<div dir="ltr">Dear Nathan:<div><br></div><div>Thank you very much, implementing now</div><div><br><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Mar 31, 2016 at 9:50 AM, <span dir="ltr"><<a href="mailto:yt-users-request@lists.spacepope.org" target="_blank">yt-users-request@lists.spacepope.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send yt-users mailing list submissions to<br>
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Today's Topics:<br>
<br>
1. Re: Inclination problem (Nathan Goldbaum)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 31 Mar 2016 09:50:31 -0500<br>
From: Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com">nathan12343@gmail.com</a>><br>
To: Discussion of the yt analysis package<br>
<<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a>><br>
Subject: Re: [yt-users] Inclination problem<br>
Message-ID:<br>
<CAJXewOnvXjZ+shfKG4SPubn_TYTAbLUu8y9ZRvovzBu=<a href="mailto:DcFZtQ@mail.gmail.com">DcFZtQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi SK,<br>
<br>
I'm going to reference this example:<br>
<br>
<a href="http://yt-project.org/doc/visualizing/streamlines.html?highlight=streamlines" rel="noreferrer" target="_blank">http://yt-project.org/doc/visualizing/streamlines.html?highlight=streamlines</a><br>
<br>
specifically this snippet:<br>
<br>
for stream in streamlines.streamlines:<br>
stream = stream[np.all(stream != 0.0, axis=1)]<br>
ax.plot3D(stream[:,0], stream[:,1], stream[:,2], alpha=0.1)<br>
<br>
Here, the 'stream' object is just a Nx3 numpy array, where N is the number<br>
of points sampled along the streamline. So each row of the numpy array is<br>
just the coordinates of the streamline along one direction.<br>
<br>
To answer your question, no, there's nothing in yt that will rotate the<br>
streamlines into a new coordinate system. Fortunately you should be able to<br>
do it yourself using e.g. an Euler angle rotation matrix. You will need to<br>
identify the new coordinate system you would like to transform to,<br>
calculate a 3D rotation matrix, then apply it using matrix multiplication<br>
(e.g. np.dot, which supports broadcasting) to each coordinate along the<br>
streamline.<br>
<br>
Hope that helps,<br>
<br>
Nathan<br>
<br>
On Thu, Mar 31, 2016 at 8:56 AM, Sushilkumar <<a href="mailto:sushil.sush19us@gmail.com">sushil.sush19us@gmail.com</a>><br>
wrote:<br>
<br>
> Dear Matt:<br>
><br>
> Pleas correct me if I am wrong but "off axis slices" takes slices of the<br>
> plot that is already plotted.<br>
><br>
> However, I would like to plot my data in a new coordinate frame (x`,y`,z`)<br>
> which is inclined at an angle of say alpha from the default (x,y,z) frame.<br>
><br>
> Or I would like to plot my data in a rotated frame (x`,y`,z`), which is<br>
> rotated at an angle of alpha from (x,y,z).<br>
><br>
><br>
><br>
><br>
> On Wed, Mar 30, 2016 at 5:01 PM, <<a href="mailto:yt-users-request@lists.spacepope.org">yt-users-request@lists.spacepope.org</a>><br>
> wrote:<br>
><br>
>> Send yt-users mailing list submissions to<br>
>> <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
>><br>
>> To subscribe or unsubscribe via the World Wide Web, visit<br>
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>> or, via email, send a message with subject or body 'help' to<br>
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>><br>
>> When replying, please edit your Subject line so it is more specific<br>
>> than "Re: Contents of yt-users digest..."<br>
>><br>
>><br>
>> Today's Topics:<br>
>><br>
>> 1. Re: load spherical polar coordinate data with mesh refinement<br>
>> in HDF5 (Jiang, Yanfei)<br>
>> 2. Re: load spherical polar coordinate data with mesh refinement<br>
>> in HDF5 (Matthew Turk)<br>
>> 3. Re: Inclination problem (Matthew Turk)<br>
>> 4. Re: load spherical polar coordinate data with mesh refinement<br>
