Dear Benedikt,

As others have pointed out, the simplest solution is to add "Coherence;" after 
"Merge" - provided that you add "SetFactory("OpenCASCADE");" before, i.e.

SetFactory("OpenCASCADE");
Merge "nanopore-rev-600.brep";
Coherence;

This is a new feature of the upcoming Gmsh 4.0 release, and is available in the 
automated snapshots. With the OpenCASCADE kernel, Coherence is actually a 
synonym for BooleanFragments. The above code is thus equivalent to:

SetFactory("OpenCASCADE");
vol() = ShapeFromFile("nanopore-rev-600.brep");
BooleanFragments{ Volume{vol()}; Delete }{}

Christophe


> On 5 Apr 2018, at 12:53, Benedikt Oswald <benedikt.oswald@lspr.swiss> wrote:
> 
> Dear gmsh developers
> 
> I recently tried to mesh a geometry (made in Freecad) which consists of
> two volumes where a smaller volume was
> 
> subtracted in Freecad from the larger one. When I mesh the two volumes I
> would need tetrahedra
> 
> and that are conformal between the two volumes. Would you have a
> suggestion on how
> 
> to achieve this ? At the moment, gmsh does not really produce a
> conformal mesh.
> 
> I attach the files in question.
> 
> Thanks a lot in advance and greetings, Benedikt
> 
> 
> 
> ----------------------------------------------------------------------------------------------------------------------
> Dr. sc. techn. Benedikt Oswald - first engineer - LSPR AG - phone +41 43 366 
> 90 74
> Grubenstrasse 9, CH-8045 Z├╝rich, benedikt.oswald@lspr.swiss
> ----------------------------------------------------------------------------------------------------------------------
> 
> <nanopore-rev-600-aux-via-brep.geo><nanopore-rev-600.brep><nanopore-rev-600.FCStd>_______________________________________________
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