> http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-selecting-data
> <
> http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-selecting-data
> >
> > > >> >> >>
> > > >> >> >> On Tue, Feb 23, 2016 at 10:18 AM, Desika Narayanan
> > > >> >> >> <desika.narayanan at gmail.com <mailto:
> desika.narayanan at gmail.com>> wrote:
> > > >> >> >> > Hi All,
> > > >> >> >> >
> > > >> >> >> > Is it possible to deposit the particles from a gadget data
> set
> > > >> onto a
> > > >> >> >> > uniform grid in yt?  Or, could it be possible to trick the
> > > octree
> > > >> >> >> > deposition
> > > >> >> >> > into doing it by forcing no refinements, but some sort of
> native
> > > >> grid
> > > >> >> >> > resolution?
> > > >> >> >> >
> > > >> >> >> > thanks,
> > > >> >> >> > desika
> > > >> >> >> >
> > > >> >> >> >
> > > >> >> >> > _______________________________________________
> > > >> >> >> > yt-users mailing list
> > > >> >> >> > yt-users at lists.spacepope.org <mailto:
> yt-users at lists.spacepope.org>
> > > >> >> >> >
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
> > > >> >> >> >
> > > >> >> >> _______________________________________________
> > > >> >> >> yt-users mailing list
> > > >> >> >> yt-users at lists.spacepope.org <mailto:
> yt-users at lists.spacepope.org>
> > > >> >> >>
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
> > > >> >> >
> > > >> >> >
> > > >> >> >
> > > >> >> > _______________________________________________
> > > >> >> > yt-users mailing list
> > > >> >> > yt-users at lists.spacepope.org <mailto:
> yt-users at lists.spacepope.org>
> > > >> >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
> > > >> >> >
> > > >> >>
> > > >> >>
> > > >> >> ------------------------------
> > > >> >>
> > > >> >> Subject: Digest Footer
> > > >> >>
> > > >> >> _______________________________________________
> > > >> >> yt-users mailing list
> > > >> >> yt-users at lists.spacepope.org <mailto:
> yt-users at lists.spacepope.org>
> > > >> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
> > > >> >>
> > > >> >>
> > > >> >> ------------------------------
> > > >> >>
> > > >> >> End of yt-users Digest, Vol 97, Issue 34
> > > >> >> ****************************************
> > > >> >
> > > >> >
> > > >> >
> > > >> >
> > > >> > --
> > > >> > SK2
> > > >> >
> > > >> > "Claiming that something can move faster than light is a good
> > > >> > conversation-stopper in physics. People edge away from you in
> cocktail
> > > >> > parties; friends never return phone calls. You just don?t mess
> with
> > > >> Albert
> > > >> > Einstein."
> > > >> >
> > > >> >
> > > >> > _______________________________________________
> > > >> > yt-users mailing list
> > > >> > yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org
> >
> > > >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
> > > >> >
> > > >>
> > > >>
> > > >> ------------------------------
> > > >>
> > > >> Message: 4
> > > >> Date: Wed, 30 Mar 2016 18:01:04 -0400
> > > >> From: Jonah Miller <jonah.maxwell.miller at gmail.com <mailto:
> jonah.maxwell.miller at gmail.com>>
> > > >> To: yt-users at lists.spacepope.org <mailto:
> yt-users at lists.spacepope.org>
> > > >> Subject: Re: [yt-users] load spherical polar coordinate data with
> mesh
> > > >>         refinement in HDF5
> > > >> Message-ID: <56FC4CA0.4030403 at gmail.com <mailto:
> 56FC4CA0.4030403 at gmail.com>>
> > > >> Content-Type: text/plain; charset=windows-1252; format=flowed
> > > >>
> > > >> Hi Yanfei,
> > > >>
> > > >> To add to Matt's comment. Here is the documentation for using
> > > >> load_hexahedral_mesh.
