Google summer of code?
by Nathan Goldbaum
Hi all,
Would anyone be interested in putting together some project ideas for
google summer of code?
OpenAstronomy will likely be applying to be an umbrella org and they've
asked me to indicate whether we'd like to participate again this year. Last
year we didn't end up getting many applications, so we should try to think
hard about writing good project ideas. We could also think about applying
under the NumFocus org instead of OpenAstronomy, since yt is increasingly
not only for astronomical simulation data.
Applications are due Feb 9, so please try to get back to me either here or
off-list so I can let the OpenAstronomy organizers know. If there's enough
interest I'll try to put together a video call so we can discuss our
portion of the application process.
-Nathan
1 year, 12 months
Issue #1312: depositing particle velocities in gadget (yt_analysis/yt)
by Desika Narayanan
New issue 1312: depositing particle velocities in gadget
https://bitbucket.org/yt_analysis/yt/issues/1312/depositing-particle-velo...
Desika Narayanan:
Trying to add a deposited particle field from gadget particle velocities (say, gas in this instance; https://paste.yt-project.org/show/6999/ ) returns error:
```
In [1]: run vel_proj
yt : [INFO ] 2017-01-17 15:27:33,808 Calculating time from 3.448e-01 to be 1.108e+17 seconds
yt : [INFO ] 2017-01-17 15:27:33,808 Assuming length units are in kpc/h (comoving)
yt : [INFO ] 2017-01-17 15:27:33,825 Parameters: current_time = 1.10758107325e+17 s
yt : [INFO ] 2017-01-17 15:27:33,825 Parameters: domain_dimensions = [2 2 2]
yt : [INFO ] 2017-01-17 15:27:33,825 Parameters: domain_left_edge = [ 0. 0. 0.]
yt : [INFO ] 2017-01-17 15:27:33,826 Parameters: domain_right_edge = [ 64000. 64000. 64000.]
yt : [INFO ] 2017-01-17 15:27:33,826 Parameters: cosmological_simulation = 1
yt : [INFO ] 2017-01-17 15:27:33,826 Parameters: current_redshift = 1.89999652869
yt : [INFO ] 2017-01-17 15:27:33,826 Parameters: omega_lambda = 0.721
yt : [INFO ] 2017-01-17 15:27:33,827 Parameters: omega_matter = 0.279
yt : [INFO ] 2017-01-17 15:27:33,827 Parameters: hubble_constant = 0.7
yt : [INFO ] 2017-01-17 15:27:33,830 Allocating for 1.191e+07 particles (index particle type 'all')
yt : [INFO ] 2017-01-17 15:27:35,746 Identified 8.088e+05 octs
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
/Users/desika/Dropbox/scratch/vel_proj.py in <module>()
6
7 ds.add_deposited_particle_field( ('PartType0', 'particle_velocity_y'),"sum")
----> 8 print ad[('deposit', 'PartType0_sum_velocity_y')]
/Users/desika/yt/yt/data_objects/data_containers.pyc in __getitem__(self, key)
279 return self.field_data[f]
280 else:
--> 281 self.get_data(f)
282 # fi.units is the unit expression string. We depend on the registry
283 # hanging off the dataset to define this unit object.