>> in HDF5 (Jonah Miller)<br>
>><br>
>><br>
>> ----------------------------------------------------------------------<br>
>><br>
>> Message: 1<br>
>> Date: Wed, 30 Mar 2016 15:49:26 -0400<br>
>> From: "Jiang, Yanfei" <<a href="mailto:yanfei.jiang@cfa.harvard.edu">yanfei.jiang@cfa.harvard.edu</a>><br>
>> To: Discussion of the yt analysis package<br>
>> <<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a>><br>
>> Subject: Re: [yt-users] load spherical polar coordinate data with mesh<br>
>> refinement in HDF5<br>
>> Message-ID:<br>
>> <<br>
>> <a href="mailto:CANixPav-VmbXfhNvmA5wb5gj19mF%2B-Ryq5YD-LrYrByDe3Ne7A@mail.gmail.com">CANixPav-VmbXfhNvmA5wb5gj19mF+-Ryq5YD-LrYrByDe3Ne7A@mail.gmail.com</a>><br>
>> Content-Type: text/plain; charset="utf-8"<br>
>><br>
>> Hi Jonah,<br>
>><br>
>> I am able to load the data to yt now using load_amr_grids(). I notice<br>
>> that it can also set geometry to spherical. This is great. But to make<br>
>> life<br>
>> more complicate. Is it possible to let yt know that the grid is<br>
>> logarithmic? Currently, load_amr_grids() just take left and right edges of<br>
>> each block. I guess yt assumes the grid is uniform between left and right<br>
>> edges. Is it possible to provide arrays of coordinate values for each cell<br>
>> in each block?<br>
>><br>
>> Thanks.<br>
>><br>
>> On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller <<br>
>> <a href="mailto:jonah.maxwell.miller@gmail.com">jonah.maxwell.miller@gmail.com</a>> wrote:<br>
>><br>
>> > Hi Yan-Feng,<br>
>> ><br>
>> > I haven't tried it, but I think there is functionality for this. You can<br>
>> > use the load_amr_grids() function which can load amr data in Cartesian,<br>
>> > spherical, or polar coordinates. Here's the documentation:<br>
>> ><br>
>> ><br>
>> <a href="http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-array" rel="noreferrer" target="_blank">http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-array</a><br>
>> ><br>
>> ><br>
>> ><br>
>> <a href="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" rel="noreferrer" target="_blank">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</a><br>
>> ><br>
>> > Best,<br>
>> > Jonah<br>
>> ><br>
>> > On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei <<br>
>> <a href="mailto:yanfei.jiang@cfa.harvard.edu">yanfei.jiang@cfa.harvard.edu</a>><br>
>> > wrote:<br>
>> ><br>
>> >> Hi,<br>
>> >> I have some data from a new version of Athena simulations. It<br>
>> is<br>
>> >> in spherical polar coordinate with mesh refinement written in HDF5. The<br>
>> >> data structure is similar to flash data but not the same. Does anyone<br>
>> have<br>
>> >> suggestions to load such data to yt directly?<br>
>> >><br>
>> >> Thank you.<br>
>> >> --<br>
>> >> Yan-Fei Jiang<br>
>> >><br>
>> >> Einstein Fellow<br>
>> >> Harvard-Smithsonian Center for Astrophysics<br>
>> >> 60 Garden Street, Cambridge MA USA 02138<br>
>> >> _______________________________________________<br>
>> >> yt-users mailing list<br>
>> >> <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
>> >> <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
>> >><br>
>> ><br>
>> > _______________________________________________<br>
>> > yt-users mailing list<br>
>> > <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
>> > <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
>> ><br>
>> ><br>
>><br>
>><br>
>> --<br>
>> Yan-Fei Jiang<br>
>><br>
>> Einstein Fellow<br>
>> Harvard-Smithsonian Center for Astrophysics<br>
>> 60 Garden Street, Cambridge MA USA 02138<br>
>> -------------- next part --------------<br>
>> An HTML attachment was scrubbed...<br>
>> URL: <<br>
>> <a href="http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160330/aedc3b19/attachment-0001.htm" rel="noreferrer" target="_blank">http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160330/aedc3b19/attachment-0001.htm</a><br>
