Hi, I am a little confused as to how to use hop_circles. I tried this but it fails... from yt.mods import * fn = "RedshiftOutput0002" pf = load(fn) halos = HaloFinder(pf) halos.modify["hop_circles"](self, hop_output, max_number=None, annotate=False, min_size=20, max_size=10000000, font_size=8, print_halo_size=False, print_halo_mass=False, width=None) halos.write_out("HopAnalysis.out") Also, I tried HaloProfiler using http://yt.enzotools.org/doc/cookbook/recipes.html#cookbook-run-halo-profiler. It generated the radial_profiles/ directory with Halo_xxxx_profile.dat files. I am printing here the first few lines from Halo_0000_profile.dat... # ActualOverdensity CellVolume Density RadiusMpc Temperature TotalMassMsun myweight 2.796608e+03 9.422900e+72 1.407563e-27 1.086579e+00 4.551426e+07 3.320010e+13 3.334302e+12 1.587191e+03 1.884580e+73 3.247510e-28 1.121908e+00 3.392715e+07 3.768487e+13 7.692859e+11 1.213350e+03 3.298015e+73 8.512354e-28 1.158386e+00 3.176131e+07 5.041525e+13 2.016447e+12 9.092253e+02 5.182595e+73 7.672296e-28 1.196051e+00 3.692482e+07 5.936658e+13 1.817450e+12 Is Halo_0000_profile.dat related to the first Halo listed in HopAnalysis.out file ? What is # ? What is the meaning of ActualOverdensity ? And units ? What is the meaning of CellVolume? And units ? What is Density referring to ? And units ? What is mywieght ? I also got the projection/ directory. But I got errors... yt.lagos INFO 2009-11-24 16:57:52,561 Writing filtered halo list to /usr/rmt_share/scratch95/a/agarwa23/0eV/512/box200/sim1/RD0002/FilteredQuantities.out. yt INFO 2009-11-24 16:57:53,873 Created plot collection with default plot-center = [0.5, 0.5, 0.5] yt.lagos INFO 2009-11-24 16:57:53,873 Projecting halo 0000 in region: [0.154949, 0.130009, 0.810277] to [0.183709, 0.158769, 0.839037]. yt INFO 2009-11-24 16:57:53,875 Generating overlap masks for level 0 Reading and masking grids 100% ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:00 yt INFO 2009-11-24 16:57:53,875 Finished calculating overlap. Projecting level 0 / 0 100% ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:01 Combining level 0 / 0 100% ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:00 yt INFO 2009-11-24 16:57:55,640 Level 0 done: 256 final yt INFO 2009-11-24 16:57:55,896 Generating overlap masks for level 0 Reading and masking grids 100% ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:00 yt INFO 2009-11-24 16:57:55,896 Finished calculating overlap. Projecting level 0 / 0 100% ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:01 Combining level 0 / 0 100% ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:00 yt INFO 2009-11-24 16:57:57,381 Level 0 done: 256 final yt INFO 2009-11-24 16:57:57,527 Generating overlap masks for level 0 Reading and masking grids 100% ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:00 yt INFO 2009-11-24 16:57:57,527 Finished calculating overlap. Traceback (most recent call last): | ETA: --:--:-- File "run_halo_profiler.py", line 37, in <module> halo_list='filtered',axes=[0,1,2]) File "/autohome/u118/agarwa23/enzo1/src/yt/yt/extensions/HaloProfiler.py", line 474, in make_projections serialize=False, **kwargs) File "/autohome/u118/agarwa23/enzo1/src/yt/yt/raven/PlotCollection.py", line 262, in add_projection return self._add_projection(PlotTypes.ProjectionPlot, *args, **kwargs) File "/autohome/u118/agarwa23/enzo1/src/yt/yt/raven/PlotCollection.py", line 285, in _add_projection center=center, **kwargs) File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/BaseDataTypes.py", line 951, in __init__ self._refresh_data() File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/BaseDataTypes.py", line 190, in _refresh_data self.get_data() File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/BaseDataTypes.py", line 1137, in get_data my_coords, my_dx, my_fields = self.__project_level(level, fields) File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/BaseDataTypes.py", line 1029, in __project_level g_coords, g_fields = self._project_grid(grid, fields, zero_out) File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/BaseDataTypes.py", line 1182, in _project_grid for field in fields] File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/BaseDataTypes.py", line 40, in save_state tr = func(self, grid, field) File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/BaseDataTypes.py", line 1222, in _get_data_from_grid return grid[field] * bad_points File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/BaseDataTypes.py", line 199, in __getitem__ self.get_data(key) File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/BaseGridType.py", line 96, in get_data self._generate_field(field) File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/BaseGridType.py", line 54, in _generate_field self.pf.field_info[field].check_available(self) File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/FieldInfoContainer.py", line 244, in check_available validator(data) File "/autohome/u118/agarwa23/enzo1/src/yt/yt/lagos/FieldInfoContainer.py", line 337, in __call__ raise NeedsDataField(doesnt_have) yt.lagos.FieldInfoContainer.NeedsDataField: (['Metal_Density']) shankar
Hi Shankar, I will answer the HaloProfiler related questions and leave the Hop questions for Stephen. However, could you post the failure output for what you tried to do with Hop. That will probably be helpful for answering your question. Is Halo_0000_profile.dat related to the first Halo listed in HopAnalysis.out
file ?
Yes, the HaloProfiler will always use the same indices for halos as all of the halo finders in yt. So, the file Halo_N_profile.dat will always refer to halo N on the halo list. What is # ?
This is just a comment character so that plotting programs don't try to read in what's on that line. The tab between it and the first field name is there to accommodate the routines that read those files back in to the HaloProfiler.
What is the meaning of ActualOverdensity ? And units ?
ActualOverdensity has the same physical meaning as the regular Overdensity field. It is (Baryon Density + Dark Matter Density) / (Mean density of the universe). If you search the literature, you will find alternate definitions that use critical density instead of mean density. The one used here is a little more common (I think, but I'm not sure). As per these definitions, overdensity is a unitless quantity. In yt, there is an Overdensity field that is calculated on a cell-by-cell basis. For calculation of virial quantities for halos, the overdensity you calculate should be explicitly the total mass (baryon + dm) / total volume / mean density, where total refers to all cells enclosed within the sphere of the radial profile, not just the shell from r_(i-1) to r_i. Technically, you could get this by doing a profile of the Overdensity field, weighted by CellVolume, with accumulation set to True. However, if for some reason, the user wanted to do profiles of the overdensity field in a different way, say weighted by CellMass, or just counting the material shell-by-shell (accumulation=False), this number would not be correct for the calculation of virial quantities. For that reason, the HaloProfiler automatically generates this ActualOverdensity field which is assured to be calculated in the correct way. That way the user doesn't accidentally override a proper calculation of the overdensity used for the virial quantities. Other than the ActualOverdensity field (which is automatically generated by the HaloProfiler, and thus does not exist outside that context) you can always get the units of any field with: lagos.fieldInfo[some_field].units For more information, see here: http://yt.enzotools.org/doc/faq.html#how-do-i-know-what-the-units-returned-a... What is the meaning of CellVolume? And units ? What is Density referring to ? And units ?
