Mailman 3 September 2013 - yt-users

Overplotting equipotential contours from total potential
by trobolo dinni 25 Sep '13

25 Sep '13

Dear yt users, I am running a binary star simulation with enzo, and in my box there is a star made up of a gas envelope and a particle as core, and a secondary star represented by a single particle (no gas). I would like to plot the equipotential surfaces of the system on a slice plot, hence, since the default Grav_Potential field does not include the particles potential, I created a custom made field as follows: * def _Total_Grav_Potential(field,data): * * #G in cgs* * grav_const_cgs = 6.674e-8* * * * #data for gas* * gas_grav_potential_cgs = data['Grav_Potential'] * (length_unit1/time_unit1)**2.0 #in units of velocity^2* * gas_position_x_cgs = data['x'] * length_unit1* * gas_position_y_cgs = data['y'] * length_unit1* * gas_position_z_cgs = data['z'] * length_unit1* * * * #initialize the array for the total grav potential to the gas grav potential* * total_grav_potential_cgs = gas_grav_potential_cgs* * * * #loops on the particles* * for i in range(len(data['ParticleMassMsun'])):* * * * #data of the current particle* * current_particle_mass_cgs= data['ParticleMassMsun'][i] * mass_unit* * current_particle_position_x_cgs = data['particle_position_x'][i] * length_unit1* * current_particle_position_y_cgs = data['particle_position_y'][i] * length_unit1* * current_particle_position_z_cgs = data['particle_position_z'][i] * length_unit1* * * * #computes the array of grav potential for the current particle* * current_particle_grav_potential_cgs = -(grav_const_cgs * current_particle_mass_cgs)/(((gas_position_x_cgs - current_particle_position_x_cgs)**2.0 + (gas_position_y_cgs - current_particle_position_y_cgs)**2.0 + (gas_position_z_cgs - current_particle_position_z_cgs)**2.0)**0.5)* * * * #adds the current particle potential to the total potential* * total_grav_potential_cgs = total_grav_potential_cgs + current_particle_grav_potential_cgs* * * * return total_grav_potential_cgs* * #adds the field to the available yt fields* * add_field("Total_Grav_Potential", function=_Total_Grav_Potential, take_log=True ,units=r"\rm{erg}/\rm{g}")* * * where the length unit and time unit variables have the function to convert my quantities in cgs. If I then call my "Total_Grav_Potential" field, I get reasonable values, but when I try to inspect the shape of the equipotential surfaces on the xy-plane by plotting the following: * sp = SlicePlot(pf, 'z', "Density", width = 1.0)* * sp.annotate_velocity(factor=16, normalize=True)* * sp.annotate_contour('Total_Grav_Potential',clim=(max_total_pot,min_total_pot)) * * sp.annotate_particles(1.0, p_size=50.0, marker='o', col='black')* * sp.annotate_text((0.7,1.05), "time = "+str(pf.current_time)+"yr") * * sp.save(plot_dir+"density_slice_z_"+str(index)+".png")* nothing happens, and the plot does not show any additional contour; while if I do the same with the default "Grav_Potential" field, the gas equipotential contours get plotted without problems. I also tried to play with the "annotate_contour" options "ncont", "factor" and "clim" to refine my plot but the result is always the same. Additionally, if I do not set the "clim" option the following error shows up: *ValueError: zero-size array to minimum.reduce without identity* * * I would like to ask if my custom definition of the Total_Grav_Potential field is correct from a yt coding point of view and if I should modify it (or if there is any improvement I can do). Also, I would like to ask if you have any idea of what could be the problem with the plotting. Thanks for the help, Roberto

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style keyword in add_projection
by Christine Simpson 23 Sep '13

23 Sep '13

Hi all, A while ago (~ 1yr) I did some projections with a plot collection that used the keyword 'style' to display the maximum value along the line of sight through a volume, e.g.: pc.add_thin_projection("GridLevel","x",thickness,figure=fig,axes=axes[1][d], use_colorbar=Fales,style='mip') It seems like in the current tip of the development repository this usage has changed perhaps? (add_thin_projection no longer seems to have a keyword argument style) Does anyone know how to do a plot like this with the current version of yt? Thanks Christine

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particle density projection plot in yt-3.0
by Junhwan Choi (최준환) 23 Sep '13

