[yt-users] star_density slices

Brian O'Shea bwoshea at gmail.com
Mon Jun 13 16:24:38 PDT 2011


Hi Matt,

Got it, my fault for not reading the entire thread.  Sorry!  (And, I like
that it'll be in the code one day, protecting us from our weird datasets.)

--Brian

On Mon, Jun 13, 2011 at 7:10 PM, Matthew Turk <matthewturk at gmail.com> wrote:

> Hi Brian,
>
> That's what the routine Elizabeth was calling does -- it utilizes a
> CIC_Deposit routine that Britton wrote to deposit the particles.  The
> problem was that the particles were located in coarse grids inside
> regions covered by finer grids.  So their deposited densities were
> overwritten in the projection routine because the were in cells that
> were "child masked."
>
> The solution to this problem I prefer is to have well-posed datasets,
> where the fluid quantities and the particle quantities are expected to
> respect the same implicit understanding that higher-resolution regions
> have the better solution to the underlying equations.  However, one
> could imagine solving this through a set of solution-projection
> routines that ensure consistency between coarse and fine grids.
>
> Such routines will ultimately be part of yt.
>
> -Matt
>
> On Mon, Jun 13, 2011 at 4:06 PM, Brian O'Shea <bwoshea at gmail.com> wrote:
> > Hi Matt,
> >
> > There is a mechanism within yt for the dark matter density to be
> > recalculated for some (all?) Enzo simulations.  Could this be extended to
> > star particles as well?  That way, the user could specify "recalculate
> this
> > field even if it already exists.  Just trust me, yt!"
> >
> > --Brian
> >
> > On Mon, Jun 13, 2011 at 6:25 PM, Matthew Turk <matthewturk at gmail.com>
> wrote:
> >>
> >> Hi all,
> >>
> >> Elizabeth, Britton and I worked on this off-list on IRC.
> >>
> >> What I have deduced is that the star particles in her simulation are
> >> not located at the finest resolution element.  After discussing it
> >> with her, this seems to me to be likely related to how she generated
> >> the data, by restarting data written by an older version of Enzo with
> >> a recent version of Enzo, having it write the potential field, and
> >> then outputting again.  What happens with data in a projection, or a
> >> slice for instance, is that higher-resolution grids are assumed to
> >> contain *better* data than the lower-resolution grids.  So while
> >> actual plots of the *particles* looked fine (I verified this) the
> >> fluid quantities, particle_density etc etc, were being generated for
> >> coarse level grids and then overwritten by finer level grids.
> >>
> >> Unfortunately, those finer level grids did not contain any particles.
> >> So their fluid values were zero, and were overwriting coarser level
> >> information which was non-zero.  This is desired behavior; but I
> >> cannot think of any solution to this problem that will work in all
> >> cases.  So, this will continue to go 'unfixed' for now, as well-formed
> >> outputs are assumed to have their particles located at the
> >> locally-finest level of resolution, and this dataset does not meet
> >> that criterion.
> >>
> >> Best,
> >>
> >> Matt
> >>
> >> On Mon, Jun 13, 2011 at 11:04 AM, Britton Smith <brittonsmith at gmail.com
> >
> >> wrote:
> >> > Ok, that at least tells us it's not a problem with the filter that's
> >> > looking
> >> > for just the star particles.  Can you run this script:
> >> > http://paste.enzotools.org/show/1704/
> >> > on your data, pipe the output to a file and send that back?  Just give
> >> > the
> >> > path to your dataset on the command line.  This should check to see if
> >> > there
> >> > are any inconsistencies in the grid dx's and positions.
