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
5 years
Problems with fields
by Cameron Hummels
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
5 years, 5 months
reading Gadget-HDF5 format in yt-3.0
by Brendan Griffen
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
5 years, 6 months
new yt website, now with gallery!
by Britton Smith
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
5 years, 6 months
Stars Particles
by Francia Riesco
Hi Everybody,
I am trying to run this example from the cookbook
from yt.mods import *
from yt.analysis_modules.star_analysis.api import *
pf = load("data0030")
# Find all the haloes, and include star particles.
haloes = HaloFinder(pf, dm_only=False)
# Set up the spectrum builder.
spec = SpectrumBuilder(pf, bcdir="/home/user/bc", model="salpeter")
# Iterate over the haloes.
for halo in haloes:
# Get the pertinent arrays.
ct = halo["creation_time"]
sm = halo["ParticleMassMsun"]
metal = halo["metallicity_fraction"]
# Select just the stars.
stars = (ct > 0)
ct = ct[stars]
sm = sm[stars]
metal = metal[stars]
# Calculate the spectrum.
spec.calculate_spectrum(star_mass=sm, star_creation_time=ct,
star_metallicity_fraction=metal)
# Write out the SED using the default flux normalization.
spec.write_out_SED(name="halo%05d.out" % halo.id)
This is my code
http://paste.yt-project.org/show/3885/
But I get this error:
Link length is 0.001000
Filling in 3697686 particles
Number of initial groups:6036
Number of groups:257
FOF CPU TIME: 10395.710700 secs
Found [ -1 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17
18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35
36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53
54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71
72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89
90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107
108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125
126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143
144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161
162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197
198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215
216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233
234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251
252 253 254 255 256 257] unique groupings
yt : [INFO ] 2013-09-25 15:15:27,721 Initializing HOP
yt : [INFO ] 2013-09-25 15:15:27,721 Getting particle_position_x using ParticleIO
yt : [INFO ] 2013-09-25 15:21:16,316 Getting particle_position_y using ParticleIO
yt : [INFO ] 2013-09-25 15:25:36,923 Getting particle_position_z using ParticleIO
yt : [INFO ] 2013-09-25 15:29:48,316 Getting ParticleMassMsun using ParticleIO
Copying arrays for 47944939 particles
Calling hop... 47944939 1.600e+02
nSmooth = 65 kd->nActive = 47944939
Building Tree...
Finding Densities...
Finding Densest Neighbors...
Grouping...
Merging Groups...
Writing Output...
All Done!Calling regroup...
No minimum group size specified. Assuming 10 particles.
ngroups = 262744
yt : [INFO ] 2013-09-25 15:52:17,649 Parsing outputs
yt : [INFO ] 2013-09-25 15:52:24,347 Getting ParticleMassMsun using ParticleIO
yt : [INFO ] 2013-09-25 15:57:00,506 Getting particle_position_x using ParticleIO
yt : [INFO ] 2013-09-25 16:01:14,743 Getting particle_position_y using ParticleIO
yt : [INFO ] 2013-09-25 16:06:14,673 Getting particle_position_z using ParticleIO
Traceback (most recent call last):
File "StarsParticleAnalysys.py", line 48, in <module>
spec = SpectrumBuilder(data_source, bcdir="/astro/py/", model="salpeter")
File "/astro/yt-dev/yt-x86_64/src/yt-hg/yt/analysis_modules/star_analysis/sfr_spectrum.py", line 278, in __init__
(100.0 * self._pf.hubble_constant),
AttributeError: 'AMRRegion' object has no attribute 'hubble_constant'
Any suggestion?
Thanks a lot in Advance!
5 years, 6 months
--parallel not working for MPT?
by Semyeong Oh
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
5 years, 6 months
accessing colorbar directly
by Luigi Iapichino
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-m... ,
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/
5 years, 6 months
Overplotting equipotential contours from total potential
by trobolo dinni
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
5 years, 6 months
style keyword in add_projection
by Christine Simpson
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
5 years, 6 months
particle density projection plot in yt-3.0
by Junhwan Choi (최준환)
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
5 years, 6 months
