.
Regards
Robert
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Hello,
the bug was introduced during with the optimization of
> https://github.com/libMesh/libmesh/pull/190
See the attached files for a modified, working version of the VTKIO.
Robert
On Tue, Jun 24, 2014 at 03:34:03PM -0400, subramanya sadasiva wrote:
> Hi,
> I am trying to run
_system().current_local_solution,u_idx,Uc);
for (unsigned int j = 0; j < u_idx.size(); ++j) {
U[j][i] = Uc.el(j);
}
}
instead of using just context.get_elem_solution(i).el(j);
Is there an easier way for doing this?
Robert
On Fri, Ma
amp;bfunc));
in a FEMSystem::init_data(..)
Are there any additional step necessary in each timestep to apply the boundary
conditions or what else am I missing?
Robert
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Hello,
after updating libmesh from git version 63581916 to d750e8c15 the files
written by VTKIO are only containing the mesh and the variables
libmesh_elem_id and subdomain_id, but none of the variables I defined.
Does any one else has this issue as well?
Robert
As someone who is also working on this code, the problem is not
uninitialized memory. Valgrind reports a clean bill of health.
On 01/02/2014 09:45 PM, Derek Gaston wrote:
> This is almost definitely not a libMesh problem. It sounds like an
> uninitialized variable. I recommend running your app
Hi,
If you don't like deriving the stuff by hand you might have a
look at AceGen (http://www.fgg.uni-lj.si/Symech/), it uses Mathematica
for the linarization and generates C code for the residual and jacobian.
Robert
On Mon, Nov 25, 2013 at 12:01:20PM -0700, Derek Gaston wrote:
> If
ield-variational formulation for
incompressibility. Is there any better type available in libmesh for
this?
Robert
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>
> Derek
>
> Sent from my iPhone
>
> On May 21, 2013, at 11:14 AM, Robert Blake wrote:
>
>> Does anyone have any advice on this question? John, maybe?
>>
>>
>> On 04/30/2013 11:29 AM, Robert Blake wrote:
>>> I am trying to run
Does anyone have any advice on this question? John, maybe?
On 04/30/2013 11:29 AM, Robert Blake wrote:
> I am trying to run a FEM simulation wherein every element has a
> variable-length C data structure defined in an external non-libmesh file
> format. What is the easiest way to get
On 05/20/2013 03:05 PM, John Peterson wrote:
> On Tue, Apr 30, 2013 at 10:02 AM, Robert Blake
> wrote:
>> Hi again,
>>
>> I'm trying to use libmesh to replace some legacy custom FEM software. I
>> need an output file where every line of text contains the val
Does anyone an idea how to write custom output code?
I'm really at a loss here. I haven't made any progress in the last
month. I might have to move to another framework.
On 04/30/2013 12:02 PM, Robert Blake wrote:
> Hi again,
>
> I'm trying to use libmesh to replac
Hi Cody,
After:
./configure CC=clang CXX=clang++
make
make check passes all tests.
Thanks a lot!
Rob J. Goedman
[email protected]
On May 12, 2013, at 2:59 PM, Robert J Goedman wrote:
> Hi Cody,
>
> Thank you. Usually configure selects clang. Will check it.
>
> Regards
quite awhile. If you are
> indeed using that compiler, let me suggest that you try either GCC
> from Mac Ports, or Clang.
>
> Cody
>
> Sent from my iPad
>
> On May 12, 2013, at 2:37 PM, Robert J Goedman wrote:
>
>> Hi,
>>
>> Just installed the librar
Hi,
Just installed the library and attempted to run 'make check'. Passed many all
tests before this test. Hope this helps.
Regards,
Rob J. Goedman
[email protected]
...
***
* Done Running Example adaptivity_ex1:
* example-opt
Hi again,
I'm trying to use libmesh to replace some legacy custom FEM software. I
need an output file where every line of text contains the value of a
solution variable at the corresponding node in a VTK input mesh. For
example, the value of the solution at node 5 in the VTK file should be
at li
I am trying to run a FEM simulation wherein every element has a
variable-length C data structure defined in an external non-libmesh file
format. What is the easiest way to get this data into libmesh and use
it in parallel?
