<div dir="ltr"><div><div>Dear yt:<br><br></div>I would like to change/customize/rotate my camera angle for my slice plots without rotating the axis.<br><br>What options do I have using yt if I want to move my camera angle by say 45 degrees?<br><br></div>Can I use the following link or can you suggest me something else<br><a href="http://yt-project.org/doc/visualizing/volume_rendering.html">http://yt-project.org/doc/visualizing/volume_rendering.html</a><br><div><div><div><div><div><div><div><div class="gmail_extra"><br></div><div class="gmail_extra">Thanks in advance<br></div><div class="gmail_extra"><br><br><br><div class="gmail_quote">On Thu, Mar 31, 2016 at 10:11 PM, <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:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Send yt-users mailing list submissions to<br>
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Today's Topics:<br>
<br>
1. Inclination problem (Sushilkumar)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 31 Mar 2016 22:11:09 -0500<br>
From: Sushilkumar <<a href="mailto:sushil.sush19us@gmail.com">sushil.sush19us@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: [yt-users] Inclination problem<br>
Message-ID:<br>
<<a href="mailto:CAKARaKXPyQedHNjW0PwFvrO0qyjFGY4FMU6c2O5_PZWt-OxKEg@mail.gmail.com">CAKARaKXPyQedHNjW0PwFvrO0qyjFGY4FMU6c2O5_PZWt-OxKEg@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear Nathan:<br>
<br>
Thank you very much, implementing now<br>
<br>
<br>
On Thu, Mar 31, 2016 at 9:50 AM, <<a href="mailto:yt-users-request@lists.spacepope.org">yt-users-request@lists.spacepope.org</a>><br>
wrote:<br>
<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=<br>
> <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>
><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<br>
> (x`,y`,z`)<br>
> > which is inclined at an angle of say alpha from the default (x,y,z)<br>
> 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>
> >> <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: 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<br>
> of<br>
> >> each block. I guess yt assumes the grid is uniform between left and<br>
> right<br>
> >> edges. Is it possible to provide arrays of coordinate values for each<br>
> 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<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>
> >><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<br>
> >> is<br>
> >> >> in spherical polar coordinate with mesh refinement written in HDF5.<br>
> 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>
> >><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<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>
> >> >><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>
> >><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>
> >><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<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>
> >> ><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>
> ><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, <<br>
> <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>
> >> >><br>
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> >> >> 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>
> >> >><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),<br>
> 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<br>
> object,<br>
> >> >> but<br>
> >> >> it does not work (here is the traceback <<br>
> <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<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>
> >><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>
> >><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>
> >><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<br>
> 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>
> >><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>
> >><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<br>
> 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>
> >><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>
> >><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<br>
> 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<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>
> >> >>> 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<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>
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> ><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 39<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>
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End of yt-users Digest, Vol 97, Issue 41<br>
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</blockquote></div><br><br clear="all"><br>-- <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 face="arial, sans-serif" color="#500050"><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>
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