Mailman 3 April 2024 - yt-users

unexpected output when using ParticlePhasePlot
by hyf＠stu.pku.edu.cn April 29, 2024

April 29, 2024

hi everyone, I am trying to use the function ParticlePhasePlot to plot particles' quantities. However, some unexpected results come out. I tried to plot (x-R-"d2center" , y-\Phi-"d2phi" , z-R-"d2center"), and the particles are colored by z-R-"d2center". Ideally, the color should vary monotonically along the x-axis, since the z - R is equal to x - R But the output figure shows that there are particles colored with red dispersed in the full figure. to see the output: https://github.com/yt-project/yt/issues/4887#issue-2268458159 I do not know why this happens and could you please give me some suggestions, thanks a lot! Here is the code: ##################### CODE ######################## import yt from yt.frontends import boxlib from yt.frontends.boxlib.data_structures import AMReXDataset import numpy as np rootdir="./Output" ds = AMReXDataset(rootdir+'/Plt00000') ptc_xname="d2center" ptc_yname="d2phi" ptc_zname="d2center" ptc_cmapname = "hsv" ptcslc = yt.ParticlePhasePlot( ds, ptc_xname, ptc_yname, [ptc_zname], x_bins=800, y_bins=800, ) ptcslc.set_log(ptc_xname,False) ptcslc.set_log(ptc_yname,False) ptcslc.set_log(ptc_zname,False) ptcslc.set_cmap(("particles", ptc_zname), ptc_cmapname) ptcslc.set_zlim(("particles", ptc_zname), 0.04, 0.065) ptcslc.save("testPTC") ##################### CODE ######################## best wishes, Yifeng He

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Find total number of halos from an existing halo catalog
by hannah.obrennan.2021＠mumail.ie April 29, 2024

April 29, 2024

I am loading an existing halo catalog to create a DataSet object: import yt ds = yt.load("test_halo_catalog.h5") I then wish to use the all_data() method: ad = ds.all_data() But if the halo catalog contains zero halos, I get this error message: yt : [INFO ] 2024-04-26 14:06:04,162 Allocating for 0.000e+00 particles Traceback (most recent call last): File "~/hc_analysis.py", line 130, in <module> ad = ds.all_data() File "/home/hannah/anaconda3/envs/yt-rockstar/lib/python3.10/site-packages/yt/data_objects/static_output.py", line 1122, in all_data self.index File "/home/hannah/anaconda3/envs/yt-rockstar/lib/python3.10/site-packages/yt/data_objects/static_output.py", line 559, in index self._instantiated_index = self._index_class( File "/home/hannah/anaconda3/envs/yt-rockstar/lib/python3.10/site-packages/yt/geometry/particle_geometry_handler.py", line 27, in __init__ self._initialize_index() File "/home/hannah/anaconda3/envs/yt-rockstar/lib/python3.10/site-packages/yt/geometry/particle_geometry_handler.py", line 164, in _initialize_index self.regions = ParticleBitmap( File "yt/geometry/particle_oct_container.pyx", line 476, in yt.geometry.particle_oct_container.ParticleBitmap.__init__ TypeError: an integer is required It seems that all_data() only works if the halo catalog contains a nonzero integer number of halos. Is there a method for a DataSet object to determine the total number of halos found? I wish to implement something like this: if ds.total_halos != 0: ad = ds.all_data() else: print("No halos found in this halo catalog") Any help would be much appreciated, thank you! Kind regards, Hannah O'Brennan

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Rays
by Daniel April 26, 2024

April 26, 2024

Hi my name is Daniel, I was trying to figure out the ray functions and seeing how they worked but I have run into the issue of the regular ray function not seeming to work how I thought it would. I have tried using the example programs that are listed in the Overplot the Path of a Ray and it seems the ray is not printing and only printing a singular value. This is my most recent efforts: my_ray = ds.ray((0.5, 0.6, 0), (0.5, 0.8, 0)) ray_sort = np.argsort(my_ray["t"]) density = my_ray[("gas", "density")][ray_sort] p = yt.ProjectionPlot(ds, "z", ("gas", "density")) p.annotate_ray(my_ray) p.show() print(density) I have also tried to do a for loop trying to go through the ray but for this and the for loop all it seems to print is [2.57707049e-27] g/cm**3. No matter what starting point or ending point I give it. I would very much appreciate some help with this if possible because I have no idea why this is doing what it is doing. Thank you, Daniel Ruvalcaba