>> ><br>
>><br>
>> ------------------------------<br>
>><br>
>> Message: 2<br>
>> Date: Wed, 30 Mar 2016 16:15:30 -0500<br>
>> From: Matthew Turk <<a href="mailto:matthewturk@gmail.com">matthewturk@gmail.com</a>><br>
>> To: Discussion of the yt analysis package<br>
>> <<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a>><br>
>> Subject: Re: [yt-users] load spherical polar coordinate data with mesh<br>
>> refinement in HDF5<br>
>> Message-ID:<br>
>> <CALO3=<br>
>> <a href="mailto:5F1-_9V5XHS4vF_eXvKoPerz3Zo20X8uPtcFjQSAQS1MA@mail.gmail.com">5F1-_9V5XHS4vF_eXvKoPerz3Zo20X8uPtcFjQSAQS1MA@mail.gmail.com</a>><br>
>> Content-Type: text/plain; charset=UTF-8<br>
>><br>
>> Hi Yanfei,<br>
>><br>
>> This is possible -- but it will also slow some things down. You can<br>
>> use the load_hexahedral_mesh function, and there're examples of this.<br>
>> This takes away some of the optimizations that regular grids can do,<br>
>> but we're hoping to add them back in shortly. Like the other<br>
>> functions it too takes a geometry argument.<br>
>><br>
>> -Matt<br>
>><br>
>> On Wed, Mar 30, 2016 at 2:49 PM, Jiang, Yanfei<br>
>> <<a href="mailto:yanfei.jiang@cfa.harvard.edu">yanfei.jiang@cfa.harvard.edu</a>> wrote:<br>
>> > Hi Jonah,<br>
>> ><br>
>> > I am able to load the data to yt now using load_amr_grids(). I notice<br>
>> > that it can also set geometry to spherical. This is great. But to make<br>
>> life<br>
>> > more complicate. Is it possible to let yt know that the grid is<br>
>> logarithmic?<br>
>> > Currently, load_amr_grids() just take left and right edges of each<br>
>> block. I<br>
>> > guess yt assumes the grid is uniform between left and right edges. Is it<br>
>> > possible to provide arrays of coordinate values for each cell in each<br>
>> block?<br>
>> ><br>
>> > Thanks.<br>
>> ><br>
>> > On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller<br>
>> > <<a href="mailto:jonah.maxwell.miller@gmail.com">jonah.maxwell.miller@gmail.com</a>> wrote:<br>
>> >><br>
>> >> Hi Yan-Feng,<br>
>> >><br>
>> >> I haven't tried it, but I think there is functionality for this. You<br>
>> can<br>
>> >> use the load_amr_grids() function which can load amr data in Cartesian,<br>
>> >> spherical, or polar coordinates. Here's the documentation:<br>
>> >><br>
>> >><br>
>> >><br>
>> <a href="http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-array" rel="noreferrer" target="_blank">http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-array</a><br>
>> >><br>
>> >><br>
>> >><br>
>> <a href="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" rel="noreferrer" target="_blank">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</a><br>
>> >><br>
>> >> Best,<br>
>> >> Jonah<br>
>> >><br>
>> >> On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei <<br>
>> <a href="mailto:yanfei.jiang@cfa.harvard.edu">yanfei.jiang@cfa.harvard.edu</a>><br>
>> >> wrote:<br>
>> >>><br>
>> >>> Hi,<br>
>> >>> I have some data from a new version of Athena simulations.<br>
>> It is<br>
>> >>> in spherical polar coordinate with mesh refinement written in HDF5.<br>
>> The data<br>
>> >>> structure is similar to flash data but not the same. Does anyone have<br>
>> >>> suggestions to load such data to yt directly?<br>
>> >>><br>
>> >>> Thank you.<br>
>> >>> --<br>
>> >>> Yan-Fei Jiang<br>
>> >>><br>
>> >>> Einstein Fellow<br>
>> >>> Harvard-Smithsonian Center for Astrophysics<br>
>> >>> 60 Garden Street, Cambridge MA USA 02138<br>
>> >>> _______________________________________________<br>
>> >>> yt-users mailing list<br>
>> >>> <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
>> >>> <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
>> >><br>
>> >><br>