CellVolume and Density are the volume of a cell and the baryon density. In this context, they are the values of those fields in the radial profile. If you did it as per the recipe, the CellVolume is the total accumulated volume for all cells within the sphere radius. Density SHOULD be the mass-weighted, mean baryon density for cells within spherical shells. However, after looking at the recipe on the website, I see that, in error, I set the weight_field of the Density profile to None, instead of CellMassMsun. Therefore, the Density profile may be meaningless as is. I will change the recipe on the website ASAP.
What is mywieght ?
The myweight field is a temporary field for keeping track of the weight field for a weight radial profile. It should be ignored and we might just want to not write it out in the future.
I also got the projection/ directory. But I got errors...
It looks like the HaloProfiler tried to do a projection of Metallicity, but your simulation data did not have the MetalDensity field. You need to set CosmologyUseMetallicityField (or something like that) to 1 in your enzo parameter file in order to get this field. You can also just remove the line in the HaloProfiler recipe that adds the metallicity field to the list of projections. Cheers, Britton
CellMassMsun. Therefore, the Density profile may be meaningless as is. I will change the recipe on the website ASAP.
Britton committed his fixes to the cookbook repository and the documentation repository, I rebuilt the docs, and I have uploaded a new build of the documentation to both the yt-1.5 repository and the website. -Matt
Hi Britton, I just wanted a clarification on the definition of ActualOverdensity. In your mail, you said... "ActualOverdensity has the same physical meaning as the regular Overdensity field. It is (Baryon Density + Dark Matter Density) / (Mean density of the universe). If you search the literature, you will find alternate definitions that use critical density instead of mean density. The one used here is a little more common." Are you sure you did not mean (Baryon Density + Dark Matter Density) / (critical density) ? Because, in halo_profiler.py, there is a virial filter... hp.add_halo_filter(HP.VirialFilter,must_be_virialized=True, overdensity_field='ActualOverdensity', virial_overdensity=200, virial_filters=[['TotalMassMsun','>=','1e14']], virial_quantities=['TotalMassMsun','RadiusMpc']) Isn't 200 w.r.t rho_ciritcal (not rho_mean_matter)? Look http://arxiv.org/abs/astro-ph/0011495 shankar -----Original Message----- From: yt-users-bounces@lists.spacepope.org on behalf of Britton Smith Sent: Wed 11/25/2009 1:30 PM To: Discussion of the yt analysis package Subject: Re: [yt-users] Hop vs HaloProfiler Hi Shankar, I will answer the HaloProfiler related questions and leave the Hop questions for Stephen. However, could you post the failure output for what you tried to do with Hop. That will probably be helpful for answering your question. Is Halo_0000_profile.dat related to the first Halo listed in HopAnalysis.out
file ?
Yes, the HaloProfiler will always use the same indices for halos as all of the halo finders in yt. So, the file Halo_N_profile.dat will always refer to halo N on the halo list. What is # ?
This is just a comment character so that plotting programs don't try to read in what's on that line. The tab between it and the first field name is there to accommodate the routines that read those files back in to the HaloProfiler.
What is the meaning of ActualOverdensity ? And units ?
ActualOverdensity has the same physical meaning as the regular Overdensity field. It is (Baryon Density + Dark Matter Density) / (Mean density of the universe). If you search the literature, you will find alternate definitions that use critical density instead of mean density. The one used here is a little more common (I think, but I'm not sure). As per these definitions, overdensity is a unitless quantity. In yt, there is an Overdensity field that is calculated on a cell-by-cell basis. For calculation of virial quantities for halos, the overdensity you calculate should be explicitly the total mass (baryon + dm) / total volume / mean density, where total refers to all cells enclosed within the sphere of the radial profile, not just the shell from r_(i-1) to r_i. Technically, you could get this by doing a profile of the Overdensity field, weighted by CellVolume, with accumulation set to True. However, if for some reason, the user wanted to do profiles of the overdensity field in a different way, say weighted by CellMass, or just counting the material shell-by-shell (accumulation=False), this number would not be correct for the calculation of virial quantities. For that reason, the HaloProfiler automatically generates this ActualOverdensity field which is assured to be calculated in the correct way. That way the user doesn't accidentally override a proper calculation of the overdensity used for the virial quantities. Other than the ActualOverdensity field (which is automatically generated by the HaloProfiler, and thus does not exist outside that context) you can always get the units of any field with: lagos.fieldInfo[some_field].units For more information, see here: http://yt.enzotools.org/doc/faq.html#how-do-i-know-what-the-units-returned-a... What is the meaning of CellVolume? And units ? What is Density referring to ? And units ?
CellVolume and Density are the volume of a cell and the baryon density. In this context, they are the values of those fields in the radial profile. If you did it as per the recipe, the CellVolume is the total accumulated volume for all cells within the sphere radius. Density SHOULD be the mass-weighted, mean baryon density for cells within spherical shells. However, after looking at the recipe on the website, I see that, in error, I set the weight_field of the Density profile to None, instead of CellMassMsun. Therefore, the Density profile may be meaningless as is. I will change the recipe on the website ASAP.
What is mywieght ?
The myweight field is a temporary field for keeping track of the weight field for a weight radial profile. It should be ignored and we might just want to not write it out in the future.
I also got the projection/ directory. But I got errors...
It looks like the HaloProfiler tried to do a projection of Metallicity, but your simulation data did not have the MetalDensity field. You need to set CosmologyUseMetallicityField (or something like that) to 1 in your enzo parameter file in order to get this field. You can also just remove the line in the HaloProfiler recipe that adds the metallicity field to the list of projections. Cheers, Britton
Shankar, As I stated in my previous email, you will find both definitions used in the literature. I'm not going to spend time in a citation battle. The good news is that both definitions differ only by a factor of Omega_matter, so you can change the value of virial_overdensity accordingly. Britton On Wed, Dec 2, 2009 at 11:27 AM, Agarwal, Shankar <sagarwal@ku.edu> wrote:
Hi Britton,
I just wanted a clarification on the definition of ActualOverdensity. In your mail, you said...
