on.
Thank you
--Junchao Zhang
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pe n_active_elem = _mesh.n_active_elem();
--Junchao Zhang
--
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patterns at an interface-level. Reveals which users, apps, and protocols are
consuming th
t;.vtk";
Inspired by your reply, I avoided using dot in file name prefixes. I
changed it to file_name << "out-" and got
out-001.vtk
out-002.vtk
out-003.vtk
out-001_0.vtu
out-002_0.vtu
out-003_0.vtu
Now I can view the mesh at each time step with ParaView.
--Junch
I get the mesh every time step so that I can see how the mesh is
adaptively refined in ParaView?
Thank you!
--Junchao Zhang
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On Wed, Jun 29, 2016 at 11:52 AM, John Peterson
wrote:
>
>
> On Wed, Jun 29, 2016 at 10:43 AM, Junchao Zhang
> wrote:
>
>>
>> On Wed, Jun 29, 2016 at 11:28 AM, John Peterson
>> wrote:
>>
>>>
>>>
>>> On Wed, Jun 29, 2016 at 10:00
On Wed, Jun 29, 2016 at 11:28 AM, John Peterson
wrote:
>
>
> On Wed, Jun 29, 2016 at 10:00 AM, Junchao Zhang
> wrote:
>
>> I usually dump a mesh into a GMVIO file and then view it with ParaView.
>> Suppose I find a cell is weird and want to examine it in debugger.
On Wed, Jun 29, 2016 at 11:04 AM, Paul T. Bauman wrote:
> On Wed, Jun 29, 2016 at 12:00 PM, Junchao Zhang
> wrote:
>
>> I usually dump a mesh into a GMVIO file and then view it with ParaView.
>>
>
> Huh. I didn't know ParaView could read output from GMVIO. TIL.
debugger? Suppose we use ReplicatedMesh.
Thank you.
--Junchao Zhang
--
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prese
algorithm used in libmesh? Or what I
can do is just to read the code?
Thanks
--Junchao Zhang
--
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In libmesh, can adjacent elements be coarsened into new elements that do
not exist before? For example, a 2x2 grid (mesh) is refined into 4x4 grid.
Can the interior 4 elements be coarsened into one?
I feel it is mathematically allowed, but don't know if it is feasible in
practice.
--Ju
I find libmesh does not accept some PETsc KSP options, such as -ksp_rtol
0. It is likely that libmesh calls KSPSetFromOptions() too early, before
other customization routines.
--Junchao Zhang
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On Fri, Jan 29, 2016 at 5:05 PM, Roy Stogner
wrote:
>
> On Fri, 29 Jan 2016, Junchao Zhang wrote:
>
> I tested the modified code with uniform refinement and
>> exact_sol.extra_quadrature_order(1). I printed out both l2 error and h1
>> error and got
>>
>&g
=
0.002569, h1_error = 0.215482
We can see l2_error monotonically decreases, however h1_error does not.
What is the possible reason?
Thanks.
--Junchao Zhang
On Thu, Jan 28, 2016 at 10:53 PM, Junchao Zhang
wrote:
> I found an example of exact_sol.extra_quadrature_order()
> in adaptivity
-elements-11-nodes mesh at the first time step for debugging purpose. Now
I know that is questionable in view of error analysis as Roy explained.
--Junchao Zhang
On Thu, Jan 28, 2016 at 6:50 PM, Derek Gaston wrote:
> Also: it can depend on integration error in the integration of the L2
>
Roy,
I tested your patch and found it did not fix the problem.
I can send you the modified example if need.
--Junchao Zhang
On Thu, Jan 28, 2016 at 2:25 PM, Roy Stogner
wrote:
>
> On Wed, 27 Jan 2016, Roy Stogner wrote:
>
> 1. DofMap::process_constraints() needs to be fixed
efinement step. The input mesh has
8 triangles and 2 quadrilaterals.