>> >> _______________________________________________<br>
>> >> yt-users mailing list<br>
>> >> <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
>> >> <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
>> >><br>
>> ><br>
>> ><br>
>> ><br>
>> > --<br>
>> > Yan-Fei Jiang<br>
>> ><br>
>> > Einstein Fellow<br>
>> > Harvard-Smithsonian Center for Astrophysics<br>
>> > 60 Garden Street, Cambridge MA USA 02138<br>
>> ><br>
>> > _______________________________________________<br>
>> > yt-users mailing list<br>
>> > <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
>> > <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
>> ><br>
>><br>
>><br>
>> ------------------------------<br>
>><br>
>> Message: 3<br>
>> Date: Wed, 30 Mar 2016 16:16:22 -0500<br>
>> From: Matthew Turk <<a href="mailto:matthewturk@gmail.com">matthewturk@gmail.com</a>><br>
>> To: Discussion of the yt analysis package<br>
>> <<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a>><br>
>> Subject: Re: [yt-users] Inclination problem<br>
>> Message-ID:<br>
>> <CALO3=5HMB=<br>
>> <a href="mailto:joejr6BBh%2BzdxkwGzJS2NPrkK9tvMJnbch5-7BgQ@mail.gmail.com">joejr6BBh+zdxkwGzJS2NPrkK9tvMJnbch5-7BgQ@mail.gmail.com</a>><br>
>> Content-Type: text/plain; charset=UTF-8<br>
>><br>
>> Hi SK,<br>
>><br>
>> I'm not sure I totally understand, but if you have an inclination<br>
>> angle you can use this directly in yt in the off axis slices and so<br>
>> on. They typically take a vector, but you should be able to convert<br>
>> one to the other.<br>
>><br>
>> -Matt<br>
>><br>
>> On Tue, Mar 29, 2016 at 1:37 PM, Sushilkumar <<a href="mailto:sushil.sush19us@gmail.com">sushil.sush19us@gmail.com</a>><br>
>> wrote:<br>
>> > Dear yt:<br>
>> ><br>
>> > I am trying to numerically solve the region around a pulsar. Now since<br>
>> > pulsar is an inclined rotator with inclination angle between rotation<br>
>> axis<br>
>> > and dipole axis I would like to include in my yt script.<br>
>> ><br>
>> > My original code written in FORTRAN incorporated this inclination but<br>
>> how<br>
>> > would I incorporate it into my visualization using yt without changing<br>
>> my<br>
>> > data.<br>
>> ><br>
>> > Could you suggest ways for the same?<br>
>> ><br>
>> > The google drive link to my script (streamline.py) and streamline plot<br>
>> > (streamline_t000.png) is included<br>
>> ><br>
>> > <a href="https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc" rel="noreferrer" target="_blank">https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc</a><br>
>> ><br>
>> > Thanks in advance<br>
>> ><br>
>> > On Tue, Mar 29, 2016 at 12:54 PM, <<a href="mailto:yt-users-request@lists.spacepope.org">yt-users-request@lists.spacepope.org</a><br>
>> ><br>
>> > wrote:<br>
>> >><br>
>> >> Send yt-users mailing list submissions to<br>
>> >> <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
>> >><br>
>> >> To subscribe or unsubscribe via the World Wide Web, visit<br>
>> >> <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
>> >> or, via email, send a message with subject or body 'help' to<br>
>> >> <a href="mailto:yt-users-request@lists.spacepope.org">yt-users-request@lists.spacepope.org</a><br>
>> >><br>
>> >> You can reach the person managing the list at<br>
>> >> <a href="mailto:yt-users-owner@lists.spacepope.org">yt-users-owner@lists.spacepope.org</a><br>
>> >><br>
>> >> When replying, please edit your Subject line so it is more specific<br>
>> >> than "Re: Contents of yt-users digest..."<br>
>> >><br>
>> >><br>
>> >> Today's Topics:<br>
>> >><br>
>> >> 1. Re: gadget onto unigrid (Carla Bernhardt)<br>
>> >> 2. Re: gadget onto unigrid (Matthew Turk)<br>
>> >><br>
>> >><br>
>> >> ----------------------------------------------------------------------<br>
>> >><br>
>> >> Message: 1<br>
