Re: [firedrake] Boundary conditions
Standard GMSH problem: if you have a physical line you also need a physical surface or GMSH will drop all the interior elements from the output. On Saturday, February 1, 2014, Cotter, Colin J <colin.cotter@imperial.ac.uk> wrote:
Dear Firedrakers, I decided to create another set of cohomology tests, this time with Dirichlet boundary conditions, since there is a nice result relating the kernels of the operators with and without Dirichlet boundary conditions (for the maths-curious, it's Poincare duality).
However, I can't get the boundary tags into Firedrake from gmsh. If I attempt to tag the boundary using "Physical Line" in gmsh (see bottom of this email for the .geo file), the line
mesh = Mesh("annulus.msh") produces: *** ERROR *** Error message: Unsupported mixture of face/element types
Removing the physical line makes the error message go away, so there is something wrong with that line.
What have I done wrong?
all the best --Colin
Point(1) = {0, 0, 0, 1.0}; Point(2) = {1, 0, 0, 1.0}; Point(3) = {1, 1, 0, 1.0}; Point(4) = {0, 1, 0, 1.0}; Point(5) = {0.3333333333333, 0.3333333333333, 0, 1.0}; Point(6) = {0.66666666666666, 0.3333333333333, 0, 1.0}; Point(7) = {0.66666666666666, 0.66666666666666, 0, 1.0}; Point(8) = {0.3333333333333, 0.66666666666666, 0, 1.0}; Line(1) = {1, 2}; Line(2) = {2, 3}; Line(3) = {3, 4}; Line(4) = {4, 1}; Line(5) = {5, 6}; Line(6) = {6, 7}; Line(7) = {7, 8}; Line(8) = {8, 5}; Line Loop(1) = {1, 2, 3, 4}; Line Loop(2) = {5, 6, 7, 8}; Plane Surface(1) = {1,2}; Physical Line(9) = {2, 3, 4, 1, 6, 7, 8, 5};
-- Dr David Ham Departments of Mathematics and Computing Imperial College London http://www.imperial.ac.uk/people/david.ham
Ah good, works, thanks. --cjc ________________________________ From: firedrake-bounces@imperial.ac.uk [firedrake-bounces@imperial.ac.uk] on behalf of David Ham [David.Ham@imperial.ac.uk] Sent: 01 February 2014 22:12 To: firedrake Subject: Re: [firedrake] Boundary conditions Standard GMSH problem: if you have a physical line you also need a physical surface or GMSH will drop all the interior elements from the output. On Saturday, February 1, 2014, Cotter, Colin J <colin.cotter@imperial.ac.uk<mailto:colin.cotter@imperial.ac.uk>> wrote: Dear Firedrakers, I decided to create another set of cohomology tests, this time with Dirichlet boundary conditions, since there is a nice result relating the kernels of the operators with and without Dirichlet boundary conditions (for the maths-curious, it's Poincare duality). However, I can't get the boundary tags into Firedrake from gmsh. If I attempt to tag the boundary using "Physical Line" in gmsh (see bottom of this email for the .geo file), the line
mesh = Mesh("annulus.msh") produces: *** ERROR *** Error message: Unsupported mixture of face/element types
Removing the physical line makes the error message go away, so there is something wrong with that line. What have I done wrong? all the best --Colin Point(1) = {0, 0, 0, 1.0}; Point(2) = {1, 0, 0, 1.0}; Point(3) = {1, 1, 0, 1.0}; Point(4) = {0, 1, 0, 1.0}; Point(5) = {0.3333333333333, 0.3333333333333, 0, 1.0}; Point(6) = {0.66666666666666, 0.3333333333333, 0, 1.0}; Point(7) = {0.66666666666666, 0.66666666666666, 0, 1.0}; Point(8) = {0.3333333333333, 0.66666666666666, 0, 1.0}; Line(1) = {1, 2}; Line(2) = {2, 3}; Line(3) = {3, 4}; Line(4) = {4, 1}; Line(5) = {5, 6}; Line(6) = {6, 7}; Line(7) = {7, 8}; Line(8) = {8, 5}; Line Loop(1) = {1, 2, 3, 4}; Line Loop(2) = {5, 6, 7, 8}; Plane Surface(1) = {1,2}; Physical Line(9) = {2, 3, 4, 1, 6, 7, 8, 5}; -- Dr David Ham Departments of Mathematics and Computing Imperial College London http://www.imperial.ac.uk/people/david.ham