/Users/desika/yt/yt/data_objects/data_containers.pyc in get_data(self, fields)
1331
1332 fields_to_generate += gen_fluids + gen_particles
-> 1333 self._generate_fields(fields_to_generate)
1334 for field in list(self.field_data.keys()):
1335 if field not in ofields:
/Users/desika/yt/yt/data_objects/data_containers.pyc in _generate_fields(self, fields_to_generate)
1351 fi = self.ds._get_field_info(*field)
1352 try:
-> 1353 fd = self._generate_field(field)
1354 if fd is None:
1355 raise RuntimeError
/Users/desika/yt/yt/data_objects/data_containers.pyc in _generate_field(self, field)
316 tr = self._generate_particle_field(field)
317 else:
--> 318 tr = self._generate_fluid_field(field)
319 if tr is None:
320 raise YTCouldNotGenerateField(field, self.ds)
/Users/desika/yt/yt/data_objects/data_containers.pyc in _generate_fluid_field(self, field)
334 finfo.check_available(gen_obj)
335 except NeedsGridType as ngt_exception:
--> 336 rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones)
337 else:
338 rv = finfo(gen_obj)
/Users/desika/yt/yt/data_objects/data_containers.pyc in _generate_spatial_fluid(self, field, ngz)
354 o = self._current_chunk.objs[0]
355 with o._activate_cache():
--> 356 ind += o.select(self.selector, self[field], rv, ind)
357 else:
358 chunks = self.index._chunk(self, "spatial", ngz = ngz)
/Users/desika/yt/yt/data_objects/data_containers.pyc in __getitem__(self, key)
279 return self.field_data[f]
280 else:
--> 281 self.get_data(f)
282 # fi.units is the unit expression string. We depend on the registry
283 # hanging off the dataset to define this unit object.
/Users/desika/yt/yt/data_objects/data_containers.pyc in get_data(self, fields)
1331
1332 fields_to_generate += gen_fluids + gen_particles
-> 1333 self._generate_fields(fields_to_generate)
1334 for field in list(self.field_data.keys()):
1335 if field not in ofields:
/Users/desika/yt/yt/data_objects/data_containers.pyc in _generate_fields(self, fields_to_generate)
1351 fi = self.ds._get_field_info(*field)
1352 try:
-> 1353 fd = self._generate_field(field)
1354 if fd is None:
1355 raise RuntimeError
/Users/desika/yt/yt/data_objects/data_containers.pyc in _generate_field(self, field)
316 tr = self._generate_particle_field(field)
317 else:
--> 318 tr = self._generate_fluid_field(field)
319 if tr is None:
320 raise YTCouldNotGenerateField(field, self.ds)
/Users/desika/yt/yt/data_objects/data_containers.pyc in _generate_fluid_field(self, field)
336 rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones)
337 else:
--> 338 rv = finfo(gen_obj)
339 return rv
340
/Users/desika/yt/yt/fields/derived_field.pyc in __call__(self, data)
218 "for %s" % (self.name,))
219 with self.unit_registry(data):
--> 220 dd = self._function(self, data)
221 for field_name in data.keys():
222 if field_name not in original_fields:
/Users/desika/yt/yt/data_objects/static_output.pyc in _deposit_field(field, data)
1215 else:
1216 d = data.ds.arr(data.deposit(pos, [data[ptype, deposit_field]],
-> 1217 method=method, kernel_name=kernel_name),
1218 input_units=units)
1219 return d
/Users/desika/yt/yt/data_objects/octree_subset.pyc in deposit(self, positions, fields, method, kernel_name)
193 fields = [np.asarray(f, dtype="float64") for f in fields]
194 op.process_octree(self.oct_handler, self.domain_ind, pos, fields,
--> 195 self.domain_id, self._domain_offset)
196 vals = op.finalize()
197 if vals is None: return
/Users/desika/yt/yt/geometry/particle_deposit.pyx in yt.geometry.particle_deposit.ParticleDepositOperation.process_octree (yt/geometry/particle_deposit.c:4579)()
61 nf = len(fields)
62 cdef np.float64_t[::cython.view.indirect, ::1] field_pointers
---> 63 if nf > 0: field_pointers = OnceIndirect(fields)
64 cdef np.float64_t pos[3]
65 cdef np.float64_t[:] field_vals = np.empty(nf, dtype="float64")
ValueError: Buffer and memoryview are not contiguous in the same dimension.
```
Responsible: MatthewTurk
2 years
Issue #1310: YTBoundsDefinitionError (yt_analysis/yt)
by Corentin Cadiou
New issue 1310: YTBoundsDefinitionError
https://bitbucket.org/yt_analysis/yt/issues/1310/ytboundsdefinitionerror
Corentin Cadiou:
HI,
I am doing a SlicePlot of a deposit field using the following code: `p = yt.SlicePlot(ds, 'z', ('deposit', 'all_cic'))`.