>> >> Date: Tue, 29 Mar 2016 15:55:27 +0200<br>
>> >> From: Carla Bernhardt <<a href="mailto:carla.j.bernhardt@gmail.com">carla.j.bernhardt@gmail.com</a>><br>
>> >> To: Discussion of the yt analysis package<br>
>> >> <<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a>><br>
>> >> Subject: Re: [yt-users] gadget onto unigrid<br>
>> >> Message-ID:<br>
>> >><br>
>> >> <CAFK0O=2vH24ViqeZ5QS3DY3uido0kEaF=<a href="mailto:UhyGS_beuiUMbw7Ag@mail.gmail.com">UhyGS_beuiUMbw7Ag@mail.gmail.com</a>><br>
>> >> Content-Type: text/plain; charset="utf-8"<br>
>> >><br>
>> >> Hi All,<br>
>> >><br>
>> >> A follow-up question: In using arbitrary_grid (but with enzo data), how<br>
>> >> does one then extract a field of an arbitrary_grid? I tried<br>
>> >> arbgrid["density"] as I have done with a smoothed_covering_grid object,<br>
>> >> but<br>
>> >> it does not work (here is the traceback <<a href="http://pastebin.com/afgcgpp0" rel="noreferrer" target="_blank">http://pastebin.com/afgcgpp0</a>><br>
>> I<br>
>> >> got).<br>
>> >><br>
>> >> Thanks,<br>
>> >> Carla<br>
>> >><br>
>> >> 2016-02-23 17:21 GMT+01:00 Matthew Turk <<a href="mailto:matthewturk@gmail.com">matthewturk@gmail.com</a>>:<br>
>> >><br>
>> >> > Hi Desika,<br>
>> >> ><br>
>> >> > Yup, this can be done reasonably easily using either the<br>
>> >> > .arbitrary_grid object (which was designed for this) or the interface<br>
>> >> > to the arbitrary grid that's in the development version, which is<br>
>> >> > ds.r[ ... ] where the ... is some combination of bounds and steps.<br>
>> >> ><br>
>> >> > <a href="http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid" rel="noreferrer" target="_blank">http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid</a><br>
>> >> ><br>
>> >> ><br>
>> >> ><br>
>> <a href="http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-selecting-data" rel="noreferrer" target="_blank">http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-selecting-data</a><br>
>> >> ><br>
>> >> > On Tue, Feb 23, 2016 at 10:18 AM, Desika Narayanan<br>
>> >> > <<a href="mailto:desika.narayanan@gmail.com">desika.narayanan@gmail.com</a>> wrote:<br>
>> >> > > Hi All,<br>
>> >> > ><br>
>> >> > > Is it possible to deposit the particles from a gadget data set<br>
>> onto a<br>
>> >> > > uniform grid in yt? Or, could it be possible to trick the octree<br>
>> >> > deposition<br>
>> >> > > into doing it by forcing no refinements, but some sort of native<br>
>> grid<br>
>> >> > > resolution?<br>
>> >> > ><br>
>> >> > > thanks,<br>
>> >> > > desika<br>
>> >> > ><br>
>> >> > ><br>
>> >> > > _______________________________________________<br>
>> >> > > yt-users mailing list<br>
>> >> > > <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
>> >> > > <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
>> >> > ><br>
>> >> > _______________________________________________<br>
>> >> > yt-users mailing list<br>
>> >> > <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
>> >> > <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
>> >> ><br>
>> >> -------------- next part --------------<br>
>> >> An HTML attachment was scrubbed...<br>
>> >> URL:<br>
>> >> <<br>
>> <a href="http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160329/e29a03a1/attachment.html" rel="noreferrer" target="_blank">http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160329/e29a03a1/attachment.html</a><br>
>> ><br>
>> >><br>
>> >> ------------------------------<br>
>> >><br>
>> >> Message: 2<br>
>> >> Date: Tue, 29 Mar 2016 08:57:08 -0500<br>
>> >> From: Matthew Turk <<a href="mailto:matthewturk@gmail.com">matthewturk@gmail.com</a>><br>
>> >> To: Discussion of the yt analysis package<br>
>> >> <<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a>><br>
>> >> Subject: Re: [yt-users] gadget onto unigrid<br>
>> >> Message-ID:<br>
