[yt-users] Over plot particles

REMUDIN RESHID MEKURIA remudin at yahoo.com
Thu May 24 14:43:55 PDT 2012


Dear Matt,

Yes, I think looking into it from that perspective sounds as a good alternative.
Thank you very much, that is really helpful. I will investigate more and let you know.

Cheers,

Remudin


On 2012 Cam 24, at 23:28, Matthew Turk wrote:

> Hi Remudin,
> 
> My understanding of the way Nyx works is that to get the original
> positions of the particles out, you have to have that parameter set.
> (If this has changed, I am unaware of it.)  *However*, you do still
> have the particle fluid information, post-deposition into grid cells
> -- this means that while you may not be able to do the particle
> overplotting, you can for instance plot slices and projections of the
> deposited particle values.  In the field list below, you can see the
> fields that might be of interest: particle_count and
> particle_mass_density.  Slicing or projecting those quantities should
> give you an idea what the particles look like.  I do recall that
> earlier versions of Nyx output only ASCII positions for particles, but
> I seem to recall that we made the decision only to support the binary
> output of particles.  (Casey, does that sound familiar to you?)
> 
> If there's been a change in how the outputting of particles is
> governed, we'd be more than happy to update the Nyx frontend code in
> yt!
> 
> -Matt
> 
> On Fri, May 25, 2012 at 6:04 AM, REMUDIN RESHID MEKURIA
> <remudin at yahoo.com> wrote:
>> 
>> Dear Matt, Casey,
>> 
>> In the list of field, I do not have any of the particle positions, I am not
>> sure if I need to.  But these is the result of your quick test:
>> 
>> print pf.h.field_list   ['density', 'xmom', 'ymom', 'zmom', 'rho_E',
>> 'rho_e', 'rho_K', 'Temp', 'rho_H', 'rho_He', 'phi_grav', 'grav_x', 'grav_y',
>> 'grav_z', 'prod_sgs', 'diss_sgs', 'turb_src', 'pressure', 'MachNumber',
>> 'magvort', 'particle_count', 'particle_mass_density']
>> 
>> print pf.use_particles           False
>> 
>> 
>> Ok, I haven't seen some thing like "particles.write_in_plotfile" in inputs.
>> I have attached the inputs
>> 
>> I used  here within.
>> 
>> Thank you again for taking much of your time.
>> 
>> 
>> Cheers,
>> 
>> Remudin
>> 
>> On 2012 Cam 24, at 22:40, Matthew Turk wrote:
>> 
>> Hi Remudin,
>> 
>> Ah, bummer.  Revisiting what Casey said, it sounds like you're trying
>> to plot and it doesn't know that there are particles.  What is the
>> output of these commands:
>> 
>> print pf.h.field_list
>> print pf.use_particles
>> 
>> And, can you check the inputs file to see what the value of
>> "particles.write_in_plotfile" is?  That parameter dictates (for Nyx)
>> whether particles are written out in the plotfiles, and without it yt
>> cannot read them.
>> 
>> -Matt
>> 
>> On Fri, May 25, 2012 at 5:36 AM, REMUDIN RESHID MEKURIA
>> <remudin at yahoo.com> wrote:
>> 
>> Dear Matt,
>> 
>> 
>> I have included the changes in the script and the error doesn't
>> 
>> change. KeyError: 'particle_position_y'.
>> 
>> 
>> Right, it will be of great simplification when those Units are clarified in
>> 
>> the recipes by you guys soon, thanks.
>> 
>> 
>> 
>> Cheers,
>> 
>> 
>> Remudin
>> 
>> 
>> On 2012 Cam 24, at 22:15, Matthew Turk wrote:
>> 
>> 
>> Hi Remudin,
