[yt-users] Inclination problem
Sushilkumar
sushil.sush19us at gmail.com
Thu Mar 31 06:56:04 PDT 2016
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>
wrote:
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> 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>
> To: Discussion of the yt analysis package
> <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>
> 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> 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/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>
> > 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
> >> 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
> >
> >
>
>
> --
> Yan-Fei Jiang
>
> Einstein Fellow
> Harvard-Smithsonian Center for Astrophysics
> 60 Garden Street, Cambridge MA USA 02138
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> ------------------------------
>
> Message: 2
> Date: Wed, 30 Mar 2016 16:15:30 -0500
> From: Matthew Turk <matthewturk at gmail.com>
> To: Discussion of the yt analysis package
> <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>
> 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> 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> 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/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>
> >> 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
> >>> 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
> >>
> >
> >
> >
> > --
> > 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
> > 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>
> To: Discussion of the yt analysis package
> <yt-users at lists.spacepope.org>
> Subject: Re: [yt-users] Inclination problem
> Message-ID:
> <CALO3=5HMB=
> joejr6BBh+zdxkwGzJS2NPrkK9tvMJnbch5-7BgQ 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>
> 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 at lists.spacepope.org>
> > wrote:
> >>
> >> Send yt-users mailing list submissions to
> >> 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
> >> or, via email, send a message with subject or body 'help' to
> >> yt-users-request at lists.spacepope.org
> >>
> >> You can reach the person managing the list at
> >> 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>
> >> To: Discussion of the yt analysis package
> >> <yt-users at lists.spacepope.org>
> >> Subject: Re: [yt-users] gadget onto unigrid
> >> Message-ID:
> >>
> >> <CAFK0O=2vH24ViqeZ5QS3DY3uido0kEaF=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>
> I
> >> got).
> >>
> >> Thanks,
> >> Carla
> >>
> >> 2016-02-23 17:21 GMT+01:00 Matthew Turk <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#slicing-syntax-for-selecting-data
> >> >
> >> > On Tue, Feb 23, 2016 at 10:18 AM, Desika Narayanan
> >> > <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
> >> > > 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
> >> >
> >> -------------- next part --------------
> >> An HTML attachment was scrubbed...
> >> URL:
> >> <
> 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>
> >> To: Discussion of the yt analysis package
> >> <yt-users at lists.spacepope.org>
> >> Subject: Re: [yt-users] gadget onto unigrid
> >> Message-ID:
> >>
> >> <CALO3=5HR=zLHujWKgLpqwei_98vBOjpYvQ4m8nnUFR=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> 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>:
> >> >>
> >> >> 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-selecting-data
> >> >>
> >> >> On Tue, Feb 23, 2016 at 10:18 AM, Desika Narayanan
> >> >> <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
> >> >> > 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
> >> >
> >>
> >>
> >> ------------------------------
> >>
> >> Subject: Digest Footer
> >>
> >> _______________________________________________
> >> yt-users mailing list
> >> yt-users at 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 at 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 at gmail.com>
> To: 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>
> 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/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> 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> 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/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>
> >>> 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
> >>>> 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
> >>>
> >>
> >>
> >> --
> >> 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
> >> 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
>
>
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.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.**"*
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