I have a simplified example of a 2x2x2 cuboid mesh with constant values on each element, stored in the variable group_0 in Exodus format (this is all done with MOOSE). My environment is Yt 3.4.1 and Python 3.6.5.
If I do a SlicePlot and try to use annotate_contour, I end up with an indexing error. I've tried to follow the traceback but frankly I'm not well versed enough with Yt to make any sense of it. Interestingly, if I instead attempt to plot a 2x2x1 mesh cut in the z-plane, the contours will plot without issue.
I've uploaded the full output, the simple (4 line) example, and my Exodus file: http://use.yt/upload/078c018a
Thank you in advance for the assistance.
Hello all,
In the rockstar call function if you dont supply a force_res for your simulation, it runs the call
if force_res is None:
tds = ts[-1] # Cache a reference
self.force_res = tds.index.get_smallest_dx().in_units("Mpc/h")
# We have to delete now to wipe the index
del tds
in the runrockstar.py file in yt.
However, I get an error
File "./runrockstar.py", line 266, in <module>
num_readers=args['num_readers'])
File "./runrockstar.py", line 198, in run_rockstar
particle_mass=dm_min_mass)
File "/home1/sflarkin/build/yt/yt/analysis_modules/halo_finding/rockstar/rockstar.py", line 221, in __init__
self.force_res = tds.index.get_smallest_dx().in_units("Mpc/h")
P014 yt : [ERROR ] 2018-07-20 13:58:08,873 AttributeError: 'numpy.float64' object has no attribute 'in_units'
I am not sure what is causing this, I have been looking in my fields for a problem but do not see any.
Hello, yt-users,
I am using yt.FITSProjection to write the field projection to a FITS file.
As stated in the documentation, it always makes projections of the width of
domain size. But I need to make the FITS projection plot with defined width
or arbitrary box size. Is there any way to do so?
I tried with Geometry Data objects as it contains the data set as a whole
but problem is that it doesn't have the coordinates attribute. Is there any
way to take out the coordinate info also, or create a small dataset of ENZO
simulation (cube of small size).
Thanks,
-Prateek
Hello all,
I am attempting to run a yt fork I made to fix the issue I noted yesterday. I installed the fork and rockstar support using the conda based install method listed on the install guide, but I can't run any scripts using this new version, as It wont override my default python program. I was wondering the correct way to do this?
Thanks
Hey All,
I am having a problem running rockstar with yt. I am updating a python 2 code that was used to run the same simulations I am running, but am getting 2 errors when running it. The first error occurs in this section of code:
if MPI.COMM_WORLD.Get_rank()==0:
print()
print('Beginning Rockstar analysis in ', sim_dir)
print('Placing output in ', out_dir)
# Generate data series
snap_base = sim_dir+ '/' + snap_base + '*'
ts = yt.DatasetSeries(snap_base)
if len(ts) > 1:
first_snap = ts[0]
last_snap = ts[-1]
if MPI.COMM_WORLD.Get_rank()==0:
print('first snapshot: ', first_snap.basename)
print('last snapshot: ', last_snap.basename)
else:
last_snap = ts[0]
if MPI.COMM_WORLD.Get_rank()==0:
print('snapshot: ', last_snap.basename)
# Create particle union if needed
particle_type = particle_types[0]
ad = last_snap.all_data()
particle_masses = yt.np.unique(ad[(particle_type, 'particle_mass')].in_units('Msun/h'))
total_particles = ad.quantities.total_quantity((particle_type, "particle_ones"))
if MPI.COMM_WORLD.Get_rank()==0:
print('Using particle(s) ', particle_types, ' with mass(es) ', particle_masses)
print()
When the script gets to the total_particles = ad.quantities...., I get this error:
File "./runrockstar.py", line 269, in <module>
num_readers=args['num_readers'])
File "./runrockstar.py", line 149, in run_rockstar