I see only a couple of ways of doing this:
1.) I can easily do this using
On Tue, Mar 05, 2013 at 12:19:50PM -0600, Roy Stogner wrote:
>
> On Tue, 5 Mar 2013, Robert wrote:
>
> > I am currently catching errors due to element inversion (det F < 0)
> > during assembly. If such an error occurs I want to reduce the timestep
> > and try ag
ust one of
the processes has an inverted element and the whole thing deadlocks.
Does anyone know how to handle this situations?
Robert
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On Thu, Nov 15, 2012 at 11:21:52AM -0500, Andrew E Slaughter wrote:
> I found two problems that may be of interest to the developers. They could
> be my problems and not yours, but just in case.
>
> (1) When using VTK there is a problem with the include directory if you use
> VTK build from source
Hi,
some time ago, I posted an example using a neo-hookean material on the
mailinglist:
> http://www.mail-archive.com/[email protected]/msg03044.html
Robert
On Thu, Aug 23, 2012 at 12:51:15AM -0500, walter kou wrote:
> Hi,
>
> Is there anyone has an example code
quite limited for application.
Thanks, Robert
On 06/07/2012 06:45 PM, John Peterson wrote:
> On Thu, Jun 7, 2012 at 10:23 AM, robert wrote:
>> I think the problem is really my computer - i installed paraview on a better
>> machine and it works with the same file.
>>
>&
But you're right, just installed paraview on a lab-computer and there it
worked fine.
thanks
On 06/07/2012 04:47 PM, Paul T. Bauman wrote:
> On Thu, Jun 7, 2012 at 9:42 AM, robert <mailto:[email protected]>> wrote:
>
> is there a size limit for writing exodus file
Thanks for the fast reply.
if I use an Exodus object I get the same result.
I'll try to find a better computer. But it's strange that ParaView asks
me which reader to use if only my computer is the problem.
On 06/07/2012 04:47 PM, Paul T. Bauman wrote:
> On Thu, Jun 7, 2012 at 9:
ty sure that the file is ok. I created it with
tetgen and can look at it with medit.
Thanks,
Robert
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Hi,
thank you for your help
Robert
On 05/24/2012 04:42 PM, John Peterson wrote:
> On Thu, May 24, 2012 at 8:31 AM, robert wrote:
>> TetGenIO found the tetgen files to read
>> Assertion `eid< _elements.size()' failed.
>> [0] src/mesh/serial_mesh.C, line 179, com
27;Assertion eid' above that what you wanted to know?
Robert
On 05/24/2012 03:54 PM, John Peterson wrote:
> On Thu, May 24, 2012 at 7:27 AM, robert wrote:
>> Hello,
>>
>> has anybody tried to use tetgen_io with one of the recent versions of
>> ubuntu (11.
1 4 8
# Generated by tetgen -pg fun.poly
I'll look at the debugging soon ...
Robert
On 05/24/2012 03:54 PM, John Peterson wrote:
> On Thu, May 24, 2012 at 7:27 AM, robert wrote:
>> Hello,
>>
>> has anybody tried to use tetgen_io with one of the recent
the following message:
/
TetGenIO found the tetgen files to read
Segmentation fault (core dumped)/
if I start it in gdb I get:
/
Program received signal SIGSEGV, Segmentation fault.
0xb7d2040c in libMesh::SerialMesh::insert_elem(libMesh::Elem*) ()
from /home/robert/software/libmesh/l
ystems. So I found no way to get all nodes on
the upper side to be constrained with dirichlet-bc in this scenario, is
there any way to do this?
regards
Robert
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On Thu, Jan 12, 2012 at 10:13:03AM +0100, Robert wrote:
> On Wed, Jan 11, 2012 at 02:10:30PM -0600, Roy Stogner wrote:
> > On Tue, 10 Jan 2012, Robert wrote:
> > > I have just tested this with the default configure options. Any
> > > suggestions for improve
Hi,
On Wed, Jan 11, 2012 at 02:10:30PM -0600, Roy Stogner wrote:
> On Tue, 10 Jan 2012, Robert wrote:
> > I have just tested this with the default configure options. Any
> > suggestions for improvements are of course welcome.
>
> Would you try running it in parallel? Th
tensor classes, I discovered a
small bug in TypeTensor::assign. See tensor.patch.