>> 
>> 
>> The units between Enzo and Nyx are different -- and to get the recipe
>> 
>> to reflect that there are a few places that have to be modified.  In
>> 
>> response to the community survey results that came in, just yesterday
>> 
>> (coincidentally enough) Britton Smith and I have been going through
>> 
>> trying to make changes to the recipes to de-enzo-ify them and to make
>> 
>> it more clear what are units and what aren't.
>> 
>> 
>> I'm not sure this will fix the problem, but it might help!
>> 
>> 
>> On Fri, May 25, 2012 at 5:08 AM, REMUDIN RESHID MEKURIA
>> 
>> <remudin at yahoo.com> wrote:
>> 
>> 
>> Thanks Casey,
>> 
>> 
>> 
>> This is the script I used from yt-cookbook Overplot particles
>> 
>> 
>> 
>> #!/usr/users/rmekuri/data/yt-x86_64/bin/python
>> 
>> 
>> 
>> 
>> from yt.mods import * # set up our namespace
>> 
>> 
>> 
>> 
>> 
>> fn = "plt00736" # parameter file to load
>> 
>> 
>> 
>> 
>> 
>> pf = load(fn) # load data
>> 
>> 
>> 
>> 
>> pc = PlotCollection(pf, [0.5, 0.5, 0.5])
>> 
>> 
>> 
>> Try changing [0.5, 0.5, 0.5] to "c" like this:
>> 
>> 
>> pc = PlotCollection(pf, "c")
>> 
>> 
>> this will put you at the domain center.
>> 
>> 
>> p = pc.add_projection("Density", 0)
>> 
>> 
>> p.modify["particles"](1.0) # 1.0 is the 'width' we want for our slab of
>> 
>> 
>> 
>> try changing this 1.0 to the full domain:
>> 
>> 
>> 1.0/pf['unitary']
>> 
>> 
>> 'unitary' is the unit meaning the full width of the domain.
>> 
>> 
>> 
>> 
>>                             # particles -- this governs the allowable
>> 
>> 
>> locations
>> 
>> 
>> 
>>                             # of particles that show up on the image
>> 
>> 
>> 
>> 
>>                             # NOTE: we can also supply a *ptype* to cut
>> 
>> 
>> based
>> 
>> 
>> 
>>                             # on a given (integer) particle type
>> 
>> 
>> 
>> 
>> pc.set_width(1.0, '1') # change width of our plot to the full domain
>> 
>> 
>> 
>> Let's set this also to the full domain:
>> 
>> 
>> pc.set_width(1.0, 'unitary')
>> 
>> 
>> 
>> -Matt
>> 
>> 
>> 
>> 
>> pc.save(fn) # save all plots
>> 
>> 
>> 
>> Cheers,
>> 
>> 
>> 
>> Remudin
>> 
>> 
>> 
>> 
>> On 2012 Cam 24, at 22:03, Casey W. Stark wrote:
>> 
>> 
>> 
>> Hi Remudin.
>> 
>> 
>> 
>> Could you include the script that is generating the error?
>> 
>> 
>> 
>> I'm not sure without the script, but it looks like you are trying to access
>> 
>> 
>> the "particle_position_y" field and it is not in the plotfile you are
>> 
>> 
>> working with.
>> 
>> 
>> 
>> Best,
>> 
>> 
>> Casey
>> 
>> 
>> 
>> 
>> On Thu, May 24, 2012 at 11:15 AM, REMUDIN RESHID MEKURIA <remudin at yahoo.com>
>> 
>> 
>> wrote:
>> 
>> 
>> 
>> Dear all,
>> 
>> 
>> 
>> Thank you for your help in advance.
>> 
>> 
>> I am currently running cosmological simulations using Nyx code.
>> 
>> 
>> And while trying to over plotting particles on the density slice, I
>> 
>> 
>> encountered the following error which I couldn't resolve. I will greatly
>> 
>> 
>> appreciate your help.
>> 
>> 
>> 
>> Traceback (most recent call last):
>> 
>> 
>>   File "./OverPlotingParticles.py", line 14, in <module>
>> 
>> 
>>     pc.set_width(1.0, '1') # change width of our plot to the full domain
>> 
>> 
>>   File
>> 
>> 
>> "/home/uni06/cosmo/rmekuri/yt-x86_64/src/yt-hg/yt/visualization/plot_collection.py",
