[yt-users] Making slices of Athena SMR data
Eve Lee
elee at cita.utoronto.ca
Tue Aug 6 00:06:45 PDT 2013
I've attached the athinput.kh.
Perhaps I didn't set up the domains correctly?
Best Regards,
Eve
On 08/06/2013 12:01 AM, John ZuHone wrote:
> Hi Eve,
>
> This is odd. I'm actually getting it to work:
>
> http://i.imgur.com/iMQttWd.png
>
> I don't get it, because it looks like your yt is up to date.
>
> Can you send your athinput.kh?
>
> John
>
> On Aug 6, 2013, at 12:56 AM, Eve Lee <elee at cita.utoronto.ca> wrote:
>
>> I've uploaded the figures here:
>>
>> http://i.imgur.com/7T5N11o.png
>> http://i.imgur.com/nOsLfQ9.png
>> http://i.imgur.com/BfojOOa.png
>>
>> Best Regards,
>>
>> Eve
>>
>> On 08/05/2013 08:56 PM, John ZuHone wrote:
>>> Also, could you send over some of the figures?
>>>
>>> John
>>>
>>> On Aug 5, 2013, at 11:30 PM, Eve Lee <elee at cita.utoronto.ca> wrote:
>>>
>>>> Hi John,
>>>>
>>>> Yes, it is. Thank you for your help.
>>>>
>>>> Best Regards,
>>>>
>>>> Eve
>>>>
>>>> On 08/05/2013 08:29 PM, John ZuHone wrote:
>>>>> Hi Eve,
>>>>>
>>>>> Is this just the 2-D K-H test simulation with SMR? If I could run it myself it would make it easier to debug.
>>>>>
>>>>> Best,
>>>>>
>>>>> John
>>>>>
>>>>> On Aug 5, 2013, at 5:28 PM, Eve Lee <elee at cita.utoronto.ca> wrote:
>>>>>
>>>>>> Hi John,
>>>>>>
>>>>>> Following is the output from yt instinfo
>>>>>>
>>>>>> yt module located at:
>>>>>> /home/evejlee/.local/lib/python2.7/site-packages/yt-2.6dev-py2.7-linux-x86_64.egg
>>>>>> The supplemental repositories are located at:
>>>>>> /pfs/sw/yt-x86_64/src/yt-supplemental
>>>>>>
>>>>>> The current version of the code is:
>>>>>>
>>>>>> ---
>>>>>> f936432ed45d yt
>>>>>> ---
>>>>>>
>>>>>> Best Regards,
>>>>>>
>>>>>> Eve
>>>>>>
>>>>>> On 08/05/2013 02:22 PM, John ZuHone wrote:
>>>>>>> Hi Eve,
>>>>>>>
>>>>>>> Sorry that you're having trouble!
>>>>>>>
>>>>>>> Just wanted to check real quick before anything else--which version of yt are you using? Also, are you using the stable branch or the development branch? Support for Athena SMR exists in yt versions 2.5.3 and later.
>>>>>>>
>>>>>>> Best,
>>>>>>>
>>>>>>> John
>>>>>>>
>>>>>>> On Aug 5, 2013, at 5:13 PM, Eve Lee <elee at cita.utoronto.ca> wrote:
>>>>>>>
>>>>>>>> Hello,
>>>>>>>>
>>>>>>>> I'm trying to make a slice plot of Athena MPI SMR data using TimeSeriesData, and I find that the code only make slices out of the base level and blanks out deeper level regions.
>>>>>>>>
>>>>>>>> Following is how I read in the Athena vtk files:
>>>>>>>>
>>>>>>>> ts = TimeSeriesData.from_filenames('id0/kh*.vtk', parallel=True)
>>>>>>>> my_storage={}
>>>>>>>> for sto,pf in ts.piter(storage=my_storage):
>>>>>>>> slc = SlicePlot(pf, 'z', 'Density')
>>>>>>>> slc.set_zlim('Density', 0.0, 3.0)
>>>>>>>> num = (pf.h.hierarchy_filename).split('.')[1]
>>>>>>>> slc.save('./slice/'+num)
>>>>>>>>
>>>>>>>> all my vtk files are in id0, ..., idn where n=number of processors I used, and I'm only using 1 more level of refinement.