> > > >>
> > > >>
> > >
> http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-data
> <
> http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-data
> >
> > > >>
> > > >>
> > >
> http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_structures.load_hexahedral_mesh.html
> <
> http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_structures.load_hexahedral_mesh.html
> >
> > > >>
> > > >> Best,
> > > >> Jonah
> > > >>
> > > >> On 16-03-30 05:15 PM, Matthew Turk wrote:
> > > >> > Hi Yanfei,
> > > >> >
> > > >> > This is possible -- but it will also slow some things down.  You
> can
> > > >> > use the load_hexahedral_mesh function, and there're examples of
> this.
> > > >> > This takes away some of the optimizations that regular grids can
> do,
> > > >> > but we're hoping to add them back in shortly.  Like the other
> > > >> > functions it too takes a geometry argument.
> > > >> >
> > > >> > -Matt
> > > >> >
> > > >> > On Wed, Mar 30, 2016 at 2:49 PM, Jiang, Yanfei
> > > >> > <yanfei.jiang at cfa.harvard.edu <mailto:
> yanfei.jiang at cfa.harvard.edu>> wrote:
> > > >> >> Hi Jonah,
> > > >> >>
> > > >> >>     I am able to load the data to yt now using load_amr_grids().
> I
> > > >> notice
> > > >> >> that it can also set geometry to spherical. This is great. But to
> > > make
> > > >> life
> > > >> >> more complicate. Is it possible to let yt know that the grid is
> > > >> logarithmic?
> > > >> >> Currently, load_amr_grids() just take left and right edges of
> each
> > > >> block. I
> > > >> >> guess yt assumes the grid is uniform between left and right
> edges. Is
> > > >> it
> > > >> >> possible to provide arrays of coordinate values for each cell in
> each
> > > >> block?
> > > >> >>
> > > >> >> Thanks.
> > > >> >>
> > > >> >> On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller
> > > >> >> <jonah.maxwell.miller at gmail.com <mailto:
> jonah.maxwell.miller at gmail.com>> wrote:
> > > >> >>> Hi Yan-Feng,
> > > >> >>>
> > > >> >>> I haven't tried it, but I think there is functionality for
> this. You
> > > >> can
> > > >> >>> use the load_amr_grids() function which can load amr data in
> > > >> Cartesian,
> > > >> >>> spherical, or polar coordinates. Here's the documentation:
> > > >> >>>
> > > >> >>>
> > > >> >>>
> > > >>
> > >
> http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-array
> <
> http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-array
> >
> > > >> >>>
> > > >> >>>
> > > >> >>>
> > > >>
> > >
> http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_structures.load_amr_grids.html#yt.frontends.stream.data_structures.load_amr_grids
> <
> http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_structures.load_amr_grids.html#yt.frontends.stream.data_structures.load_amr_grids
> >
> > > >> >>>
> > > >> >>> Best,
> > > >> >>> Jonah
> > > >> >>>
> > > >> >>> On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei <
> > > >> yanfei.jiang at cfa.harvard.edu <mailto:yanfei.jiang at cfa.harvard.edu>>
> > > >> >>> wrote:
> > > >> >>>> Hi,
> > > >> >>>>           I have some data from a new version of Athena
> > > simulations.
> > > >> It is
> > > >> >>>> in spherical polar coordinate with mesh refinement written in
> HDF5.
> > > >> The data
> > > >> >>>> structure is similar to flash data but not the same. Does
> anyone
> > > have
> > > >> >>>> suggestions to load such data to yt directly?
> > > >> >>>>
> > > >> >>>> Thank you.
