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[Robert Caulk <1666339@xxxxxxxxxxxxxxxxxx>]

I've narrowed it down to the cell1 and cell2 declarations. These objects
are not playing nicely with CGAL's is_infinite, mirror_index, and
neighbor functions.

Here is my working theory:

The cell1 and cell2 handles originate down at the facet_circulator on
line 195 where an arbitrary facet is defined by dereferencing the edge
of interest.

195: RTriangulation::Facet_circulator facet1 =
Tri.incident_facets(*edge);

This is where I believe there may be a problem. facet1 does not appear
to be the address of a facet, instead it appears to be the circulator.
Am I right to say that in this case *facet1 is the facet that we are
interested in using [1]? If so, we should be able to change lines 174
and 175 to:

const CellHandle& cell1 = *facet->first;
const CellHandle& cell2 = *facet->first->neighbor(*facet->second);

But of course, the compiler says this is an invalid initialization of
reference.

[1] http://doc.cgal.org/latest/Circulator/index.html

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https://bugs.launchpad.net/bugs/1666339

Title:
  DFNflow crashes for compiled trunk but not non-optimized debug
  compiled trunk

Status in Yade:
  New

Bug description:
  Distro: Xenial 16.04LTS
  Yade Version: yade-2017-0207.git-11c276f
  Compilation: default compilation with debug flags and '#define DFNFLOW' uncommented in DFNFlow.cpp

  
  Summary:

  DFNFlowEngine crashes for compiled yade-2017-0207.git-11c276f sources.
  The segmentation fault also occurs for a debug compiled version and
  yields the attached core dump. Interestingly, the DFNFlowEngine does
  not crash for a non-optimized debug compilation of the same sources.

  
  Description of failure:

  According to the core dump, the failure can be traced back to
  DFNFlow.cpp:176, where it is checking if the cell is inifinite
  (although I have also had it fail at the permeability assignment
  directly below line 176 for a modified version of DFNflow.cpp).

   DFNFlow.cpp:

   176: if ( Tri.is_infinite(cell1) || Tri.is_infinite(cell2)) cerr<<"Infinite cell found in    trickPermeability, should be handled somehow, maybe"<<endl;
   177:	cell1->info().kNorm()[facet->second]=cell2->info().kNorm()[Tri.mirror_index(cell1, facet- >second)] = pow((aperture+residualAperture),3)/(12*viscosity);

  I am unsure why this line is causing a crash in the optimized-debug
  compiled code, but not the non-optimized-debug compiled code.

  My optimized-debug compiled executable is simply built with the flag
  -DDEBUG=ON. My non-optimized debug compiled code uses an edited
  CMakeLists.txt to avoid optimization:

  IF(CMAKE_COMPILER_IS_GNUCC)
    SET(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -O0")
    SET(CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS_DEBUG} -O0")
  ENDIF(CMAKE_COMPILER_IS_GNUCC)

  The attached zip contains:
    mwe.py  // input script 
    liteSpecimen2mm.spheres  // packing file
    jointSurf.stl  // stl for smooth joint
    coreDump2.txt  // core dump after executing mwe.py with optimized debug compiled yade

  Any assistance with this bug is greatly appreciated.

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