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] Rescale, Inc. 589 Howard Street, Ste. 2 San Francisco, CA 94105 [email protected]<mailto:[email protected]> P: (855) 737-2253 enc <delta_wing.tgz> -- You received this message because you are subscribed to the Google Groups "PyFR Mailing List" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]<mailto:[email protected]>. To post to this group, send email to [email protected]<mailto:[email protected]>. Visit this group at http://groups.google.com/group/pyfrmailinglist. For more options, visit https://groups.google.com/d/optout. -- You received this message because you are subscribed to the Google Groups "PyFR Mailing List" group. 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