> >> >
> >> > Britton
> >> >
> >> > On Mon, Jun 13, 2011 at 1:38 PM, Elizabeth Tasker <
> taskere at mcmaster.ca>
> >> > wrote:
> >> >>
> >> >> Hi,
> >> >>
> >> >> Doesn't dm_density require the particle creation time to be less than
> >> >> or
> >> >> equal to zero? That is:
> >> >>
> >> >>
> >> >> field = pf.field_info["dm_density"]
> >> >> ------> print(field.get_source())
> >> >> def _dmpdensity(field, data):
> >> >>   blank = na.zeros(data.ActiveDimensions, dtype='float32')
> >> >>   if data.NumberOfParticles == 0: return blank
> >> >>   filter = data['creation_time'] <= 0.0
> >> >>   if not filter.any(): return blank
> >> >>
> >> >>
> >> >>
> amr_utils.CICDeposit_3(data["particle_position_x"][filter].astype(na.float64),
> >> >>
> >> >>  data["particle_position_y"][filter].astype(na.float64),
> >> >>
> >> >>  data["particle_position_z"][filter].astype(na.float64),
> >> >>
> >> >>  data["particle_mass"][filter].astype(na.float32),
> >> >>                          na.int64(na.where(filter)[0].size),
> >> >>                          blank,
> >> >> na.array(data.LeftEdge).astype(na.float64),
> >> >>
> >> >>  na.array(data.ActiveDimensions).astype(na.int32),
> >> >>                          na.float64(data['dx']))
> >> >>   return blank
> >> >>
> >> >>
> >> >> It is zero in my simulation; I checked.
> >> >>
> >> >> The particle_density field though works ok (well.... it looks the
> same
> >> >> as
> >> >> the stars!) and I've attached a projection of it.
> >> >>
> >> >> Elizabeth
> >> >>
> >> >>
> >> >>
> >> >>
> >> >> Matthew Turk wrote:
> >> >>>
> >> >>> Hi Elizabeth,
> >> >>>
> >> >>> We're basically trying to break down where the problem is.
> >> >>>
> >> >>> Here are the definitions of star_density:
> >> >>>
> >> >>>
> http://hg.enzotools.org/yt/src/tip/yt/frontends/enzo/fields.py#cl-269
> >> >>>
> >> >>>
> >> >>>
> http://hg.enzotools.org/yt/src/tip/yt/data_objects/universal_fields.py#cl-384
> >> >>>
> >> >>> Alternately to plotting the dm_density would just be
> particle_density:
> >> >>>
> >> >>>
> >> >>>
> >> >>>
> http://hg.enzotools.org/yt/src/tip/yt/data_objects/universal_fields.py#cl-906
> >> >>>
> >> >>> Additionally, trying without the grid overplot would also be
> helpful.
> >> >>> The specific item we're focusing on with the particle_density etc is
> >> >>> whether it's the grids that are causing a problem or the particle
> >> >>> selection.
> >> >>>
> >> >>> Thanks,
> >> >>>
> >> >>> -Matt
> >> >>>
> >> >>> On Mon, Jun 13, 2011 at 9:11 AM, Elizabeth Tasker
> >> >>> <taskere at mcmaster.ca>
> >> >>> wrote:
> >> >>>
> >> >>>>
> >> >>>> Hi Britton,
> >> >>>>
> >> >>>> I don't have any DM in my simulations, so I don't think that will
> >> >>>> produce
> >> >>>> anything?
> >> >>>>
> >> >>>> Elizabeth
> >> >>>>
> >> >>>>
> >> >>>> Britton Smith wrote:
> >> >>>>
> >> >>>>>
> >> >>>>> Hi Elizabeth,
> >> >>>>>
> >> >>>>> Matt and I are still puzzling over this.  It's not clear right now
> >> >>>>> if
> >> >>>>> the
> >> >>>>> issue is related to projecting particles in general in your data
> or
> >> >>>>> projecting star particles specifically.  Can you do another full
> box
> >> >>>>> projection for us, but this time with the field dm_density?  That
> >> >>>>> should
> >> >>>>> help us to narrow down the problem.
> >> >>>>>
> >> >>>>> Britton
> >> >>>>>
> >> >>>>> On Mon, Jun 13, 2011 at 10:31 AM, Elizabeth Tasker
> >> >>>>> <taskere at mcmaster.ca
> >> >>>>> <mailto:taskere at mcmaster.ca>> wrote:
> >> >>>>>
> >> >>>>>   Hi Matt and Britton,
> >> >>>>>
> >> >>>>>   I've attached the image for the stars over the whole disk; it
> >> >>>>>   shows the same issue, with the grids (and also any gas property)
