Problem during transition from CGAL to mshr

Question

Hi everyone.
I am running on linux mint 17 [~ Ubuntu Trusty] and I recently got updates from apt for fenics from the custom PPA which broke the support for CSG.

I am aware of this conversation, dated July 2014, in which is said that the transition from CGAL to mshr should be seamless but, at least in my case, I have been less lucky than expected.

My programs using CSG now fail with

Error: Unable to create mesh from CSG geometry.
Reason: Mesh generation not available. Dolfin has been compiled without CGAL..
Where: This error was encountered inside CSGMeshGenerator.cpp.

How can I fix this?
Thanks for help,
Massimiliano

Comments

More or less seamless. You need to use the methods from mshr, see its demos.

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Ok, I finally got it to work; it asked me to learn another bit of CMake, but that can't hurt :)

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Im having the same error and trouble solving this problem. How did you do it?

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Are you talking about using mshr or setting CMakeLists.txt?

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I have to admit, I'm not quite sure. I guess im using the right mshr syntax but it somehow doesn't work:

Using the old syntax
dolfin::CircleMesh mesh(dolfin::Point(0.0,0.0), radius, 0.03);

gives me the error

*** Error: Unable to generate ellipse mesh.
*** Reason: Generation of ellipse meshes requires DOLFIN to be configured with CGAL.
*** Where: This error was encountered inside EllipseMesh.cpp.
*** Process: unknown

What would be the correct translation into new mshr syntax? I tried

dolfin::Circle circle(0.0, 0.0, radius);
dolfin::Mesh mesh(circle, 0.03);

but that gives me the error

*** Error: Unable to create mesh from CSG geometry.
*** Reason: Mesh generation not available. Dolfin has been compiled without CGAL..
*** Where: This error was encountered inside CSGMeshGenerator.cpp.
*** Process: unknown

which is the same as your error. I have reinstalled fenics via purging and adding the repository, but that didn't help. How did you solve this problem?

edit: What is the c++ alternative/syntax for from mshr import *? Using #include gives a mshr could be resolved error, like it hasn't been installed.

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Try

#include <mshr.h>
[...]
mshr::Circle obstacle(Point(xc,yc,0),r);
Mesh mesh;
mshr::generate(mesh,obstacle,resolution);

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Thanks it is finally working. After using your code I just had to add the line

env.Append(LIBS = ['mshr'])

to my SCons file.

Answer 1

Hi!

Here is a simple example of what you would do earlier:

from dolfin import *

res = 100
r1 = Rectangle(0, 0, 1, 2)
r2 = Rectangle(0.4, 0.4, 0.6, 0.7)

mesh = Mesh(r1 - r2, res)

This chunk of code as you have discovered returns the CGAL error. When applying mshr the syntax is slightly different:

from dolfin import *
from mshr import *

r1 = Rectangle(Point(0,0), Point(1,2))
r2 = Rectangle(Point(0.4, 0.4), Point(0.6, 0.7))

# Define domain and resolution
domain = r1 - r2
res = 100

# Generate mesh
mesh = generate_mesh(domain, res)

Just a basic example but you get the idea, check out mshr on bitbucket for more info: https://bitbucket.org/benjamik/mshr

Answer 2

Yes, I had figured that out earlier, reading through the API.
Also, the C++ interface is slightly different as the method is generate and has different signature.
However, I got it to work now, we can close this.