>> >><br>
>> >> <CALO3=5HR=zLHujWKgLpqwei_98vBOjpYvQ4m8nnUFR=<a href="mailto:P098utA@mail.gmail.com">P098utA@mail.gmail.com</a>><br>
>> >> Content-Type: text/plain; charset=UTF-8<br>
>> >><br>
>> >> Hi Carla,<br>
>> >><br>
>> >> This functionality was recently implemented and is in the development<br>
>> >> version, but not yet in the stable. We're hoping for a release very<br>
>> >> shortly, but you can also try the dev version if you'd like!<br>
>> >><br>
>> >> -Matt<br>
>> >><br>
>> >> On Tue, Mar 29, 2016 at 8:55 AM, Carla Bernhardt<br>
>> >> <<a href="mailto:carla.j.bernhardt@gmail.com">carla.j.bernhardt@gmail.com</a>> wrote:<br>
>> >> > Hi All,<br>
>> >> ><br>
>> >> > A follow-up question: In using arbitrary_grid (but with enzo data),<br>
>> how<br>
>> >> > does<br>
>> >> > one then extract a field of an arbitrary_grid? I tried<br>
>> >> > arbgrid["density"] as<br>
>> >> > I have done with a smoothed_covering_grid object, but it does not<br>
>> work<br>
>> >> > (here<br>
>> >> > is the traceback I got).<br>
>> >> ><br>
>> >> > Thanks,<br>
>> >> > Carla<br>
>> >> ><br>
>> >> > 2016-02-23 17:21 GMT+01:00 Matthew Turk <<a href="mailto:matthewturk@gmail.com">matthewturk@gmail.com</a>>:<br>
>> >> >><br>
>> >> >> Hi Desika,<br>
>> >> >><br>
>> >> >> Yup, this can be done reasonably easily using either the<br>
>> >> >> .arbitrary_grid object (which was designed for this) or the<br>
>> interface<br>
>> >> >> to the arbitrary grid that's in the development version, which is<br>
>> >> >> ds.r[ ... ] where the ... is some combination of bounds and steps.<br>
>> >> >><br>
>> >> >><br>
>> <a href="http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid" rel="noreferrer" target="_blank">http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid</a><br>
>> >> >><br>
>> >> >><br>
>> >> >><br>
>> <a href="http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-selecting-data" rel="noreferrer" target="_blank">http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-selecting-data</a><br>
>> >> >><br>
>> >> >> On Tue, Feb 23, 2016 at 10:18 AM, Desika Narayanan<br>
>> >> >> <<a href="mailto:desika.narayanan@gmail.com">desika.narayanan@gmail.com</a>> wrote:<br>
>> >> >> > Hi All,<br>
>> >> >> ><br>
>> >> >> > Is it possible to deposit the particles from a gadget data set<br>
>> onto a<br>
>> >> >> > uniform grid in yt? Or, could it be possible to trick the octree<br>
>> >> >> > deposition<br>
>> >> >> > into doing it by forcing no refinements, but some sort of native<br>
>> grid<br>
>> >> >> > resolution?<br>
>> >> >> ><br>
>> >> >> > thanks,<br>
>> >> >> > desika<br>
>> >> >> ><br>
>> >> >> ><br>
>> >> >> > _______________________________________________<br>
>> >> >> > yt-users mailing list<br>
>> >> >> > <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
>> >> >> > <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
>> >> >> ><br>
>> >> >> _______________________________________________<br>
>> >> >> yt-users mailing list<br>
>> >> >> <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
>> >> >> <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
>> >> ><br>
>> >> ><br>
>> >> ><br>
>> >> > _______________________________________________<br>
>> >> > yt-users mailing list<br>
>> >> > <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
>> >> > <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
>> >> ><br>
>> >><br>
>> >><br>
>> >> ------------------------------<br>
>> >><br>
>> >> Subject: Digest Footer<br>
>> >><br>
>> >> _______________________________________________<br>
>> >> yt-users mailing list<br>
>> >> <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
>> >> <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
>> >><br>
>> >><br>
>> >> ------------------------------<br>
>> >><br>
>> >> End of yt-users Digest, Vol 97, Issue 34<br>
