[yt-users] Accessing particle_density in a Castro pure nbody simulation
Matthew Turk
matthewturk at gmail.com
Fri Jun 10 07:04:24 PDT 2011
Hi Steffen,
This is, funnily enough, two problems.
The one for yt stats is actually just telling you that it wanted to do
something with the Density, but you have an N-body only calculation,
so it can't. I've made this conditional.
The second issue is that of units. Right now the Nyx units are a bit
uncertain and unknown to yt, so I have erred on the side of failing
rather than returning bad data. I think that you should be able to
project "particle_mass_density" without trouble. Today and early next
week, in a weird coincidence, was when we were supposed to work on
units for this frontend; I'll keep you in the loop on that. The
ticket I was going to keep track of this with is here:
http://hg.enzotools.org/yt/issue/281/nyx-units-are-incorrect
If you wouldn't mind, it'd be very helpful if you could fill in a bit
about what you know -- from a pragmatic point of view -- about the
units in that ticket.
Thanks,
Matt
On Fri, Jun 10, 2011 at 1:32 AM, Steffen Klemer <moh at gmx.org> wrote:
> Hey,
>
> I'm trying to access die derived field "particle_density" via the
> following script:
>
> from yt.mods import *
>
> pf = load('plt00000')
> my_sphere = pf.h.sphere([0,0,0], 1000.0/pf['kpc'])
> print my_sphere["particle_density"]
>
>
> Result:
> http://pastebin.com/Hukh7ahB
>
>
> The data is from a pure nbody Castro run and contains no
> "Density"-Field in the output.
>
>
> Like this:
>
> gurke: ~/castro/runs/test_my_ic > yt stats plt00000
> yt : [WARNING ] 2011-06-10 10:29:56,591 Setting 1.0 in code units to be 1.0 cm
> yt : [WARNING ] 2011-06-10 10:29:56,591 No time units. Setting 1.0 = 1 second.
> yt : [INFO ] 2011-06-10 10:29:56,592 Parameters: current_time = 0.0
> yt : [INFO ] 2011-06-10 10:29:56,592 Parameters: domain_dimensions = [64, 64, 64]
> yt : [INFO ] 2011-06-10 10:29:56,592 Parameters: domain_left_edge = [ 0. 0. 0.]
> yt : [INFO ] 2011-06-10 10:29:56,592 Parameters: domain_right_edge = [ 90. 90. 90.]
> yt : [INFO ] 2011-06-10 10:29:56,593 Parameters: cosmological_simulation = 0.0
> yt : [INFO ] 2011-06-10 10:29:56,598 Adding particle_count to list of fields
> yt : [INFO ] 2011-06-10 10:29:56,598 Adding particle_mass_density to list of fields
> Warning: invalid value encountered in sqrt
> Warning: divide by zero encountered in divide
> Warning: divide by zero encountered in divide
> Warning: invalid value encountered in sqrt
> level # grids # cells
> ---------------------------
> 0 8 262144
> ----------------------------
> 8 262144
>
>
> t = 0.00000000e+00 = 0.00000000e+00 s = 0.00000000e+00 years
>
> Smallest Cell:
> Width: 4.557e-25 mpc
> Width: 4.557e-22 kpc
> Width: 4.557e-19 pc
> Width: 9.402e-14 au
> Width: 2.022e-11 rsun
> Width: 8.736e-06 miles
> Width: 1.562e-02 unitary
> Width: 1.406e+00 1
> Width: 1.406e+00 cm
> Traceback (most recent call last):
> File "/home/sklemer/yt/yt-x86_64/bin/yt", line 9, in <module>
> load_entry_point('yt==2.1dev', 'console_scripts', 'yt')()
> File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/utilities/command_line.py", line 1061, in run_main
> sys.exit(YT.main())
> File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/utilities/cmdln.py", line 257, in main
> return self.cmd(args)
> File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/utilities/cmdln.py", line 280, in cmd
> retval = self.onecmd(argv)
> File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/utilities/cmdln.py", line 412, in onecmd
> return self._dispatch_cmd(handler, argv)
> File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/utilities/cmdln.py", line 1100, in _dispatch_cmd
> return handler(argv[0], opts, *args)
> File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/utilities/command_line.py", line 224, in arg_iterate
> func(self, subcmd, opts, arg)
> File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/utilities/command_line.py", line 535, in do_stats
> v, c = pf.h.find_max("Density")
> File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 55, in find_max
> mg, mc, mv, pos = self.find_max_cell_location(field, finest_levels)
> File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 68, in find_max_cell_location
> source.quantities["MaxLocation"]( field, lazy_reader=True)
> File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 91, in __call__
> return self._call_func_lazy(args, kwargs)
> File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 98, in _call_func_lazy
> rv = self.func(GridChildMaskWrapper(g, self._data_source), *args, **kwargs)
> File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 603, in _MaxLocation
> if data[field].size > 0:
> File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 60, in __getitem__
> data = self.data_source._get_data_from_grid(self.grid, item)
> File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 73, in save_state
> tr = func(self, grid, field)
> File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 2313, in _get_data_from_grid
> if grid[field].size == 1: # dx, dy, dz, cellvolume
> File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line 147, in __getitem__
> self.get_data(key)
> File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line 190, in get_data
> self._generate_field(field)
> File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line 135, in _generate_field
> self[field] = self.pf.field_info[field](self)
> File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.py", line 309, in __call__
> dd = self._function(self, data)
> File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/frontends/castro/fields.py", line 84, in <lambda>
> add_field(theirs, function=lambda a, b: b[mine], take_log=True)
> File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line 147, in __getitem__
> self.get_data(key)
> File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line 190, in get_data
> self._generate_field(field)
> File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line 125, in _generate_field
> self.pf.field_info[field].check_available(self)
> File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.py", line 276, in check_available
> validator(data)
> File "/home/sklemer/yt/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.py", line 374, in __call__
> raise NeedsDataField(doesnt_have)
> yt.data_objects.field_info_container.NeedsDataField: (['density'])
>
>
>
> Or here like this:
>
>
> In [27]: pf.keys()
> Out[27]:
> ['miles',
> 'rsun',
> 'mpc',
> 'cm',
> 'unitary',
> '1',
> 'pc',
> 'kpc',
> 'au',
> '1',
> 'days',
> 'years',
> 'DualEnergyFormalism',
> 'cosmology_calculator',
> 'TopGridDimensions',
> 'CosmologyHubbleConstantNow',
> 'TopGridRank',
> 'CosmologyOmegaLambdaNow',
> 'Time',
> 'HydroMethod',
> 'CosmologyOmegaMatterNow',
> 'EOSType',
> 'particle_velocity_z',
> 'particle_position_z',
> 'particle_position_x',
> 'particle_position_y',
> 'particle_mass',
> 'particle_velocity_x',
> 'particle_velocity_y']
>
>
>
>
> bye
> /Steffen
>
> PS: Sorry for not using the yt-pastebin script but the lodge_it script
> seems to not work via the http proxy from my mashine.
>
> --
> () ascii ribbon campaign - against html e-mail
> /\ www.asciiribbon.org - against proprietary attachments
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