Hello yt-users,
I have a question about the disk data object. The first input it needs is
center, which according to your website is the coordinates of the
geometrical center of the disk on the simulation length units. So, the
center of the computational domain is c=[0.5,0.5,0.5].
I set the center of two different cylinders in a way that they don’t
overlap. The axis of these cylinders are parallel to the x axis and one is
on the negative X coordinate region while the other one on the positive
region. But, I found that they actually have exactly the same cell centers.
Did I do something wrong?
On the following code the box side is 256 pc, so the center of the first
disk c_1=[0.25,0.5,0.5] with a height of 32 pc does not overlap with the
second disk of center c_2=[0.75,0.5,0.5] also with height 32 pc.
http://paste.yt-project.org/show/275/
I’m using :
---
Version = 3.6.dev0
And the snapshot used is here:
http://use.yt/upload/c58a4c0f
--
Guido
Hi all,
I'm trying to do a volume render of the temperature field inside a
sphere with the following code:
val, loc = ds.find_max('density')
sp = ds.sphere(loc, SP_DIST)
source = VolumeSource(sp, 'temperature')
scene = Scene()
scene.add_source(source)
# v is calculated based on angular momentum
camera = scene.add_camera(sp, lens_type= 'perspective')
cam_position = loc + v * CAM_DIST
camera.set_position(cam_position)
camera.set_focus(loc)
source.set_field('temperature')
source.set_log(True)
bounds = (UPPER, LOWER)
tf = yt.ColorTransferFunction(np.log10(bounds))
tf.add_layers(12, colormap='jet')
source.tfh.tf = tf
source.tfh.bounds = bounds
source.tfh.plot('transfer_function.png', profile_field='temperature')
scene.save("render_t={:.3f}".format(times[i]), sigma_clip= 1)
Upon saving though I encounter the error:
Traceback (most recent call last):
File "plot_3d.py", line 51, in <module>
scene.save("render_t={:.3f}".format(times[i]), sigma_clip= 1)
#last sigma = 2
File
"/opt/apps/pkgs/cpython/3.7.1/intel64/intel_2019.2/lib/python3.7/site-packages/yt/visualization/volume_rendering/scene.py",
line 310, in save
yt : [INFO ] 2020-09-15 10:34:02,783 Saving render render_t=0.000.png
self._last_render.write_png(fname, sigma_clip=sigma_clip)
File
"/opt/apps/pkgs/cpython/3.7.1/intel64/intel_2019.2/lib/python3.7/site-packages/yt/data_objects/image_array.py",
line 289, in write_png
scaled = self.rescale(inline=False)
File
"/opt/apps/pkgs/cpython/3.7.1/intel64/intel_2019.2/lib/python3.7/site-packages/yt/data_objects/image_array.py",
line 242, in rescale
np.clip(out, 0.0, 1.0, out)
File "<__array_function__ internals>", line 6, in clip
File
"/opt/apps/pkgs/cpython/3.7.1/intel64/intel_2019.2/lib/python3.7/site-packages/numpy/core/fromnumeric.py",
line 2084, in clip
return _wrapfunc(a, 'clip', a_min, a_max, out=out, **kwargs)
File
"/opt/apps/pkgs/cpython/3.7.1/intel64/intel_2019.2/lib/python3.7/site-packages/numpy/core/fromnumeric.py",
line 61, in _wrapfunc
return bound(*args, **kwds)
File
"/opt/apps/pkgs/cpython/3.7.1/intel64/intel_2019.2/lib/python3.7/site-packages/numpy/core/_methods.py",
line 132, in _clip
um.clip, a, min, max, out=out, casting=casting, **kwargs)
File
"/opt/apps/pkgs/cpython/3.7.1/intel64/intel_2019.2/lib/python3.7/site-packages/numpy/core/_methods.py",
line 85, in _clip_dep_invoke_with_casting
return ufunc(*args, out=out, **kwargs)
File
"/opt/apps/pkgs/cpython/3.7.1/intel64/intel_2019.2/lib/python3.7/site-packages/yt/units/yt_array.py",
line 1401, in __array_ufunc__
"added to YTArray." % (str(ufunc), len(inputs)))
RuntimeError: Support for the <ufunc 'clip'> ufunc with 3 inputs has not
beenadded to YTArray.
I would also like to eventually add a colorbar to the side of the
created image which represents the transfer function and annotate text
as well. Does the render functionality allow me to do this? Any help on
these topics would be much appreciated.
Many thanks,
Sam Patrick
Hello,
data_source in SlicePlot does not work (data_source in ProjectionPlot works). Would you explain how to enable it or fix the problem?
ds= yt.load("../DD2000/jf2000")
ad = ds.all_data()
dense_ad = ad.cut_region(["obj['Density'] >= 0"])
p = yt.SlicePlot(ds, 'x',"density",center=[6.5536/2, 6.5536/2,(15.5/2+2.5)],origin=["lower", "center", "domain"]
,data_source=dense_ad )
I chose 0 so that it will pick up all the gas but it does not.
There is no error message. It just does not show anything much in the figure. How can I attach figures here?
Hello again,
I am using yt slices and projections with scale annotation. I have my plots in comoving units ("Mpccm/h") but whenever I want to use the same units for annotation:
slc.annotate_scale(corner='lower_right', coeff=10, units='Mpccm/h'),
yt does not recognize these units. Am I missing something or only the physical scale annotation is possible ?
