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From: Steffen Petersen <steffen.petersen@tu...>  20060117 20:55:55

Shengli Xu schrieb: > In example 8 : > ...... > if (fabs(curr_node(2)z_coo) < TOLERANCE) > { > // The global number of the respective degree of freedom. > unsigned int dn = curr_node.dof_number(0,0,0); > > // The penalty parameter. > const Real penalty = 1.e10; > ...... > > the function dof_number(0,0,0) is unsigned int > DofObject::dof_number(const unsigned int s, const unsigned int var, > const unsigned int comp). What is comp? Is it for parallel? Comp is the number of components (for variable var in system s) associated with a specific DofObject. For the Lagrange elements used here, each node has exactly one degree of freedom (and ther is only one variable), which means that there is only one component (0) and we get the corresponding dof number from the call dof_number(0,0,0). Note that for other finite element types more than one degree of freedom can be associated with one node, and there can also be dofs that belong to elements. > For example in 2D , the first defined variable is u, the second defined > variable is v. If I want to set the boundary of v. Is it right that > dof_number(0,1,0)? Yes. > Can libMesh read boundary information from input file? What is the > format ? Is there some examples about it? > Can libMesh read all information from input file. Don't set the node > boundary condition like in Example 8 manually. You may have a look at example 7. In this example the rhs vector is read from a file. In a similar manner other boundary conditions can be defined in such an input file. Steffen 
From: Ondrej Certik <ondrej@ce...>  20060117 20:53:13

> The actual slepc version (2.3.0) also offers a Lanczos > solver (for Hermitian problems) that can be used to compute the > smallest values in the spectrum (since I have been using > an older slepc version so far I have not tested this solver yet). > I have just commited some changes to also include the > Lanczos algorithm that comes with the current version. I tried Lanczos, and unfortunately, it always says, the solver didn't converge. And my external solver (pysparse) works fine on the same matrix. > For computing the smallest eigenvalues I have used slepc > (2.2.1) together with the arpack package, but it seems that > I need to change some cunfiguration stuff to get everything > working with the 2.3.0 version. The arpack++ package looks good, thanks for the tip. Ondrej 
From: KIRK, BENJAMIN (JSCEG) (NASA) <benjamin.kirk1@na...>  20060117 16:19:16

Many apologies. It seems the make rule we have for rsync'ing the xda_format directory for the web page was in error. I have manually updated the file and will fix the rule shortly. Ben Original Message From: libmeshusersadmin@... [mailto:libmeshusersadmin@...] On Behalf Of David Knezevic Sent: Friday, January 13, 2006 3:48 AM To: Roy Stogner Cc: Shengli Xu; libmeshusers@... Subject: Re: [Libmeshusers] Where can I find the description of XDA and UNV file format used by LibMesh? I updated the xda_format.pdf file a while ago. I added the updated version to the CVS repository but I guess it never got uploaded to the website. Check in your libmesh/doc/latex/xda_format directory.  Dave On 13/01/2006, at 2:01 AM, Roy Stogner wrote: > On Fri, 13 Jan 2006, Shengli Xu wrote: > >> Title String >> 0 4 8 7 >> 8 5 2 6 >> 7 9 3 >> ....... >> Is this the node information of element? > > These are the node numbers in each element, one element per line. > >> But it does not fit with the Figure. 1. > > No, it doesn't. > >> The element nodes is >> "1,2,3,4" of element 1 in Figure.1. Is "0 >> 4 8 7" right ? I think it maybe "0 1 2 3" ? > > The nodes in Fig. 1 appear to be misnumbered. The node numbers in the > .xda file do fit with the node coordinates later in the file. > > Someone should fix that figure... but it probably won't get done until > we update the whole description document, which doesn't cover the new > libMesh .xda support for storing refined meshes. >  > Roy Stogner > > >  > This SF.net email is sponsored by: Splunk Inc. Do you grep through log > files for problems? Stop! Download the new AJAX search engine that > makes searching your log files as easy as surfing the web. DOWNLOAD > SPLUNK! > http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click > _______________________________________________ > Libmeshusers mailing list > Libmeshusers@... > https://lists.sourceforge.net/lists/listinfo/libmeshusers  This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click _______________________________________________ Libmeshusers mailing list Libmeshusers@... https://lists.sourceforge.net/lists/listinfo/libmeshusers 
From: KIRK, BENJAMIN (JSCEG) (NASA) <benjamin.kirk1@na...>  20060117 15:45:36

