Mailman 3 June 2015 - yt-users

adding quantities to halo catalogs
by Professor Maller 22 Jun '15

22 Jun '15

Hi Everyone, I'm trying to add a quantity to my halo catalog which is cold gas mass. We can assume I've already defined the field cold_gas_mass, but I'm having trouble understanding how to add it to my halo catalog. The examples all seem to be for profiles and it isn't clear to me what to do if you aren't looking for a profile. Does anyone have an example of doing something like this they could share? The total gas mass or any other sum of fluid quantities would probably be close enough for me understand the syntax. Thanks, Ari

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Re: [yt-users] Getting error in Worked Example of Halo Analysis
by Chen Jingjing 22 Jun '15

22 Jun '15

Hi Britton, When I set critical_density=500, does it mean 500 times of the average density, or 500 times of the critical density? Thanks, Jingjing 2015-03-20 4:22 GMT-04:00 Britton Smith <brittonsmith(a)gmail.com>: > Hi Reju, > > It looks like the version of the notebook you are working from is a little > out of date as the syntax for some of those callbacks has changed. Please, > have a look here for an updated version: > http://yt-project.org/doc/cookbook/halo_analysis_example.html > I just ran this myself and confirmed everything to be working. > > As for your other questions: > > 1) How to find the center of mass of the halos( >> hc.add_quantity('center_of_mass') is not working ) >> > > By default, the halo catalog is storing the center of the halo as > calculated by the halo finder that you used. If you reload the halo > catalog that you produce, the x, y, and z position of each halo are the > "particle_position_x", "particle_position_y", "particle_position_z" > fields. For example, you could do: > ds = yt.load(your_halo_catalog) > ad = ds.all_data() > print ad["particle_position_x"] > > Additionally, the halo catalog has a callback called > "iterative_center_of_mass" which starts from the original center and > iteratively recalculates the center of mass while reducing the radius of > the sphere. I have found this to work very well for calculating halo > centers. If you use this callback, it will rewrite the particle_position > fields to contain the new center for each halo. To get more information on > this callback, do the following: > > from yt.analysis_modules.halo_analysis.halo_callbacks import * > help(iterative_center_of_mass) > > >> 2) How to find virial mass (both M_500 and M_200 ) of the halas >> > > You can find these using the virial_quantities callback. In the example > you are working from, you can add another field to the virial_quantities > callback you use and it would calculate the value of that field where the > overdensity = 200. For total mass, the field you want is called > "matter_mass". To get M_500 instead of M_200, you can call the > virial_quantities callback again and give the keyword argument > critical_density=500. > > Britton > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > -- Jingjing Chen [ chenjj235(a)gmail.com ] Department of Astronomy Columbia University 550 West 120th Street New York, New York 10027 Cell Phone: +1(347)5746709

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3D physical properties from projection plot
by Desika Narayanan 22 Jun '15

22 Jun '15

Hi All, I'm trying to calculate some physical properties from a gadget data set on a similar grid as projection plot, but in 3D. That is, if I calculate a projection plot: >px_gas = yt.ProjectionPlot(ds,"z",("gas","density")) >px_gas_frb = px_gas.frb then I can access the gas surface density values in some 800x800 (or whatever) 2D array. What I would like is to be able to get the gas physical properties in the 800x800x800 (or whatever) grid that yt is integrating along to give me the Projection Plot (in particular the gas mass, and the gas velocity vectors). Is this possible? Thanks a lot, -d

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Simple Visualizations: No images displaying
by Carla Carroll 22 Jun '15

22 Jun '15

Hi yt users, I am new to yt and working through through the Simple Visualization tutorial ( http://yt-project.org/docs/3.1/quickstart/simple_visualization.html). Within ipython, when I try to display any image, I always only get the text output with no image. For example, >p.show() <yt.visualization.plot_window.ProjectionPlot at 0x109cd4550> I have tried this on two machines and get the same result. There is no error, but I also do not get an image like I should (on the tutorial there are many multiple variations of display, otherwise I would just use p.save() and display the image outside of ipython). Ideas? Suggestions? Kind regards, Carla Carroll

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projection plot smoothing
by Yang Luo 22 Jun '15

22 Jun '15

Hi I am trying to use yt to make a projection plot from gadget data. for the plot, I set the field to be plotted as ('deposit', 'PartType0_smoothed_density'). But the final plot shows some cell structures, so I want to know how to smooth or render this plot. In splash, the plot is better rendered. could this be done in yt ? I am grateful for your comments. Yang

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another cut_region question
by Stephanie Tonnesen 19 Jun '15

19 Jun '15

Hi all, I tried to work around the no boolean operators in yt3.1 thing that Cameron told me about by using two cut_regions [image: Inline image 1] but then I get this error: [image: Inline image 2] It doesn't make a different what order I use for the two cut_region calls. I guess that this is something else that hasn't made it into yt3.1? It seems strange, though, so I thought I would check. Thanks! Stephanie -- Dr. Stephanie Tonnesen Alvin E. Nashman Postdoctoral Fellow Carnegie Observatories, Pasadena, CA stonnes(a)gmail.com

