Notebook server question
by Andrew Myers
Hello yt users,
I have a (perhaps naive) ssh question related to the yt notebook. I would
like to run a yt notebook server on machine A. However, machine A cannot be
directly accessed via ssh from the wider internet. Instead, I must first
ssh into machine B, and then ssh from B to A. Machine B cannot run the
notebook server itself. Does anyone know how I can configure things -
perhaps by using a more complicated ssh tunnel command - so I that access a
notebook server running on machine A through machine B?
Thanks,
Andrew
4 years, 8 months
change size of phase plot
by Stephanie Tonnesen
Hi all,
I am trying to make my phase plots smaller so they can fit more nicely into
a paper. Alternatively, I would be fine with upping the font size so when
I shrink them you can read the axes. I found advise on how to do this for
slices, but not for phase_objects.
pc = PlotCollection(pf)
tracerp25 = alld.cut_region(["grid['specific_scalar[0]'] > 0.5", "grid['z']
< 0.192","grid['z'] > -0.192","grid['cyl_RCode'] < 1.2"])
pc.add_phase_object(tracerp25,["Density","z-velocity","CellMassSolar"],weight=None,x_bins=50,y_bins=50,y_bounds
= [-4e7,8e7],x_bounds=[5e-28,5e-23],x_log=True,y_log=False)
Any help is much appreciated!
Thanks,
Stephanie
4 years, 8 months
Light Cone Projection
by Pengfei Chen
Hi all,
I downloaded the example script of light cone projectoin(
http://yt-project.org/doc/cookbook/cosmological_analysis.html#light-cone-...)
to my laptop and changed the Enzo simulation parameter file and redshifts.
But when I ran it the following error occurred:
File "light_cone_projection.py", line 19, in <module>
find_outputs=False)
File
"/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/analysis_modules/cosmological_observation/light_cone/light_cone.py",
line 158, in __init__
find_outputs=find_outputs)
File
"/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/analysis_modules/cosmological_observation/cosmology_splice.py",
line 44, in __init__
find_outputs=find_outputs)
File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/convenience.py", line
131, in simulation
find_outputs=find_outputs)
File
"/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/frontends/enzo/simulation_handling.py",
line 81, in __init__
find_outputs=find_outputs)
File
"/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/data_objects/time_series.py",
line 343, in __init__
self._parse_parameter_file()
File
"/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/frontends/enzo/simulation_handling.py",
line 273, in _parse_parameter_file
param, vals = (i.strip() for i in line.split("="))
ValueError: need more than 1 value to unpack
Does the parameters "near_redshift" and "far_redshift" in LightCone need to
be the same with "CosmologyFinalRedshift" and "CosmologyInitialRedshift" in
enzo parameter file?
Does anyone know how to solve this?
Thank you all!
Pengfei
4 years, 9 months
chemical species abundances discrepancy
by poetaste＠gmail.com
Hi Guys,
I did a simple test with enzo and I tried to plot a radial profile of
the chemical species fractions with YT.
The problem is that if I use the YT function which intrinsically plot
the fraction for a species, let's say H2I_Fraction (as usual), and
compare this with a direct evaluation of the mass fraction:
data['H2I_Density']/data['Density']
I obtain some slightly different results, mostly at large radii.
Anyone might explain this discrepancy!? This happens with all the
species.
Thank you in advance
Stefano
4 years, 10 months
More PhasePlots questions
by Stephanie Tonnesen
Hi everyone!
I have a few more PhasePlots questions.
1) I would like to force my axes to be a particular range. I am looking
at several times in my simulation, and the length of the stripped tail
increases, so different PhasePlots end up with different height above the
disk x-axis ranges, which makes comparison more annoying.
2) I would like for the last tick label to be blank--to not print out on
the figure (in the attachment, I would like for '100' to not be there).
3) On a slightly different note, I want the bin size to be bigger. The
PhasePlots look very streaky, see attached.
I will paste my current set of commands for making my PhasePlot. Thanks
for any help!
Stephanie
plot =
PhasePlot(tracerp25,"zkpc","zvelocity8",["CellMassMsun"],weight_field=None,fontsize=19)#,x_bounds=[3e-28,5e-23],y_bounds=[-0.7,1.2])
plot.set_log("zkpc",False)
plot.set_log("zvelocity8",False)
plot.set_zlim("CellMassMsun",1e4,1e9)
plot.set_figure_size(3)
ax = plot.plots['CellMassMsun'].axes
ax.set_ylabel(r'z-velocity (10$^8$ cm/s)',fontsize=10)
ax.set_xlabel(r'Height above disk (kpc)',fontsize=10)
print r'z-velocity (10$^8$ cm/s)'
for label in ax.xaxis.get_ticklabels():
#label.set_color('red')
label.set_rotation(35)
label.set_fontsize(11)
for label in ax.yaxis.get_ticklabels():
label.set_fontsize(10)
plot.save()
4 years, 10 months
Trouble with SciPy Install
by Nathan Butcher
Hello,
I am trying to install yt with SciPy on Michigan State University's HPCC
system and am running into errors that I cannot resolve by following the
instructions in the install script. I have tried uncommenting each of the
NUMPY_ARGS statements and had no success. I have attached the log file from
my most recent installation attempt as the error message is long. My guess
is that it has to do with the "recompile with -fPIC" message but I cannot
figure out what that means.
Can anybody explain what this error message means and how to resolve it.
Thank you,
Nathan Butcher
4 years, 10 months
Mailing list issues
by Matthew Turk
Hi all,
We were having some mailing list issues earlier in the day, but I have
been assured they are now fixed. So if you're seeing this, and got a
bounce earlier, the clog seems to have been resolved. Sorry about
that.
-Matt
4 years, 10 months
ProjectionTransferFunction with Camera
by Munier Azzam Salem
Hey Guys,
I'm trying to get simple projections, but using the Camera interface,
to allow skewed perspectives. I've tried simply allowing the camera to use
the default ProjectionTransferFunction, in lieu of prettier color transfer
functions ... this seems to yield an all-black image. I've also tried
explicitly setting it's bounds (both with log and non-log limits). This
doesn't seem to help. I see this issue came up about a year ago
here<http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2013-January/...>
.
My script's included below. I'm tempted to just tweak my inputs to
the color trasnfer function to mimic a simple projection.
thanks!
Munier
My script:
*from yt.mods import **
*import yt.visualization.volume_rendering.api as vr*
*from yt.visualization.volume_rendering.transfer_functions import
ProjectionTransferFunction as PTF*
*pf = load("DD0179/DD0179")*
*field = 'Density'*
*use_log = True*
*# Find the bounds in log space of for your field*
*dd = pf.h.all_data()*
*limits = np.array(dd.quantities["Extrema"](field)[0]) * pf.units['cm']*
*#if use_log:*
*# limits = np.log(limits)*
*# Set up the camera parameters: center, looking direction, width,
resolution*
*c = np.array([.333]*3)*
*L = np.array([1.0, 1.0, 1.0])*
*W = 0.3 / pf["unitary"]*
*N = 1028*
*# Create a camera object*
*cam = vr.Camera(c, L, W, (N,N), transfer_function=PTF(limits),pf=pf)*
*im = cam.snapshot('density.png')*
--
Munier A. Salem // 845.489.6450
4 years, 10 months