If I do the slice in the `x` or `y` directions, it works fine. But if I slice in the `z` direction, I get:
```
#!python
---------------------------------------------------------------------------
YTBoundsDefinitionError Traceback (most recent call last)
<ipython-input-11-d477c9a88f02> in <module>()
----> 1 p = yt.SlicePlot(ds, 'z', ('deposit', 'all_cic'))
/home/cadiou/anaconda2/lib/python2.7/site-packages/yt-3.4.dev0-py2.7-linux-x86_64.egg/yt/visualization/plot_window.pyc
in SlicePlot(ds, normal, fields, axis, *args, **kwargs)
1999 del kwargs['north_vector']
2000
-> 2001 return AxisAlignedSlicePlot(ds, normal, fields, *args, **kwargs)
/home/cadiou/anaconda2/lib/python2.7/site-packages/yt-3.4.dev0-py2.7-linux-x86_64.egg/yt/visualization/plot_window.pyc
in __init__(self, ds, axis, fields, center, width, axes_unit, origin, right_handed, fontsize, field_parameters, window_
size, aspect, data_source)
1324 slc = ds.slice(axis, center[axis], field_parameters=field_parameters,
1325 center=center, data_source=data_source)
-> 1326 slc.get_data(fields)
1327 validate_mesh_fields(slc, fields)
1328 PWViewerMPL.__init__(self, slc, bounds, origin=origin,
/home/cadiou/anaconda2/lib/python2.7/site-packages/yt-3.4.dev0-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.p
yc in get_data(self, fields)
1331
1332 fields_to_generate += gen_fluids + gen_particles
-> 1333 self._generate_fields(fields_to_generate)
1334 for field in list(self.field_data.keys()):
1335 if field not in ofields:
/home/cadiou/anaconda2/lib/python2.7/site-packages/yt-3.4.dev0-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.p
yc in _generate_fields(self, fields_to_generate)
1351 fi = self.ds._get_field_info(*field)
1352 try:
-> 1353 fd = self._generate_field(field)
1354 if fd is None:
1355 raise RuntimeError
/home/cadiou/anaconda2/lib/python2.7/site-packages/yt-3.4.dev0-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.p
yc in _generate_field(self, field)
316 tr = self._generate_particle_field(field)
317 else:
--> 318 tr = self._generate_fluid_field(field)
319 if tr is None:
320 raise YTCouldNotGenerateField(field, self.ds)
/home/cadiou/anaconda2/lib/python2.7/site-packages/yt-3.4.dev0-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.p
yc in _generate_fluid_field(self, field)
334 finfo.check_available(gen_obj)
335 except NeedsGridType as ngt_exception:
--> 336 rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones)
337 else:
338 rv = finfo(gen_obj)
/home/cadiou/anaconda2/lib/python2.7/site-packages/yt-3.4.dev0-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.p
yc in _generate_spatial_fluid(self, field, ngz)
354 o = self._current_chunk.objs[0]
355 with o._activate_cache():
--> 356 ind += o.select(self.selector, self[field], rv, ind)
357 else:
358 chunks = self.index._chunk(self, "spatial", ngz = ngz)
/home/cadiou/anaconda2/lib/python2.7/site-packages/yt-3.4.dev0-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.p
yc in __getitem__(self, key)
279 return self.field_data[f]
280 else:
--> 281 self.get_data(f)
282 # fi.units is the unit expression string. We depend on the registry
283 # hanging off the dataset to define this unit object.