--Junchao Zhang
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> // initialize parent data
> Base::reinit();
>
> // Project the old & older vectors to the new mesh
> // The System::reinit handles this now
> // this->project_vector (*old_local_solution);
> // this->project_vector (*older_local_solution);
> }
>
ect_vector (*older_local_solution);
}
--Junchao Zhang
On Wed, Jan 27, 2016 at 3:43 PM, Roy Stogner
wrote:
>
> On Wed, 27 Jan 2016, Junchao Zhang wrote:
>
> I slightly modified adaptivity_ex2.C ( see the outline below). I find
>> after the mesh is refined, the old solution i
Hello,
I slightly modified adaptivity_ex2.C ( see the outline below). I find
after the mesh is refined, the old solution is not correctly projected to
the new mesh.
I print out old solution in each refinement step. At the beginning, time
= 0.025, r_step = 0, old_local_solution->print() prints t
That is awesome. That solves my problem.
Thanks
--Junchao Zhang
On Fri, Jan 22, 2016 at 9:52 AM, Paul T. Bauman wrote:
> You need to make sure you call System::reinit_constraints (
> http://libmesh.github.io/doxygen/classlibMesh_1_1System.html#ad12672358a8e9796a42bd7f42888c54f)
> a
same time.
Any thoughts?
--Junchao Zhang
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Monitor end-to-end web transactions and
Yeah, that solves my problem. I now can use DirichletBoundary in
adaptivity_ex2.C
Thanks.
--Junchao Zhang
On Wed, Jan 20, 2016 at 5:58 PM, John Peterson wrote:
>
>
> On Wed, Jan 20, 2016 at 4:33 PM, John Peterson
> wrote:
>
>>
>>
>> On Wed, Jan 20, 2016 at
I guess that is because the input mesh is read from a file in adaptivity_ex2,
however the input file does not boundary info.
I am trying to add this to the input file. It looks the format of .xda
files is not well documented.
--Junchao Zhang
On Wed, Jan 20, 2016 at 3:31 PM, Junchao Zhang
wrote
and
nodes. I don't know what is wrong.
I attach my modified adaptivity_ex2.C and the diff to see if someone can
help on that.
Thank you!
--Junchao Zhang
diff --git a/examples/adaptivity/adaptivity_ex2/adaptivity_ex2.C
b/examples/adaptivity/adaptivity_ex2/adaptivity_ex2.C
index 741
Thanks, that is helpful.
--Junchao Zhang
On Tue, Jan 19, 2016 at 4:10 PM, David Knezevic
wrote:
> Assemble the Uexact vector, then compute the difference e = U - Uexact.
>
> You can also refer to error_estimation/exact_solution.h, but I believe
> that's used for computing L2
How to get e = U - Uex? Is there a libmesh interface for that?
--Junchao Zhang
On Tue, Jan 19, 2016 at 3:57 PM, David Knezevic
wrote:
> Assuming you've already assembled K, so you can just do a matvec
> (SparseMatrix::vector_mult) followed by a dot product (NumericVector::dot)
Hello,
I want to compute e^TKe as a measure of the error of a solution. Here e =
U - Uex, supposing I know the analytic answer to the PDE.
How can I do it in libmesh? Is there an example?
Thank you.
--Junchao Zhang
Thanks to David and John for your hints. I need to further digest it.
--Junchao Zhang
On Wed, Jan 13, 2016 at 4:33 PM, John Peterson wrote:
>
>
> On Wed, Jan 13, 2016 at 3:23 PM, Junchao Zhang
> wrote:
>
>> Hello,
>> I tried to follow the textbook to write weak f
libmesh
examples still do not have boundary terms in weak form. Why?
Thank you.
--Junchao Zhang
--
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APM + Mobile APM + RUM: Monitor 3 App instances at just
Thanks to David and Vikram, your explanation helps me a lot. I'll do
further exploration from your points.
My current work is just to repeat what adaptivity_ex2.C does, with aim of
showing we can solve PDEs with another programming model.
--Junchao Zhang
On Tue, Jan 12, 2016 at 3:06 PM, V
the boundary all zeros.
I am a guy from computer science. Understanding FE is hard for me. Hope I
can get some hints here.
Thank you.
--Junchao Zhang
On Mon, Jan 11, 2016 at 5:46 PM, Geordie McBain
wrote:
> 2016-01-12 8:44 GMT+11:00 Junchao Zhang :
> > Hello,
> >I am
no idea on how to interpret them.