Sure... The CBS method ends up adding streamline diffusion in a clever way, much like the SUPG or TaylorGalerkin formulations. I've played with it for scalar convectiondiffusion problems, but it is easily applicable to systems. All you need to do is write out the stabilized weak form and implement all the terms using the test and trial functions (and their gradients) provided in the library. The only reason stabilized methods are not implemented in the examples is to avoid "endorsing" any single approach. I routinely use SUPG stabilization for the compressible NavierStokes equations. Ben _____ From: libmeshusersadmin@... [mailto:libmeshusersadmin@...] On Behalf Of Shengli Xu Sent: Thursday, January 12, 2006 7:07 PM To: libmeshusers@... Subject: [Libmeshusers] Can the characteristicbased split (CBS) algorithm for NS function be worked with libMesh? Does anybody have experience on it? Thanks! ShengliXu 
From: Steffen Petersen <steffen.petersen@tu...>  20060117 14:15:57

> Hi, I also use the generalized eigenvalue problem and it=20 > works fine. Many > thanks. I have a question: I have a real symmetric problem,=20 > so I get only real > eigenvalues, but I need to get the lowest ones. So I use: >=20 > eigen_system.eigen_solver>set_position_of_spectrum(SMALLEST_M AGNITUDE); >=20 > The problem is, that all the solvers from slepc package=20 > (ARNOLDI, SUBSPACE, > POWER) don't support the "SMALLEST_MAGNITUDE" option, see=20 > their sources, for > example slepc2.3.0/src/eps/impls/arnoldi/arnoldi.c, line 38: >=20 > if (eps>which!=3DEPS_LARGEST_MAGNITUDE) > SETERRQ(1,"Wrong value of eps>which"); >=20 > Except the "LAPACK" solver. Lapack works fine, but it=20 > retrieves all the > eigenvalues and is really slow, in fact for a bigger mesh=20 > it's completely > unusable (but works). Is there a way how to get the lowest=20 > eigenvalues with > slepc (maybe using some trick)? The actual slepc version (2.3.0) also offers a Lanczos solver (for Hermitian problems) that can be used to compute the smallest values in the spectrum (since I have been using an older slepc version so far I have not tested this solver yet). I have just commited some changes to also include the Lanczos algorithm that comes with the current version. For computing the smallest eigenvalues I have used slepc (2.2.1) together with the arpack package, but it seems that I need to change some cunfiguration stuff to get everything working with the 2.3.0 version. Steffen =20 > In the meantime, I export the element matrices to a file and=20 > use external > solver, pysparse >=20 > http://people.web.psi.ch/geus/pyfemax/pysparse.html >=20 > so I have a small (88 lines) python script, which assembles=20 > the global matrices > (they are called A and B in libmesh), and calls Jacobi=20 > Davidson method from > pysparse module. The solver is written in C (exported to=20 > python), it's fast and > it works.=20 >=20 > Ondrej >=20 > On Mon, Jan 16, 2006 at 12:25:50AM +0100, Steffen Petersen wrote: > > Hello Michael, > >=20 > > a few weeks ago you have asked for > > solving generalized eigenvalue problems with libMesh. > > Meanwhile, I have extended the slepc interface > > to also support generalized problems > > (with a few modifaications example 16 > > may be used for solving a generalized eigenvalue > > problem). > > Feel free to ask if you are interested in some > > more details. > >=20 > > Steffen > >=20 > >=20 > >=20 > > Michael Povolotskyi schrieb: > > >Dear Libmesh developers, > > >I have to solve an eigenvalue problem for a quantum=20 > physics calculations. > > >My questions are: > > >1) Is it possible to solve a general eigenvalue problem=20 > like Hx =3D Sx,=20 > > >where H and S are known matrixes. > > >2) Is it possible to have complex (selfconjugated) matrixes? > > > > > >Thank you, > > >Michael. > > >=20 > > >=20 > This SF.net=20 > > >email is sponsored by: Splunk Inc. Do you grep through log=20 > files for=20 > > >problems? Stop! Download the new AJAX search engine that=20 > makes searching=20 > > >your log files as easy as surfing the web. DOWNLOAD SPLUNK!=20 > > >http://ads.osdn.com/?ad_idv37&alloc_id=16865&op=3Dclick=20 > > >_______________________________________________=20 > Libmeshusers mailing=20 > > >list Libmeshusers@...=20 > > >https://lists.sourceforge.net/lists/listinfo/libmeshusers > >=20 > >=20 > >=20 > >  > > This SF.net email is sponsored by: Splunk Inc. Do you grep=20 > through log files > > for problems? Stop! Download the new AJAX search engine that makes > > searching your log files as easy as surfing the web. =20 > DOWNLOAD SPLUNK! > > http://ads.osdn.com/?ad_id=3D7637&alloc_id=3D16865&op=3Dclick > > _______________________________________________ > > Libmeshusers mailing list > > Libmeshusers@... > > https://lists.sourceforge.net/lists/listinfo/libmeshusers >=20 