>>>>>>>>
>>>>>>>> Thanks in advance!
>>>>>>>>
>>>>>>>> Best Regards,
>>>>>>>>
>>>>>>>> Eve
>>>>>>>>
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-------------- next part --------------
<comment>
problem = KH instability of slip surface # runs KH test on Athena webpage
author = J. Stone and T. Gardiner
config = --with-gas=hydro --with-problem=kh
<job>
problem_id = kh # problem ID: basename of output filenames
maxout = 100 # Output blocks number from 1 -> maxout
num_domains = 3 # number of Domains in Mesh
<output1>
out_fmt = hst # History data dump
dt = 0.05 # time increment between outputs
<output2>
out_fmt = vtk # Binary data dump
dt = 0.1 # time increment between outputs
<output3>
out_fmt = rst # Restart dump
dt = 0.1 # time increment
<time>
cour_no = 0.8 # The Courant, Friedrichs, & Lewy (CFL) Number
nlim = 5000 # cycle limit
tlim = 50.0 # time limit
<domain1>
level = 0 # refinement level this Domain (root=0)
Nx1 = 64 # Number of zones in X1-direction
x1min = -1.0 # minimum value of X1
x1max = 1.0 # maximum value of X1
bc_ix1 = 4 # boundary condition flag for inner-I (X1)
bc_ox1 = 4 # boundary condition flag for outer-I (X1)
Nx2 = 32 # Number of zones in X2-direction
x2min = -0.5 # minimum value of X2
x2max = 0.5 # maximum value of X2
bc_ix2 = 4 # boundary condition flag for inner-J (X2)
bc_ox2 = 4 # boundary condition flag for outer-J (X2)
Nx3 = 1 # Number of zones in X3-direction
x3min = -0.5 # minimum value of X3
x3max = 0.5 # maximum value of X3
bc_ix3 = 4 # boundary condition flag for inner-K (X3)
bc_ox3 = 4 # boundary condition flag for outer-K (X3)
NGrid_x1 = 2
NGrid_x2 = 2
<domain2>
level = 1 # refinement level this Domain (root=0)
Nx1 = 128 # Number of zones in X1-direction
Nx2 = 16 # Number of zones in X2-direction
Nx3 = 1 # Number of zones in X3-direction
iDisp = 0 # i-displacement measured in cells of this level
jDisp = 8 # j-displacement measured in cells of this level
kDisp = 0 # k-displacement measured in cells of this level
NGrid_x1 = 2
NGrid_x2 = 2
<domain3>
level = 1 # refinement level this Domain (root=0)
Nx1 = 128 # Number of zones in X1-direction
Nx2 = 16 # Number of zones in X2-direction
Nx3 = 1 # Number of zones in X3-direction
iDisp = 0 # i-displacement measured in cells of this level
jDisp = 40 # j-displacement measured in cells of this level
kDisp = 0 # k-displacement measured in cells of this level
NGrid_x1 = 2
NGrid_x2 = 2
<domain4>
level = 2 # refinement level this Domain (root=0)
Nx1 = 256 # Number of zones in X1-direction
Nx2 = 16 # Number of zones in X2-direction
Nx3 = 1 # Number of zones in X3-direction
iDisp = 0 # i-displacement measured in cells of this level
jDisp = 24 # j-displacement measured in cells of this level
kDisp = 0 # k-displacement measured in cells of this level
NGrid_x1 = 4
NGrid_x2 = 1
<domain5>
level = 2 # refinement level this Domain (root=0)
Nx1 = 256 # Number of zones in X1-direction
Nx2 = 16 # Number of zones in X2-direction
Nx3 = 1 # Number of zones in X3-direction
iDisp = 0 # i-displacement measured in cells of this level
jDisp = 88 # j-displacement measured in cells of this level
kDisp = 0 # k-displacement measured in cells of this level
NGrid_x1 = 4
NGrid_x2 = 1
<problem>
gamma = 1.4 # gamma = C_p/C_v
iprob = 1
amp = 1.0e-2
drat = 2.0
vflow = 0.5
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