Hi all,
I downloaded the example script of light cone projectoin(
http://yt-project.org/doc/cookbook/cosmological_analysis.html#light-cone-pr…)
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
Hello fellow yt'ers:
I'm having some issues with some fields that I don't think are behaving the
way they should be in yt. I'm encountering a number of problems with a
simple 2D enzo dataset (x and y), so I put together a notebook
demonstrating my various issues.
https://hub.yt-project.org/nb/727j2j
To summarize the weirdness from the notebook:
1) The 'dx' field doesn't seem to be able to be displayed (i.e. when I try
to slice it), whereas the 'dy' field is fine. 'dz' even exists, but it's
just uniformly 0, as is expected from a 2D dataset.
2) When I try to produce a new field which is 2^GridLevel, I get weird
results (ignored levels and more).
3-5) I get strange behavior when trying to make a new field combining
GridLevel and 'dy', since GridLevel has twice as many indices as any of
the spatial fields (in the z direction no less). This results in some odd
behavior when I try to pair various subsets of GridLevel with 'dy'.
Any clarification of these ideas is welcome. The docs and source haven't
yet revealed what is going on here. Thanks!
Cameron
--
Cameron Hummels
Postdoctoral Researcher
Steward Observatory
University of Arizona
http://chummels.org
Hi,
I noticed in the update log of yt-3.0 you can now read Gadget HDF5 format
(for OWLS project), but it is possible for Rockstar to read the exact same
formats? I have some HDF5 data and I'd like to run Rockstar on it through
yt if it has this capability in 3.0.
Are there any examples of carrying out such a process? Thanks.
Thanks.
Brendan
Hi everyone,
Today we launched a completely redesigned yt website. It's still at
yt-project.org, but with a completely new look. One of the brand new
features is the yt Gallery (http://yt-project.org/gallery.html). The
gallery is designed to show off examples of yt in the real world and to
give new users an idea of all that's possible.
We have a few really nice contributions up there now, but we want many
more! If you have a figure made at least in part with yt that you're
particularly proud from a paper, poster, talk, press release, or just
something really cool, please consider submitting it to the gallery. To
add something to the gallery, simply fork the yt website repository here:
https://bitbucket.org/yt_analysis/website
Then, add your image (400 pixels wide, preferably) to the directory
img/gallery, add an entry to the gallery.html file, and submit a pull
request. We will also accept embedded movies from vimeo or youtube. Make
sure to add a caption with a brief explanation of the figure, what
functionality you used to make it, and a citation if it appears in a
publication. Also, make sure to add your figure to the top of the gallery
page so it's easy to see what's new.
We look forward to seeing what amazing things people have done!
Britton
Hi all,
I want to divide ENZO simulation into certain regions, do some operation
and save some files in parallel. I used parallel_objects for this.
If I use openMPI and do
$mpirun -np 6 python script.py --parallel
it works fine.
But if I use MPT(a variety of MPICH, I think) and run the exact same
command,
it ignores --parallel and just does things in serial.
Is this expected? I'm new to parallel computation, and kind of stuck here.
Thanks for your help.
Best regards,
Semyeong
Dear all,
I am in the process of moving most of my visualisation scripts from
PlotCollection to the PlotWindow interface. One feature that now I am not
able to find is the capability of customising the tick values in the colorbar
of a plot. Inspired by the example script found in
http://yt-project.org/docs/2.5/cookbook/simple_plots.html#accessing-and-mod… ,
I was thinking about interacting with a matplotlib object directly, but I am
not able to find a suitable one. Could you please suggest me a workaround for
this issue?
Thanks in advance,
Luigi
--
---------------------------------------------------------------
Luigi Iapichino
Universität Heidelberg, Zentrum für Astronomie
Institut für Theoretische Astrophysik
Philosophenweg 12, D-69120 Heidelberg, Germany
Tel: +49 6221 548983, Fax: +49 6221 544221
e-mail: luigi(a)uni-heidelberg.de
URL: http://www.ita.uni-heidelberg.de/~luigi/
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
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
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