"ActualOverdensity has the same physical meaning as the regular Overdensity field. It is (Baryon Density + Dark Matter Density) / (Mean density of the universe). If you search the literature, you will find alternate definitions that use critical density instead of mean density. The one used here is a little more common."
Are you sure you did not mean (Baryon Density + Dark Matter Density) / (critical density) ?
Because, in halo_profiler.py, there is a virial filter...
hp.add_halo_filter(HP.VirialFilter,must_be_virialized=True, overdensity_field='ActualOverdensity', virial_overdensity=200, virial_filters=[['TotalMassMsun','>=','1e14']], virial_quantities=['TotalMassMsun','RadiusMpc'])
Isn't 200 w.r.t rho_ciritcal (not rho_mean_matter)? Look http://arxiv.org/abs/astro-ph/0011495
shankar
-----Original Message----- From: yt-users-bounces@lists.spacepope.org on behalf of Britton Smith Sent: Wed 11/25/2009 1:30 PM To: Discussion of the yt analysis package Subject: Re: [yt-users] Hop vs HaloProfiler
Hi Shankar,
I will answer the HaloProfiler related questions and leave the Hop questions for Stephen. However, could you post the failure output for what you tried to do with Hop. That will probably be helpful for answering your question.
Is Halo_0000_profile.dat related to the first Halo listed in HopAnalysis.out
file ?
Yes, the HaloProfiler will always use the same indices for halos as all of the halo finders in yt. So, the file Halo_N_profile.dat will always refer to halo N on the halo list.
What is # ?
This is just a comment character so that plotting programs don't try to read in what's on that line. The tab between it and the first field name is there to accommodate the routines that read those files back in to the HaloProfiler.
What is the meaning of ActualOverdensity ? And units ?
ActualOverdensity has the same physical meaning as the regular Overdensity field. It is (Baryon Density + Dark Matter Density) / (Mean density of the universe). If you search the literature, you will find alternate definitions that use critical density instead of mean density. The one used here is a little more common (I think, but I'm not sure). As per these definitions, overdensity is a unitless quantity.
In yt, there is an Overdensity field that is calculated on a cell-by-cell basis. For calculation of virial quantities for halos, the overdensity you calculate should be explicitly the total mass (baryon + dm) / total volume / mean density, where total refers to all cells enclosed within the sphere of the radial profile, not just the shell from r_(i-1) to r_i. Technically, you could get this by doing a profile of the Overdensity field, weighted by CellVolume, with accumulation set to True. However, if for some reason, the user wanted to do profiles of the overdensity field in a different way, say weighted by CellMass, or just counting the material shell-by-shell (accumulation=False), this number would not be correct for the calculation of virial quantities. For that reason, the HaloProfiler automatically generates this ActualOverdensity field which is assured to be calculated in the correct way. That way the user doesn't accidentally override a proper calculation of the overdensity used for the virial quantities.
Other than the ActualOverdensity field (which is automatically generated by the HaloProfiler, and thus does not exist outside that context) you can always get the units of any field with: lagos.fieldInfo[some_field].units For more information, see here:
http://yt.enzotools.org/doc/faq.html#how-do-i-know-what-the-units-returned-a...
What is the meaning of CellVolume? And units ?
What is Density referring to ? And units ?
CellVolume and Density are the volume of a cell and the baryon density. In this context, they are the values of those fields in the radial profile. If you did it as per the recipe, the CellVolume is the total accumulated volume for all cells within the sphere radius. Density SHOULD be the mass-weighted, mean baryon density for cells within spherical shells. However, after looking at the recipe on the website, I see that, in error, I set the weight_field of the Density profile to None, instead of CellMassMsun. Therefore, the Density profile may be meaningless as is. I will change the recipe on the website ASAP.
What is mywieght ?
The myweight field is a temporary field for keeping track of the weight field for a weight radial profile. It should be ignored and we might just want to not write it out in the future.
I also got the projection/ directory. But I got errors...
It looks like the HaloProfiler tried to do a projection of Metallicity, but your simulation data did not have the MetalDensity field. You need to set CosmologyUseMetallicityField (or something like that) to 1 in your enzo parameter file in order to get this field. You can also just remove the line in the HaloProfiler recipe that adds the metallicity field to the list of projections.
Cheers,
Britton
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Shankar and Britton, I have gone through this argument extensively, and discovered that both definitions are used, with roughly equal frequency in the literature. Lately, it has been trending toward OD = density/mean density (matter). I think the main reason for the density with respect to critical in the past has been due to an historical preference for omega_m=1 universes (SCDM). cheers, On Dec 2, 2009, at 11:50 AM, Britton Smith wrote:
Shankar,
As I stated in my previous email, you will find both definitions used in the literature. I'm not going to spend time in a citation battle. The good news is that both definitions differ only by a factor of Omega_matter, so you can change the value of virial_overdensity accordingly.
Britton
On Wed, Dec 2, 2009 at 11:27 AM, Agarwal, Shankar <sagarwal@ku.edu> wrote: Hi Britton,
I just wanted a clarification on the definition of ActualOverdensity. In your mail, you said...
"ActualOverdensity has the same physical meaning as the regular Overdensity field. It is (Baryon Density + Dark Matter Density) / (Mean density of the universe). If you search the literature, you will find alternate definitions that use critical density instead of mean density. The one used here is a little more common."
Are you sure you did not mean (Baryon Density + Dark Matter Density) / (critical density) ?
Because, in halo_profiler.py, there is a virial filter...
hp.add_halo_filter(HP.VirialFilter,must_be_virialized=True, overdensity_field='ActualOverdensity', virial_overdensity=200, virial_filters=[['TotalMassMsun','>=','1e14']], virial_quantities=['TotalMassMsun','RadiusMpc'])
Isn't 200 w.r.t rho_ciritcal (not rho_mean_matter)? Look http://arxiv.org/abs/astro-ph/0011495
shankar
-----Original Message----- From: yt-users-bounces@lists.spacepope.org on behalf of Britton Smith Sent: Wed 11/25/2009 1:30 PM To: Discussion of the yt analysis package Subject: Re: [yt-users] Hop vs HaloProfiler
Hi Shankar,
I will answer the HaloProfiler related questions and leave the Hop questions for Stephen. However, could you post the failure output for what you tried to do with Hop. That will probably be helpful for answering your question.
Is Halo_0000_profile.dat related to the first Halo listed in HopAnalysis.out
file ?
Yes, the HaloProfiler will always use the same indices for halos as all of the halo finders in yt. So, the file Halo_N_profile.dat will always refer to halo N on the halo list.
What is # ?
This is just a comment character so that plotting programs don't try to read in what's on that line. The tab between it and the first field name is there to accommodate the routines that read those files back in to the HaloProfiler.
