[yt-users] yt.extensions.EnzoSimulation gorne
Matthew Turk
matthewturk at gmail.com
Mon Nov 8 06:58:03 PST 2010
Hi all,
As a brief followup to the list, there were data corruption errors --
yt was detecting the fields correctly, but the .hierarchy file was
misreporting them, which caused a mismatch.
-Matt
On Wed, Nov 3, 2010 at 10:35 AM, Matthew Turk <matthewturk at gmail.com> wrote:
> Hi Elizabeth,
>
> Looks like an oddity of how it's masking child cells. These show up
> from time to time and are usually because of a combination of domain
> size, refinement parameter, and grid index placement. If you don't
> mind, could you (off list) send me a link to the dataset (we can't use
> drop.io anymore -- they got bought by facebook and shut down!) and
> I'll see if I can fix it up tonight.
>
> -Matt
>
> On Wed, Nov 3, 2010 at 1:31 PM, Elizabeth Tasker <taskere at mcmaster.ca> wrote:
>> Hi Britton,
>>
>> It just fails in the same way. The entire output in all it's glory is:
>>
>>
>> [taskere at saw377 sedov]$ /work/taskere/yt-2/yt/bin/iyt total_energy.py
>> yt INFO 2010-11-03 13:29:08,135 Loaded 11 total data outputs.
>> yt INFO 2010-11-03 13:29:08,414 Getting the binary hierarchy
>> yt INFO 2010-11-03 13:29:08,418 Finished with binary hierarchy
>> reading
>> Warning: divide by zero encountered in divide
>> Warning: divide by zero encountered in divide
>> Warning: invalid value encountered in sqrt
>> Warning: invalid value encountered in divide
>> Warning: invalid value encountered in divide
>> Warning: invalid value encountered in sqrt
>> ---------------------------------------------------------------------------
>> IndexError Traceback (most recent call last)
>>
>> /saw_sfs/work/taskere/yt-2/scripts/iyt in <module>()
>> 15 # calculate total energy for the simulation volume
>> 16 data = pf.h.all_data()
>> ---> 17 print data.quantities["TotalQuantity"]("TotalEnergy")[0]
>> 18 # ETot.append(data.quantities["TotalQuantity"]("TotalEnergy")[0])
>> 19
>>
>> /saw_sfs/work/taskere/yt-2/yt/data_objects/derived_quantities.pyc in
>> __call__(self, *args, **kwargs)
>> 88 self._data_source.pf.h.io)
>> 89 if lazy_reader and not self.force_unlazy:
>> ---> 90 return self._call_func_lazy(args, kwargs)
>> 91 else:
>> 92 return self._call_func_unlazy(args, kwargs)
>>
>> /saw_sfs/work/taskere/yt-2/yt/data_objects/derived_quantities.pyc in
>> _call_func_lazy(self, args, kwargs)
>> 95 self.retvals = [ [] for i in range(self.n_ret)]
>> 96 for gi,g in enumerate(self._get_grids()):
>> ---> 97 rv = self.func(GridChildMaskWrapper(g,
>> self._data_source), *args, **kwargs)
>> 98 for i in range(self.n_ret): self.retvals[i].append(rv[i])
>> 99 g.clear_data()
>> /saw_sfs/work/taskere/yt-2/yt/data_objects/derived_quantities.pyc in
>> _TotalQuantity(data, fields)
>> 493 totals = []
>> 494 for field in fields:
>> --> 495 if data[field].size < 1:
>> 496 totals.append(0)
>> 497 continue
>>
>> /saw_sfs/work/taskere/yt-2/yt/data_objects/derived_quantities.pyc in
>> __getitem__(self, item)
>> 57 def __getitem__(self, item):
>> 58 if item not in self.local_cache:
>> ---> 59 data = self.data_source._get_data_from_grid(self.grid,
>> item)
>> 60 self.local_cache[item] = data
>> 61 return self.local_cache[item]
>>
>> /saw_sfs/work/taskere/yt-2/yt/data_objects/data_containers.pyc in
>> save_state(self, grid, field)
>> 68 old_keys = grid.data.keys()
>> 69 grid.field_parameters = self.field_parameters
>> ---> 70 tr = func(self, grid, field)
>> 71 grid.field_parameters = old_params
>> 72 grid.data = dict( [(k, grid.data[k]) for k in old_keys] )
>>
>> /saw_sfs/work/taskere/yt-2/yt/data_objects/data_containers.pyc in
>> _get_data_from_grid(self, grid, field)
>> 1939 t = grid[field] * na.ones(grid.ActiveDimensions,
>> dtype='float64')
>> 1940 return t[pointI].ravel()
>> -> 1941 return grid[field][pointI].ravel()
>> 1942
>> 1943 def _flush_data_to_grids(self, field, default_val,
>> dtype='float32'):
>>
>> IndexError: index (100) out of range (0<=index<99) in dimension 0
>> WARNING: Failure executing file: <total_energy.py>
>>
>> Welcome to yt!