2) The code uses the penalty method to impose boundary conditions. I was
told the penalty method is bad and a smoothing function with zero on
boundary is preferred. Could someone point me to literatures or examples on
smoothing?
Thank you!
--Jun
Hello,
I am debugging a libmesh example code to learn libmesh. Is there a
method to print out the matrix and the vector, or even visualize them?
Thanks.
--Junchao Zhang
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On Fri, Aug 14, 2015 at 4:58 PM, John Peterson wrote:
>
>
> On Fri, Aug 14, 2015 at 2:28 PM, Junchao Zhang
> wrote:
>
>> Hello,
>> I have a simple AMR code using SerialMesh. I run it 70 refinements on 12
>> cores.
>
>
> 2^70 = 1180591620717411303424,
d I found libMesh uses number of nodes as weight (in
my case, it should be 3). I tried to changed &vwgt[0] to NULL when calling
METIS. From the printf, I got a quite balanced partitioning. However, the
program execution time incr
remote processors. But I could not find this communication in libmesh
source code.
Could some tell me where this functionality is triggered if my
understanding is correct?
Thank you!
--Junchao Zhang
rtion with
libmesh_dbg.so
Assertion `incoming_header == node_magic_header' failed.
incoming_header = 96
node_magic_header = 1234567890
[0] src/parallel/parallel_node.C, line 194
It seems the conclusion is Parallel Mesh repartitioning is not ready in
libmesh?
--Junchao Zhang
On Wed, Aug 5,
the error again, I will report it here.
Thanks a lot.
--Junchao Zhang
On Wed, Aug 5, 2015 at 3:15 PM, Roy Stogner
wrote:
>
> On Wed, 5 Aug 2015, Junchao Zhang wrote:
>
> In addition, I did more experiments. I increased the input mesh size, let
>> it has 64 elements and ran
rial meshes may not be ready for repartitioning here.
376 else if(!skip_partitioning() &&
377 partitioner().get() &&
378 this->is_serial())
379 {
380 partitioner()->partition (*this, n_parts);
381 }
--Junchao Zhang
On Wed, Aug 5, 2015 at
I used GMVIO(mesh).write("output.gmv");
--Junchao Zhang
On Wed, Aug 5, 2015 at 2:32 PM, Derek Gaston wrote:
> What file format were you using to write the mesh out and view it in
> Paraview?
>
> Derek
>
> On Wed, Aug 5, 2015 at 12:14 PM Junchao Zhang
> wrote:
&
output mesh
in paraview.
So the question is under what conditions mesh repartitioning will be
triggered in libmesh?
Thank you very much.
--Junchao Zhang
On Tue, Aug 4, 2015 at 2:58 PM, Junchao Zhang
wrote:
> Hi, John,
>
> Attached are my naive AMR (adapted from adaptivity_ex2.C) a
So, why are non-serial meshes not repartitioned?
Thanks.
--Junchao Zhang
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OK. I find I can output a mesh into a file and then view it with Paraview.
Thanks.
--Junchao Zhang
On Thu, Jul 30, 2015 at 4:05 PM, Junchao Zhang
wrote:
> Hello,
> Is there a way to dump a mesh into figures, e.g., using Cairo? If run
> in parallel, it is great if I can dump multi
Hello,
Is there a way to dump a mesh into figures, e.g., using Cairo? If run in
parallel, it is great if I can dump multiple files showing partitions on
each process.
Thanks.
--Junchao Zhang
On Thu, Jul 30, 2015 at 8:31 AM, Roy Stogner
wrote:
>
> On Thu, 30 Jul 2015, li@siat.ac.cn wrote:
>
> > For a parallel mesh, is that every processor has a global mesh?
>
> For SerialMesh, for every properly initialized mesh every processor
> has a full copy of the mesh.
>
I guess after refin
itself should be refined into two children, instead of four.
However, I find Elem::refine() always generates n_children(), which is four
in this case. How and where does libmesh handle this case?
Thank you.
--Junchao Zhang
On Tue, Jul 28, 2015 at 9:07 AM, John Peterson wrote:
>
>
> On
refined too, since new nodes are introduced on their sides.
Can someone point me to code doing that?
Thanks.
--Junchao Zhang
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