What is the meaning of ActualOverdensity ? And units ?
ActualOverdensity has the same physical meaning as the regular Overdensity field. It is (Baryon Density + Dark Matter Density) / (Mean density of the universe). If you search the literature, you will find alternate definitions that use critical density instead of mean density. The one used here is a little more common (I think, but I'm not sure). As per these definitions, overdensity is a unitless quantity.
In yt, there is an Overdensity field that is calculated on a cell-by- cell basis. For calculation of virial quantities for halos, the overdensity you calculate should be explicitly the total mass (baryon + dm) / total volume / mean density, where total refers to all cells enclosed within the sphere of the radial profile, not just the shell from r_(i-1) to r_i. Technically, you could get this by doing a profile of the Overdensity field, weighted by CellVolume, with accumulation set to True. However, if for some reason, the user wanted to do profiles of the overdensity field in a different way, say weighted by CellMass, or just counting the material shell-by-shell (accumulation=False), this number would not be correct for the calculation of virial quantities. For that reason, the HaloProfiler automatically generates this ActualOverdensity field which is assured to be calculated in the correct way. That way the user doesn't accidentally override a proper calculation of the overdensity used for the virial quantities.
Other than the ActualOverdensity field (which is automatically generated by the HaloProfiler, and thus does not exist outside that context) you can always get the units of any field with: lagos.fieldInfo[some_field].units For more information, see here: http://yt.enzotools.org/doc/faq.html#how-do-i-know-what-the-units-returned-a...
What is the meaning of CellVolume? And units ?
What is Density referring to ? And units ?
CellVolume and Density are the volume of a cell and the baryon density. In this context, they are the values of those fields in the radial profile. If you did it as per the recipe, the CellVolume is the total accumulated volume for all cells within the sphere radius. Density SHOULD be the mass-weighted, mean baryon density for cells within spherical shells. However, after looking at the recipe on the website, I see that, in error, I set the weight_field of the Density profile to None, instead of CellMassMsun. Therefore, the Density profile may be meaningless as is. I will change the recipe on the website ASAP.
What is mywieght ?
The myweight field is a temporary field for keeping track of the weight field for a weight radial profile. It should be ignored and we might just want to not write it out in the future.
I also got the projection/ directory. But I got errors...
It looks like the HaloProfiler tried to do a projection of Metallicity, but your simulation data did not have the MetalDensity field. You need to set CosmologyUseMetallicityField (or something like that) to 1 in your enzo parameter file in order to get this field. You can also just remove the line in the HaloProfiler recipe that adds the metallicity field to the list of projections.
Cheers,
Britton
_______________________________________________ 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
Dr. Eric J. Hallman NSF Astronomy and Astrophysics Postdoctoral Fellow Center for Astrophysics and Space Astronomy University of Colorado at Boulder hallman (at) casa.colorado.edu Phone: (312) 725-4626 http://solo.colorado.edu/~hallman/
Britton and Eric, So I guess if the convention in halo_profiler is (Baryon + Dark Matter Density) / (Mean density) , then I should use virial_overdensity = 200/Omega_matter = 200/0.258 = 775 instead of 200. A separate stupid question : I have run a Box=200Mpc/h with 512^3 dark matter particle simulation. http://drop.io/slice The most dense point in the box is only 1.3e-27 gm/cm^3, which is about 520*matter_mean_density (for omega_matter=0.26). Then I ran halo_profiler.py on it. Here are the first few lines... ActualOverdensity CellVolume Density RadiusMpc Temperature TotalMassMsun myweight 1.411083e+03 1.884580e+73 5.022445e-28 1.086579e+00 3.470612e+07 3.350352e+13 4.667973e+12 1.349560e+03 2.826870e+73 2.846061e-28 1.108807e+00 2.697442e+07 4.806416e+13 1.054647e+12 1.199229e+03 3.298015e+73 3.425752e-28 1.131491e+00 2.577368e+07 4.982850e+13 8.115086e+11 1.029234e+03 5.653740e+73 2.792583e-28 1.154639e+00 3.303925e+07 7.331169e+13 2.847611e+12 1.135776e+03 7.538320e+73 3.070320e-28 1.178260e+00 3.784802e+07 1.078674e+14 2.675091e+12 1.135776e+03 7.538320e+73 nan 1.202365e+00 nan 1.078674e+14 0.000000e+00 1.135776e+03 7.538320e+73 nan 1.226962e+00 nan 1.078674e+14 0.000000e+00 1.018853e+03 8.951755e+73 3.040255e-28 1.252063e+00 3.025227e+07 1.149060e+14 1.974464e+12 9.159449e+02 1.083633e+74 1.950294e-28 1.277677e+00 3.573580e+07 1.250475e+14 1.774217e+12 9.158806e+02 1.177862e+74 1.275998e-28 1.303816e+00 3.568055e+07 1.359117e+14 5.672694e+11 8.432311e+02 1.413435e+74 1.915018e-28 1.330489e+00 2.360579e+07 1.501570e+14 1.880053e+12 7.995894e+02 1.649007e+74 2.735319e-28 1.357708e+00 2.651133e+07 1.661165e+14 2.674878e+12 Looking at ActualOverdensity column, Is it possible to have a halo with overdensities in 1000's when the peak overdensity is 520. And do the "nan" correspond to some kind of profile maxima ? regards shankar -----Original Message----- From: yt-users-bounces@lists.spacepope.org on behalf of Eric Hallman Sent: Wed 12/2/2009 12:56 PM To: Discussion of the yt analysis package Subject: Re: [yt-users] HaloProfiler ActualOverdensity Shankar and Britton, I have gone through this argument extensively, and discovered that both definitions are used, with roughly equal frequency in the literature. Lately, it has been trending toward OD = density/mean density (matter). I think the main reason for the density with respect to critical in the past has been due to an historical preference for omega_m=1 universes (SCDM). cheers, On Dec 2, 2009, at 11:50 AM, Britton Smith wrote:
Shankar,
As I stated in my previous email, you will find both definitions used in the literature. I'm not going to spend time in a citation battle. The good news is that both definitions differ only by a factor of Omega_matter, so you can change the value of virial_overdensity accordingly.
Britton
On Wed, Dec 2, 2009 at 11:27 AM, Agarwal, Shankar <sagarwal@ku.edu> wrote: Hi Britton,
I just wanted a clarification on the definition of ActualOverdensity. In your mail, you said...
"ActualOverdensity has the same physical meaning as the regular Overdensity field. It is (Baryon Density + Dark Matter Density) / (Mean density of the universe). If you search the literature, you will find alternate definitions that use critical density instead of mean density. The one used here is a little more common."
