Hi Peter, As you noted I included a pole in my mesh. I’ve gone another route with the meshing, and that seems to have resolved my initial issue. However, now during the course of simulation I get a runtime error indicating the “Minimum sized time step rejected”. I’m looking for some clarification here—does this indicate my min-fact is too small, or too large? Or does it have to do with the actual tolerance values that I've set? Thanks!
Best Regards,
Zach Davis
Rescale, Inc.
589 Howard Street, Ste. 2
San Francisco, CA 94105
[email protected]
P: (855) 737-2253
> On Nov 17, 2014, at 2:47 PM, Vincent, Peter E <[email protected]>
> wrote:
>
> Hi Zach,
>
> We have had a quick look at the mesh. I think the hexes that converge at the
> `nose' of the delta wing config are invalid. I think you have hexes with one
> face collapsing to a single point?
>
> Cheers
>
> Peter
>
> Dr Peter Vincent MSci ARCS DIC PhD
> Senior Lecturer and EPSRC Early Career Fellow
> Department of Aeronautics
> Imperial College London
> South Kensington
> London
> SW7 2AZ
> UK
>
> web: www.imperial.ac.uk/aeronautics/research/vincentlab
> <http://www.imperial.ac.uk/aeronautics/research/vincentlab>
> twitter: @Vincent_Lab <https://twitter.com/Vincent_Lab>
>
>
>
>
>
> On 17 Nov 2014, at 16:32, Vincent, Peter E <[email protected]
> <mailto:[email protected]>> wrote:
>
>> Hi Zach,
>>
>> I am at SC14 with Freddie. We think this may be a mesh problem.
>>
>>> /Users/zdavis/Applications/PyFR/pyfr/solvers/base/elements.py:208:
>>> RuntimeWarning: invalid value encountered in divide
>>> self._norm_pnorm_fpts = pnorm_fpts / mag_pnorm_fpts[...,None]
>>
>> Looks like mag_pnorm_fpts may be zero somewhere - resulting from an element
>> with a zero Jacobian (invalid element). This is causing the out of index
>> problem later on.
>>
>> Could you send us the .geo Gmsh file?
>>
>> Cheers
>>
>> Peter
>>
>> Dr Peter Vincent MSci ARCS DIC PhD
>> Senior Lecturer and EPSRC Early Career Fellow
>> Department of Aeronautics
>> Imperial College London
>> South Kensington
>> London
>> SW7 2AZ
>> UK
>>
>> web: www.imperial.ac.uk/aeronautics/research/vincentlab
>> <http://www.imperial.ac.uk/aeronautics/research/vincentlab>
>> twitter: @Vincent_Lab <https://twitter.com/Vincent_Lab>
>>
>>
>>
>>
>>
>> On 17 Nov 2014, at 16:23, Zach Davis <[email protected]
>> <mailto:[email protected]>> wrote:
>>
>>> Monday, 17 November 2014
>>>
>>>
>>>
>>>
>>> Hi all,
>>>
>>> In my continuing effort to familiarize myself with some of the recent
>>> additions to PyFR, Gmsh, and compare the available backends I seem to have
>>> encountered what I believe may be a numpy issue. I’m getting an out of
>>> index error in nputil.py. Stack trace is:
>>>
>>> /Users/zdavis/Applications/PyFR/pyfr/solvers/base/elements.py:208:
>>> RuntimeWarning: invalid value encountered in divide
>>> self._norm_pnorm_fpts = pnorm_fpts / mag_pnorm_fpts[...,None]
>>> Traceback (most recent call last):
>>> File "/Users/zdavis/Applications/PyFR/pyfr/scripts/pyfr-sim", line 112,
>>> in <module>
>>> main()
>>> File "/usr/local/lib/python2.7/site-packages/mpmath/ctx_mp.py", line
>>> 1301, in g
>>> return f(*args, **kwargs)
>>> File "/Users/zdavis/Applications/PyFR/pyfr/scripts/pyfr-sim", line 88, in
>>> main
>>> solver = get_solver(backend, rallocs, mesh, soln, cfg)