Regards
Robert
On Mon, Jan 09, 2012 at 09:02:29AM +1300, Mark Davies wrote:
> Hi Guys,
>
> I'm just getting started with the library and was wondering if there are
> any examples dealing wi
?
Regards,
Robert
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Dear all,
I want to read a mesh on a BlueGene/P computer, then partition it and
write a mesh-file for each partition:
/* READ TETGEN FILE*/
...
/* prepare and partition mesh */
mesh.find_neighbors();
tilities for semi-structured grids
>* NodeConstraints calculations for moving mesh users
I am assuming that this change should help me to get my periodic BC
problem (See thread "Change sparsity pattern of system matrix") on
a moving mesh fixed. Can you provide some lines of code (or
Am Donnerstag, den 10.11.2011, 07:17 -0700 schrieb Cody Permann:
> On Nov 10, 2011, at 4:22 AM, robert wrote:
>
> > Am Mittwoch, den 24.08.2011, 22:16 -0500 schrieb Roy Stogner:
> >
> >>
> >> Hi Robert,
> >>
> >> My experience wi
> >
>
> I see three warnings here but I don't see any errors. Are there additional
> messages that you didn't paste here?
Hi Cody,
thanks for your reply.
That's exactly the strange thing - I couldn't find any error messages
either. It just aborts with error 1.
I tried to build the same libm
Am Mittwoch, den 24.08.2011, 22:16 -0500 schrieb Roy Stogner:
>
> Hi Robert,
>
> My experience with the BIG machines is that many of them don't support
> dynamic linking. This static build produces bigger
> binaries but simplifies the runtime environment on the comput
+mass+matrix+integration&source=bl&ots=SvCQZQEcGB&sig=ERkG7r7yTgGWOugp3COUMjfqx1E&hl=en&ei=IuG2Tof9OcqAhQeYrfn3Aw&sa=X&oi=book_result&ct=result&resnum=7&ved=0CFwQ6AEwBg#v=onepage&q=lumped
ore I build the
EquationSystems object, the n_dofs() correspond to the
coarse mesh, not to the refined one.
Any suggestions?
Robert
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e I don't use the class
ParallelMesh - so I was wondering if the data-structure,
which I get with --enable-parmesh, allows refinement and
coarsening.
So, although I read in 1 file per processor the
n_partitions() has changed.
Thank you,
Robert
-
Hello,
I haven't tried the suggestion of Derek yet. Instead, I
wanted to try to split a smaller mesh with nemesis and see
if my code runs in parallel (configure with
--enable-parmesh)
I split the mesh with the following code:
Mesh mesh;
TetGenIO TETGEN(mesh);
e nemesis files.
>
> nem_spread is a _serial_ process that produces "n" number
> of nemesis files (it is doing an "offline" partitioning).
> You will need a machine with quite a bit of RAM.
>
> Derek
Hi Derek,
thanks for your help. I have to do some labw
r problem more than a month ago but still, I could't
solve the problem.
Thanks very much for your help in advance,
Robert
> thank you,
> Robert
>
>
>
> > > >> You'd either need to borrow a large memory machine
> > > for >> long enoug
Mesh mesh;
TetGenIO TETGEN(mesh);
TETGEN.read("meshfile");
mesh.find_neighbors();
> thank you,
> Robert
>
>
>
> > > >> You'd either need to borrow a large memory machine
> > > for >> long enough to read in the
ng in the serial tetgen mesh on one processor?
I am sure it is quite easy - unfortunately I don't progress
any more without help.
thank you,
Robert
> > >> You'd either need to borrow a large memory machine
> > for >> long enough to read in the Tetgen file and
n running with 'mpiexec -np
8 ./tryRead-opt'
I get a long error message - see at the end of the mail.
For configuring of libmesh I used the following options:
./configure --enable-slepc --enable-mpi --enable-parmesh
--enable-petsc
Do I maybe have to change something there?
thanks, Robert
9:6: error: class
libMesh::Nemesis_IO has no member named write
Could you give me some lines of example code how you would
do it?
Thank you, Robert
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Hello,
could someone give me an example of how to use parallelmesh?