Are you sure you did not mean (Baryon Density + Dark Matter Density) / (critical density) ?
Because, in halo_profiler.py, there is a virial filter...
hp.add_halo_filter(HP.VirialFilter,must_be_virialized=True, overdensity_field='ActualOverdensity', virial_overdensity=200, virial_filters=[['TotalMassMsun','>=','1e14']], virial_quantities=['TotalMassMsun','RadiusMpc'])
Isn't 200 w.r.t rho_ciritcal (not rho_mean_matter)? Look http://arxiv.org/abs/astro-ph/0011495
shankar
-----Original Message----- From: yt-users-bounces@lists.spacepope.org on behalf of Britton Smith Sent: Wed 11/25/2009 1:30 PM To: Discussion of the yt analysis package Subject: Re: [yt-users] Hop vs HaloProfiler
Hi Shankar,
I will answer the HaloProfiler related questions and leave the Hop questions for Stephen. However, could you post the failure output for what you tried to do with Hop. That will probably be helpful for answering your question.
Is Halo_0000_profile.dat related to the first Halo listed in HopAnalysis.out
file ?
Yes, the HaloProfiler will always use the same indices for halos as all of the halo finders in yt. So, the file Halo_N_profile.dat will always refer to halo N on the halo list.
What is # ?
This is just a comment character so that plotting programs don't try to read in what's on that line. The tab between it and the first field name is there to accommodate the routines that read those files back in to the HaloProfiler.
What is the meaning of ActualOverdensity ? And units ?
ActualOverdensity has the same physical meaning as the regular Overdensity field. It is (Baryon Density + Dark Matter Density) / (Mean density of the universe). If you search the literature, you will find alternate definitions that use critical density instead of mean density. The one used here is a little more common (I think, but I'm not sure). As per these definitions, overdensity is a unitless quantity.
In yt, there is an Overdensity field that is calculated on a cell-by- cell basis. For calculation of virial quantities for halos, the overdensity you calculate should be explicitly the total mass (baryon + dm) / total volume / mean density, where total refers to all cells enclosed within the sphere of the radial profile, not just the shell from r_(i-1) to r_i. Technically, you could get this by doing a profile of the Overdensity field, weighted by CellVolume, with accumulation set to True. However, if for some reason, the user wanted to do profiles of the overdensity field in a different way, say weighted by CellMass, or just counting the material shell-by-shell (accumulation=False), this number would not be correct for the calculation of virial quantities. For that reason, the HaloProfiler automatically generates this ActualOverdensity field which is assured to be calculated in the correct way. That way the user doesn't accidentally override a proper calculation of the overdensity used for the virial quantities.
Other than the ActualOverdensity field (which is automatically generated by the HaloProfiler, and thus does not exist outside that context) you can always get the units of any field with: lagos.fieldInfo[some_field].units For more information, see here: http://yt.enzotools.org/doc/faq.html#how-do-i-know-what-the-units-returned-a...
What is the meaning of CellVolume? And units ?
What is Density referring to ? And units ?
CellVolume and Density are the volume of a cell and the baryon density. In this context, they are the values of those fields in the radial profile. If you did it as per the recipe, the CellVolume is the total accumulated volume for all cells within the sphere radius. Density SHOULD be the mass-weighted, mean baryon density for cells within spherical shells. However, after looking at the recipe on the website, I see that, in error, I set the weight_field of the Density profile to None, instead of CellMassMsun. Therefore, the Density profile may be meaningless as is. I will change the recipe on the website ASAP.
What is mywieght ?
The myweight field is a temporary field for keeping track of the weight field for a weight radial profile. It should be ignored and we might just want to not write it out in the future.
I also got the projection/ directory. But I got errors...
It looks like the HaloProfiler tried to do a projection of Metallicity, but your simulation data did not have the MetalDensity field. You need to set CosmologyUseMetallicityField (or something like that) to 1 in your enzo parameter file in order to get this field. You can also just remove the line in the HaloProfiler recipe that adds the metallicity field to the list of projections.
Cheers,
Britton
_______________________________________________ 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
Dr. Eric J. Hallman NSF Astronomy and Astrophysics Postdoctoral Fellow Center for Astrophysics and Space Astronomy University of Colorado at Boulder hallman (at) casa.colorado.edu Phone: (312) 725-4626 http://solo.colorado.edu/~hallman/
For question 1, you would use that only if you believe the *correct* OD for virialization is 200 only with respect to either mean matter density or critical density. The number 200 is somewhat arbitrary. But for your purposes, your conversion is correct. As to which number you should use for virial overdensity, I would recommend looking through linear collapse theory in an expanding universe if you are concerned at this level which is correct (e.g. Peebles or the Press- Schechter papers, or any of the new ones) On Dec 2, 2009, at 3:40 PM, Agarwal, Shankar wrote:
Britton and Eric,
So I guess if the convention in halo_profiler is (Baryon + Dark Matter Density) / (Mean density) , then I should use
virial_overdensity = 200/Omega_matter = 200/0.258 = 775
instead of 200.
A separate stupid question :
I have run a Box=200Mpc/h with 512^3 dark matter particle simulation. http://drop.io/slice The most dense point in the box is only 1.3e-27 gm/cm^3, which is about 520*matter_mean_density (for omega_matter=0.26).
Then I ran halo_profiler.py on it. Here are the first few lines...
ActualOverdensity CellVolume Density RadiusMpc Temperature TotalMassMsun myweight 1.411083e+03 1.884580e+73 5.022445e-28 1.086579e+00 3.470612e+07 3.350352e+13 4.667973e+12 1.349560e+03 2.826870e+73 2.846061e-28 1.108807e+00 2.697442e+07 4.806416e+13 1.054647e+12 1.199229e+03 3.298015e+73 3.425752e-28 1.131491e+00 2.577368e+07 4.982850e+13 8.115086e+11 1.029234e+03 5.653740e+73 2.792583e-28 1.154639e+00 3.303925e+07 7.331169e+13 2.847611e+12 1.135776e+03 7.538320e+73 3.070320e-28 1.178260e+00 3.784802e+07 1.078674e+14 2.675091e+12 1.135776e+03 7.538320e+73 nan 1.202365e+00 nan 1.078674e+14 0.000000e+00 1.135776e+03 7.538320e+73 nan 1.226962e+00 nan 1.078674e+14 0.000000e+00 1.018853e+03 8.951755e+73 3.040255e-28 1.252063e+00 3.025227e+07 1.149060e+14 1.974464e+12 9.159449e+02 1.083633e+74 1.950294e-28 1.277677e+00 3.573580e+07 1.250475e+14 1.774217e+12 9.158806e+02 1.177862e+74 1.275998e-28 1.303816e+00 3.568055e+07 1.359117e+14 5.672694e+11 8.432311e+02 1.413435e+74 1.915018e-28 1.330489e+00 2.360579e+07 1.501570e+14 1.880053e+12 7.995894e+02 1.649007e+74 2.735319e-28 1.357708e+00 2.651133e+07 1.661165e+14 2.674878e+12
Looking at ActualOverdensity column, Is it possible to have a halo with overdensities in 1000's when the peak overdensity is 520.