OK, next question is whether I can output a numpy matrix for a bilinear form assembled with boundary conditions, i.e. whether I can get the reduced matrix with the boundary rows and columns removed? I can see that the bcs are postponed until the solve, so if this exists it would just be a utility for testing. If it doesn't I can remove them myself. --cjc ________________________________ From: firedrake-bounces@imperial.ac.uk [firedrake-bounces@imperial.ac.uk] on behalf of Cotter, Colin J [colin.cotter@imperial.ac.uk] Sent: 02 February 2014 08:54 To: firedrake Subject: Re: [firedrake] Boundary conditions Ah good, works, thanks. --cjc ________________________________ From: firedrake-bounces@imperial.ac.uk [firedrake-bounces@imperial.ac.uk] on behalf of David Ham [David.Ham@imperial.ac.uk] Sent: 01 February 2014 22:12 To: firedrake Subject: Re: [firedrake] Boundary conditions Standard GMSH problem: if you have a physical line you also need a physical surface or GMSH will drop all the interior elements from the output. On Saturday, February 1, 2014, Cotter, Colin J <colin.cotter@imperial.ac.uk<mailto:colin.cotter@imperial.ac.uk>> wrote: Dear Firedrakers, I decided to create another set of cohomology tests, this time with Dirichlet boundary conditions, since there is a nice result relating the kernels of the operators with and without Dirichlet boundary conditions (for the maths-curious, it's Poincare duality). However, I can't get the boundary tags into Firedrake from gmsh. If I attempt to tag the boundary using "Physical Line" in gmsh (see bottom of this email for the .geo file), the line
mesh = Mesh("annulus.msh") produces: *** ERROR *** Error message: Unsupported mixture of face/element types
Removing the physical line makes the error message go away, so there is something wrong with that line. What have I done wrong? all the best --Colin Point(1) = {0, 0, 0, 1.0}; Point(2) = {1, 0, 0, 1.0}; Point(3) = {1, 1, 0, 1.0}; Point(4) = {0, 1, 0, 1.0}; Point(5) = {0.3333333333333, 0.3333333333333, 0, 1.0}; Point(6) = {0.66666666666666, 0.3333333333333, 0, 1.0}; Point(7) = {0.66666666666666, 0.66666666666666, 0, 1.0}; Point(8) = {0.3333333333333, 0.66666666666666, 0, 1.0}; Line(1) = {1, 2}; Line(2) = {2, 3}; Line(3) = {3, 4}; Line(4) = {4, 1}; Line(5) = {5, 6}; Line(6) = {6, 7}; Line(7) = {7, 8}; Line(8) = {8, 5}; Line Loop(1) = {1, 2, 3, 4}; Line Loop(2) = {5, 6, 7, 8}; Plane Surface(1) = {1,2}; Physical Line(9) = {2, 3, 4, 1, 6, 7, 8, 5}; -- Dr David Ham Departments of Mathematics and Computing Imperial College London http://www.imperial.ac.uk/people/david.ham
On 2 Feb 2014, at 09:04, "Cotter, Colin J" <colin.cotter@imperial.ac.uk> wrote:
OK, next question is whether I can output a numpy matrix for a bilinear form assembled with boundary conditions, i.e. whether I can get the reduced matrix with the boundary rows and columns removed?
We don't give you the matrix with the bc rows and cols removed, we just zero them and slap a 1 on the diagonal, you'll have to do it yourself. Note that you can get the dof indices of the bc nodes by accessing bc.nodes where bc is a DirichletBC object. Lawrence
Oh, neat! Thanks. --cjc ________________________________________ From: firedrake-bounces@imperial.ac.uk [firedrake-bounces@imperial.ac.uk] on behalf of Lawrence Mitchell [lawrence@duffch.at] Sent: 02 February 2014 14:47 To: firedrake Subject: Re: [firedrake] Boundary conditions
On 2 Feb 2014, at 09:04, "Cotter, Colin J" <colin.cotter@imperial.ac.uk> wrote:
OK, next question is whether I can output a numpy matrix for a bilinear form assembled with boundary conditions, i.e. whether I can get the reduced matrix with the boundary rows and columns removed?
We don't give you the matrix with the bc rows and cols removed, we just zero them and slap a 1 on the diagonal, you'll have to do it yourself. Note that you can get the dof indices of the bc nodes by accessing bc.nodes where bc is a DirichletBC object. Lawrence _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
participants (3)
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Cotter, Colin J
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David Ham
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Lawrence Mitchell