I think that the main mapping functions that stellar people are thinking about are these: http://math.boisestate.edu/~calhoun/www_personal/papers/ca-he-le-2008.pdf On Mon, Apr 4, 2016 at 5:35 PM, Matthew Turk <matthewturk@gmail.com> wrote:
Hi Mike and Sam,
That makes sense; one thing we need to be slightly careful about is if the shape function needs to be modified considerably, or if it's multi-variate. Sam, I'm sorry I missed your message or didn't put things together, but I think this is worth looking into further. If you'd like to correspond about this, yt-dev might be a better choice, or we can chat offline and I'll send a summary.
This mapped grid capability is similar to what Sam Jones e-mailed the
about a week or two ago. Their grid is logically Cartesian, but a mapping function transforms it to a different shape.
On Mon, Apr 4, 2016 at 5:13 PM, Matthew Turk <matthewturk@gmail.com> wrote:
Hi Yan-Fei,
I've thought about this a bunch. I *think* that it's feasible, with only very minor modifications to the existing system, as long as there's a mapping we can construct for the spacing, and that mapping is unique across the grids at fixed levels.
What I mean by that is, if we can have a function that operates such that it's given a set of integer values (integer coordinate [xyz], resolution level) and it can return a position and a width (in linear space), we can implement this without too much trouble. I can see some tricky things relating to how to switch between log/lin visualization, but they should be surmountable. (And presumably, if you have a log spaced dataset, you won't want linear viz terribly frequently anyway.) Generating the integer coordinate might be the funniest part; in linear space it's just (pos-domain_left_edge)/local_dx, but I don't know the specifics of your data format.
-Matt
On Thu, Mar 31, 2016 at 9:55 AM, Jonah Miller <jonah.maxwell.miller@gmail.com> wrote:
Hi Yan-Fei,
I don't think this will work out of the box. Matt may have more
insight
here.
Best, Jonah
On 16-03-31 01:03 AM, Jiang, Yanfei wrote:
Hi Matt and Jonah,
I think I can use load_hexahedral_mesh to load data from each mesh block. But it cannot use three arrays (xgrid, ygrid, zgrid) to define the whole mesh due to mesh refinement. I guess I can create a dict to collect the data from each mesh block, as in load_amr_grids (but not the same). The question is will such a data structure (a dict of hexahedral_mesh) be recognized by yt?
On Wed, Mar 30, 2016 at 6:01 PM, Jonah Miller <jonah.maxwell.miller@gmail.com> wrote:
Hi Yanfei,
To add to Matt's comment. Here is the documentation for using load_hexahedral_mesh.
http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-d...
http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s...
Best, Jonah
On 16-03-30 05:15 PM, Matthew Turk wrote:
Hi Yanfei,
This is possible -- but it will also slow some things down. You can use the load_hexahedral_mesh function, and there're examples of
On Mon, Apr 4, 2016 at 4:31 PM, Michael Zingale <michael.zingale@stonybrook.edu> wrote: list this.
This takes away some of the optimizations that regular grids can do, but we're hoping to add them back in shortly. Like the other functions it too takes a geometry argument.
-Matt
On Wed, Mar 30, 2016 at 2:49 PM, Jiang, Yanfei <yanfei.jiang@cfa.harvard.edu> wrote: > > Hi Jonah, > > I am able to load the data to yt now using load_amr_grids(). I > notice > that it can also set geometry to spherical. This is great. But to > make > life > more complicate. Is it possible to let yt know that the grid is > logarithmic? > Currently, load_amr_grids() just take left and right edges of each > block. I > guess yt assumes the grid is uniform between left and right edges. Is > it > possible to provide arrays of coordinate values for each cell in each > block? > > Thanks. > > On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller > <jonah.maxwell.miller@gmail.com> wrote: >> >> Hi Yan-Feng, >> >> I haven't tried it, but I think there is functionality for this. You >> can >> use the load_amr_grids() function which can load amr data in >> Cartesian, >> spherical, or polar coordinates. Here's the documentation: >> >> >> >> >> http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar... >> >> >> >> >> http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s... >> >> Best, >> Jonah >> >> On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei >> <yanfei.jiang@cfa.harvard.edu> >> wrote: >>> >>> Hi, >>> I have some data from a new version of Athena >>> simulations. >>> It is >>> in spherical polar coordinate with mesh refinement written in HDF5. >>> The data >>> structure is similar to flash data but not the same. Does anyone >>> have >>> suggestions to load such data to yt directly? >>> >>> Thank you. >>> -- >>> Yan-Fei Jiang >>> >>> Einstein Fellow >>> Harvard-Smithsonian Center for Astrophysics >>> 60 Garden Street, Cambridge MA USA 02138 >>> _______________________________________________ >>> yt-users mailing list >>> yt-users@lists.spacepope.org >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> >> _______________________________________________ >> yt-users mailing list >> yt-users@lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> > > > -- > Yan-Fei Jiang > > Einstein Fellow > Harvard-Smithsonian Center for Astrophysics > 60 Garden Street, Cambridge MA USA 02138 > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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-- Yan-Fei Jiang
Einstein Fellow Harvard-Smithsonian Center for Astrophysics 60 Garden Street, Cambridge MA USA 02138
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-- Michael Zingale Associate Professor
Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800 phone: 631-632-8225 e-mail: Michael.Zingale@stonybrook.edu web: http://www.astro.sunysb.edu/mzingale github: http://github.com/zingale
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-- Michael Zingale Associate Professor Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800 *phone*: 631-632-8225 *e-mail*: Michael.Zingale@stonybrook.edu *web*: http://www.astro.sunysb.edu/mzingale github: http://github.com/zingale