And do the "nan" correspond to some kind of profile maxima ?
regards shankar
-----Original Message----- From: yt-users-bounces@lists.spacepope.org on behalf of Eric Hallman Sent: Wed 12/2/2009 12:56 PM To: Discussion of the yt analysis package Subject: Re: [yt-users] HaloProfiler ActualOverdensity
Shankar and Britton, I have gone through this argument extensively, and discovered that both definitions are used, with roughly equal frequency in the literature. Lately, it has been trending toward OD = density/mean density (matter). I think the main reason for the density with respect to critical in the past has been due to an historical preference for omega_m=1 universes (SCDM).
cheers,
On Dec 2, 2009, at 11:50 AM, Britton Smith wrote:
Shankar,
As I stated in my previous email, you will find both definitions used in the literature. I'm not going to spend time in a citation battle. The good news is that both definitions differ only by a factor of Omega_matter, so you can change the value of virial_overdensity accordingly.
Britton
On Wed, Dec 2, 2009 at 11:27 AM, Agarwal, Shankar <sagarwal@ku.edu> wrote: Hi Britton,
I just wanted a clarification on the definition of ActualOverdensity. In your mail, you said...
"ActualOverdensity has the same physical meaning as the regular Overdensity field. It is (Baryon Density + Dark Matter Density) / (Mean density of the universe). If you search the literature, you will find alternate definitions that use critical density instead of mean density. The one used here is a little more common."
Are you sure you did not mean (Baryon Density + Dark Matter Density) / (critical density) ?
Because, in halo_profiler.py, there is a virial filter...
hp.add_halo_filter(HP.VirialFilter,must_be_virialized=True, overdensity_field='ActualOverdensity', virial_overdensity=200, virial_filters=[['TotalMassMsun','>=','1e14']], virial_quantities=['TotalMassMsun','RadiusMpc'])
Isn't 200 w.r.t rho_ciritcal (not rho_mean_matter)? Look http://arxiv.org/abs/astro-ph/0011495
shankar
-----Original Message----- From: yt-users-bounces@lists.spacepope.org on behalf of Britton Smith Sent: Wed 11/25/2009 1:30 PM To: Discussion of the yt analysis package Subject: Re: [yt-users] Hop vs HaloProfiler
Hi Shankar,
I will answer the HaloProfiler related questions and leave the Hop questions for Stephen. However, could you post the failure output for what you tried to do with Hop. That will probably be helpful for answering your question.
Is Halo_0000_profile.dat related to the first Halo listed in HopAnalysis.out
file ?
Yes, the HaloProfiler will always use the same indices for halos as all of the halo finders in yt. So, the file Halo_N_profile.dat will always refer to halo N on the halo list.
What is # ?
This is just a comment character so that plotting programs don't try to read in what's on that line. The tab between it and the first field name is there to accommodate the routines that read those files back in to the HaloProfiler.
What is the meaning of ActualOverdensity ? And units ?
ActualOverdensity has the same physical meaning as the regular Overdensity field. It is (Baryon Density + Dark Matter Density) / (Mean density of the universe). If you search the literature, you will find alternate definitions that use critical density instead of mean density. The one used here is a little more common (I think, but I'm not sure). As per these definitions, overdensity is a unitless quantity.
In yt, there is an Overdensity field that is calculated on a cell-by- cell basis. For calculation of virial quantities for halos, the overdensity you calculate should be explicitly the total mass (baryon + dm) / total volume / mean density, where total refers to all cells enclosed within the sphere of the radial profile, not just the shell from r_(i-1) to r_i. Technically, you could get this by doing a profile of the Overdensity field, weighted by CellVolume, with accumulation set to True. However, if for some reason, the user wanted to do profiles of the overdensity field in a different way, say weighted by CellMass, or just counting the material shell-by-shell (accumulation=False), this number would not be correct for the calculation of virial quantities. For that reason, the HaloProfiler automatically generates this ActualOverdensity field which is assured to be calculated in the correct way. That way the user doesn't accidentally override a proper calculation of the overdensity used for the virial quantities.
Other than the ActualOverdensity field (which is automatically generated by the HaloProfiler, and thus does not exist outside that context) you can always get the units of any field with: lagos.fieldInfo[some_field].units For more information, see here: http://yt.enzotools.org/doc/faq.html#how-do-i-know-what-the-units-returned-a...
What is the meaning of CellVolume? And units ?
What is Density referring to ? And units ?
CellVolume and Density are the volume of a cell and the baryon density. In this context, they are the values of those fields in the radial profile. If you did it as per the recipe, the CellVolume is the total accumulated volume for all cells within the sphere radius. Density SHOULD be the mass-weighted, mean baryon density for cells within spherical shells. However, after looking at the recipe on the website, I see that, in error, I set the weight_field of the Density profile to None, instead of CellMassMsun. Therefore, the Density profile may be meaningless as is. I will change the recipe on the website ASAP.
What is mywieght ?
The myweight field is a temporary field for keeping track of the weight field for a weight radial profile. It should be ignored and we might just want to not write it out in the future.
I also got the projection/ directory. But I got errors...
It looks like the HaloProfiler tried to do a projection of Metallicity, but your simulation data did not have the MetalDensity field. You need to set CosmologyUseMetallicityField (or something like that) to 1 in your enzo parameter file in order to get this field. You can also just remove the line in the HaloProfiler recipe that adds the metallicity field to the list of projections.