23 Sep '13

Now, I try to move on yt-3.0. For the test, I tried the following projection plot for DM and gas from the enzo simulation. ============================= from yt.mods import * import matplotlib.pylab as pylab pf = load("../DD0023/DD0023") pc = ProjectionPlot(pf, "x", "ComovingDensity", width = (1.0, 'mpccm')) pc.save("cen_L1M") pc = ProjectionPlot(pf, "x", "particle_density", width = (1.0, 'mpccm')) pc.save("cen_L1M") ============================= I found that the gas Projection density plot works but the DM projection plot crashs and gives me following message ============================ yt : [INFO ] 2013-09-18 12:00:51,613 Parameters: current_time = 23.8165517864 yt : [INFO ] 2013-09-18 12:00:51,613 Parameters: domain_dimensions = [128 128 128] yt : [INFO ] 2013-09-18 12:00:51,614 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2013-09-18 12:00:51,614 Parameters: domain_right_edge = [ 1. 1. 1.] yt : [INFO ] 2013-09-18 12:00:51,614 Parameters: cosmological_simulation = 1 yt : [INFO ] 2013-09-18 12:00:51,614 Parameters: current_redshift = 20.1060163976 yt : [INFO ] 2013-09-18 12:00:51,614 Parameters: omega_lambda = 0.721 yt : [INFO ] 2013-09-18 12:00:51,614 Parameters: omega_matter = 0.279 yt : [INFO ] 2013-09-18 12:00:51,614 Parameters: hubble_constant = 0.701 Parsing Hierarchy100% |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:\ 00:00 yt : [INFO ] 2013-09-18 12:00:52,334 Gathering a field list (this may take a moment.) Traceback (most recent call last): File "test.py", line 11, in <module> pc = ProjectionPlot(pf, "x", "particle_density", width = (1.0, 'mpccm')) File "/Users/jhchoi/common/src/yt-3.0-hg/yt/visualization/plot_window.py", line 1410, in __init__ field_parameters = field_parameters) File "/Users/jhchoi/common/src/yt-3.0-hg/yt/data_objects/construction_data_containers.py", line 234, in __init__ self.get_data(field) File "/Users/jhchoi/common/src/yt-3.0-hg/yt/data_objects/construction_data_containers.py", line 278, in get_data chunk_fields, "io")): File "/Users/jhchoi/common/src/yt-3.0-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 434, in parallel_objects for obj_id, obj in oiter: File "/Users/jhchoi/common/src/yt-3.0-hg/yt/data_objects/data_containers.py", line 450, in chunks self.get_data(fields) File "/Users/jhchoi/common/src/yt-3.0-hg/yt/data_objects/data_containers.py", line 536, in get_data self._generate_fields(fields_to_generate) File "/Users/jhchoi/common/src/yt-3.0-hg/yt/data_objects/data_containers.py", line 552, in _generate_fields self.field_data[field] = self._generate_field(field) File "/Users/jhchoi/common/src/yt-3.0-hg/yt/data_objects/data_containers.py", line 219, in _generate_field tr = self._generate_fluid_field(field) File "/Users/jhchoi/common/src/yt-3.0-hg/yt/data_objects/data_containers.py", line 236, in _generate_fluid_field rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones) File "/Users/jhchoi/common/src/yt-3.0-hg/yt/data_objects/data_containers.py", line 252, in _generate_spatial_fluid ind += o.select(self.selector, self[field], rv, ind) File "/Users/jhchoi/common/src/yt-3.0-hg/yt/data_objects/data_containers.py", line 189, in __getitem__ self.get_data(f) File "/Users/jhchoi/common/src/yt-3.0-hg/yt/data_objects/data_containers.py", line 536, in get_data self._generate_fields(fields_to_generate) File "/Users/jhchoi/common/src/yt-3.0-hg/yt/data_objects/data_containers.py", line 552, in _generate_fields self.field_data[field] = self._generate_field(field) File "/Users/jhchoi/common/src/yt-3.0-hg/yt/data_objects/data_containers.py", line 219, in _generate_field tr = self._generate_fluid_field(field) File "/Users/jhchoi/common/src/yt-3.0-hg/yt/data_objects/data_containers.py", line 238, in _generate_fluid_field rv = finfo(gen_obj) File "/Users/jhchoi/common/src/yt-3.0-hg/yt/data_objects/field_info_container.py", line 488, in __call__ dd = self._function(self, data) File "/Users/jhchoi/common/src/yt-3.0-hg/yt/data_objects/universal_fields.py", line 991, in _pdensity pmass = data[('deposit','all_mass')] File "/Users/jhchoi/common/src/yt-3.0-hg/yt/data_objects/grid_patch.py", line 85, in __getitem__ tr = super(AMRGridPatch, self).__getitem__(key) File "/Users/jhchoi/common/src/yt-3.0-hg/yt/data_objects/data_containers.py", line 189, in __getitem__ self.get_data(f) File "/Users/jhchoi/common/src/yt-3.0-hg/yt/data_objects/data_containers.py", line 536, in get_data self._generate_fields(fields_to_generate) File "/Users/jhchoi/common/src/yt-3.0-hg/yt/data_objects/data_containers.py", line 552, in _generate_fields self.field_data[field] = self._generate_field(field) File "/Users/jhchoi/common/src/yt-3.0-hg/yt/data_objects/data_containers.py", line 221, in _generate_field raise YTCouldNotGenerateField(field, self.pf) yt.utilities.exceptions.YTCouldNotGenerateField: Could field '('all', 'particle_position_x')' in DD0023 could not be generated. ===================================== Do you have any idea what is the problem? This script has been working fine in yt-2.5.4. Thank you in advance, Junhwan

