On Wed, 28 Oct 2009, Joa Ljungvall wrote:
> Since I produce the first mesh inside my code, using OpenCASCADE+Gmsh I'm
> thinking maybe I can let Gmsh regenerate a mesh for at each iteration, with
> the refined mesh of libmesh as a background mesh...
If by "each iteration" you mean each refinemen
Hm...
I almost giving up on this one... Looping through the elements, and moving
nodes on the boundaries, it is not too difficult to make sure that the element
I'm looking at isn't modified in a bad way. However, that node also belongs
to a hole line of other elements, that might get destroyed. On
On Mon, 26 Oct 2009, Joa Ljungvall wrote:
> What I'm trying to do is:
>
> 1) Refine the mesh
> 2) Find and store hanging nodes
> 3) Move points on boundary to the "real" boundary
> then I do a do{...}While() including
> 4) Check that Jacobian>0, if not switch node 0 and 2 (the pointers in the
>
Hi,
I've tried to get this running, but still have some problems...
What I'm trying to do is:
1) Refine the mesh
2) Find and store hanging nodes
3) Move points on boundary to the "real" boundary
then I do a do{...}While() including
4) Check that Jacobian>0, if not switch node 0 and 2 (the pointe
Hi,
Yes, it looks like the thing we need, expect that it only works for QUAD4...
But I guess I could use it as a model and write a function in my program. If
it works we add it to the svn version.
Thanks for all the help. I think I understood the problem and how to fix it.
I'll get back with new
On Wed, 14 Oct 2009, Derek Gaston wrote:
> I thought I ran into similar problems when I did mesh redistribution /
> smoothing + adaptivity. I was able to go in and "fix" the hanging
> nodes somehow... But I don't remember where I did it ( I thought it
> was down inside the library and I committ
I thought I ran into similar problems when I did mesh redistribution /
smoothing + adaptivity. I was able to go in and "fix" the hanging
nodes somehow... But I don't remember where I did it ( I thought it
was down inside the library and I committed it back).
I'm not near a computer right now whe
On Wed, 14 Oct 2009, Joa Ljungvall wrote:
> So returning to the "fix" using the constraint equations... I don't quite
> understand the idea behind this. If my hanging node no longer is at the right
> position, my mesh is broken, no?
Not quite. If your hanging node is no longer at the right posi
So returning to the "fix" using the constraint equations... I don't quite
understand the idea behind this. If my hanging node no longer is at the right
position, my mesh is broken, no? So fixing this with the constraint equations
is a way of making the calculations go on, assuming that the error we
On Wed, 14 Oct 2009, Joa Ljungvall wrote:
> When I loop over the nodes, find a face that is on the boundary, and
> then move the nodes the problem is, if I understood it correct, that
> I might move a hanging node out of the line between the nodes of the
> not so refined neighbour.
This is not t
Hi again,
When I loop over the nodes, find a face that is on the boundary, and then move
the nodes the problem is, if I understood it correct, that I might move a
hanging node out of the line between the nodes of the not so refined neighbour.
But I can check if this is the case, and instead of mo
That'll work out of the box, but you can't coarsen the "base" mesh that
you load in to libmesh --- you can only refine the base mesh and then
subsequently coarsen the elements that have been refined by libmesh. But
if you can represent the geometry with a coarser mesh than is required
to resolv
I've been running in devel mode. Things start to look complicated... What
about this as an approach, escentially what was proposed to me in the
beginning.
1) Use gmsh to generate a mesh that is fine enough to describe the geometry
to the precision it is known
2) Solve the equations
3) Refine
On Tue, 13 Oct 2009, Roy Stogner wrote:
> Anyway, the solution is probably to, after you've looped over all
> nodes, loop over all constraint equations in the dof map and apply
> them to nodes' xyz coordinates.
Thinking about it again, this is an oversimplification. For it to
work, you'd need
On Tue, 13 Oct 2009, Joa Ljungvall wrote:
> #5 0x7fff81116bfc in __cxa_throw ()
> #6 0x00010512afa4 in RemoteElem::n_nodes ()
> #7 0x00010510acf4 in DofMap::dof_indices ()
> #8 0x00010510e2d9 in DofMap::add_neighbors_to_send_list ()
>
> This I don't understand at all...
Hmm..