I have the problem that I have 12GB of RAM, 8 CPU's, but a
mesh which has several GB (generated with tetgen). Now, if I
understood everything right, a copy of the mesh is kept on
every processor. I am reading the mesh with tetgen_i
Hello,
I had success using the exodusII file format, which I had generated with
cubit[1]. In addition to generating the geometry and meshing it, you
have to create "sidesets" containing the surfaces on which you want to
apply your BC.
Robert
[1] http://cubit.sandia.gov/
On Wed, Oc
Hi,
On Fri, Oct 07, 2011 at 10:23:57AM -0500, Roy Stogner wrote:
>
> On Fri, 7 Oct 2011, robert wrote:
>
> > I am doing solid mechanics calculations with FEMSystem and a moving mesh
> > and need periodic boundary conditions. As the PR-BC code in libmesh only
> > wor
ing of the matrix while adding the PR-BCs. So how can I influence
the default sparsity pattern used to create the system matrix to avoid
these performance issues?
Robert
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Am Mittwoch, den 31.08.2011, 16:55 +0200 schrieb robert:
> Am Mittwoch, den 31.08.2011, 08:46 -0600 schrieb John Peterson:
> > On Wed, Aug 31, 2011 at 1:31 AM, robert wrote:
> > >
> > > running the job with --enable-parmesh doesn't change. I run only one
> &
Am Mittwoch, den 31.08.2011, 08:46 -0600 schrieb John Peterson:
> On Wed, Aug 31, 2011 at 1:31 AM, robert wrote:
> >
> > running the job with --enable-parmesh doesn't change. I run only one
> > mpi-job per node but it is still quite slow.
>
> You need to **rec
Am Dienstag, den 30.08.2011, 21:19 +0200 schrieb robert:
> >
> > > It is possible to run 1, 2 or 4 processes per node. If I run 2 or 4
> > > processes I get:
> > > Error! ***Memory allocation failed for SetUpCoarseGraph: gdata.
> > > Requested size:
>
> > It is possible to run 1, 2 or 4 processes per node. If I run 2 or 4
> > processes I get:
> > Error! ***Memory allocation failed for SetUpCoarseGraph: gdata.
> > Requested size: 107754020 bytesError! ***Memory allocation failed for
> > SetUpCoarseGraph: gdata. Requested size: 107754020 byte
Am Dienstag, den 30.08.2011, 12:34 -0600 schrieb John Peterson:
> On Tue, Aug 30, 2011 at 12:23 PM, robert wrote:
> >
> >> 32 nodes or 32 cores? I don't know the details of your cluster so it
> >> may be obvious, but make sure you aren't accidentally run
Am Dienstag, den 30.08.2011, 10:48 -0600 schrieb John Peterson:
> It will be extremely slow if it goes into swap.
>
> > Would this option just work with the existing code or do I have to
> > change to ParallelMesh?
>
> Should work with existing code. Hopefully.
>
> >
> > – SMP mode : 4 GB of
Am Dienstag, den 30.08.2011, 10:08 -0600 schrieb John Peterson:
> On Tue, Aug 30, 2011 at 9:56 AM, robert wrote:
> >
> > The mesh.uniformly_refine(1) takes some minutes when I do it in serial
> > on my PC. However, on the BlueGene/P it doesn't come to an end (I
>
Hello,
I am trying to get to run my libmesh code in parallel. Thanks to the
help of you guys most of the code already works. However, I still have
some small problems where I still don't have enough understanding of
libmesh to solve them alone.
One of them is to do mesh refinement in parallel:
Am Freitag, den 26.08.2011, 09:09 -0500 schrieb Roy Stogner:
>
> On Fri, 26 Aug 2011, robert wrote:
>
> > probably not - it's the first time that I am working in parallel so I
> > don't know how to do it yet.
>
> Instead of this:
>
> &
Roy,
probably not - it's the first time that I am working in parallel so I
don't know how to do it yet.
Would be great if you could give me a hint.
Thanks in advance,
Robert
Here function I am using:
std::cout << "set boundary_id's ...&qu
ne. In contrast, if I do
it after setting the boundary ids, I can't write it any more (except
with gmv).