> > > >> >>>> --
> > > >> >>>> Yan-Fei Jiang
> > > >> >>>>
> > > >> >>>> Einstein Fellow
> > > >> >>>> Harvard-Smithsonian Center for Astrophysics
> > > >> >>>> 60 Garden Street, Cambridge MA USA 02138
> > > >> >>>> _______________________________________________
> > > >> >>>> yt-users mailing list
> > > >> >>>> yt-users at lists.spacepope.org <mailto:
> yt-users at lists.spacepope.org>
> > > >> >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
> > > >> >>>
> > > >> >>> _______________________________________________
> > > >> >>> yt-users mailing list
> > > >> >>> yt-users at lists.spacepope.org <mailto:
> yt-users at lists.spacepope.org>
> > > >> >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
> > > >> >>>
> > > >> >>
> > > >> >>
> > > >> >> --
> > > >> >> Yan-Fei Jiang
> > > >> >>
> > > >> >> Einstein Fellow
> > > >> >> Harvard-Smithsonian Center for Astrophysics
> > > >> >> 60 Garden Street, Cambridge MA USA 02138
> > > >> >>
> > > >> >> _______________________________________________
> > > >> >> yt-users mailing list
> > > >> >> yt-users at lists.spacepope.org <mailto:
> yt-users at lists.spacepope.org>
> > > >> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
> > > >> >>
> > > >> > _______________________________________________
> > > >> > yt-users mailing list
> > > >> > yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org
> >
> > > >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
> > > >>
> > > >>
> > > >>
> > > >> ------------------------------
> > > >>
> > > >> Subject: Digest Footer
> > > >>
> > > >> _______________________________________________
> > > >> yt-users mailing list
> > > >> yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>
> > > >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
> > > >>
> > > >>
> > > >> ------------------------------
> > > >>
> > > >> End of yt-users Digest, Vol 97, Issue 37
> > > >> ****************************************
> > > >>
> > > >
> > > >
> > > >
> > > > --
> > > > *SK2*
> > > >
> > > > *"**Claiming that something can move faster than light is a good
> > > > conversation-stopper in physics. People edge away from you in
> cocktail
> > > > parties; friends never return phone calls. You just don?t mess with
> > > Albert
> > > > Einstein.**"*
> > > >
> > > >
> > > > _______________________________________________
> > > > yt-users mailing list
> > > > yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>
> > > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
> > > >
> > > >
> > > -------------- next part --------------
> > > An HTML attachment was scrubbed...
> > > URL: <
> > >
> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160331/b739cfe9/attachment.htm
> <
> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160331/b739cfe9/attachment.htm
> >
> > > >
> > >
> > > ------------------------------
> > >
> > > Subject: Digest Footer
> > >
> > > _______________________________________________
> > > yt-users mailing list
> > > yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>
> > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
> > >
> > >
> > > ------------------------------
> > >
> > > End of yt-users Digest, Vol 97, Issue 39
> > > ****************************************
> > >
> >
> >
> >
> > --
> > *SK2*
> >
> > *"**Claiming that something can move faster than light is a good
> > conversation-stopper in physics. People edge away from you in cocktail
> > parties; friends never return phone calls. You just don?t mess with
> Albert
> > Einstein.**"*
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL: <
> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160331/f4f56e5d/attachment.htm
> <
> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160331/f4f56e5d/attachment.htm
> >>
> >
> > ------------------------------
> >
> > Subject: Digest Footer
> >
> > _______________________________________________
> > yt-users mailing list
> > yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
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> > ------------------------------
> >
> > End of yt-users Digest, Vol 97, Issue 41
> > ****************************************
> >
> >
> >
> > --
> > SK2
> >
> > "Claiming that something can move faster than light is a good
> conversation-stopper in physics. People edge away from you in cocktail
> parties; friends never return phone calls. You just don?t mess with Albert
> Einstein."
> >
> > _______________________________________________
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> Subject: Digest Footer
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> End of yt-users Digest, Vol 98, Issue 14
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>



-- 
*SK2*

*"**Claiming that something can move faster than light is a good
conversation-stopper in physics. People edge away from you in cocktail
parties; friends never return phone calls. You just don’t mess with Albert
Einstein.**"*
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