Hi Christine and Matt, Unfortunately, I don't have a Dark_Matter_Density field, just the position, velocities, type, mass and index. (From looking directly at the contents of XXXX.cpu0000). I'm afraid I also need my hand held more to use Matt's suggestion! Would it be possible to give me an example of how to call those functions? I tried to guess and failed miserably. Thank you~ Elizabeth Matthew Turk wrote:

Hi Elizabeth,

It should be. You can either do the CIC deposited DM density using the field "particle_density_pyx" ( http://yt.enzotools.org/doc/api/field_list.html#particle-density-pyx ) if you're on the 'stable' branch of the field "particle_density" if you're on the current development trunk. That will convert the DM to be like a baryon quantity.

If you'd rather do raw particle binning, there is also functionality for that by using the x field "ParticleRadius" ( http://yt.enzotools.org/doc/api/field_list.html#particleradius ) or one of its derivatives, and the y field "ParticleMassMsun".

-Matt

On Mon, Oct 25, 2010 at 5:27 PM, Elizabeth Tasker wrote:

...

Hi,

I'd like to plot dark matter particle density as a function of radius for my particle-only simulation. Can I use add_profile_sphere, but for particles rather than gas? I only have a single halo and I know the halo it's centred in the middle of my box (or it better be, since I put it there!).

Is this possible?

Thanks,

Elizabeth _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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To expand a little on what Matt said ealier, if you don't have the Dark_Matter_Density field, you should still be able to use the field particle_density_pyx. This uses a yt implementation of the cic_deposit routine to take the particle data and make a grid field out of it. Depending on the version of yt you're using, the field will either be called particle_density_pyx or just particle_density. Britton On Tue, Oct 26, 2010 at 12:07 PM, Matthew Turk wrote:

Hi Elizabeth,

Here's a script that does it; you can get this with "yt_lodgeit.py --download=1294".

http://paste.enzotools.org/show/1294/

Also, on re-reading your initial question, my initial suggestion of adding a profile using "ParticleRadius" and "ParticleMassMsun" *will* function, but it's not what you wanted.

Best,

Matt

...

Hi Christine and Matt,

Unfortunately, I don't have a Dark_Matter_Density field, just the

...

velocities, type, mass and index. (From looking directly at the contents of XXXX.cpu0000).

I'm afraid I also need my hand held more to use Matt's suggestion! Would it be possible to give me an example of how to call those functions? I tried to guess and failed miserably.

Thank you~

Elizabeth

Matthew Turk wrote:

...

Hi Elizabeth,

It should be. You can either do the CIC deposited DM density using the field "particle_density_pyx" ( http://yt.enzotools.org/doc/api/field_list.html#particle-density-pyx ) if you're on the 'stable' branch of the field "particle_density" if you're on the current development trunk. That will convert the DM to be like a baryon quantity.

If you'd rather do raw particle binning, there is also functionality for that by using the x field "ParticleRadius" ( http://yt.enzotools.org/doc/api/field_list.html#particleradius ) or one of its derivatives, and the y field "ParticleMassMsun".

-Matt

On Mon, Oct 25, 2010 at 5:27 PM, Elizabeth Tasker wrote:

...

Hi,

I'd like to plot dark matter particle density as a function of radius

for

...

...

my particle-only simulation. Can I use add_profile_sphere, but for

On Tue, Oct 26, 2010 at 8:08 AM, Elizabeth Tasker wrote: position, particles

...

...

...

rather than gas? I only have a single halo and I know the halo it's centred in the middle of my box (or it better be, since I put it there!).

Is this possible?

Thanks,

Elizabeth _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Hi Elizabeth, That's a bug; it actually was trying to call the Enzo CIC routines. I've fixed it in the stable branch now. -Matt On Tue, Oct 26, 2010 at 3:09 PM, Elizabeth Tasker wrote:

Sorry, this still isn't working for me.

I don't have the field dark_matter_density and it hates cloud in cell too!

NameError: global name 'cic_deposit' is not defined

Elizabeth

Matthew Turk wrote:

...

Hi Elizabeth,

Here's a script that does it; you can get this with "yt_lodgeit.py --download=1294".

http://paste.enzotools.org/show/1294/

Also, on re-reading your initial question, my initial suggestion of adding a profile using "ParticleRadius" and "ParticleMassMsun" *will* function, but it's not what you wanted.

Best,

Matt

On Tue, Oct 26, 2010 at 8:08 AM, Elizabeth Tasker wrote:

...

Hi Christine and Matt,

Unfortunately, I don't have a Dark_Matter_Density field, just the position, velocities, type, mass and index. (From looking directly at the contents of XXXX.cpu0000).

I'm afraid I also need my hand held more to use Matt's suggestion! Would it be possible to give me an example of how to call those functions? I tried to guess and failed miserably.

Thank you~

Elizabeth

Matthew Turk wrote:

...