particle_masses = yt.np.unique(ad[(particle_type, 'particle_mass')].in_units('Msun/h'))
File "/home1/sflarkin/build/yt-conda/src/yt-git/yt/data_objects/data_containers.py", line 282, in __getitem__
self.get_data(f)
File "/home1/sflarkin/build/yt-conda/src/yt-git/yt/data_objects/data_containers.py", line 1334, in get_data
particles, self, self._current_chunk)
File "/home1/sflarkin/build/yt-conda/src/yt-git/yt/geometry/geometry_handler.py", line 227, in _read_particle_fields
fields_to_read)
File "/home1/sflarkin/build/yt-conda/src/yt-git/yt/utilities/io_handler.py", line 199, in _read_particle_selection
psize = self._count_particles_chunks(chunks, ptf, selector)
File "/home1/sflarkin/build/yt-conda/src/yt-git/yt/utilities/io_handler.py", line 170, in _count_particles_chunks
for ptype, (x, y, z) in self._read_particle_coords(chunks, ptf):
File "/home1/sflarkin/build/yt-conda/src/yt-git/yt/frontends/art/io.py", line 102, in _read_particle_coords
x = self._get_field((ptype, "particle_position_x"))
File "/home1/sflarkin/build/yt-conda/src/yt-git/yt/frontends/art/io.py", line 139, in _get_field
tr[field] = rp([ax])[0]/dd - off
File "/home1/sflarkin/build/yt-conda/src/yt-git/yt/frontends/art/io.py", line 134, in <lambda>
idxb=idxb, fields=ax)
File "/home1/sflarkin/build/yt-conda/src/yt-git/yt/frontends/art/io.py", line 458, in read_particles
ranges = get_ranges(skip, count, field, **kwargs)
File "/home1/sflarkin/build/yt-conda/src/yt-git/yt/frontends/art/io.py", line 425, in get_ranges
for page in range(num_pages):
P001 yt : [ERROR ] 2018-07-17 15:24:08,955 TypeError: 'float' object cannot be interpreted as an integer
P001 yt : [ERROR ] 2018-07-17 15:24:08,955 Error occured on rank 1.
I am not sure why this is occuring, and if I am missing something obvious.
The other error occurs when attempting to clear the cache, done as follows:
if len(ts) > 1 : del first_snap
del last_snap
_cached_datasets.clear()
but _cached_datasets is said as not defined, despite being called by an earlier call of:
from yt.data_objects.static_output import _cached_datasets
I am wondering if this is the correct way to go about that?
Thanks
I am having a problem running rockstar with yt. I am updating a python 2
code that was used to run the same simulations I am running, but am getting
2 errors when running it. The first error occurs in this section of code:
if MPI.COMM_WORLD.Get_rank()==0:
print()
print('Beginning Rockstar analysis in ', sim_dir)
print('Placing output in ', out_dir)
# Generate data series
snap_base = sim_dir+ '/' + snap_base + '*'
ts = yt.DatasetSeries(snap_base)
if len(ts) > 1:
first_snap = ts[0]
last_snap = ts[-1]
if MPI.COMM_WORLD.Get_rank()==0:
print('first snapshot: ', first_snap.basename)
print('last snapshot: ', last_snap.basename)
else:
last_snap = ts[0]
if MPI.COMM_WORLD.Get_rank()==0:
print('snapshot: ', last_snap.basename)
# Create particle union if needed
particle_type = particle_types[0]
ad = last_snap.all_data()
particle_masses = yt.np.unique(ad[(particle_type,
'particle_mass')].in_units('Msun/h'))
total_particles = ad.quantities.total_quantity((particle_type,
"particle_ones"))
if MPI.COMM_WORLD.Get_rank()==0:
print('Using particle(s) ', particle_types, ' with mass(es) ',
particle_masses)
print()
When the script gets to the total_particles = ad.quantities...., I get this
error:
File "./runrockstar.py", line 269, in <module>
num_readers=args['num_readers'])
File "./runrockstar.py", line 149, in run_rockstar
particle_masses = yt.np.unique(ad[(particle_type,
'particle_mass')].in_units('Msun/h'))
File
"/home1/sflarkin/build/yt-conda/src/yt-git/yt/data_objects/data_containers.py",
line 282, in __getitem__
self.get_data(f)
File
"/home1/sflarkin/build/yt-conda/src/yt-git/yt/data_objects/data_containers.py",