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Dealing with time averages
by taj30＠cam.ac.uk April 17, 2024

April 17, 2024

Dear all, I am a new yt user, working with idefix data. I was wondering if there is an easy way to do time averages in yt. For example, if I have two vtk files data.0.vtk and data.1.vtk that I can easily load with ds0=yt.load("data.0.vtk") and ds1=yt.load("data.1.vtk"). Is there an easy way to create a datafile dsmean where all fields are means of the fields in ds1 and ds2 ? Sorry if this question has already been asked, or if it's answered in the documentation, but I didn't see it. Thanks in advance, Best wishes, Thomas

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Minimum and Maximum Mass Using Arbitrary Grids Objects and Deposit Field
by Hữu Thịnh Nguyễn April 16, 2024

April 16, 2024

Hi yt developers, When using the Arbitrary Grids Objects and Deposit Field, to speed up my code, I want to obtain the minimum and maximum dark matter mass of each grid. However, it seems like the deposit field only allows total mass or density. Is there another way to work around this? Or how do I manually modify the source code itself to do it? Thank you very much for your help. Best regards, Thinh

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SlicePlot of 3D cylindrical coordinates for FLASH
by sanbackup313＠gmail.com April 6, 2024

April 6, 2024

Hello, First of all, thanks to the yt community for developing the toolkit for visualizing various forms of data. I am working on FLASH simulations in 3D cylindrical coordinates. A SlicePlot of density along 'z' creates a plot of the x-y plane (I assume that yt performs the coordinate transformation internally, converts the radial coordinate 'r' into 'x' and 'y' and generates the plot in the x-y plane), whereas SlicePlot along 'theta' creates a plot of 'r' vs 'z' which understandably considers only the positive values for 'r'. I would like to plot a cross-section of my domain (that considers both postive and negative values of the radial direction either in terms of 'x' or 'y'). i.e., I would like to SlicePlot along 'theta' that creates a plot of 'z' vs 'y' or 'z' vs 'x'. Can someone please guide me how to do it? I am very new to yt and in general to a coding language. Therefore, I request you to kindly elaborate your answer to a level that a layman like me can understand and benefit from it. Thanks in advance :)

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SlicePlot of 3D cylindrical coordinates for FLASH
by sanbackup313＠gmail.com April 5, 2024

April 5, 2024

Hello, First of all, thanks to the yt community for developing the toolkit for visualizing various forms of data. I am working on FLASH simulations in 3D cylindrical coordinates. A SlicePlot of density along 'z' creates a plot of the x-y plane (I assume that yt performs the coordinate transformation internally, converts the radial coordinate 'r' into 'x' and 'y' and generates the plot in the x-y plane), whereas SlicePlot along 'theta' creates a plot of 'r' vs 'z' which understandably considers only the positive values for 'r'. I would like to plot a cross-section of my domain (that considers both postive and negative values of the radial direction either in terms of 'x' or 'y'). i.e., I would like to SlicePlot along 'theta' that creates a plot of 'z' vs 'y' or 'z' vs 'x'. Can someone please guide me how to do it? I am very new to yt and in general to a coding language. Therefore, I request you to kindly elaborate your answer to a level that a layman like me can understand and benefit from it. Thanks in advance :)

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Fastest way to mirror the auto-generation of fields for gas particles?
by Jacob Morgan April 5, 2024

April 5, 2024

yt generates many fields from the few that are saved on the disk. I am doing something weird with TNG data where I basically have 'PartType0' and 'PartType0_78', where 'PartType0_78' holds data on the gas particles at a different snapshot (namely, 78). I basically want yt to act like I have two different names for gas particles and generate the temperature, cylindrical coordinates, entropy, magnetic field, etc for 'PartType0_78' just as it does for 'PartType0'. The fields on disk are named the same. I tracked the fields down to yt/frontends/gadget/fields and/or yt/frontends/gadget/fields, and the setup_gas_particle_fields function. I tried doing it all from the plugins file, but the more I look, the more I feel like there's just a few lines where I'd need to change >>>if ptype=='PartType0': to >>>if ptype in ('PartType0', 'PartType0_78'): in the fields-related scripts and most of my work would be done automatically. Does anyone know where those few places might be?