Thanks,
Salome
Hi!
Working on the FLASH code (dynamic mesh refinement), I am looking for how could I get from the HDF5 Outputs the spatial positions (in physical units).
Idealy, if I run a 2D simulation, I would like to obtain x and y arrays at a given time.
It is not necessarally a YT issue but it is obvious that some modules could help a lot.
Tell me if you have any idea!
Thanks
--
Thibault Goudal
PhD Student CEA
CELIA CNRS UMR5107 laboratory
+33664160842
thibault.goudal(a)u-bordeaux.fr
Dear all,
I am trying to annotate quiver over the projection plot of density field
using the following code line:
* p.annotate_quiver("velocity_x", "velocity_y", factor = 35,
normalize = True, plot_args = {"color":'Red'})*
but it shows an *error*:
File "/home/user1/yt/yt/visualization/plot_window.py", line 997, in
run_callbacks
callback = CallbackMaker(*args[1:], **kwargs)
*TypeError: __init__() got an unexpected keyword argument 'plot_args'*
Without *'plot_args'* keyword argument annotation works fine but I need to
adjust the color and the width of the vectors.
I am using yt Version = 3.5.dev0.
It may be a silly question: while annotating vectors (velocity_x and
velocity_y, say) over the projection plot, is the annotation done after the
weighted line integration of velocity_x and velocity_y over the width of
the projection? and for this also the weight field is the same as we
specified in the field projection method! If so, Is there any way to change
the weight field for the annotation?
Many thanks and regards,
-Prateek
Hi all,
I am attempting to add a divergence field and am running into the issue apparent in the plot below:
The grid artifacts appear to be the meshblocks for mpi parallelization when running the simulation. This doesn’t occur for any other field.
I am working with an Athena++ athdf dataset and using yt version 3.7.dev0.
Here is the script I used to add the desired field:
import yt
from yt.fields.derived_field import ValidateSpatial
import yt.units as u
kappa0 = 9.68e4
ds = yt.load('../pleiades/grf/grf_pr_2_3_nm5_3/TI.uov.00200.athdf',\
units_override=units_override,unit_system="cgs")
grad_fields = ds.add_gradient_fields(("gas","temperature"))
def _therm_cond(field,data):
kappa = kappa0*u.erg/(u.cm*u.K*u.s)
sl_left = slice(None, -2, None)
sl_right = slice(2, None, None)
div_fac = 2.0
ds = div_fac * data['dx'].flat[0]
f = data["temperature_gradient_x"][sl_right,1:-1,1:-1]/ds
f -= data["temperature_gradient_x"][sl_left ,1:-1,1:-1]/ds
if data.ds.dimensionality > 1:
ds = div_fac * data['dy'].flat[0]
f += data["temperature_gradient_y"][1:-1,sl_right,1:-1]/ds
f -= data["temperature_gradient_y"][1:-1,sl_left ,1:-1]/ds
if data.ds.dimensionality > 2:
ds = div_fac * data['dz'].flat[0]
f += data["temperature_gradient_z"][1:-1,1:-1,sl_right]/ds
f -= data["temperature_gradient_z"][1:-1,1:-1,sl_left ]/ds
new_field = np.zeros(data["temperature_gradient_x"].shape, dtype='float64')
new_field = data.ds.arr(new_field,'K/cm**2')
new_field[1:-1,1:-1,1:-1] = f
return kappa*new_field/data['density']
ds.add_field(('gas','therm_cond'), function=_therm_cond, units="erg/(g*s)", sampling_type="cell", take_log=False,
display_name=r'$\nabla \cdot (\kappa\nabla T)/\rho$', force_override=True, validators = [ValidateSpatial(1,
['temperature_gradient_x','temperature_gradient_y','temperature_gradient_z'])])
Has anyone come across this issue before? Is this a known bug or am I just implementing the divergence field incorrectly? Any help is greatly appreciated.
Thanks,
Michael
Hi all,
I'm trying to use the 'density' method for the smooth() function (which points to the class SmoothedDensityEstimate), but I can't find any documentation about how to use the 'density' method of smooth (i.e. what fields, index fields, etc. I should feed it.) Could someone give me an example of how this method should be used? I'm using yt 3.6 with FLASH particle data. The link to the SmoothedDensityEstimate class code is https://github.com/yt-project/yt/blob/6befef2bc0427250fd62395962599be41b193….
Thanks,
Camryn
Hi! I'm working with a FLASH dataset and am trying to use the add_nearest_neighbor_field() function as briefly described here https://yt-project.org/doc/analyzing/fields.html#computing-the-nth-nearest-…. However, when I run the short script (with the input data replaced with my own FLASH dataset), I get the errors yt.fields.field_exceptions.NeedsGridType: (0, None) and NotImplementedError. Is this function not available for FLASH datasets, and is there a workaround? My final goal is to create a smoothed particle field, so if there is a better way than using the nearest_neighbor_distance_64 field in place of a smoothing_length field, please let me know!
Input data:
plt file - http://use.yt/upload/a94cdffd
part file - http://use.yt/upload/dec62ce5
Test Script: http://paste.yt-project.org/show/259/
Camryn
Hi,
Just wondering if it is possible to find the ellipticity of the model. I assume one should first start with all the (x,y,z) coordinates and fit them to an ellipsoid. Is it already implemented in yt?
Thank you
Robin
