Dear YT Users,
To better understand covering_grid (or smoothed_covering_grid), can someone
explain what dimensions I should use when I have multiple levels of
refinement? If I have 1 level of refinement from AMR data, the dimensions
should be the same, I believe, but what if I have 2 or 3 levels of
refinement? Should the fixed resolution region then have dimensions of
dims*2^2 and dims*3^2 respectively?
Here is one example from a tutorial
<http://yt-project.org/doc/examining/low_level_inspection.html#examining-gri…>
if that helps isolate my question:
all_data_level_2 = ds.covering_grid(level=2, left_edge=[0,0.0,0.0],
dims=ds.domain_dimensions * 2**2)
Thanks in advance,
Carla
Hi everyone,
I'm letting anaconda handle my yt install. I have a workstation with yt
3.2.3 running that is now unable to load any enzo data set I have... it
crashes with the following error when trying to access the data (and
crashes with a call to "ds.field_list" with the same error):
http://paste.yt-project.org/show/6387/
However, this doesn't seem to be a problem on my laptop which I haven't
updated (yt 3.2.2) and also isn't a problem on FLASH data I have.
Anyone have the same problem?
Thanks,
Andrew
--
Graduate Student
Columbia University
Department of Astronomy
Dear Nathan:
Thank you very much, implementing now
On Thu, Mar 31, 2016 at 9:50 AM, <yt-users-request(a)lists.spacepope.org>
wrote:
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>
>
> Today's Topics:
>
> 1. Re: Inclination problem (Nathan Goldbaum)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 31 Mar 2016 09:50:31 -0500
> From: Nathan Goldbaum <nathan12343(a)gmail.com>
> To: Discussion of the yt analysis package
> <yt-users(a)lists.spacepope.org>
> Subject: Re: [yt-users] Inclination problem
> Message-ID:
> <CAJXewOnvXjZ+shfKG4SPubn_TYTAbLUu8y9ZRvovzBu=
> DcFZtQ(a)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
>
> 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(a)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(a)lists.spacepope.org>
> > wrote:
> >
> >> Send yt-users mailing list submissions to
> >> yt-users(a)lists.spacepope.org
> >>
> >> To subscribe or unsubscribe via the World Wide Web, visit
> >> 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(a)lists.spacepope.org
> >>
> >> You can reach the person managing the list at
> >> yt-users-owner(a)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(a)cfa.harvard.edu>
> >> To: Discussion of the yt analysis package
> >> <yt-users(a)lists.spacepope.org>
> >> Subject: Re: [yt-users] load spherical polar coordinate data with mesh
> >> refinement in HDF5
> >> Message-ID:
> >> <
> >> CANixPav-VmbXfhNvmA5wb5gj19mF+-Ryq5YD-LrYrByDe3Ne7A(a)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(a)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-a…
> >> >
> >> >
> >> >
> >>
> http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_…
> >> >
> >> > Best,
> >> > Jonah
> >> >
> >> > On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei <
> >> yanfei.jiang(a)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(a)lists.spacepope.org
> >> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >> >>
> >> >
> >> > _______________________________________________
> >> > yt-users mailing list
> >> > yt-users(a)lists.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/201…
> >> >
> >>
> >> ------------------------------
> >>
> >> Message: 2
> >> Date: Wed, 30 Mar 2016 16:15:30 -0500
> >> From: Matthew Turk <matthewturk(a)gmail.com>
> >> To: Discussion of the yt analysis package
> >> <yt-users(a)lists.spacepope.org>
> >> Subject: Re: [yt-users] load spherical polar coordinate data with mesh
> >> refinement in HDF5
> >> Message-ID:
> >> <CALO3=
> >> 5F1-_9V5XHS4vF_eXvKoPerz3Zo20X8uPtcFjQSAQS1MA(a)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(a)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(a)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-a…
> >> >>
> >> >>
> >> >>
> >>
> http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_…
> >> >>
> >> >> Best,
> >> >> Jonah
> >> >>
> >> >> On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei <
> >> yanfei.jiang(a)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(a)lists.spacepope.org
> >> >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >> >>
> >> >>
> >> >> _______________________________________________
> >> >> yt-users mailing list
> >> >> yt-users(a)lists.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(a)lists.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(a)gmail.com>
> >> To: Discussion of the yt analysis package
> >> <yt-users(a)lists.spacepope.org>
> >> Subject: Re: [yt-users] Inclination problem
> >> Message-ID:
> >> <CALO3=5HMB=
> >> joejr6BBh+zdxkwGzJS2NPrkK9tvMJnbch5-7BgQ(a)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(a)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
> >> >
> >> > Thanks in advance
> >> >
> >> > On Tue, Mar 29, 2016 at 12:54 PM, <
> yt-users-request(a)lists.spacepope.org
> >> >
> >> > wrote:
> >> >>
> >> >> Send yt-users mailing list submissions to
> >> >> yt-users(a)lists.spacepope.org
> >> >>
> >> >> To subscribe or unsubscribe via the World Wide Web, visit
> >> >>
> 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(a)lists.spacepope.org
> >> >>
> >> >> You can reach the person managing the list at
> >> >> yt-users-owner(a)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(a)gmail.com>
> >> >> To: Discussion of the yt analysis package
> >> >> <yt-users(a)lists.spacepope.org>
> >> >> Subject: Re: [yt-users] gadget onto unigrid
> >> >> Message-ID:
> >> >>
> >> >> <CAFK0O=2vH24ViqeZ5QS3DY3uido0kEaF=UhyGS_beuiUMbw7Ag(a)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>
> >> I
> >> >> got).