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Issue with ART tutorial
by Alex Bogert 23 Sep '13

23 Sep '13

Following the ART data tutorial on the site http://yt-project.org/doc/analyzing/loading_data.html#art-data I tried this : from yt.mods import * file = "/u/cmoody3/data/art_snapshots/SFG1/10MpcBox_csf512_a0.460.d" pf = load(file,discover_particles=True,grid_particles=2,limit_level=3) and in return I see : TypeError: __init__() got an unexpected keyword argument 'grid_particles' TypeError: __init__() got an unexpected keyword argument 'discover_particles' Version info: >>> import yt >>> print yt.__version__ 3.0-dev

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Mapping Particle Velocities to a Field
by Alex Bogert 21 Sep '13

21 Sep '13

Hi all, I was wondering if yt has the ability to map particle velocities to an evenly divided field or grid. I was unable to resolve this using resources on the website. Does anyone have any suggestions on how to accomplish this using yt? Thanks, Alex

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field parameters for off-axis projections
by John ZuHone 21 Sep '13

21 Sep '13

Hello, Does anyone know a way to use a field with a field parameter in an off-axis projection? Best, John Z

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New PyNE / yt / MOAB IPython notebook for neutron diffussion
by Anthony Scopatz 20 Sep '13

20 Sep '13

Hello All, In case you have otherwise missed it, Matt Turk and I spent the past week getting yt and PyNE and MOAB all working nicely together. We produced this awesome IPython notebook which simulation a fuel pin in a reactor. The video at the bottom of the page I think is hands down one of the coolest things I have ever done. http://nbviewer.ipython.org/urls/raw.github.com/pyne/sandbox/master/ndiff.i… Be Well Anthony

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Sorry, re: off-axis projections and field parameters
by John ZuHone 20 Sep '13

20 Sep '13

I just realized an essentially equivalent question was asked recently--doh! Sorry about the spam. JZ

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"Partial" Projection
by Munier Azzam Salem 19 Sep '13

19 Sep '13

Hey Guys, I'm a bit confused on the projection plot. By default, when you hand YT a width, does it use that width to restrict the depth of the projection (i.e. limits the entire analysis to a cube?) or does it sum along the entire line-of-sight through the whole simulation box (a french fry?). If the latter is the default, is there a way to override this? thanks! Munier -- Munier A. Salem // 845.489.6450

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Proposing changing the way parameter files get accessed
by Matthew Turk 19 Sep '13

19 Sep '13

Hi all, Because yt is primarily exposed as a library on top of which scripts and analysis can be built, we have recently (wow, actually, it's been almost a year!) attempted to start a mechanism of proposing, discussing and then finally implementing changes that touch the API. (YTEPs, or "yt Enhancement Proposals.") Because this particular change would be quite wide-ranging, I wanted to bring it up before it got much further in the discussion. https://bitbucket.org/yt_analysis/ytep/pull-request/24/ytep-0018-reducing-d… Essentially, what this would do is eliminate this operation: 1.0/pf["cm"] or 128.0/pf["mpc"] to specify length units. Any accessing of a parameter file (static output, dataset, whatever) like a dictionary would be changed. The initial implementation of the YTEP suggests that this be limited to just allowing parameters (i.e., this would be things that the simulation frontend identifies as controlling the simulation) but not units, conversion factors, etc etc, to be accessed this way. But, there have been discussions in the pull request about making it so that a "pf" cannot be accessed like a dictionary at all. This would exclusively change in yt 3.0, and would not propagate to the current releases. However, since we're hoping to shift development over to 3.0 not too long from now, I think getting input on this possible change would be extremely valuable. So if you're interested, head on over to the YTEP and share your feelings. This would likely break a lot of scripts, but it's also a ways off, and you can always stick with the current version of yt you're using. Thanks, Matt

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