Re: brain anatomy boundary conditions

[Konstantinos Poulios]

I just had a mistake in the order of the Interpolate arguments, it should be

md.add_interpolate_transformation_from_expression("head_to_tf", meshh, meshtf, "X")

md.add_filtered_fem_variable("multmortar", mfutf, EDGE_RG)

md.add_nonlinear_generic_assembly_brick(mim, "(u_tf-Interpolate(u_head, head_to_tf)).multmortar", EDGE_RG)

On Fri, Nov 19, 2021 at 12:11 AM Konstantinos Poulios <logari81@googlemail.com> wrote:

There are different ways to bind a surface mesh to a volume mesh. If your meshes are conformal, i.e. sharing nodes along the interface, you can merge all meshes into one mixed mesh and create a mesh_fem on the combined mesh. The following example shows a mesh_fem defined on a mixed mesh with common nodes between surface and volume elements:

import getfem as gf
m0 = gf.Mesh('cartesian',[0,1,2,3],[0,1,2],[-1,0])
m0.add_convex(gf.GeoTrans('GT_QK(2,1)'),[[0,0,-.8, -1],
                                         [0,1,  0,1.1],
                                         [0,0,  0,  0]])
mf0 = gf.MeshFem(m0);
mf0.set_classical_fem(1)
mf0.export_to_vtk('mixed_mesh.vtk','ascii')
print(mf0.nbdof())

The other approach, which is more general is to keep the separate meshes and implement a mortar condition between the edge of the surface mesh and the volume mesh. To implement such a condition you will need to define a multiplier and an interpolation operation between the two domains with something like

md.add_interpolate_transformation_from_expression("head_to_tf", meshh, meshtf, "X")

md.add_filtered_fem_variable("multmortar", mfutf, EDGE_RG)

md.add_nonlinear_generic_assembly_brick(mim, "(u_tf-Interpolate(head_to_tf,u_head)).multmortar", EDGE_RG)

Haven't tested it but conceptually it should work

BR

Kostas

On Thu, Nov 18, 2021 at 9:37 PM Lesage,Anne Cecile J <AJLesage@mdanderson.org> wrote:

Dear all

 

To describe a brain geometrical space contrains, I have three meshes part in my python script

 

meshb=gf.Mesh('import','gid','brainr25tet4h5.GiD.msh')

meshtf=gf.Mesh('import','gid','tentoriumfalxr25h5.GiD.msh')

meshh=gf.Mesh('import','gid','headr25tet4h5.GiD.msh')

 

meshb and mesh are 3d and meshtf is a fine membrane described by a triangle mesh surface

 

mesh and meshtf are attached at several places (nodes in common), how do I ensure that the fem takes this boundary condition in account?

 

To set up that the brain is sliding without friction inside the head, I wrote the following python lines

 

fbb = meshb.outer_faces()  # Boundary of the brain

fbh = meshh.outer_faces()  # Boundary of the head

 

HEAD_BOUND = 1;

BRAIN_BOUND = 2;

 

# selection of faces for contact condition

meshh.set_region(HEAD_BOUND, fbh)

meshb.set_region(BRAIN_BOUND, fbb)

 

md.add_penalized_contact_between_nonmatching_meshes_brick(mim3h, uh, ub, datanamer, HEAD_BOUND, BRAIN_BOUND, 1, lambda1_n)

 

Is it a good option? How to choose the parameters datanamer and lambda1?

 

I would like the brain to slide along the whole meshtf. How to define a set of faces that contains the entire triangles mesh?

 

Thank you

Regards

Anne-Cecile

 

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