>> >> ****************************************<br>
>> ><br>
>> ><br>
>> ><br>
>> ><br>
>> > --<br>
>> > SK2<br>
>> ><br>
>> > "Claiming that something can move faster than light is a good<br>
>> > conversation-stopper in physics. People edge away from you in cocktail<br>
>> > parties; friends never return phone calls. You just don?t mess with<br>
>> Albert<br>
>> > Einstein."<br>
>> ><br>
>> ><br>
>> > _______________________________________________<br>
>> > yt-users mailing list<br>
>> > <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
>> > <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
>> ><br>
>><br>
>><br>
>> ------------------------------<br>
>><br>
>> Message: 4<br>
>> Date: Wed, 30 Mar 2016 18:01:04 -0400<br>
>> From: Jonah Miller <<a href="mailto:jonah.maxwell.miller@gmail.com">jonah.maxwell.miller@gmail.com</a>><br>
>> To: <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
>> Subject: Re: [yt-users] load spherical polar coordinate data with mesh<br>
>> refinement in HDF5<br>
>> Message-ID: <<a href="mailto:56FC4CA0.4030403@gmail.com">56FC4CA0.4030403@gmail.com</a>><br>
>> Content-Type: text/plain; charset=windows-1252; format=flowed<br>
>><br>
>> Hi Yanfei,<br>
>><br>
>> To add to Matt's comment. Here is the documentation for using<br>
>> load_hexahedral_mesh.<br>
>><br>
>> <a href="http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-data" rel="noreferrer" target="_blank">http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-data</a><br>
>><br>
>> <a href="http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_structures.load_hexahedral_mesh.html" rel="noreferrer" target="_blank">http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_structures.load_hexahedral_mesh.html</a><br>
>><br>
>> Best,<br>
>> Jonah<br>
>><br>
>> On 16-03-30 05:15 PM, Matthew Turk wrote:<br>
>> > Hi Yanfei,<br>
>> ><br>
>> > This is possible -- but it will also slow some things down. You can<br>
>> > use the load_hexahedral_mesh function, and there're examples of this.<br>
>> > This takes away some of the optimizations that regular grids can do,<br>
>> > but we're hoping to add them back in shortly. Like the other<br>
>> > functions it too takes a geometry argument.<br>
>> ><br>
>> > -Matt<br>
>> ><br>
>> > On Wed, Mar 30, 2016 at 2:49 PM, Jiang, Yanfei<br>
>> > <<a href="mailto:yanfei.jiang@cfa.harvard.edu">yanfei.jiang@cfa.harvard.edu</a>> wrote:<br>
>> >> Hi Jonah,<br>
>> >><br>
>> >> I am able to load the data to yt now using load_amr_grids(). I<br>
>> notice<br>
>> >> that it can also set geometry to spherical. This is great. But to make<br>
>> life<br>
>> >> more complicate. Is it possible to let yt know that the grid is<br>
>> logarithmic?<br>
>> >> Currently, load_amr_grids() just take left and right edges of each<br>
>> block. I<br>
>> >> guess yt assumes the grid is uniform between left and right edges. Is<br>
>> it<br>
>> >> possible to provide arrays of coordinate values for each cell in each<br>
>> block?<br>
>> >><br>
>> >> Thanks.<br>
>> >><br>
>> >> On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller<br>
>> >> <<a href="mailto:jonah.maxwell.miller@gmail.com">jonah.maxwell.miller@gmail.com</a>> wrote:<br>
>> >>> Hi Yan-Feng,<br>
>> >>><br>
>> >>> I haven't tried it, but I think there is functionality for this. You<br>
>> can<br>
>> >>> use the load_amr_grids() function which can load amr data in<br>
>> Cartesian,<br>
>> >>> spherical, or polar coordinates. Here's the documentation:<br>
>> >>><br>
>> >>><br>
>> >>><br>
>> <a href="http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-array" rel="noreferrer" target="_blank">http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-array</a><br>
>> >>><br>
>> >>><br>
>> >>><br>