> >> >>>>>   showing the region correctly, but the stars only appearing in a
> >> >>>>>   small patch.
> >> >>>>>
> >> >>>>>   Matt, your script gives:
> >> >>>>>
> >> >>>>>   Min: [('x', 5.6774955112245706), ('y', 5.7878015648296586),
> ('z',
> >> >>>>>   15.07668303734844)]
> >> >>>>>   Max: [('x', 26.537083788811703), ('y', 25.802074691296504),
> ('z',
> >> >>>>>   17.201602159672426)]
> >> >>>>>
> >> >>>>>
> >> >>>>>   Which are the values I expect.
> >> >>>>>
> >> >>>>>   It could be, as Britton suggests, a problem with the box size
> not
> >> >>>>>   being 0-1. Although, that is a particularly random patch it's
> >> >>>>>   decided to fill in.
> >> >>>>>
> >> >>>>>   Elizabeth
> >> >>>>>
> >> >>>>>
> >> >>>>>
> >> >>>>>   Matthew Turk wrote:
> >> >>>>>
> >> >>>>>       Hi Elizabeth,
> >> >>>>>
> >> >>>>>       Weird.
> >> >>>>>
> >> >>>>>       This script should help us find out where the stars live.
> >> >>>>>        What's it
> >> >>>>>       give you?  (Replace the loaded dataset with your own.)
> >> >>>>>
> >> >>>>>       http://paste.enzotools.org/show/1696/
> >> >>>>>
> >> >>>>>       Also, it'd be nice to see that image Britton requested.
> >> >>>>>
> >> >>>>>       -Matt
> >> >>>>>
> >> >>>>>       On Fri, Jun 10, 2011 at 2:02 PM, Elizabeth Tasker
> >> >>>>>       <taskere at mcmaster.ca <mailto:taskere at mcmaster.ca>> wrote:
> >> >>>>>
> >> >>>>>           Oddly, neither of those make any difference.
> >> >>>>>
> >> >>>>>           Elizabeth
> >> >>>>>
> >> >>>>>
> >> >>>>>
> >> >>>>>           Britton Smith wrote:
> >> >>>>>
> >> >>>>>               I would also suggest trying some projections instead
> >> >>>>>               of slices as well.
> >> >>>>>                Both of those fields are created using the
> >> >>>>>               CIC_deposit interpolation method
> >> >>>>>               with just the star particles.  I could see a field
> >> >>>>>               like that being
> >> >>>>>               problematic when doing slices.
> >> >>>>>
> >> >>>>>               Britton
> >> >>>>>
> >> >>>>>               On Fri, Jun 10, 2011 at 4:10 PM, Cameron Hummels
> >> >>>>>               <chummels at astro.columbia.edu
> >> >>>>>               <mailto:chummels at astro.columbia.edu>
> >> >>>>>               <mailto:chummels at astro.columbia.edu
> >> >>>>>               <mailto:chummels at astro.columbia.edu>>> wrote:
> >> >>>>>
> >> >>>>>                 Try using the field StarMassMsun instead of
> >> >>>>>               star_density and see
> >> >>>>>                 what it yields.  I've had better luck with that
> >> >>>>> field.
> >> >>>>>
> >> >>>>>                 Cameron
> >> >>>>>
> >> >>>>>
> >> >>>>>                 On 6/10/11 4:00 PM, Elizabeth Tasker wrote:
> >> >>>>>
> >> >>>>>                     Hi,
> >> >>>>>
> >> >>>>>                     Slices of the star_density field are only
> >> >>>>>                   showing a tiny patch of
> >> >>>>>                     the area in the corner, rather than the whole
> >> >>>>>                   region. My script
> >> >>>>>                     looks like:
> >> >>>>>
> >> >>>>>                     pc = PlotCollection(pf, center=[17.,11.5, 16])
> >> >>>>>                     p = pc.add_slice("star_density", 2)
> >> >>>>>                     pc.set_width(10, 'kpc')
> >> >>>>>                     p.modify["grids"]()
> >> >>>>>
> >> >>>>>                     Density comes out fine and the grids are drawn
> >> >>>>>                   in but then only a
> >> >>>>>                     few of them get stars.
> >> >>>>>
> >> >>>>>                     Elizabeth
> >> >>>>>
> >> >>>>>
> >> >>>>>
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