Dear Phuoc,
Yes, the export can also have some problems with the singular
transformation ... I robustified a bit the evaluation. Can you try
?
Best regards,
Yves
Le 19/06/2018 à 12:48, Huu Phuoc BUI a écrit :
Dear Yves,
I now faced with mixed elements of higher order. In the
enclosed script, I use degree = 2 for all elements, and set the
integration method mim = gf.MeshIm(m, 8), but after resolution,
there are 'nan' values in displacement filed. The 'nan' values
are shown by yellow color in Paraview as
I tried to change the order for integration method but without
success.
Please let me know if you have an idea. Thanks a lot.
Best regards,
Phuoc
On 19/06/2018 10:21, Huu Phuoc BUI
wrote:
Dear Yves,
Thanks a lot for your help. I think the fact that assigning
the integration method by only providing the degree of
interpolation is very useful. That solved my problem now.
Thank you also for your remark about using macro for models.
It's really helpful.
Best regards,
Phuoc
On 18/06/2018 17:32, Yves Renard
wrote:
Dear Phuoc,
The main reason is that you use a NewtonCotes integration
methods on the prism. The NewtonCotes integration method
has Gauss points on the geometrical nodes which is not
convenient at all for the pyramid. You can use instead
mim = gf.MeshIm(m, 3)
which will select an integration of order at least 3 on each
element.
Just an additional remark. You can use the macro system
which can give clearer expressions. For instance
sig_u = "(lambda_para*Trace(Grad_u)*Id(qdim(u)) +
mu_para*(Grad_u + Grad_u'))"
stress_jump_inner = "{sig_u} .... ".format(sig_u=sig_u)
can also be entered has
md.add_macro('sig_u',
"(lambda_para*Trace(Grad_u)*Id(qdim(u)) + mu_para*(Grad_u +
Grad_u'))")
stress_jump_inner = "sig_u ... "
or
stress_jump_inner = "Def sig_u :=
(lambda_para*Trace(Grad_u)*Id(qdim(u)) + mu_para*(Grad_u +
Grad_u')); sig_u ..."
you can also define macros with parameters, see http://getfem.org/userdoc/gasm_high.html#macrodefinition
Best regards,
Yves
Le 18/06/2018 à 13:35, Huu Phuoc BUI a écrit :
Dear Yves,
Please find enclosed the smallest python script. I made
an mistake when assigning Lamé coefficients for 3D
problems (sorry!). Now the problem seems to be different
than the 'nan' ouput.
By using generic assembly, it says:
"RuntimeError: (Getfem::InterfaceError)  Error in
bgeot_geometric_trans.cc, line 245 bgeot::scalar_type
bgeot::lu_inverse(bgeot::scalar_type*, bgeot::size_type,
bool):
Non invertible matrix
"
Best regards,
Phuoc
On 18/06/2018 10:57, Yves
Renard wrote:
Dear Phuoc,
Do you compute some gradient quantities on the finite
element nodes ? If not, it should not pose any problem
since using the generic assembly, the computation are
located on the Gauss points which are not located on the
nodes.
can
you extract the smallest possible program on which
the error occurs ?
Best regards,
Yves
Le 18/06/2018 à 10:35, Huu Phuoc BUI a écrit :
Dear
Yves,
Sorry I email you again on this topics. In fact, the
generic assembly did some computation on pyramid
elements but the output is 'nan'. On elements of others
types (of the mixed mesh), the output is fine.
Please let me know if you have an idea. Thanks.
Best regards,
Phuoc
On 15/06/2018 16:43, Huu Phuoc BUI wrote:
Dear Yves,
That's great! It's indeed working now. Thank you very
much for your help.
Best regards,
Phuoc
On 15/06/2018 16:38, Yves Renard wrote:
Dear Phuoc,
The problem is indeed the same, to compute the
location of gauss points on a neighbour element, the