>> <a href="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" rel="noreferrer" target="_blank">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</a><br>
>> >>><br>
>> >>> Best,<br>
>> >>> Jonah<br>
>> >>><br>
>> >>> On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei <<br>
>> <a href="mailto:yanfei.jiang@cfa.harvard.edu">yanfei.jiang@cfa.harvard.edu</a>><br>
>> >>> wrote:<br>
>> >>>> Hi,<br>
>> >>>> I have some data from a new version of Athena simulations.<br>
>> It is<br>
>> >>>> in spherical polar coordinate with mesh refinement written in HDF5.<br>
>> The data<br>
>> >>>> structure is similar to flash data but not the same. Does anyone have<br>
>> >>>> suggestions to load such data to yt directly?<br>
>> >>>><br>
>> >>>> Thank you.<br>
>> >>>> --<br>
>> >>>> Yan-Fei Jiang<br>
>> >>>><br>
>> >>>> Einstein Fellow<br>
>> >>>> Harvard-Smithsonian Center for Astrophysics<br>
>> >>>> 60 Garden Street, Cambridge MA USA 02138<br>
>> >>>> _______________________________________________<br>
>> >>>> yt-users mailing list<br>
>> >>>> <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
>> >>>> <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
>> >>><br>
>> >>> _______________________________________________<br>
>> >>> yt-users mailing list<br>
>> >>> <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
>> >>> <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
>> >>><br>
>> >><br>
>> >><br>
>> >> --<br>
>> >> Yan-Fei Jiang<br>
>> >><br>
>> >> Einstein Fellow<br>
>> >> Harvard-Smithsonian Center for Astrophysics<br>
>> >> 60 Garden Street, Cambridge MA USA 02138<br>
>> >><br>
>> >> _______________________________________________<br>
>> >> yt-users mailing list<br>
>> >> <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
>> >> <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
>> >><br>
>> > _______________________________________________<br>
>> > yt-users mailing list<br>
>> > <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
>> > <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
>><br>
>><br>
>><br>
>> ------------------------------<br>
>><br>
>> Subject: Digest Footer<br>
>><br>
>> _______________________________________________<br>
>> yt-users mailing list<br>
>> <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
>> <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
>><br>
>><br>
>> ------------------------------<br>
>><br>
>> End of yt-users Digest, Vol 97, Issue 37<br>
>> ****************************************<br>
>><br>
><br>
><br>
><br>
> --<br>
> *SK2*<br>
><br>
> *"**Claiming that something can move faster than light is a good<br>
> conversation-stopper in physics. People edge away from you in cocktail<br>
> parties; friends never return phone calls. You just don?t mess with Albert<br>
> Einstein.**"*<br>
><br>
><br>
> _______________________________________________<br>
> yt-users mailing list<br>
> <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
> <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
><br>
><br>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature"><span style="border-collapse:collapse"><div style="color:rgb(80,0,80);font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px;border-collapse:collapse"><b><i>SK<sup>2</sup></i></b></span></div><div style="color:rgb(80,0,80);font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px;border-collapse:collapse"><b><i><sup><br></sup></i></b></span></div><div><span style="color:rgb(80,0,80);font-family:arial,sans-serif;border-collapse:collapse"><b><sup>"</sup></b></span><font color="#500050" face="arial, sans-serif"><b>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.</b></font><b style="color:rgb(80,0,80);font-family:arial,sans-serif"><sup>"</sup></b></div><div style="color:rgb(80,0,80);font-family:arial,sans-serif;font-size:13px"><br></div></span></div>
</div></div></div>