Robert
Am Freitag, den 26.08.2011, 12:49 +0200 schrieb robert:
> Hello,
>
> My calculation consists of several parts. For each part the geometry
> changes and I create a n
sh.xdr");'
the program gets stuck. There is no error and it doesn't abort, it just
seems to take quite a long time. In contrast, the
new_equation_systems.write("../bgscratch/old_equation_systems.xdr");
take
Am Donnerstag, den 25.08.2011, 09:48 +0200 schrieb Robert:
> Hi,
>
> you might also think about changing the settings of the
> mailinglist software in such way, that a "Reply-To" header pointing to
> the List is added to every message (Option "reply_goes_to_list"
hitting the reply-button" mails to the mailinglist instead of single
persons.
(another) Robert
On Wed, Aug 24, 2011 at 10:16:55PM -0500, Roy Stogner wrote:
>
>
> Okay, that's two in a row, from two different sources even.
>
> New rules:
>
> People who send h
t;&1 | tee mi.txt
in .bashrc: PATH=/home//mpich2-install/bin:$PATH ; export PATH
Then I downloaded petsc and compiled it with the following:
./config/configure.py --download-f-blas-lapack=1 --download-mpich=0
--with-mpich-dir=/home//include/mpich2-install
make PETSC_DIR=/home/robert
Am Montag, den 15.08.2011, 08:03 -0600 schrieb John Peterson:
> On Fri, Aug 12, 2011 at 4:21 AM, robert wrote:
> > Hello,
> >
> > again, I have a question as far as reading meshes with tetgen is
> > concered.
> > I read a mesh by
> >
> > Mesh new_m
processor ids and use a code like
ex9, everything works like if I created the mesh with libmesh?
thanks,
Robert
Am Donnerstag, den 04.08.2011, 11:48 +0200 schrieb robert:
> Hi,
>
> could you just tell me how you implemented the public members
> 'element_attributes' and
contrast to this, xdr_io works fine.
Robert
Am Montag, den 08.08.2011, 17:29 +0200 schrieb robert:
> Hello,
>
> I have seen that there has already been a topic like this one some years
> ago. However, I couldn't find a solution for the problem.
>
> At the end of a calculation
Hello,
I have seen that there has already been a topic like this one some years
ago. However, I couldn't find a solution for the problem.
At the end of a calculation I want to evaluate the results by using
system.point_value(int,Point). Everything works fine if I do it
immediately. However, if
ction is defined as
'short int boundary_id (const Elem *const elem, const unsigned short int
side) const'
with the element constant, it did not work. How can I set the
boundary_id?
Thank you,
Robert
Am Donnerstag, den 04.08.2011, 08:12 -0600 schrieb John Peterson:
> On Thu, A
::TetGenIO’ has no member
named ‘node_attributes’
make: *** [ThermoPaine3d.i686-pc-linux-gnu.opt.o] Fehler 1
robert@robert:~/Desktop/THERMO_PAINE/3D$
Am Mittwoch, den 03.08.2011, 16:48 -0600 schrieb John Peterson:
> On Wed, Aug 3, 2011 at 12:36 PM, robert wrote:
> > Hi John,
> >
> >
ned as public: std::vector<
std::vector > in tetgen_io.h. I did the same for node_attributes.
However, I get some bad alloc when reading the mesh.
Thank you,
Robert
Am Mittwoch, den 03.08.2011, 16:48 -0600 schrieb John Peterson:
> On Wed, Aug 3, 2011 at 12:36 PM, robert wrote:
> &
ing the mesh and before any refinement.
This is maybe not the most elegant way to do it. However, it seems to
work.
Regards,
Robert
Am Mittwoch, den 03.08.2011, 09:01 -0600 schrieb John Peterson:
> On Wed, Aug 3, 2011 at 7:10 AM, robert wrote:
> > Hi to all,
> >
> > I wa
n_id();
when looping through the elements. But since the new_mesh.n_subdomains()
returns 1, this didn't work.
Thank you for your help,
Robert
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On Mon, Jul 04, 2011 at 05:45:10PM -0500, Roy Stogner wrote:
>
> On Mon, 4 Jul 2011, Robert wrote:
>
> > I have some trouble with the accuracy of the displacement gradient in
> > moving mesh situations.