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a way annotate a piece of a grid?
by Jonah Miller 18 Jun '15

18 Jun '15

Hi Everybody, I am looking for something similar to the annotate_grids function, but that can annotate arbitrary pieces of a single grid (or more precisely, of a hexahedral mesh). Is there a reasonable way to do this? Thanks in advance! Best, Jonah Miller

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Cylindrical VTK data
by Elizabeth Tasker 17 Jun '15

17 Jun '15

Hi everyone, We have a file created with Fargo 3D that’s been exported to Athena VTK format. When we try and load this into yt 3.0, we hit the error: In [1]: ds = yt.load("gasdens1000.vtk") --------------------------------------------------------------------------- KeyError Traceback (most recent call last) /home/kanagawa/work/yt-x86_64/src/yt-hg/scripts/iyt in <module>() ----> 1 ds = yt.load("gasdens1000.vtk") /home/kanagawa/work/yt-x86_64/src/yt-hg/yt/convenience.pyc in load(*args, **kwargs) 78 if c._is_valid(*args, **kwargs): candidates.append(n) 79 if len(candidates) == 1: ---> 80 return output_type_registry[candidates[0]](*args, **kwargs) 81 if len(candidates) == 0: 82 if ytcfg.get("yt", "enzo_db") != '' \ /home/kanagawa/work/yt-x86_64/src/yt-hg/yt/frontends/athena/data_structures.pyc in __init__(self, filename, dataset_type, storage_filename, parameters) 358 parameters = {} 359 self.specified_parameters = parameters --> 360 Dataset.__init__(self, filename, dataset_type) 361 self.filename = filename 362 if storage_filename is None: /home/kanagawa/work/yt-x86_64/src/yt-hg/yt/data_objects/static_output.pyc in __init__(self, filename, dataset_type, file_style) 178 179 self._create_unit_registry() --> 180 self._parse_parameter_file() 181 self.set_units() 182 self._setup_coordinate_handler() /home/kanagawa/work/yt-x86_64/src/yt-hg/yt/frontends/athena/data_structures.pyc in _parse_parameter_file(self) 409 line = self._handle.readline() 410 --> 411 self.domain_left_edge = grid['left_edge'] 412 mylog.info("Temporarily setting domain_right_edge = -domain_left_edge."+ 413 " This will be corrected automatically if it is not the case.") KeyError: ‘left_edge' I’m guessing this is because the data set is in polar coordinates? Is that right? I’ve seen that yt can handle polars in FLASH but does it need to be explicitly FLASH data? Thanks very much, Elizabeth

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Creating a ring
by Stephanie Tonnesen 17 Jun '15

17 Jun '15

Hi yt-users! I am trying to analyze a cylindrical loop in my dataset. So what I want to do is to create two disks: d1 = ds.disk([0.5, 0.5, 0.5], [0., 0., 1.], (8, 'kpc'), (1, 'kpc')) d2 = ds.disk([0.5, 0.5, 0.5], [0., 0., 1.], (7, 'kpc'), (1, 'kpc')) and have r1 be the region containing all the cells in d1 and NOT in d2. I feel like there must be an easy way to do this, but can't think of it. Also, searching the yt-users archive kept coming up with an error. Thanks in advance! Stephanie -- Dr. Stephanie Tonnesen Alvin E. Nashman Postdoctoral Fellow Carnegie Observatories, Pasadena, CA stonnes(a)gmail.com

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question about derived fields that require field_parameters
by Brian O'Shea 17 Jun '15

17 Jun '15

Hi folks, I'm doing some analysis on an Enzo simulation using the tip of yt-3, and would like to find the maximum and minimum of the field "baryon_overdensity", which is a derived field. If I were to make a projection or slice of this field, I'd have to feed in omega_baryon so that baryon_overdensity can be created on the fly, e.g., plot1 = yt.ProjectionPlot(ds,'z',"baryon_overdensity",weight_field="baryon_overdensity", center=c,data_source=my_region, field_parameters = {'omega_baryon': 0.046}) However, if I try to run find_max("baryon_overdensity") on my dataset, it complains that the derived field needs omega_baryon, with an error message ending in this: /Users/bwoshea/Desktop/yt-3/src/yt-hg/yt/fields/derived_field.pyc in __call__(self, data) 237 doesnt_have.append(p) 238 if len(doesnt_have) > 0: --> 239 raise NeedsParameter(doesnt_have) 240 return True 241 NeedsParameter: (['omega_baryon']) This makes sense; however, I can't feed omega_baryon to find_max() in the same way that I can feed field_parameters into ProjectionPlot. Is there a way to either (1) force yt to generate the baryon_overdensity field prior to calling find_max(), or (2) feed omega_baryon into find_max()? I think that option #2 is not trivial, since the source code for find_max (in src/yt-hg/yt/data_objects/static_objects.py) only takes the name of the field. I suspect that #1 is possible, though I can't find anything in the documentation about it. Any suggestions would be greatly appreciated. Thanks! --Brian

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