line 1334, in get_data
particles, self, self._current_chunk)
File
"/home1/sflarkin/build/yt-conda/src/yt-git/yt/geometry/geometry_handler.py",
line 227, in _read_particle_fields
fields_to_read)
File
"/home1/sflarkin/build/yt-conda/src/yt-git/yt/utilities/io_handler.py",
line 199, in _read_particle_selection
psize = self._count_particles_chunks(chunks, ptf, selector)
File
"/home1/sflarkin/build/yt-conda/src/yt-git/yt/utilities/io_handler.py",
line 170, in _count_particles_chunks
for ptype, (x, y, z) in self._read_particle_coords(chunks, ptf):
File "/home1/sflarkin/build/yt-conda/src/yt-git/yt/frontends/art/io.py",
line 102, in _read_particle_coords
x = self._get_field((ptype, "particle_position_x"))
File "/home1/sflarkin/build/yt-conda/src/yt-git/yt/frontends/art/io.py",
line 139, in _get_field
tr[field] = rp([ax])[0]/dd - off
File "/home1/sflarkin/build/yt-conda/src/yt-git/yt/frontends/art/io.py",
line 134, in <lambda>
idxb=idxb, fields=ax)
File "/home1/sflarkin/build/yt-conda/src/yt-git/yt/frontends/art/io.py",
line 458, in read_particles
ranges = get_ranges(skip, count, field, **kwargs)
File "/home1/sflarkin/build/yt-conda/src/yt-git/yt/frontends/art/io.py",
line 425, in get_ranges
for page in range(num_pages):
P001 yt : [ERROR ] 2018-07-17 15:24:08,955 TypeError: 'float' object
cannot be interpreted as an integer
P001 yt : [ERROR ] 2018-07-17 15:24:08,955 Error occured on rank 1.
I am not sure why this is occuring, and if I am missing something obvious.
The other error occurs when attempting to clear the cache, done as follows:
if len(ts) > 1 : del first_snap
del last_snap
_cached_datasets.clear()
but _cached_datasets is said as not defined, despite being called by an
earlier call of:
from yt.data_objects.static_output import _cached_datasets
I am wondering if this is the correct way to go about that?
Thanks
Hi all,
I'm here at the scipy conference this week where they just announced the
winners of the John Hunter Excellence in Plotting Contest.
This year the second prize winner was Enrico Garaldi, who made a very nice
visualization of a cosmological RAMSES simulation using yt to extract the
data and matplotlib to make the plot.
You can see more details about this plot here:
http://droettboom.com/jhepc2018-judge-packet/entry19.html
Congratulations Enrico and congratulations to the other winners and
honorable mentions as well.
-Nathan
Dear yt-users,
Hi, I want to know about the function "extract_connected_sets". I want to
extract SuperNova enriched bubbles (which I define as Z > -4 or something)
and analyze its size or mass or some other values. I'm working with
cosmological simulation by enzo, and there are many SN enriched bubbles.
What I need is the set of "bubble regions" of (probably) YTRegions. For
this purpose, it seemed to me that "extract_connected_sets" would be the
perfect function, but I don't understand what this object is, or how I can
analyze the object, because when I tried projection plot of the objects,
nothing appeared.
Could you tell me how I can use "extract_connected_sets"? Or, is there any
other way to extract SN enriched region?
Best,
YT
Dear yt-users,
Hello. I am Eun-jin.
I tried to visualize Gadget's simulations(Gadget2) and followed
https://yt-project.org/docs/dev/cookbook/gadget_notebook.html
But It plots only 1/4 (upper and right side).
I wondered whether my simulation data has some problems,
so I checked some gadget snapshots from yt sample datasets 'Gadget3-snap-format2', 'IsothermalCollapse',
but the first one gives 1/4 and the last one is fine.
I also tried the same with the latest stable version yt-3.4.1 (before I used yt-3.5 dev),
and it gave me the same results.
Can I ask how to resolve this?
Any suggestions would be greatly appreciated.
Thank you,
Eun-jin