>> 
>> 
>> line 267, in set_width
>> 
>> 
>>     plot.set_width(width, unit)
>> 
>> 
>>   File
>> 
>> 
>> "/home/uni06/cosmo/rmekuri/yt-x86_64/src/yt-hg/yt/visualization/plot_types.py",
>> 
>> 
>> line 441, in set_width
>> 
>> 
>>     self._refresh_display_width()
>> 
>> 
>>   File
>> 
>> 
>> "/home/uni06/cosmo/rmekuri/yt-x86_64/src/yt-hg/yt/visualization/plot_types.py",
>> 
>> 
>> line 459, in _refresh_display_width
>> 
>> 
>>     self._redraw_image()
>> 
>> 
>>   File
>> 
>> 
>> "/home/uni06/cosmo/rmekuri/yt-x86_64/src/yt-hg/yt/visualization/plot_types.py",
>> 
>> 
>> line 406, in _redraw_image
>> 
>> 
>>     self._run_callbacks()
>> 
>> 
>>   File
>> 
>> 
>> "/home/uni06/cosmo/rmekuri/yt-x86_64/src/yt-hg/yt/visualization/plot_types.py",
>> 
>> 
>> line 259, in _run_callbacks
>> 
>> 
>>     cb(self)
>> 
>> 
>>   File
>> 
>> 
>> "/home/uni06/cosmo/rmekuri/yt-x86_64/src/yt-hg/yt/visualization/plot_modifications.py",
>> 
>> 
>> line 985, in __call__
>> 
>> 
>>     &   ( reg[field_y] >= y0 ) & ( reg[field_y] <= y1 ) )
>> 
>> 
>>   File
>> 
>> 
>> "/home/uni06/cosmo/rmekuri/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>> 
>> 
>> line 319, in __getitem__
>> 
>> 
>>     self.get_data(key)
>> 
>> 
>>   File
>> 
>> 
>> "/home/uni06/cosmo/rmekuri/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>> 
>> 
>> line 2410, in get_data
>> 
>> 
>>     if self._generate_field(field):
>> 
>> 
>>   File
>> 
>> 
>> "/home/uni06/cosmo/rmekuri/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>> 
>> 
>> line 352, in _generate_field
>> 
>> 
>>     raise KeyError(field)
>> 
>> 
>> KeyError: 'particle_position_y'
>> 
>> 
>> 
>> With best regards,
>> 
>> 
>> 
>> 
>> Cheers,
>> 
>> 
>> 
>> Remudin
>> 
>> 
>> 
>> ------
>> 
>> 
>> 
>> Remudin Reshid Mekuria                              phone: +49 (0)551
>> 
>> 
>> 39-13805
>> 
>> 
>> 
>> IAG, Friedrich-Hund-Plaz 1                           fax: +49 (0)551
>> 
>> 
>> 39-5043
>> 
>> 
>> 
>> D-37077 Goettingen
>> 
>> 
>> 
>> Germany
>> 
>> 
>> 
>> 
>> 
>> 
>> 
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>> 
>> Remudin Reshid Mekuria                              phone: +49 (0)551
>> 
>> 
>> 39-13805
>> 
>> 
>> 
>> IAG, Friedrich-Hund-Plaz 1                           fax: +49 (0)551 39-5043
>> 
>> 
>> 
>> D-37077 Goettingen
>> 
>> 
>> 
>> Germany
>> 
>> 
>> 
>> 
>> 
>> 
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>> ------
>> 
>> 
>> Remudin Reshid Mekuria                              phone: +49 (0)551
>> 
>> 39-13805
>> 
>> 
>> IAG, Friedrich-Hund-Plaz 1                           fax: +49 (0)551 39-5043
>> 
>> 
>> D-37077 Goettingen
>> 
>> 
>> Germany
>> 
>> 
>> 
>> 
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>> ------
>> 
>> Remudin Reshid Mekuria                              phone: +49 (0)551
>> 39-13805
>> 
>> IAG, Friedrich-Hund-Plaz 1                           fax: +49 (0)551 39-5043
>> 
>> D-37077 Goettingen
>> 
>> Germany
>> 
>> 
>> 
>> 
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------
Remudin Reshid Mekuria                              phone: +49 (0)551 39-13805
IAG, Friedrich-Hund-Plaz 1                           fax: +49 (0)551 39-5043
D-37077 Goettingen
Germany



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