inversion of the geometric transformation is called.
This inversion used a Newton algorithm whose
starting point is a node of the element ...
(function find_initial_guess in
bgeot_geotrans_inv.cc).
I changed a bit the starting point, so it should
work now. But this is clear that the fact that the
transformation is singular at the pyramid tip is a
difficulty.
Best regards,
Yves
Le 15/06/2018 à 11:53, Huu Phuoc BUI a écrit :
Dear Yves,
Thank you very much for your help.
Now it worked when computing the outer faces. But
I faced another problem of this mixed mesh. In
fact, I'd like to compute the stress jump at the
inner faces using generic assembly, and GetFEM++
showed an error like this:
"
File
"/usr/local/lib/python2.7/distpackages/getfem/getfem.py",
line 5591, in asm_generic
return getfem('asm', 'generic', mim, order,
_expression_, region, model, *args)
RuntimeError: (Getfem::InterfaceError)  Error in
getfem_generic_assembly_compile_and_exec.cc, line
3887 virtual int
getfem::ga_instruction_neighbour_transformation_call::exec():
Geometric transformation inversion has failed in
neighbour transformation
"
So, as you said, this error comes from geometric
transformation of pyramid elements. Do you have an
idea how to fix it?
Best regards,
Phuoc
On 15/06/2018 11:10, Yves Renard wrote:
Dear Phuoc,
The problem come from the fact that the test is
made on the mean unit normal vector on a face.
This mean unit normal vector is computed by
averaging the unit normal vector on each
geometrical node of a face. Unfortunately, for a
pyramid element, the transformation is singular
on the geometrical nodes.
I replaced the mean of normal vector by the
normal vector on the mean of geometrical nodes
of the face. It fixes the problem. (I push the
change on the master branch).
Best regards,
Yves
Le 14/06/2018 à 15:40, Huu Phuoc BUI a écrit :
Dear Yves,
Please find the mesh attached.
Thank you for your help.
Best regards,
Phuoc
On 14/06/2018 14:52, Yves Renard wrote:
Dear Phuoc,
No, I see no reason. If you can just send me
the mesh in a format readable by GetFEM, I
could check what is wrong.
Best regards,
Yves
Le 14/06/2018 à 10:24, Huu Phuoc BUI a
écrit :
Dear Getfemusers,
I have a problem with computing the outer
faces when using a mixed mesh (having
tetras, hexa, prisms and pyramids).
The error is:
face_left =
m.outer_faces_with_direction([0, 0.,
1.0], 0.01)
File
"/usr/local/lib/python2.7/distpackages/getfem/getfem.py",
line 1372, in outer_faces_with_direction
return
self.get("outer_faces_with_direction", v,
angle, CVIDs)
File
"/usr/local/lib/python2.7/distpackages/getfem/getfem.py",
line 1152, in get
return getfem('mesh_get',self.id,
*args)
RuntimeError: (Getfem::InterfaceError) 
Error in bgeot_geometric_trans.cc, line
381 const base_matrix&
bgeot::geotrans_interpolation_context::B()
const:
Non invertible matrix
Please let me know if you have any idea.
Thank you.
Best regards,
Phuoc

Yves Renard (address@hidden) tel : (33) 04.72.43.87.08
Pole de Mathematiques, INSALyon fax : (33) 04.72.43.85.29
20, rue Albert Einstein
69621 Villeurbanne Cedex, FRANCE
http://math.univlyon1.fr/~renard


Yves Renard (address@hidden) tel : (33) 04.72.43.87.08
Pole de Mathematiques, INSALyon fax : (33) 04.72.43.85.29
20, rue Albert Einstein
69621 Villeurbanne Cedex, FRANCE
http://math.univlyon1.fr/~renard


Yves Renard (address@hidden) tel : (33) 04.72.43.87.08
Pole de Mathematiques, INSALyon fax : (33) 04.72.43.85.29
20, rue Albert Einstein
69621 Villeurbanne Cedex, FRANCE
http://math.univlyon1.fr/~renard