Hi Elizabeth,

It should be.  You can either do the CIC deposited DM density using the field "particle_density_pyx" ( http://yt.enzotools.org/doc/api/field_list.html#particle-density-pyx ) if you're on the 'stable' branch of the field "particle_density" if you're on the current development trunk.  That will convert the DM to be like a baryon quantity.

If you'd rather do raw particle binning, there is also functionality for that by using the x field "ParticleRadius" ( http://yt.enzotools.org/doc/api/field_list.html#particleradius ) or one of its derivatives, and the y field "ParticleMassMsun".

-Matt

On Mon, Oct 25, 2010 at 5:27 PM, Elizabeth Tasker wrote:

...

Hi,

I'd like to plot dark matter particle density as a function of radius for my particle-only simulation. Can I use add_profile_sphere, but for particles rather than gas? I only have a single halo and I know the halo it's centred in the middle of my box (or it better be, since I put it there!).

Is this possible?

Thanks,

Elizabeth _______________________________________________ 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

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Looks like yt doesn't understand your units. It should understand all the units in Enzo 2.0, so if you could off-list send me your parameter file that'd be great. I think what's probably happening is that it's a dark matter only simulation, but since yt relies on the DensityCGS conversion factor Enzo provides to convert code density (which particles are stored in) to CGS density, it doesn't know how to deal since Enzo provides no explicit Density conversion factor. -Matt On Tue, Oct 26, 2010 at 4:13 PM, Elizabeth Tasker wrote:

More, yet different hatred:

I now get:

KeyError                                  Traceback (most recent call last)

/1/home/taskere/yt_hg/yt/src/yt-hg/scripts/iyt in <module>()    22    23 #pc.add_profile_object(data, ["Radius", "Dark_Matter_Density"]) ---> 24 pc.add_profile_object(data, ["Radius", "particle_density"])    25    26 pc.save(fn) # save all plots

/1/home/taskere/yt_hg/yt/src/yt-hg/yt/raven/plot_collection.py in add_profile_object(self, data_source, fields, weight, accumulation, x_bins, x_log, x_bounds, lazy_reader, id, figure, axes)   808                                      lazy_reader)   809         if len(fields) > 1: --> 810             profile.add_fields(fields[1], weight=weight, accumulation=accumulation)   811         if id is None: id = self._get_new_id()   812         p = self._add_plot(PlotTypes.Profile1DPlot(profile, fields, id,

/1/home/taskere/yt_hg/yt/src/yt-hg/yt/lagos/Profiles.py in add_fields(self, fields, weight, accumulation, fractional)   136         fields = ensure_list(fields)   137         if self._lazy_reader: --> 138             self._lazy_add_fields(fields, weight, accumulation)   139         else:   140             self._unlazy_add_fields(fields, weight, accumulation)

/1/home/taskere/yt_hg/yt/src/yt-hg/yt/lagos/Profiles.py in _lazy_add_fields(self, fields, weight, accumulation)    95                 # We get back field values, weight values, used bins    96                 f, w, u = self._bin_field(grid, field, weight, accumulation, ---> 97                                           args=args, check_cut=True)    98                 self.__data[field] += f        # running total    99                 self.__weight_data[field] += w # running total

/1/home/taskere/yt_hg/yt/src/yt-hg/yt/lagos/Profiles.py in save_state(*args, **kwargs)    45             old_params = source.field_parameters    46             source.field_parameters = prof._data_source.field_parameters ---> 47             tr = func(*args, **kwargs)    48             source.field_parameters = old_params    49         else:

/1/home/taskere/yt_hg/yt/src/yt-hg/yt/lagos/Profiles.py in _bin_field(self, source, field, weight, accumulation, args, check_cut)   232         # check_cut is set if source != self._data_source   233         # (i.e., lazy_reader) --> 234         source_data = self._get_field(source, field, check_cut)[mi]   235         if weight: weight_data = self._get_field(source, weight, check_cut)[mi]   236         binned_field = self._get_empty_field()

/1/home/taskere/yt_hg/yt/src/yt-hg/yt/lagos/Profiles.py in _get_field(self, source, this_field, check_cut)   172                 else:   173                     pointI = self._data_source._get_point_indices(source) --> 174 data.append(source[field][pointI].ravel().astype('float64'))   175         return na.concatenate(data, axis=0)   176

/1/home/taskere/yt_hg/yt/src/yt-hg/yt/lagos/BaseGridType.py in __getitem__(self, key)   136         """   137         if not self.data.has_key(key): --> 138             self.get_data(key)   139         return self.data[key]   140

/1/home/taskere/yt_hg/yt/src/yt-hg/yt/lagos/BaseGridType.py in get_data(self, field)   179                     else: raise   180             else: --> 181                 self._generate_field(field)   182         return self.data[field]   183

