[yt-users] Dark matter + yt

[Matthew Turk]

Hi Elizabeth,

> Does yt have trouble if there is no gas but only particles in an output? I'm
> seeing:
>
> In [2]: fn="Gasoline_32static_dmonly_0000"
>
> In [3]: pf = load(fn)
>
> In [4]: pc = PlotCollection(pf)
> yt         INFO       2010-08-20 17:32:36,447 Getting the binary hierarchy
> yt         INFO       2010-08-20 17:32:36,451 Finished with binary hierarchy
> reading
> ---------------------------------------------------------------------------
> NeedsDataField                            Traceback (most recent call last)
>
> /1/home/taskere/yt/src/yt-1.7-svn/scripts/iyt in <module>()
> ----> 1
>     2
>     3
>     4
>     5
>
> /1/home/taskere/yt/src/yt-1.7-svn/yt/raven/plot_collection.py in
> __init__(self, pf, center)
>    81         self.pf = pf
>    82         if center == None:
> ---> 83             v,self.c = pf.h.find_max("Density") # @todo: ensure no
> caching
>    84         elif center == "center" or center == "c":
>    85             self.c = (pf["DomainRightEdge"] +
> pf["DomainLeftEdge"])/2.0
>
> /1/home/taskere/yt/src/yt-1.7-svn/yt/lagos/object_finding_mixin.py in
> find_max(self, field, finest_levels)
>    53         if (field, finest_levels) in self._max_locations:
>    54             return self._max_locations[(field, finest_levels)]
> ---> 55         mg, mc, mv, pos = self.find_max_cell_location(field,
> finest_levels)
>    56         self._max_locations[(field, finest_levels)] = (mv, pos)
>    57         return mv, pos
>
> /1/home/taskere/yt/src/yt-1.7-svn/yt/lagos/object_finding_mixin.py in
> find_max_cell_location(self, field, finest_levels)
>    66                     len(source._grids), field)
>    67         max_val, maxi, mx, my, mz, mg = \
> ---> 68             source.quantities["MaxLocation"]( field,
> lazy_reader=True)
>    69         max_grid = self.grids[mg]
>    70         mc = na.unravel_index(maxi, max_grid.ActiveDimensions)
>
> /1/home/taskere/yt/src/yt-1.7-svn/yt/lagos/DerivedQuantities.py in
> __call__(self, *args, **kwargs)
>    70                           self._data_source.pf.h.io)
>    71         if lazy_reader and not self.force_unlazy:
> ---> 72             return self._call_func_lazy(args, kwargs)
>    73         else:
>    74             return self._call_func_unlazy(args, kwargs)
>
> /1/home/taskere/yt/src/yt-1.7-svn/yt/lagos/DerivedQuantities.py in
> _call_func_lazy(self, args, kwargs)
>    77         self.retvals = [ [] for i in range(self.n_ret)]
>    78         for gi,g in enumerate(self._get_grids()):
> ---> 79             rv = self.func(GridChildMaskWrapper(g,
> self._data_source), *args, **kwargs)
>    80             for i in range(self.n_ret): self.retvals[i].append(rv[i])
>    81             g.clear_data()
>
> /1/home/taskere/yt/src/yt-1.7-svn/yt/lagos/DerivedQuantities.py in
> _MaxLocation(data, field)
>   445     """
>   446     ma, maxi, mx, my, mz, mg = -1e90, -1, -1, -1, -1, -1
> --> 447     if data[field].size > 0:
>   448         maxi = na.argmax(data[field])
>   449         ma = data[field][maxi]
>
> /1/home/taskere/yt/src/yt-1.7-svn/yt/lagos/DerivedQuantities.py in
> __getitem__(self, item)
>    41         return getattr(self.grid, attr)
>    42     def __getitem__(self, item):
> ---> 43         return self.data_source._get_data_from_grid(self.grid, item)
>    44
>    45 class DerivedQuantity(ParallelAnalysisInterface):
>
> /1/home/taskere/yt/src/yt-1.7-svn/yt/lagos/BaseDataTypes.py in
> save_state(self, grid, field)
>    41         old_keys = grid.data.keys()
>    42         grid.field_parameters = self.field_parameters
> ---> 43         tr = func(self, grid, field)
>    44         grid.field_parameters = old_params
>    45         grid.data = dict( [(k, grid.data[k]) for k in old_keys] )
>
> /1/home/taskere/yt/src/yt-1.7-svn/yt/lagos/BaseDataTypes.py in
> _get_data_from_grid(self, grid, field)
>  1681         else:
>  1682             pointI = self._get_point_indices(grid)
> -> 1683             if grid[field].size == 1: # dx, dy, dz, cellvolume
>  1684                 t = grid[field] * na.ones(grid.ActiveDimensions,
> dtype='float64')
>  1685                 return t[pointI].ravel()
>
> /1/home/taskere/yt/src/yt-1.7-svn/yt/lagos/BaseGridType.py in
> __getitem__(self, key)
>   133         """
>   134         if not self.data.has_key(key):
> --> 135             self.get_data(key)
>   136         return self.data[key]
>   137
>
> /1/home/taskere/yt/src/yt-1.7-svn/yt/lagos/BaseGridType.py in get_data(self,
> field)
>   176                     else: raise
>   177             else:
> --> 178                 self._generate_field(field)
>   179         return self.data[field]
>   180
>
> /1/home/taskere/yt/src/yt-1.7-svn/yt/lagos/BaseGridType.py in
> _generate_field(self, field)
>   111             # First we check the validator
>   112             try:
> --> 113                 self.pf.field_info[field].check_available(self)
>   114             except NeedsGridType, ngt_exception:
>   115                 # This is only going to be raised if n_gz > 0
>
> /1/home/taskere/yt/src/yt-1.7-svn/yt/lagos/field_info_container.py in
> check_available(self, data)
>   283         """
>   284         for validator in self.validators:
> --> 285             validator(data)
>   286         # If we don't get an exception, we're good to go
>   287         return True
>
> /1/home/taskere/yt/src/yt-1.7-svn/yt/lagos/field_info_container.py in
> __call__(self, data)
>   381                 doesnt_have.append(f)
>   382         if len(doesnt_have) > 0:
> --> 383             raise NeedsDataField(doesnt_have)
>   384         return True
>   385
>
> NeedsDataField: (['Density'])
>
>
> Which looks like it is requiring a density field?
>
> Elizabeth
>
>

Yup, it's trying to center on the most dense point.  You can specify a
center with:

pc = PlotCollection(pf, center = [0.5, 0.5, 0.5])

I believe it has correctly guessed the data type, but if you run into
another issue with this try:

pf = EnzoStaticOutput(fn, data_style="enzo_packed_3d")

Best,

Matt