[yt-users] Error in reading the hydrodynamics dataset in Ramses

Wed Nov 20 14:56:33 PST 2013

Thank you, now it works.
Junhwan

On Wed, Nov 20, 2013 at 4:33 PM, Romain Teyssier
<romain.teyssier at gmail.com> wrote:
> In the Makefile you should have NVAR=6.
>
> Romain
>
>> Le 20 nov. 2013 à 23:15, Junhwan Choi (최준환) <choi.junhwan at gmail.com> a écrit :
>>
>> Hi Romain,
>>
>> Yes, it is Pierre's cudaton simulation.
>> If this is the case where do I find how many  variables the simulation
>> use and what he names are?
>> I can ask to pierre, if there is no such a information in the simulation output.
>>
>> Thank you,
>> Junhwan
>>
>> On Wed, Nov 20, 2013 at 3:53 PM, Romain Teyssier
>> <romain.teyssier at gmail.com> wrote:
>>> Hi Junhwan,
>>>
>>> The name of your repository “rhd” suggests that you are using the radiation solver.
>>> In this case, you must have more than 5 variables, probably 6 or more.
>>> So you need to use :
>>> fields = ["Density","x-velocity", "y-velocity","z-velocity",”Pressure”,”var6”,”var7”,...]).
>>>
>>> Romain
>>>
>>>
>>>
>>>
>>>> On 20 Nov 2013, at 22:50, Junhwan Choi (최준환) <choi.junhwan at gmail.com> wrote:
>>>>
>>>> Thank you, Kearn.
>>>>
>>>> I tried your suggestion that I used
>>>> ds = load("/lustre/widow2/proj/ast031/test11_rhd_fesc=0.05/output_00048/info_00048.txt",
>>>> fields = ["Density","x-velocity", "y-velocity",
>>>> "z-velocity","Pressure"]).
>>>> But, it results in the identical error message.
>>>> I still do not know what I need to do.
>>>>
>>>> Regard,
>>>> Junhwan
>>>>
>>>>
>>>>
>>>>> On Wed, Nov 20, 2013 at 10:37 AM,  <k.grisdale at surrey.ac.uk> wrote:
>>>>> Hi Junhwan
>>>>>
>>>>> I think the problem you might the having is you need to specify the fields you read into yt. To do this just modify you load command to this:
>>>>>
>>>>> ds = load("/lustre/widow2/proj/ast031/test11_rhd_fesc=0.05/output_00048/info_00048.txt”, fields = ["Density","x-velocity", "y-velocity", "z-velocity", "Pressure”])
>>>>>
>>>>> (Assuming that you are running a 3d Simulation with NVAR set as 5)
>>>>>
>>>>> Hope that helps
>>>>>
>>>>> Kearn
>>>>>
>>>>>
>>>>>> On 20 Nov 2013, at 16:26, Junhwan Choi (최준환) <choi.junhwan at gmail.com> wrote:
>>>>>>
>>>>>> Hi yt users,
>>>>>>
>>>>>> I try to make a basic visualization for the Ramses simulation using
>>>>>> following script:
>>>>>> ==========================
>>>>>> from yt.mods import *
>>>>>>
>>>>>> ds = load("/lustre/widow2/proj/ast031/test11_rhd_fesc=0.05/output_00048/info_00048.txt")
>>>>>> center = [0.5, 0.5, 0.5]
>>>>>>
>>>>>> pw = ProjectionPlot(ds, "x", ("deposit", "all_density"))
>>>>>> pw.zoom(1.01)
>>>>>> pw.save("allview")
>>>>>>
>>>>>> pw = ProjectionPlot(ds, "x", "Density")
>>>>>> pw.zoom(1.01)
>>>>>> pw.save("allviewGas")
>>>>>> ============================
>>>>>> It WORKS for the particle projection (for allview) but it does not
>>>>>> work for gas projection.
>>>>>>
>>>>>> When the yt try to deal with gas dataset, I got the following error
>>>>>> message and the script crash.
>>>>>> You are running with the wrong number of fields.
>>>>>> Please specify these in the load command.
>>>>>> We are looking for 6 fields.
>>>>>> The last set of field sizes was: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
>>>>>> 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
>>>>>> 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2]
>>>>>> Traceback (most recent call last):
>>>>>> File "DenVis_DM_Gas.py", line 10, in <module>
>>>>>>  pw = ProjectionPlot(ds, "x", ("gas", "Density"))
>>>>>> File "/autofs/na3_home1/jhchoi/common/src/yt-hg/yt/visualization/plot_window.py",
>>>>>> line 1441, in __init__
>>>>>>  field_parameters = field_parameters)
>>>>>> File "/autofs/na3_home1/jhchoi/common/src/yt-hg/yt/data_objects/construction_data_containers.py",
>>>>>> line 234, in __init__
>>>>>>  self.get_data(field)
>>>>>> File "/autofs/na3_home1/jhchoi/common/src/yt-hg/yt/data_objects/construction_data_containers.py",
>>>>>> line 278, in get_data
>>>>>>  chunk_fields, "io")):
>>>>>> File "/autofs/na3_home1/jhchoi/common/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py",
>>>>>> line 434, in parallel_objects
>>>>>>  for obj_id, obj in oiter:
>>>>>> File "/autofs/na3_home1/jhchoi/common/src/yt-hg/yt/data_objects/data_containers.py",
>>>>>> line 453, in chunks
>>>>>>  self.get_data(fields)
>>>>>> File "/autofs/na3_home1/jhchoi/common/src/yt-hg/yt/data_objects/data_containers.py",
>>>>>> line 531, in get_data
>>>>>>  fluids, self, self._current_chunk)
>>>>>> File "/autofs/na3_home1/jhchoi/common/src/yt-hg/yt/geometry/geometry_handler.py",
>>>>>> line 520, in _read_fluid_fields
>>>>>>  chunk_size)
>>>>>> File "/autofs/na3_home1/jhchoi/common/src/yt-hg/yt/frontends/ramses/io.py",
>>>>>> line 41, in _read_fluid_selection
>>>>>>  rv = subset.fill(content, fields, selector)
>>>>>> File "/autofs/na3_home1/jhchoi/common/src/yt-hg/yt/frontends/ramses/data_structures.py",
>>>>>> line 304, in fill
>>>>>>  for level, offset in enumerate(self.domain.hydro_offset):
>>>>>> File "/autofs/na3_home1/jhchoi/common/src/yt-hg/yt/frontends/ramses/data_structures.py",
>>>>>> line 102, in hydro_offset
>>>>>>  hvals = fpu.read_attrs(f, header, "=")
>>>>>> File "/autofs/na3_home1/jhchoi/common/src/yt-hg/yt/utilities/fortran_utils.py",
>>>>>> line 74, in read_attrs
>>>>>>  assert(s1 == s2)
>>>>>> AssertionError
>>>>>>
>>>>>> I do not understand what is the problem since it is such a basic visualization.
>>>>>> Since I am new for Ramses data, I may take a simple mistake.
>>>>>> Can anyone explain what the error message means and how to resolve the problem?
>>>>>>
>>>>>> Thank you in advance,
>>>>>> Junhwan
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