Hi there,
As I received the advice the other day,
I converted the Gadget2 data to arbitrary_grid data by referring to the following URL,
https://yt-project.org/docs/dev/analyzing/objects.html
https://yt-project.org/docs/dev/analyzing/saving_data.html
and reloaded it.
As I received the advice the other day,
I converted the Gadget2 data to arbitrary_grid data by referring to the following URL, and reloaded it.
Then, probably because the converted data does not have the necessary data elements, an error is displayed and clamp finding is not possible.
What elements should be added to the arbitrary_grid data in order to perform the clamp finding introduced on the homepage?
We apologize for the inconvenience, but thank you for your reply.
Below are all the results of the execution.
It's very hard to see, but please forgive me.
=================================================================================
import numpy as np
import yt
from yt.data_objects.level_sets.api import *
fname = "Gadget2.0090"
bbox_lim = 70 # pc
bbox = [[-bbox_lim, bbox_lim], [-bbox_lim, bbox_lim], [-bbox_lim, bbox_lim]]
ds = yt.load(fname, bounding_box=bbox)
ds.index
sorted(ds.field_list)
print(ds.field_list)
obj = ds.arbitrary_grid([-10, -10, -10], [10, 10, 10], dims=[128, 128, 128])
print(obj)
ds2 = obj.save_as_dataset(fields=[("deposit", "all_density"), ("deposit", "all_mass")])
print(ds2)
-------------------------------------------------------------------------------------------------------------------------------------------
yt : [INFO ] 2021-12-15 11:52:05,207 Omega Lambda is 0.0, so we are turning off Cosmology.
yt : [INFO ] 2021-12-15 11:52:05,209 Assuming length units are in kpc (physical)
yt : [INFO ] 2021-12-15 11:52:05,280 Parameters: current_time = 10.68
yt : [INFO ] 2021-12-15 11:52:05,282 Parameters: domain_dimensions = [2 2 2]
yt : [INFO ] 2021-12-15 11:52:05,284 Parameters: domain_left_edge = [-70. -70. -70.]
yt : [INFO ] 2021-12-15 11:52:05,286 Parameters: domain_right_edge = [70. 70. 70.]
yt : [INFO ] 2021-12-15 11:52:05,289 Parameters: cosmological_simulation = 0
yt : [INFO ] 2021-12-15 11:52:05,295 Allocating for 2.198e+06 particles (index particle type 'all')
yt : [INFO ] 2021-12-15 11:52:05,780 Identified 1.478e+05 octs
[('Gas', 'Coordinates'), ('Gas', 'Density'), ('Gas', 'InternalEnergy'), ('Gas', 'Mass'), ('Gas', 'ParticleIDs'), ('Gas', 'SmoothingLength'), ('Gas', 'Velocities'), ('Stars', 'Coordinates'), ('Stars', 'Mass'), ('Stars', 'ParticleIDs'), ('Stars', 'Velocities'), ('all', 'Coordinates'), ('all', 'Mass'), ('all', 'ParticleIDs'), ('all', 'Velocities')]
YTArbitraryGrid (Gadget2): , left_edge=[-3.08567758e+22 -3.08567758e+22 -3.08567758e+22] cm, right_edge=[3.08567758e+22 3.08567758e+22 3.08567758e+22] cm, ActiveDimensions=[128 128 128]
yt : [INFO ] 2021-12-15 11:52:09,509 Saving field data to yt dataset: Gadget2_arbitrary_grid.h5.
Gadget2_arbitrary_grid.h5
=================================================================================
import yt
fname2 = 'Gadget2_arbitrary_grid.h5'
sphere_ds = yt.load(fname2)
sphere_ds.index
sorted(sphere_ds.field_list)
-------------------------------------------------------------------------------------------------------------------------------------------
yt : [INFO ] 2021-12-15 11:52:15,177 Parameters: current_time = 10.68 code_time
yt : [INFO ] 2021-12-15 11:52:15,179 Parameters: domain_dimensions = [128 128 128]
yt : [INFO ] 2021-12-15 11:52:15,181 Parameters: domain_left_edge = [-10. -10. -10.] code_length
yt : [INFO ] 2021-12-15 11:52:15,183 Parameters: domain_right_edge = [10. 10. 10.] code_length
yt : [INFO ] 2021-12-15 11:52:15,187 Parameters: cosmological_simulation = 0
[('grid', 'all_density'),
('grid', 'all_mass'),
('grid', 'dx'),
('grid', 'dy'),
('grid', 'dz'),
('grid', 'x'),
('grid', 'y'),
('grid', 'z')]
=================================================================================
import numpy as np
import yt
from yt.data_objects.level_sets.api import *
fname2 = 'Gadget2_arbitrary_grid.h5'
ds = yt.load(fname2)
data_source = ds.disk([0.5, 0.5, 0.5], [0.0, 0.0, 1.0], (8, "pc"), (1, "pc"))
master_clump = Clump(ds, ("grid", "all_density"))
master_clump.add_validator("min_cells", 20)
master_clump.add_info_item("center_of_mass")
c_min = data_source["grid", "all_density"].min()
c_max = data_source["grid", "all_density"].max()
step = 2.0
print(c_min)
print(c_max)
find_clumps(master_clump, c_min, c_max, step)
-------------------------------------------------------------------------------------------------------------------------------------------
yt : [INFO ] 2021-12-15 13:11:53,189 Parameters: current_time = 10.68 code_time
yt : [INFO ] 2021-12-15 13:11:53,191 Parameters: domain_dimensions = [128 128 128]
yt : [INFO ] 2021-12-15 13:11:53,193 Parameters: domain_left_edge = [-10. -10. -10.] code_length
yt : [INFO ] 2021-12-15 13:11:53,195 Parameters: domain_right_edge = [10. 10. 10.] code_length
yt : [INFO ] 2021-12-15 13:11:53,198 Parameters: cosmological_simulation = 0
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
<ipython-input-1-f88c4eeda40e> in <module>()
17 #master_clump = Clump(data_source, ("gas", "cell_density"))
18
---> 19 master_clump = Clump(ds, ("grid", "all_density"))
20
21 master_clump.add_validator("min_cells", 20)
/home/salty1840/anaconda3/envs/yt3/lib/python2.7/site-packages/yt/data_objects/level_sets/clump_handling.pyc in __init__(self, data, field, parent, clump_info, validators, base, contour_key, contour_id)
61 self.field = field
62 self.parent = parent
---> 63 self.quantities = data.quantities
64 self.min_val = self.data[field].min()
65 self.max_val = self.data[field].max()
AttributeError: 'YTGridDataset' object has no attribute 'quantities'
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