>>> File "/Users/zdavis/Applications/PyFR/pyfr/solvers/__init__.py", line 14,
>>> in get_solver
>>> return get_integrator(backend, systemcls, rallocs, mesh, initsoln, cfg)
>>> File "/Users/zdavis/Applications/PyFR/pyfr/integrators/__init__.py", line
>>> 29, in get_integrator
>>> return integrator(backend, systemcls, rallocs, mesh, initsoln, cfg)
>>> File "/Users/zdavis/Applications/PyFR/pyfr/integrators/controllers.py",
>>> line 92, in __init__
>>> super(PIController, self).__init__(*args, **kwargs)
>>> File "/Users/zdavis/Applications/PyFR/pyfr/integrators/controllers.py",
>>> line 11, in __init__
>>> super(BaseController, self).__init__(*args, **kwargs)
>>> File "/Users/zdavis/Applications/PyFR/pyfr/integrators/steppers.py", line
>>> 147, in __init__
>>> super(RKVdH2RStepper, self).__init__(*args, **kwargs)
>>> File "/Users/zdavis/Applications/PyFR/pyfr/integrators/steppers.py", line
>>> 11, in __init__
>>> super(BaseStepper, self).__init__(*args, **kwargs)
>>> File "/Users/zdavis/Applications/PyFR/pyfr/integrators/writers.py", line
>>> 68, in __init__
>>> super(FileWriter, self).__init__(*args, **kwargs)
>>> File "/Users/zdavis/Applications/PyFR/pyfr/integrators/writers.py", line
>>> 16, in __init__
>>> super(BaseWriter, self).__init__(*args, **kwargs)
>>> File "/Users/zdavis/Applications/PyFR/pyfr/integrators/base.py", line 50,
>>> in __init__
>>> self._system = systemcls(backend, rallocs, mesh, initsoln, nreg, cfg)
>>> File "/Users/zdavis/Applications/PyFR/pyfr/solvers/base/system.py", line
>>> 31, in __init__
>>> eles, elemap = self._load_eles(rallocs, mesh, initsoln)
>>> File "/Users/zdavis/Applications/PyFR/pyfr/solvers/base/system.py", line
>>> 66, in _load_eles
>>> elemap[t] = self.elementscls(basismap[t], mesh[f], self._cfg)
>>> File "/Users/zdavis/Applications/PyFR/pyfr/solvers/base/elements.py",
>>> line 64, in __init__
>>> for ffpts in basis.facefpts]
>>> File "/Users/zdavis/Applications/PyFR/pyfr/nputil.py", line 73, in
>>> fuzzysort
>>> srtdidx[i:j] = fuzzysort(arr, srtdidx[i:j], dim + 1, tol)
>>> File "/Users/zdavis/Applications/PyFR/pyfr/nputil.py", line 77, in
>>> fuzzysort
>>> srtdidx[i:] = fuzzysort(arr, srtdidx[i:], dim + 1, tol)
>>> File "/Users/zdavis/Applications/PyFR/pyfr/nputil.py", line 77, in
>>> fuzzysort
>>> srtdidx[i:] = fuzzysort(arr, srtdidx[i:], dim + 1, tol)
>>> File "/Users/zdavis/Applications/PyFR/pyfr/nputil.py", line 66, in
>>> fuzzysort
>>> arrd = arr[dim]
>>> IndexError: list index out of range
>>>
>>> I’m using the openmp backend, and I’ve invoked pyfr to run using the
>>> following:
>>>
>>> pyfr-sim -n 100 -p -b openmp run delta_wing.pyfrm delta_wing.ini
>>>
>>> Is this an issue with my numpy installation, or perhaps something amiss
>>> with my configuration file? I’ve attached both mesh and configuration
>>> files for your review. Note, I’ve converted the mesh included as an
>>> attachment prior to running PyFR, but it was more economical to send just
>>> the Gmsh file itself.
>>>
>>> Best Regards,
>>>
>>>
>>>
>>>
>>> Zach Davis
>>> Rescale, Inc.
>>> 589 Howard Street, Ste. 2
>>> San Francisco, CA 94105
>>>
>>> [email protected] <mailto:[email protected]>
>>> P: (855) 737-2253
>>>
>>> enc
>>>
>>> <delta_wing.tgz>
>>
>>
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