Cheers,
Britton
_______________________________________________ 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
Dr. Eric J. Hallman NSF Astronomy and Astrophysics Postdoctoral Fellow Center for Astrophysics and Space Astronomy University of Colorado at Boulder hallman (at) casa.colorado.edu Phone: (312) 725-4626 http://solo.colorado.edu/~hallman/
<winmail.dat>_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Dr. Eric J. Hallman NSF Astronomy and Astrophysics Postdoctoral Fellow Center for Astrophysics and Space Astronomy University of Colorado at Boulder hallman (at) casa.colorado.edu Phone: (312) 725-4626 http://solo.colorado.edu/~hallman/
Shankar, The overdensity in the profile is referring to dark matter + baryons. The field called "Density" is just baryon density. The nans come from spherical shells of the radial profile that had nothing in them. If you look at the TotalMassMsun field, you'll notice that it is flat over the points where you get the nans and the value of myweight is 0. Britton On Wed, Dec 2, 2009 at 3:49 PM, Eric Hallman <Eric.Hallman@colorado.edu>wrote:
For question 1, you would use that only if you believe the *correct* OD for virialization is 200 only with respect to either mean matter density or critical density. The number 200 is somewhat arbitrary. But for your purposes, your conversion is correct. As to which number you should use for virial overdensity, I would recommend looking through linear collapse theory in an expanding universe if you are concerned at this level which is correct (e.g. Peebles or the Press-Schechter papers, or any of the new ones)
On Dec 2, 2009, at 3:40 PM, Agarwal, Shankar wrote:
Britton and Eric,
So I guess if the convention in halo_profiler is (Baryon + Dark Matter Density) / (Mean density) , then I should use
virial_overdensity = 200/Omega_matter = 200/0.258 = 775
instead of 200.
A separate stupid question :
I have run a Box=200Mpc/h with 512^3 dark matter particle simulation. http://drop.io/slice The most dense point in the box is only 1.3e-27 gm/cm^3, which is about 520*matter_mean_density (for omega_matter=0.26).
Then I ran halo_profiler.py on it. Here are the first few lines...
ActualOverdensity CellVolume Density RadiusMpc Temperature TotalMassMsun myweight 1.411083e+03 1.884580e+73 5.022445e-28 1.086579e+00 3.470612e+07 3.350352e+13 4.667973e+12 1.349560e+03 2.826870e+73 2.846061e-28 1.108807e+00 2.697442e+07 4.806416e+13 1.054647e+12 1.199229e+03 3.298015e+73 3.425752e-28 1.131491e+00 2.577368e+07 4.982850e+13 8.115086e+11 1.029234e+03 5.653740e+73 2.792583e-28 1.154639e+00 3.303925e+07 7.331169e+13 2.847611e+12 1.135776e+03 7.538320e+73 3.070320e-28 1.178260e+00 3.784802e+07 1.078674e+14 2.675091e+12 1.135776e+03 7.538320e+73 nan 1.202365e+00 nan 1.078674e+14 0.000000e+00 1.135776e+03 7.538320e+73 nan 1.226962e+00 nan 1.078674e+14 0.000000e+00 1.018853e+03 8.951755e+73 3.040255e-28 1.252063e+00 3.025227e+07 1.149060e+14 1.974464e+12 9.159449e+02 1.083633e+74 1.950294e-28 1.277677e+00 3.573580e+07 1.250475e+14 1.774217e+12 9.158806e+02 1.177862e+74 1.275998e-28 1.303816e+00 3.568055e+07 1.359117e+14 5.672694e+11 8.432311e+02 1.413435e+74 1.915018e-28 1.330489e+00 2.360579e+07 1.501570e+14 1.880053e+12 7.995894e+02 1.649007e+74 2.735319e-28 1.357708e+00 2.651133e+07 1.661165e+14 2.674878e+12
Looking at ActualOverdensity column, Is it possible to have a halo with overdensities in 1000's when the peak overdensity is 520.
And do the "nan" correspond to some kind of profile maxima ?
regards shankar
-----Original Message----- From: yt-users-bounces@lists.spacepope.org on behalf of Eric Hallman Sent: Wed 12/2/2009 12:56 PM To: Discussion of the yt analysis package Subject: Re: [yt-users] HaloProfiler ActualOverdensity
Shankar and Britton, I have gone through this argument extensively, and discovered that both definitions are used, with roughly equal frequency in the literature. Lately, it has been trending toward OD = density/mean density (matter). I think the main reason for the density with respect to critical in the past has been due to an historical preference for omega_m=1 universes (SCDM).
cheers,
On Dec 2, 2009, at 11:50 AM, Britton Smith wrote:
Shankar,
As I stated in my previous email, you will find both definitions
used in the literature. I'm not going to spend time in a citation
battle. The good news is that both definitions differ only by a
factor of Omega_matter, so you can change the value of
virial_overdensity accordingly.
Britton
On Wed, Dec 2, 2009 at 11:27 AM, Agarwal, Shankar <sagarwal@ku.edu>
wrote:
Hi Britton,
I just wanted a clarification on the definition of
ActualOverdensity. In your mail, you said...
"ActualOverdensity has the same physical meaning as the regular
Overdensity
field. It is (Baryon Density + Dark Matter Density) / (Mean
density of the
universe). If you search the literature, you will find alternate
definitions that use critical density instead of mean density. The
one used
here is a little more common."
Are you sure you did not mean (Baryon Density + Dark Matter
Density) / (critical density) ?
Because, in halo_profiler.py, there is a virial filter...
hp.add_halo_filter(HP.VirialFilter,must_be_virialized=True,
overdensity_field='ActualOverdensity',
virial_overdensity=200,
virial_filters=[['TotalMassMsun','>=','1e14']],
virial_quantities=['TotalMassMsun','RadiusMpc'])
Isn't 200 w.r.t rho_ciritcal (not rho_mean_matter)? Look http://arxiv.org/abs/astro-ph/0011495
shankar
-----Original Message-----
From: yt-users-bounces@lists.spacepope.org on behalf of Britton Smith
Sent: Wed 11/25/2009 1:30 PM
To: Discussion of the yt analysis package
Subject: Re: [yt-users] Hop vs HaloProfiler
Hi Shankar,
I will answer the HaloProfiler related questions and leave the Hop
questions
for Stephen. However, could you post the failure output for what
you tried
to do with Hop. That will probably be helpful for answering your
question.
Is Halo_0000_profile.dat related to the first Halo listed in
HopAnalysis.out
file ?
Yes, the HaloProfiler will always use the same indices for halos as
all of
the halo finders in yt. So, the file Halo_N_profile.dat will always
refer
to halo N on the halo list.
What is # ?
This is just a comment character so that plotting programs don't try
to read
in what's on that line. The tab between it and the first field name
is
there to accommodate the routines that read those files back in to the
HaloProfiler.
What is the meaning of ActualOverdensity ? And units ?
ActualOverdensity has the same physical meaning as the regular
Overdensity
field. It is (Baryon Density + Dark Matter Density) / (Mean density
of the
universe). If you search the literature, you will find alternate
definitions that use critical density instead of mean density. The
one used
here is a little more common (I think, but I'm not sure). As per
these
definitions, overdensity is a unitless quantity.
In yt, there is an Overdensity field that is calculated on a cell-by-
cell
basis. For calculation of virial quantities for halos, the
overdensity you
calculate should be explicitly the total mass (baryon + dm) / total
volume /
mean density, where total refers to all cells enclosed within the
sphere of
the radial profile, not just the shell from r_(i-1) to r_i.