The problem with a negative jacobian seems solved. It was indeed a node that
was moved in the wrong way by my code. Now the program iterates two
times but then I get (running in gdb)
EquationSystems
n_systems()=1
System "Laplace"
Type "LinearImplicit"
Variables="u"
Finite Elemen
On Tue, 13 Oct 2009, Joa Ljungvall wrote:
> As for getting inverted element, this means I've moved a node to the other
> side of the opposite face of my tet? This could very well be a bug in my
> code. I can, and will, check that I don't move nodes in an unreasnoble way.
If you're sticking to f
Hi again,
Ok. Seems sensible to me. Now, I'm a nuclear physicist so FEM is not quite
what I do for a living, but presently I'm giving it a try to see if it can
improve some detector simulations we are doing, presently done with finite
difference solvers, so bare with me even if I'm not 100% on tar
On Tue, 13 Oct 2009, Joa Ljungvall wrote:
> If I change the locations of the new nodes when they are made, i.e. somewhere
> deep down in the MeshRefinement class, can I do what I would like to do?
I don't think that would make any difference. If moving nodes
eventually gives you an inverted ele
Hmmm...
If I change the locations of the new nodes when they are made, i.e. somewhere
deep down in the MeshRefinement class, can I do what I would like to do? If I've
understood everything correct a tet is subdivided by adding vertices halfway
between the old ones. But there is nothing magic abou
> 3) Copies all active elements to a new mesh, i.e. my new mesh have the right
> nodes locations etc. but no "refinement" (is this true if I do it right?)
This won't work if there's any adaptive refinement in the original
mesh - libMesh relies on the parent element hierarchy to figure out
hangi
Hi again,
If I:
0) Solve the equations one time...
1) Refine my mesh
2) Move my nodes
3) Copies all active elements to a new mesh, i.e. my new mesh have the right
nodes locations etc. but no "refinement" (is this true if I do it right?)
4) I change mesh in my equation system
5) build my matrix
On Tue, 13 Oct 2009, John Peterson wrote:
> On Tue, Oct 13, 2009 at 11:40 AM, Joa Ljungvall wrote:
>> It is quite possible that I move the wrong nodes the wrong way, but is my
>> problem ;). The general question is, is this a possible route to take? I call
>> this routine after refinement and c
On Tue, Oct 13, 2009 at 11:40 AM, Joa Ljungvall wrote:
> It is quite possible that I move the wrong nodes the wrong way, but is my
> problem ;). The general question is, is this a possible route to take? I call
> this routine after refinement and coursening, before
> equation_systems.reinit().
I
Hi again,
during the day I been working a bit on the problem: Currently I have the
exact geometry inside my program (implemented via CGS and GEANT4). What I
have tried is to, after the refinement move the new boundary points using
a code like this one (it tries to move all nodes on a boundary to
On Tue, Oct 13, 2009 at 10:36 AM, Joa Ljungvall wrote:
> Hi,
>
> The problem is that I have to solve my equation on the same domain with
> very different boundary conditions, making a uniform refinement very
> inefficient and a waste of time, and worse in my case, RAM. So I do need
> to start with
Hi,
The problem is that I have to solve my equation on the same domain with
very different boundary conditions, making a uniform refinement very
inefficient and a waste of time, and worse in my case, RAM. So I do need
to start with a very course mesh and refine.
cheers
Joa
On Tue, Oct 13, 2
Hi,
I'm not sure I understood the answer. I want to start with a very course mesh,
and refine it based on the solution on the course(r) mesh, i.e. adaptive
refinment. So using gmsh I would have to communicate the solution in each step
and tell gmsh which regions to refine, or? And if so, how? Fu
If you generate a mesh in gmsh that is sufficiently fine that a mesh of
second order elements captures the geometry well enough, then you can
read that mesh into libMesh, and just use libMesh's adaptive refinement
as in the examples. In that situation, libMesh's adaptive refinement
will interpo
I think the simplest thing to do is use second order elements in gmsh. Then
when you refine the new nodes will interpolate the quadratic
approximation to
the boundary of your domain.
- Dave
Joa Ljungvall wrote:
> Hi all,
>
> I would like to use libmesh to solve a rather simple equation
> (Lap
Hi all,
I would like to use libmesh to solve a rather simple equation (Laplace/poisson)
but in a domain with a somewhat funny shape of the boundary. To do this I
created a mesh using gmsh, modified example 14 a bit so it reads my mesh
instead of the l-shaped domain. My problem is that when I refi
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