<div dir="ltr"><div>Dear Matt:<br><br></div>Pleas correct me if I am wrong but "off axis slices" takes slices of the plot that is already plotted. <br><div><div><br>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. <br><br></div><div>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).<br></div><div><div><br><br><br><div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Mar 30, 2016 at 5:01 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:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">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>
<<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 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>
> <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>
> <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 <<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 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 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: <<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>
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=<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 life<br>
> more complicate. Is it possible to let yt know that the grid is logarithmic?<br>
> Currently, load_amr_grids() just take left and right edges of each 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 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>
>> <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 <<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 is<br>
>>> in spherical polar coordinate with mesh refinement written in HDF5. 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=<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>> 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 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 how<br>
> would I incorporate it into my visualization using yt without changing 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>
> 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>> 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>
>> > <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 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 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>
>> <<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>
>> 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), 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 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 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>
>> >> <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 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 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 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>
<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>
<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 notice<br>
>> that it can also set geometry to spherical. This is great. But to make life<br>
>> more complicate. Is it possible to let yt know that the grid is logarithmic?<br>
>> Currently, load_amr_grids() just take left and right edges of each 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 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 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>
>>> <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 <<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. It is<br>
>>>> in spherical polar coordinate with mesh refinement written in HDF5. 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>
</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>
</div></div></div></div></div></div>