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
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
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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@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
_______________________________________________ yt-users mailing listyt-users@lists.spacepope.orghttp://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
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@astro.columbia.edu <mailto:chummels@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
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto: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
Hi Elizabeth, It's difficult to tell from just the image you sent. It's possible this is an issue with your computational domain not being 0 to 1. Can you do a projection of star_density of the entire box? That might help us figure out what is going on. Britton On Fri, Jun 10, 2011 at 5:02 PM, Elizabeth Tasker <taskere@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@astro.columbia.edu <mailto:chummels@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
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org>
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto: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
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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@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@astro.columbia.edu <mailto:chummels@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
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto: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
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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@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@astro.columbia.edu <mailto:chummels@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
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto: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
_______________________________________________ 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
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@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@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@astro.columbia.edu <mailto:chummels@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
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto: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
_______________________________________________ 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
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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@mcmaster.ca <mailto:taskere@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@mcmaster.ca <mailto:taskere@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@astro.columbia.edu <mailto:chummels@astro.columbia.edu> <mailto:chummels@astro.columbia.edu <mailto:chummels@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
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org>>
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org>>
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
------------------------------------------------------------------------
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto: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
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-38... 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-90... 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@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@mcmaster.ca <mailto:taskere@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@mcmaster.ca <mailto:taskere@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@astro.columbia.edu <mailto:chummels@astro.columbia.edu> <mailto:chummels@astro.columbia.edu <mailto:chummels@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
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org>>
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org>>
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
------------------------------------------------------------------------
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org>
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto: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
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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-38...
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-90...
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@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@mcmaster.ca <mailto:taskere@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@mcmaster.ca <mailto:taskere@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@astro.columbia.edu <mailto:chummels@astro.columbia.edu> <mailto:chummels@astro.columbia.edu <mailto:chummels@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
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org>>
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org>>
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
------------------------------------------------------------------------
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org>
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto: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
_______________________________________________ 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
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@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-38...
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-90...
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@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@mcmaster.ca <mailto:taskere@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@mcmaster.ca <mailto:taskere@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@astro.columbia.edu <mailto:chummels@astro.columbia.edu> <mailto:chummels@astro.columbia.edu <mailto:chummels@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
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org>>
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org>>
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
------------------------------------------------------------------------
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org>
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org>
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto: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
_______________________________________________ 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
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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@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@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-38...
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-90...
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@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@mcmaster.ca <mailto:taskere@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@mcmaster.ca <mailto:taskere@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@astro.columbia.edu <mailto:chummels@astro.columbia.edu> <mailto:chummels@astro.columbia.edu <mailto:chummels@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
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org>>
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org>>
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
------------------------------------------------------------------------
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org>
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org>
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto: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
_______________________________________________ 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
_______________________________________________ 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
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@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
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
path to your dataset on the command line. This should check to see if
On Mon, Jun 13, 2011 at 11:04 AM, Britton Smith <brittonsmith@gmail.com> wrote: the there
are any inconsistencies in the grid dx's and positions.
Britton
On Mon, Jun 13, 2011 at 1:38 PM, Elizabeth Tasker <taskere@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-38...
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-90...
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@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@mcmaster.ca
<mailto:taskere@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@mcmaster.ca <mailto:taskere@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@astro.columbia.edu <mailto:chummels@astro.columbia.edu> <mailto:chummels@astro.columbia.edu <mailto:chummels@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
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org>>
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org>>
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org>
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org>
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto: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
_______________________________________________ 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
_______________________________________________ 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
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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@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@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@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@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-38...
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-90...
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@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@mcmaster.ca > <mailto:taskere@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@mcmaster.ca <mailto:taskere@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@astro.columbia.edu > <mailto:chummels@astro.columbia.edu> > <mailto:chummels@astro.columbia.edu > <mailto:chummels@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 > > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org> > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org> > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org <mailto: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 > >
_______________________________________________ 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
_______________________________________________ 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
_______________________________________________ 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
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@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
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
field even if it already exists. Just trust me, yt!"
--Brian
On Mon, Jun 13, 2011 at 6:25 PM, Matthew Turk <matthewturk@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@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@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-38...
Alternately to plotting the dm_density would just be
On Mon, Jun 13, 2011 at 4:06 PM, Brian O'Shea <bwoshea@gmail.com> wrote: this particle_density:
http://hg.enzotools.org/yt/src/tip/yt/data_objects/universal_fields.py#cl-90...
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@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@mcmaster.ca >> <mailto:taskere@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@mcmaster.ca <mailto:taskere@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@astro.columbia.edu >> <mailto:chummels@astro.columbia.edu> >> <mailto:chummels@astro.columbia.edu >> <mailto:chummels@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 >> >> >>
>> yt-users mailing list >> yt-users@lists.spacepope.org >> <mailto:yt-users@lists.spacepope.org> >> <mailto:yt-users@lists.spacepope.org >> <mailto:yt-users@lists.spacepope.org>> >> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> >> _______________________________________________ >> yt-users mailing list >> yt-users@lists.spacepope.org >> <mailto:yt-users@lists.spacepope.org> >> <mailto:yt-users@lists.spacepope.org >> <mailto:yt-users@lists.spacepope.org>> >> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> >> >> >> >>
>> >> _______________________________________________ >> yt-users mailing list >> yt-users@lists.spacepope.org >> <mailto:yt-users@lists.spacepope.org> >> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> >> _______________________________________________ >> yt-users mailing list >> yt-users@lists.spacepope.org >> <mailto:yt-users@lists.spacepope.org> >> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> >> _______________________________________________ >> yt-users mailing list >> yt-users@lists.spacepope.org >> <mailto:yt-users@lists.spacepope.org> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> >> >> _______________________________________________ >> yt-users mailing list >> yt-users@lists.spacepope.org <mailto: 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 >> >> > > _______________________________________________ > 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
_______________________________________________ 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
_______________________________________________ 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
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
participants (5)
-
Brian O'Shea -
Britton Smith -
Cameron Hummels -
Elizabeth Tasker -
Matthew Turk