Technically,
you could get this by doing a profile of the Overdensity field,
weighted by
CellVolume, with accumulation set to True. However, if for some
reason, the
user wanted to do profiles of the overdensity field in a different
way, say
weighted by CellMass, or just counting the material shell-by-shell
(accumulation=False), this number would not be correct for the
calculation
of virial quantities. For that reason, the HaloProfiler automatically
generates this ActualOverdensity field which is assured to be
calculated in
the correct way. That way the user doesn't accidentally override a
proper
calculation of the overdensity used for the virial quantities.
Other than the ActualOverdensity field (which is automatically
generated by
the HaloProfiler, and thus does not exist outside that context) you
can
always get the units of any field with:
lagos.fieldInfo[some_field].units
For more information, see here:
http://yt.enzotools.org/doc/faq.html#how-do-i-know-what-the-units-returned-a...
What is the meaning of CellVolume? And units ?
What is Density referring to ? And units ?
CellVolume and Density are the volume of a cell and the baryon
density. In
this context, they are the values of those fields in the radial
profile. If
you did it as per the recipe, the CellVolume is the total
accumulated volume
for all cells within the sphere radius. Density SHOULD be the
mass-weighted, mean baryon density for cells within spherical shells.
However, after looking at the recipe on the website, I see that, in
error, I
set the weight_field of the Density profile to None, instead of
CellMassMsun. Therefore, the Density profile may be meaningless as
is. I
will change the recipe on the website ASAP.
What is mywieght ?
The myweight field is a temporary field for keeping track of the
weight
field for a weight radial profile. It should be ignored and we
might just
want to not write it out in the future.
I also got the projection/ directory. But I got errors...
It looks like the HaloProfiler tried to do a projection of
Metallicity, but
your simulation data did not have the MetalDensity field. You need
to set
CosmologyUseMetallicityField (or something like that) to 1 in your
enzo
parameter file in order to get this field. You can also just remove
the
line in the HaloProfiler recipe that adds the metallicity field to
the list
of projections.
Cheers,
Britton
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Dr. Eric J. Hallman NSF Astronomy and Astrophysics Postdoctoral Fellow Center for Astrophysics and Space Astronomy University of Colorado at Boulder hallman (at) casa.colorado.edu Phone: (312) 725-4626 http://solo.colorado.edu/~hallman/ <http://solo.colorado.edu/%7Ehallman/>
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Dr. Eric J. Hallman NSF Astronomy and Astrophysics Postdoctoral Fellow Center for Astrophysics and Space Astronomy University of Colorado at Boulder hallman (at) casa.colorado.edu Phone: (312) 725-4626 http://solo.colorado.edu/~hallman/ <http://solo.colorado.edu/%7Ehallman/>
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Shankar,
from yt.mods import *
fn = "RedshiftOutput0002" pf = load(fn) halos = HaloFinder(pf) halos.modify["hop_circles"](self, hop_output, max_number=None, annotate=False, min_size=20, max_size=10000000, font_size=8, print_halo_size=False, print_halo_mass=False, width=None) halos.write_out("HopAnalysis.out")
hop_circles makes a plot of hop haloes on an existing projection. You need to create the projection first. So... ... halos = HaloFinder(pf) pc = PlotCollection(pf) p = pc.add_projection("Density",0) p.modify["hop_circles"](halos, max_number=etc...) pc.set_width(1.0, '1') pc.save('plotname') My advice is, when you try to use a new function, you should figure out what it's doing and what the inputs are. For example, even if your input was formatted correctly, you haven't defined 'self' or 'hop_output' before you use them in the function call, and it would have failed anyway. Also, 'self' is a special variable in python that is never used as an argument of a function call. Good luck! _______________________________________________________ sskory@physics.ucsd.edu o__ Stephen Skory http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student ________________________________(_)_\(_)_______________
Hi Stephen, I am using the following statement... p.modify["hop_circles"](halos, max_number=None, annotate=True, min_size=400, max_size=100000, font_size=8, print_halo_size=True, print_halo_mass=True, width=None) The plot is at http://drop.io/hop_circles Why is it not printing the print_halo_mass ? What are the options for width ? shankar -----Original Message----- From: yt-users-bounces@lists.spacepope.org on behalf of Stephen Skory Sent: Wed 11/25/2009 3:30 PM To: Discussion of the yt analysis package Subject: Re: [yt-users] Hop vs HaloProfiler Shankar,
from yt.mods import *
fn = "RedshiftOutput0002" pf = load(fn) halos = HaloFinder(pf) halos.modify["hop_circles"](self, hop_output, max_number=None, annotate=False, min_size=20, max_size=10000000, font_size=8, print_halo_size=False, print_halo_mass=False, width=None) halos.write_out("HopAnalysis.out")
hop_circles makes a plot of hop haloes on an existing projection. You need to create the projection first. So... ... halos = HaloFinder(pf) pc = PlotCollection(pf) p = pc.add_projection("Density",0) p.modify["hop_circles"](halos, max_number=etc...) pc.set_width(1.0, '1') pc.save('plotname') My advice is, when you try to use a new function, you should figure out what it's doing and what the inputs are. For example, even if your input was formatted correctly, you haven't defined 'self' or 'hop_output' before you use them in the function call, and it would have failed anyway. Also, 'self' is a special variable in python that is never used as an argument of a function call. Good luck! _______________________________________________________ sskory@physics.ucsd.edu o__ Stephen Skory http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student ________________________________(_)_\(_)_______________ _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Shankar,
I am using the following statement...
p.modify["hop_circles"](halos, max_number=None, annotate=True, min_size=400, max_size=100000, font_size=8, print_halo_size=True, print_halo_mass=True, width=None)
The plot is at http://drop.io/hop_circles
Why is it not printing the print_halo_mass ?
It can't print both the halo mass and halo size. Pick one 'True', and make the other 'False'.
What are the options for width ?
Whether you mean image size or domain coverage, they are both options for the plot, see 'set_width' and 'set_lim' http://yt.enzotools.org/doc/modules/plotting.html _______________________________________________________ sskory@physics.ucsd.edu o__ Stephen Skory http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student ________________________________(_)_\(_)_______________
Shankar,
Whether you mean image size or domain coverage, they are both options for the plot, see 'set_width' and 'set_lim'
Also look at the 'fig_size' argument when creating an image, like in add_projection, or add_slice. _______________________________________________________ sskory@physics.ucsd.edu o__ Stephen Skory http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student ________________________________(_)_\(_)_______________
participants (5)
-
Agarwal, Shankar -
Britton Smith -
Eric Hallman -
Matthew Turk -
Stephen Skory