[yt-dev] Vertex-centred AMR data?

[Matthew Turk]

Hi Erik,

OK -- here are the changes that will need to be made.  For a stopgap,
your AMRGridPatch subclass should call select_cells such that the
values computed by LeftEdge + 0.5dx + i*dx are the vertex centered
points.  For longer term, this will be a selection routine that is
called "select_vertices" which does the math internally; this is
placed in yt/geometry/selection_routines.pyx .  This will ensure that
the

The next step is ensuring that the notion of a "volume" is meaningful.
Typically this is computed by taking the product of fwidth, which is
the "spatial extent" in all three dimensions of each point.  This is
where the impedance mismatch will be the most difficult, because
either each vertex will need to be part of a cell, or it will need to
be regarded as its principle "extent", i.e., the domain over which is
it considered "valid."

The final step is going to be modifying the pixelization routine to
recognize vertex centered data.  This is probably the easiest, as I
suspect that it will work reasonably well out of the box as-is.

The second step is the one that is the most troublesome, as I think it
will be necessary to ensure that fwidth is not used elsewhere in a way
that doesn't make sense for vertex-centered data.  One of the reasons
I would be most careful with this is that the notion of masking and
overlapping vertices means not all vertices will have the same
conceptual "width."  For instance, at coarse-fine boundaries.

On Wed, Nov 11, 2015 at 8:55 AM, Erik Schnetter <schnetter at gmail.com> wrote:
> Matt
>
> For the moment, anything that works would be fine. I always selecting full
> cells is easier I'd be happy to try this first.
>
> -erik
>
> On Wed, Nov 11, 2015 at 9:53 AM, Matthew Turk <matthewturk at gmail.com> wrote:
>>
>> Hi Erik,
>>
>> Thanks, this helps.  This means that for the specific case of your
>> data, we will need to use a different selection method than that used
>> for finite element data, where we select full cells rather than
>> allowing partial selection.  Instead of "rounding up" we should be
>> using a method similar to particle selection, where discrete points
>> are sampled.
>>
>> For the case of changing a set of points into a pixel buffer, this
>> means we will use nearest-neighbor interpolation (with no sub-cellular
>> interpolation).  This should be straightforward, as it will suffice to
>> define an edge of a zone (which will be truncated at boundaries) and
>> width, which we do already for cell-centered data.
>>
>> On Wed, Nov 11, 2015 at 8:50 AM, Erik Schnetter <schnetter at gmail.com>
>> wrote:
>> > Matt
>> >
>> > In my notion, there are no cells, only vertices. Or if you want to
>> > renaming
>> > things, then there are only cells, no vertices, but the fine a coarse
>> > grid
>> > cells do not share faces.
>> >
>> > To answer your question specifically: no, it does not matter whether
>> > the
>> > centre of a "cell" is selected. Only the vertices that are selected
>> > should
>> > be part of the selection.
>> >
>> > -erik
>> >
>> > On Wed, Nov 11, 2015 at 8:57 AM, Matthew Turk <matthewturk at gmail.com>
>> > wrote:
>> >>
>> >> Hi Erik,
>> >>
>> >> I have some ideas about this, but it relies heavily on the notion of
>> >> how to regard "vertices" as separate from "cells", or if they should
>> >> not be.  In terms of things like visualization, vertex centered data
>> >> is not a huge leap in functionality, but in terms of data selection we
>> >> need to be careful.  The canonical question is, if you have a region
>> >> selector that includes the *center* of a zone, should all of its
>> >> vertices be selected?  For instance, imagine you have a region
>> >> selector whose corner resides at the center of a (3D) cell.  Does one
>> >> select all eight vertices, since the "cell" is nominally selected, or
>> >> just the one vertex that is included?  If we can answer that, we can
>> >> start the work of implementing.
>> >>
>> >> On Tue, Nov 10, 2015 at 7:11 PM, Nathan Goldbaum
>> >> <nathan12343 at gmail.com>
>> >> wrote:
>> >> >
>> >> >
>> >> > On Tuesday, November 10, 2015, Erik Schnetter <schnetter at gmail.com>
>> >> > wrote:
>> >> >>
>> >> >> I have implemented a front-end for cell-centred Cactus AMR data.
>> >> >>
>> >> >
>> >> > Awesome! We'd love to have this in the public distribution of yt.
>> >> >
>> >> >>
>> >> >>
>> >> >> However, many Cactus simulations use vertex-centred AMR. That is,
>> >> >> data
>> >> >> is
>> >> >> stored at the vertices of a grid (not in the cells), and coarse
>> >> >> vertices are
>> >> >> at the same locations as fine vertices.
>> >> >>
>> >> >> How do I present such data to yt? Do I need to set grid coordinates
>> >> >> differently, or is there a "vertex centred" flag?
>> >> >>
>> >> >> When vertex-centred data are displayed, then I expect either a
>> >> >> "control
>> >> >> volume" around each vertex to have the same value, or to use e.g.
>> >> >> linear
>> >> >> interpolation in the cells from the respective boundaries.
>> >> >
>> >> >
>> >> > We don't have good support for vertex-centered AMR data. I think Matt
>> >> > would
>> >> > have a better idea of what approaches we might take here.
>> >> >
>> >> >>
>> >> >>
>> >> >> -erik
>> >> >>
>> >> >> --
>> >> >> Erik Schnetter <schnetter at gmail.com>
>> >> >> http://www.perimeterinstitute.ca/personal/eschnetter/
>> >> >
>> >> >
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>> >
>> > --
>> > Erik Schnetter <schnetter at gmail.com>
>> > http://www.perimeterinstitute.ca/personal/eschnetter/
>> >
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>
>
>
>
> --
> Erik Schnetter <schnetter at gmail.com>
> http://www.perimeterinstitute.ca/personal/eschnetter/
>
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