[yt-users] Error in reading the hydrodynamics dataset in Ramses
Sam Geen
samgeen at astro.ox.ac.uk
Mon Nov 25 03:18:02 PST 2013
Hi,
I ran into this problem as well; turns out I was running a simulation
with 11 variables and not 8 as the Makefile said (apparently the MHD
module silently adds 3). A few things that might be worth looking at:
1) When I re-ran load() with a new field array in the same ipython
instance, it kept the old one (i.e. "We are looking for 8 fields." even
when I'd changed it to 11 elements) unless I restarted Python.
2) The 2nd Fortran record in the hydro files in RAMSES is a 4-byte
integer containing NVAR; this could be a useful thing to read to check
against the user's fields array to say, e.g. "You provided [len(fields)]
fields, but this output contains [NVAR] fields".
3) It could also be nice if an output would work anyway if the user
provides fewer fields than are in the file, since it's possible to, say,
read the density without reading the metallicity (a lot of RAMSES
simulations have different versions depending on what patches you're
using, but all RAMSES outputs will have [density, [x/y/z]-velocity*,
pressure]. It depends how YT reads RAMSES hydro files, but it shouldn't
be necessary to a priori know the number of fields as long as you don't
try to read more than NVAR.
Cheers,
Sam
*Depending on the number of dimensions, which is the record after NVAR.
On 20/11/13 23:56, Junhwan Choi (최준환) wrote:
> 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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