> >> >>
> >> >> Thanks,
> >> >> Carla
> >> >>
> >> >> 2016-02-23 17:21 GMT+01:00 Matthew Turk <matthewturk(a)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#slicing-syntax-for-se…
> >> >> >
> >> >> > On Tue, Feb 23, 2016 at 10:18 AM, Desika Narayanan
> >> >> > <desika.narayanan(a)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(a)lists.spacepope.org
> >> >> > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >> >> > >
> >> >> > _______________________________________________
> >> >> > yt-users mailing list
> >> >> > yt-users(a)lists.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/201…
> >> >
> >> >>
> >> >> ------------------------------
> >> >>
> >> >> Message: 2
> >> >> Date: Tue, 29 Mar 2016 08:57:08 -0500
> >> >> From: Matthew Turk <matthewturk(a)gmail.com>
> >> >> To: Discussion of the yt analysis package
> >> >> <yt-users(a)lists.spacepope.org>
> >> >> Subject: Re: [yt-users] gadget onto unigrid
> >> >> Message-ID:
> >> >>
> >> >> <CALO3=5HR=zLHujWKgLpqwei_98vBOjpYvQ4m8nnUFR=P098utA(a)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(a)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(a)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#slicing-syntax-for-se…
> >> >> >>
> >> >> >> On Tue, Feb 23, 2016 at 10:18 AM, Desika Narayanan
> >> >> >> <desika.narayanan(a)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(a)lists.spacepope.org
> >> >> >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >> >> >> >
> >> >> >> _______________________________________________
> >> >> >> yt-users mailing list
> >> >> >> yt-users(a)lists.spacepope.org
> >> >> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >> >> >
> >> >> >
> >> >> >
> >> >> > _______________________________________________
> >> >> > yt-users mailing list
> >> >> > yt-users(a)lists.spacepope.org
> >> >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >> >> >
> >> >>
> >> >>
> >> >> ------------------------------
> >> >>
> >> >> Subject: Digest Footer
> >> >>
> >> >> _______________________________________________
> >> >> yt-users mailing list
> >> >> yt-users(a)lists.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(a)lists.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(a)gmail.com>
> >> To: yt-users(a)lists.spacepope.org
> >> Subject: Re: [yt-users] load spherical polar coordinate data with mesh
> >> refinement in HDF5
> >> Message-ID: <56FC4CA0.4030403(a)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-…
> >>
> >>
> http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_…
> >>
> >> 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(a)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(a)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-a…
> >> >>>
> >> >>>
> >> >>>
> >>
> http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_…
> >> >>>
> >> >>> Best,
> >> >>> Jonah
> >> >>>
> >> >>> On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei <
> >> yanfei.jiang(a)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(a)lists.spacepope.org
> >> >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >> >>>
> >> >>> _______________________________________________
> >> >>> yt-users mailing list
> >> >>> yt-users(a)lists.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(a)lists.spacepope.org
> >> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >> >>
> >> > _______________________________________________
> >> > yt-users mailing list
> >> > yt-users(a)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 37
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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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--
*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.**"*