/1/home/taskere/yt_hg/yt/src/yt-hg/yt/lagos/BaseGridType.py in _generate_field(self, field)   124                 self[field] = temp_array[sl]   125             else: --> 126                 self[field] = self.pf.field_info[field](self)   127         else: # Can't find the field, try as it might   128             raise exceptions.KeyError, field

/1/home/taskere/yt_hg/yt/src/yt-hg/yt/lagos/field_info_container.py in __call__(self, data)   317         original_fields = data.keys() # Copy   318         dd = self._function(self, data) --> 319         dd *= self._convert_function(data)   320         for field_name in data.keys():   321             if field_name not in original_fields:

/1/home/taskere/yt_hg/yt/src/yt-hg/yt/lagos/UniversalFields.py in _convertDensity(data)   780   781 def _convertDensity(data): --> 782     return data.convert("Density")   783 def _pdensity_pyx(field, data):   784     blank = na.zeros(data.ActiveDimensions, dtype='float32')

/1/home/taskere/yt_hg/yt/src/yt-hg/yt/lagos/BaseGridType.py in convert(self, datatype)   101         It either returns the multiplicative factor or throws a KeyError.   102         """ --> 103         return self.pf[datatype]   104   105     def __repr__(self):

/1/home/taskere/yt_hg/yt/src/yt-hg/yt/lagos/OutputTypes.py in __getitem__(self, key)   108                   self.conversion_factors]:   109             if key in d: return d[key] --> 110         raise KeyError(key)   111   112     def keys(self):

KeyError: 'Density' WARNING: Failure executing file: WARNING: Readline services not available on this platform. WARNING: The auto-indent feature requires the readline librar

:\

Elizabeth

Matthew Turk wrote:

...

Hi Elizabeth,

That's a bug; it actually was trying to call the Enzo CIC routines. I've fixed it in the stable branch now.

-Matt

On Tue, Oct 26, 2010 at 3:09 PM, Elizabeth Tasker wrote:

...

Sorry, this still isn't working for me.

I don't have the field dark_matter_density and it hates cloud in cell too!

NameError: global name 'cic_deposit' is not defined

Elizabeth

Matthew Turk wrote:

...

Hi Elizabeth,

Here's a script that does it; you can get this with "yt_lodgeit.py --download=1294".

http://paste.enzotools.org/show/1294/

Also, on re-reading your initial question, my initial suggestion of adding a profile using "ParticleRadius" and "ParticleMassMsun" *will* function, but it's not what you wanted.

Best,

Matt

On Tue, Oct 26, 2010 at 8:08 AM, Elizabeth Tasker wrote:

...

Hi Christine and Matt,

Unfortunately, I don't have a Dark_Matter_Density field, just the position, velocities, type, mass and index. (From looking directly at the contents of XXXX.cpu0000).

I'm afraid I also need my hand held more to use Matt's suggestion! Would it be possible to give me an example of how to call those functions? I tried to guess and failed miserably.

Thank you~

Elizabeth

Matthew Turk wrote:

...

Hi Elizabeth,

It should be.  You can either do the CIC deposited DM density using the field "particle_density_pyx" ( http://yt.enzotools.org/doc/api/field_list.html#particle-density-pyx ) if you're on the 'stable' branch of the field "particle_density" if you're on the current development trunk.  That will convert the DM to be like a baryon quantity.

If you'd rather do raw particle binning, there is also functionality for that by using the x field "ParticleRadius" ( http://yt.enzotools.org/doc/api/field_list.html#particleradius ) or one of its derivatives, and the y field "ParticleMassMsun".

-Matt

On Mon, Oct 25, 2010 at 5:27 PM, Elizabeth Tasker wrote:

> > Hi, > > I'd like to plot dark matter particle density as a function of radius > for > my > particle-only simulation. Can I use add_profile_sphere, but for > particles > rather than gas? I only have a single halo and I know the halo it's > centred > in the middle of my box (or it better be, since I put it there!). > > Is this possible? > > Thanks, > > Elizabeth > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > >

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Yeah ... my face is a bit red. This solution will almost certainly work, and if it does it will be much faster. In Enzo, the Dark_Matter_Density field (if it's in your output) is a pre-computed deposited field -- the same thing as particle_density[_pyx], except without having to compute it on the fly in yt. Thanks, Christine! :) -Matt On Mon, Oct 25, 2010 at 5:39 PM, Christine Simpson wrote:

I believe you can use the field "Dark_Matter_Density" with add_profile_sphere, i.e.:

pc.add_profile_sphere(25.0, "kpc",["RadiusMpc", "Dark_Matter_Density"], x_bounds = (4e-4, 0.025))

Christine

On Mon, 2010-10-25 at 20:27 -0400, Elizabeth Tasker wrote:

...

Hi,

I'd like to plot dark matter particle density as a function of radius for my particle-only simulation. Can I use add_profile_sphere, but for particles rather than gas? I only have a single halo and I know the halo it's centred in the middle of my box (or it better be, since I put it there!).

Is this possible?

Thanks,

Elizabeth _______________________________________________ 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