>
> Sadly that may not be the end of your troubles in moving mesh
d --enable-petsc --enable-slepc --enable-laspack
--enable-gzstreams --enable-bzip2 --enable-vtk --enable-tecplot
--enable-exodus
Robert
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On Fri, Jun 24, 2011 at 10:35:18AM -0500, Roy Stogner wrote:
>
> On Fri, 24 Jun 2011, Robert wrote:
>
> > I was trying to build a TransientSystem
>
> Any reason why? FEMSystem already has a mechanism for transient
> solves, via the TimeSolver subclasses.
I
user-code and give therefore more flexibility.
Robert
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not add nodes, resp.
Is there a better way to do so? Wouldn't it maybe smarter to solve both
meshes in seperate systems and to combine them with the boundary
conditions (although I have problems to figure out how to set the
boundary conditions)?
Thanks for your help,
R
Hi to all,
is there a possibility of mesh-deformation in libmesh? I would need it
to model tectonic emplacement of lithospheric plates.
Thanks,
Robert
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Hello,
when trying to build against VTK I had to modify the libmesh-Makefiles
to make it work:
Index: m4/vtk.m4
===
--- m4/vtk.m4 (Revision 4437)
+++ m4/vtk.m4 (Arbeitskopie)
@@ -111,7 +111,7 @@
dnl If both the header file
reassembled when using MPI. I intend to use this e.g. to
for store the progress of damage or other internal state of the material.
Robert
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Hi,
I am trying to build a model which solves the same equation as in ex9.
I would like to specify the boundary conditions in a way that the flux
out of the system on the left side equals the flux coming in on the
right side.
I am trying to use something like:
for (unsigned int side=0; siden_s
it?
I thought I could write it to a file and read it afterwards again, but
this might not be very efficient.
Thanks,
Robert
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Hi,
if I use
./configure --disable-mpi
I get the same problem
Running the samples directly doesn't work either. If you don't have time
- maybe someone else has any suggestion?
thankes,
Robert
Am Mittwoch, den 15.12.2010, 12:39 -0700 schrieb Cody Permann:
> Robert,
>
>
anything else - at least not on
purpose.
Thanks for your help.
Robert
###
# the following lines will be replaced by the output
# of ./configure
hosttype = i686-pc-linux-gnu
hostos= linux-gnu
27;/usr/include/libmesh-0.7.0.3/examples'
make: *** [run_examples] Fehler 2
Before I used some oder version of libmesh and everything worked fine.
thanks,
Robert
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and nothing can happen any more - this changes at every time step.
Furthermore, for my simplified model the holes should have circular
shapes
thanks,
Robert
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Hi,
I have tried to modify example code 9. I am using a starting
concentration of one everywhere but want to set the condition for one
(or more) boundary to zero.
for (unsigned int qp=0; qphttp://p.sf.net/sfu/therealnews-com
___
Libmesh-users mailing
blem: During my calculation I am creating holes
in the grid. When I then want to impose boundary conditions for this
hole in the next time step (let's say the value of the concentration was
1 at this position and i set it to 0) I get oscillations.
thanks, Robert
Am Mittwoch, den 08.12.2010, 09
*/
std::cout<<"boundary_id: "<
> On Tue, 7 Dec 2010, robert wrote:
>
> > How can I specify different boundary conditions for my domain
> > boundary and for the 'inner' boundaries surrounding the holes?
> >
> > Is ther
How can I specify different boundary conditions for my domain
boundary and for the 'inner' boundaries surrounding the holes?
Is there something like:
if (elem->neighbor(s) == NULL)
that I can use for the hole boundaries?
Thanks,
Robert
Am Montag, den 06.12.2010, 10:57
0 at 10:26 AM, robert wrote:
> > Hi,
> > I just have a problem with my next step: The holes in my domain
> > represent minerals in which no diffusion is happening. However, the
> > minerals are growing with time. Now I have the following problem:
> >
> >
> >
Hi,
How can I create a mesh which has something like a whole in the middle?
I need to have something which works in runtime because during my model
(based on diffusion equation) chemical reactions and phase transitions
occur.
thanks.
Robert
h time step. Thus, after each step I have
to search the elements, which lie within the crystal now.
How would you do this? I have problems in finding the right element
boundaries and afterwards also in implementing an efficient routine
which
finds those elem
--
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