/home/cadiou/anaconda2/lib/python2.7/site-packages/yt-3.4.dev0-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.pyc in get_data(self, fields)
1331
1332 fields_to_generate += gen_fluids + gen_particles
-> 1333 self._generate_fields(fields_to_generate)
1334 for field in list(self.field_data.keys()):
1335 if field not in ofields:
/home/cadiou/anaconda2/lib/python2.7/site-packages/yt-3.4.dev0-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.pyc in _generate_fields(self, fields_to_generate)
1351 fi = self.ds._get_field_info(*field)
1352 try:
-> 1353 fd = self._generate_field(field)
1354 if fd is None:
1355 raise RuntimeError
/home/cadiou/anaconda2/lib/python2.7/site-packages/yt-3.4.dev0-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.pyc in _generate_field(self, field)
316 tr = self._generate_particle_field(field)
317 else:
--> 318 tr = self._generate_fluid_field(field)
319 if tr is None:
320 raise YTCouldNotGenerateField(field, self.ds)
/home/cadiou/anaconda2/lib/python2.7/site-packages/yt-3.4.dev0-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.pyc in _generate_fluid_field(self, field)
336 rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones)
337 else:
--> 338 rv = finfo(gen_obj)
339 return rv
340
/home/cadiou/anaconda2/lib/python2.7/site-packages/yt-3.4.dev0-py2.7-linux-x86_64.egg/yt/fields/derived_field.pyc in __call__(self, data)
218 "for %s" % (self.name,))
219 with self.unit_registry(data):
--> 220 dd = self._function(self, data)
221 for field_name in data.keys():
222 if field_name not in original_fields:
/home/cadiou/anaconda2/lib/python2.7/site-packages/yt-3.4.dev0-py2.7-linux-x86_64.egg/yt/fields/particle_fields.pyc in particle_cic(field, data)
141 def particle_cic(field, data):
142 pos = data[ptype, coord_name]
--> 143 d = data.deposit(pos, [data[ptype, mass_name]], method = "cic")
144 d = data.apply_units(d, data[ptype, mass_name].units)
145 d /= data["index", "cell_volume"]
/home/cadiou/anaconda2/lib/python2.7/site-packages/yt-3.4.dev0-py2.7-linux-x86_64.egg/yt/data_objects/octree_subset.pyc in deposit(self, positions, fields, method, kernel_name)
184 # We allocate number of zones, not number of octs
185 op = cls(nvals, kernel_name)
--> 186 op.initialize()
187 mylog.debug("Depositing %s (%s^3) particles into %s Octs",
188 positions.shape[0], positions.shape[0]**0.3333333, nvals[-1])
/home/cadiou/anaconda2/lib/python2.7/site-packages/yt-3.4.dev0-py2.7-linux-x86_64.egg/yt/geometry/particle_deposit.pyx in yt.geometry.particle_deposit.CICDeposit.initialize (yt/geometry/particle_deposit.c:8068)()
332 if not all(_ > 1 for _ in self.nvals):
333 from yt.utilities.exceptions import YTBoundsDefinitionError
--> 334 raise YTBoundsDefinitionError(
335 "CIC requires minimum of 2 zones in all dimensions",
336 self.nvals)
YTBoundsDefinitionError: This operation has encountered a bounds error: CIC requires minimum of 2 zones in all dimensions Specified bounds are (2, 2, 2, 1)
```
I am using the yt 3.4-dev version.
2 years
[hub] update
by Kacper Kowalik
Hi all,
I just rolled out new version of hub.yt. Most notable changes:
* girder API was upgraded to 2.1.0.
* hub can now spawn different containers.
The latter is probably the most interesting feature. Before the update,
all you could do with the data was launching jupyter notebook that had
the proper files mounted. Right now when you try to run the notebook,
you'll be instead asked about your preferred "frontend" to expose the
data with.
Currently available frontends are: Jupyter Notebook and Jupyter Lab.
I know it's not really much of a choice, but it merely serves as a proof
of concept. The bottom line is: if you have a specific software that
you'd like to run with the data hosted on hub.yt, we can make that happen!
As always, if you notice anything not working, please let me know.
Cheers,
Kacper
2 years
