[yt-users] particle density projection plot in yt-3.0

Nathan Goldbaum nathan12343 at gmail.com
Fri Sep 20 12:30:17 PDT 2013


Hi Junhwan,

This is described in this YTEP:
http://ytep.readthedocs.org/en/latest/YTEPs/YTEP-0013.html (although it
looks like the YTEP is somewhat out of date as it doesn't describe the
field tuple syntax we've standardized on).

Unfortunately yt-3.0 is still in flux.  As we get closer to a final
release, we will improve documentation but to do so now would only
introduce documentation that could become rapidly obsolete.

For now it's probably best to keep in contact on IRC or the mailing lists
as you run into issues.

-Nathan


On Fri, Sep 20, 2013 at 12:21 PM, Junhwan Choi (최준환) <choi.junhwan at gmail.com
> wrote:

> Thank you Matt, the pc = ProjectionPlot(pf, "x",
> ("deposit","all_density"), width = (1.0, 'mpccm')) looks work.
> But, I do not know what ("deposit","all_density") means. Is it new yt-3.0
> thing?
> If there is document about new change for yt-3.0, it could be very helpful.
>
> Thanks again,
> Junhwan
>
>
> On Thu, Sep 19, 2013 at 2:43 PM, Matthew Turk <matthewturk at gmail.com>wrote:
>
>> Hi Junhwan,
>>
>> We're still working some of the kinks out, but I think you will be
>> able to get what you are looking for by projecting the field
>> ("deposit", "all_density") .  This would look like:
>>
>> pc = ProjectionPlot(pf, "x", ("deposit","all_density"), width = (1.0,
>> 'mpccm'))
>>
>> On Thu, Sep 19, 2013 at 12:14 PM, Junhwan Choi (최준환)
>> <choi.junhwan at gmail.com> wrote:
>> > 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
>> >
>> >
>> >
>> > _______________________________________________
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>> >
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