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Precise Data
by Daniel Ruvalcaba April 4, 2024

April 4, 2024

Hello I am a new user to yt and am also new to python as a coding language. I do have past coding experiences but that is not important. I have been making graphs based on the files given on yt_data and am now trying to see if I can grab specific data from points within the graph. I saw that yt can do that with a sphere and its radius but I would like to see if there was a way to do the same with projection plots (other graphs as well). Specifically what I want to ask is if I can grab data from a graph at specific points within it or if I can draw a line within the graph and grab the data from those lines, and how I would be able to do that. I would be really grateful if someone could help, but if not it is okay. Thank you, Daniel56

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Trouble adding a field to TNG data
by Jacob Morgan April 4, 2024

April 4, 2024

Hey there! I have a relatively extensive plugins file that adds lots of fields. I changed how one of the fields is calculated, but now I am getting an error about an undefined variable. I have the following function: def _get_scalar_func(_ptype, field_name, unit_dict): def _scalar(_ptype, field, data): if field_name in only_gas_fields: _ptype='gas' return data[_ptype, field_name] elif 'velocity_los' in field_name and data.ds.head('RAY')==0: pass else: old_data=data[_ptype, field_name] x_old_units=unyt.unyt_array(old_data.value*unit_dict[field_name][0], units=unit_dict[field_name][1], registry=data.ds.unit_registry) return x_old_units.to(unit_dict[field_name][2]) return _scalar it converts some scalar fields for me based on "unit_dict", which holds what units I want for each property. It also adds the field ('PartType0', 'entropy'), which is just a copy of ('gas', 'entropy') with the first "if" statement. However, it says that the variable "_ptype" is referenced before assignment, and none of my plugins stuff is added. When I try to add a field manually outside the plugins file like so: ds.add_field(('PartType0', 'Density_msun_pc3'), function=_get_scalar_func('PartType0', 'Density', gas_scalar_conversions), sampling_type='particle', units='Msun/pc**3') I get the following long error: Traceback (most recent call last): File "file_loader_tester.py", line 35, in <module> new_yt.add_field(('PartType0', 'Density_msun_pc3'), function=_get_scalar_func('PartType0', 'Density', gas_scalar_conversions), sampling_type='particle', units='Msun/pc**3') File "/home/jacob/.local/lib/python3.8/site-packages/yt/data_objects/static_output.py", line 1593, in add_field self.index File "/home/jacob/.local/lib/python3.8/site-packages/yt/data_objects/static_output.py", line 539, in index self.create_field_info() File "/home/jacob/.local/lib/python3.8/site-packages/yt/data_objects/static_output.py", line 613, in create_field_info self.field_info.load_all_plugins(self.default_fluid_type) File "/home/jacob/.local/lib/python3.8/site-packages/yt/fields/field_info_container.py", line 402, in load_all_plugins self.find_dependencies(loaded) File "/home/jacob/.local/lib/python3.8/site-packages/yt/fields/field_info_container.py", line 415, in find_dependencies deps, unavailable = self.check_derived_fields(loaded) File "/home/jacob/.local/lib/python3.8/site-packages/yt/fields/field_info_container.py", line 612, in check_derived_fields fd = fi.get_dependencies(ds=self.ds) File "/home/jacob/.local/lib/python3.8/site-packages/yt/fields/derived_field.py", line 253, in get_dependencies e[self.name] File "/home/jacob/.local/lib/python3.8/site-packages/yt/fields/field_detector.py", line 125, in __missing__ vv = finfo(self) File "/home/jacob/.local/lib/python3.8/site-packages/yt/fields/derived_field.py", line 294, in __call__ dd = self._function(self, data) File "/home/jacob/.config/yt/my_plugins.py", line 69, in _scalar old_data=data[_ptype, field_name] UnboundLocalError: local variable '_ptype' referenced before assignment This has been working for literally years, and I only made minor changes to the inner _scalar function recently. But this almost seems like an issue with the add_field() function, which I don't think I have ever touched. Any ideas?

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