>>
>>
>> (I find that last line amusing in such circumstances :) )
>>
>>
>> Also, my total script is:
>>
>> from yt.mods import *
>> from yt.analysis_modules.api import EnzoSimulation
>>
>> ETot = []
>> time = []
>> i=0
>>
>> es = EnzoSimulation("SedovBlastAMR.enzo", initial_time=0.0, final_time=0.1)
>>
>> for output in es.allOutputs:
>> # load up a dataset
>> pf = load(output['filename'])
>>
>> # calculate total energy for the simulation volume
>> data = pf.h.all_data()
>> print data.quantities["TotalQuantity"]("TotalEnergy")[0]
>> # ETot.append(data.quantities["TotalQuantity"]("TotalEnergy")[0])
>>
>>
>> # calculate the time of output
>> time.append(0.01*i)
>> i = i + 1
>>
>> pylab.xlabel("Time")
>> pylab.ylabel("Total Energy")
>> pylab.plot(time, ETot, 'b')
>> pylab.savefig('TotEnergy.png')
>> pylab.show()
>>
>>
>>
>> Thank you~
>>
>>
>> Britton Smith wrote:
>>>
>>> Hi Elizabeth,
>>>
>>> It's not totally clear to me what's failing. Can you change that line to
>>> just
>>> print data.quantities["TotalQuantity"]("TotalEnergy")[0]
>>> just to see what's coming out of that.
>>>
>>> Britton
>>>
>>> On Wed, Nov 3, 2010 at 1:10 PM, Elizabeth Tasker <taskere at mcmaster.ca
>>> <mailto:taskere at mcmaster.ca>> wrote:
>>>
>>> Actually, it turns out this is still giving me problems. I'm now
>>> using yt 2.0 and have:
>>>
>>>
>>> from yt.analysis_modules.api import EnzoSimulation
>>> es = EnzoSimulation("SedovBlastAMR.enzo", initial_time=0.0,
>>> final_time=0.1)
>>>
>>> ETot = []
>>>
>>> for output in es.allOutputs:
>>> pf = load(output['filename'])
>>> data = pf.h.all_data()
>>> ETot.append(data.quantities["TotalQuantity"]("TotalEnergy")[0])
>>> .
>>> .
>>> .
>>>
>>> But I get:
>>>
>>> IndexError Traceback (most recent
>>> call last)
>>>
>>> /saw_sfs/work/taskere/yt-2/scripts/iyt in <module>()
>>> 15 # calculate total energy for the simulation volume
>>> 16 data = pf.h.all_data()
>>> ---> 17
>>> ETot.append(data.quantities["TotalQuantity"]("TotalEnergy")[0])
>>> 18
>>> 19 # calculate the time of output
>>> .
>>> .
>>> .
>>> IndexError: index (100) out of range (0<=index<99) in dimension 0
>>> WARNING: Failure executing file: <total_energy.py>
>>>
>>>
>>>
>>> What did I do wrong?
>>>
>>> Elizabeth
>>>
>>>
>>>
>>>
>>>
>>>
>>> Elizabeth Tasker wrote:
>>>
>>> Hi Jeff,
>>>
>>> I think it might be enzo 1.7, but inspired by your comment I
>>> controversially checked the code and found
>>>
>>> import yt.extensions.enzo_simulation as ES
>>>
>>> works.
>>>
>>> Thanks, Elizabeth
>>>
>>>
>>> j s oishi wrote:
>>>
>>> Hi Elizabeth,
>>>
>>> Are you on yt-2.0? If so, then it should be
>>>
>>> from yt.analysis_modules.api import EnzoSimulation as ES
>>>
>>> j
>>>
>>>
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>>
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