Re: [Libmesh-users] Periodic Boundary Conditions

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Dear All,

After analyzing both of the matrices (A and B) in matlab as John suggested,
I found my B matrix had an empty row (as pointed out in the error message).
Position of the row is related to the size of the mesh and type of element:

using QUAD8:
2x2 mesh --- B has an empty row at 18 from 21  dif: 3
3x3 mesh --- B has an empty row at 34 from 40  dif: 6
4x4 mesh --- B has an empty row at 56 from 65  dif: 9
5x5 mesh --- B has an empty row at 84 from 96  dif: 12

using QUAD9
Quad9
2x2 mesh --- B.m has an empty row at 21 from 25  dif: 4
3x3 mesh --- B.m has an empty row at 31 from 49  dif: 8
..

I must be forgetting to add something when imposing the PBCs,

If anyone sees it please let me know.

Thank you

Peter

On Fri, Jan 25, 2013 at 4:48 AM, Nachiket Gokhale <gok...@gm...>wrote:

> You might want to try using MUMPS for LU factorization. It is robust.
> Petsc and SlepC make using it very easy.
>
>
>
>
> On Jan 24, 2013, at 10:12 PM, David Knezevic <dkn...@se...>
> wrote:
>
> > Hi Peter,
> >
> > You're using SLEPc, right? Have you tried using the LAPACK eigensolver
> > via SLEPc (this tends to be very robust, but it treats the matrices as
> > dense so only works for small problems). To do this, use the command
> > line option:
> >
> > -eps_type lapack
> >
> > David
> >
> >
> >
> > On 01/24/2013 03:29 PM, Peter Zajac wrote:
> >> Hi Roy,
> >>
> >> after constraining the matrices I get the correct eigenvalues and
> >> wavefunctions -- thank you for helping me solve the problem.
> >>
> >> There is one last thing I wanted to ask. When I run the code now (with
> the
> >> constrains), despite obtaining the correct results I get the following
> >> error message:
> >>
> >> [0]PETSC ERROR: --------------------- Error Message
> >> ------------------------------------
> >> [0]PETSC ERROR: Detected zero pivot in LU factorization:
> >> see http://www.mcs.anl.gov/petsc/documentation/faq.html#ZeroPivot!
> >> [0]PETSC ERROR: Empty row in matrix: row in original ordering 1223 in
> >> permuted ordering 20!
> >> [0]PETSC ERROR:
> >> ------------------------------------------------------------------------
> >> [0]PETSC ERROR: Petsc Release Version 3.3.0, Patch 3, Wed Aug 29
> 11:26:24
> >> CDT 2012
> >> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> >> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> >> [0]PETSC ERROR: See docs/index.html for manual pages.
> >> [0]PETSC ERROR:
> >> ------------------------------------------------------------------------
> >> [0]PETSC ERROR: ./femvib on a arch-linu named peter-VirtualBox by peter
> Thu
> >> Jan 24 09:25:57 2013
> >> [0]PETSC ERROR: Libraries linked from
> >> /home/peter/petsc-3.3-p3/arch-linux2-c-debug/lib
> >> [0]PETSC ERROR: Configure run at Fri Nov 23 19:14:06 2012
> >> [0]PETSC ERROR: Configure options --download-f2cblaslapack=1
> >> [0]PETSC ERROR:
> >> ------------------------------------------------------------------------
> >> [0]PETSC ERROR: MatLUFactorSymbolic_SeqAIJ() line 334 in
> >> src/mat/impls/aij/seq/aijfact.c
> >> [0]PETSC ERROR: MatLUFactorSymbolic() line 2750 in
> >> src/mat/interface/matrix.c
> >> [0]PETSC ERROR: PCSetUp_LU() line 135 in src/ksp/pc/impls/factor/lu/lu.c
> >> [0]PETSC ERROR: PCSetUp() line 832 in src/ksp/pc/interface/precon.c
> >> [0]PETSC ERROR: KSPSetUp() line 278 in src/ksp/ksp/interface/itfunc.c
> >> [0]PETSC ERROR: PCSetUp_Redundant() line 176 in
> >> src/ksp/pc/impls/redundant/redundant.c
> >> [0]PETSC ERROR: PCSetUp() line 832 in src/ksp/pc/interface/precon.c
> >> [0]PETSC ERROR: KSPSetUp() line 278 in src/ksp/ksp/interface/itfunc.c
> >> [0]PETSC ERROR: STSetUp_Shift() line 94 in src/st/impls/shift/shift.c
> >> [0]PETSC ERROR: STSetUp() line 280 in src/st/interface/stsolve.c
> >> [0]PETSC ERROR: EPSSetUp() line 204 in src/eps/interface/setup.c
> >> [0]PETSC ERROR: EPSSolve() line 109 in src/eps/interface/solve.c
> >> [0]PETSC ERROR: SlepcAbs() line 486 in
> >> "unknowndirectory/"src/solvers/slepc_eigen_solver.C
> >> application called MPI_Abort(comm=0x84000000, 71) - process 0
> >>
> >> According to the PETSC documentation zero pivot does not always mean the
> >> matrix is singular and since I am getting the correct results I am
> ignoring
> >> the error. Could my ignorance in this case cause a serious problem in
> the
> >> future I should be aware of?
> >>
> >> thank you again
> >>
> >> best
> >>
> >> Peter Zajac
> >> Computational Science Research Center
> >> San Diego
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> On Wed, Jan 23, 2013 at 11:33 AM, Roy Stogner <roy...@ic...
> >wrote:
> >>
> >>> On Wed, 23 Jan 2013, Peter Zajac wrote:
> >>>
> >>>  I am not applying the constraint matrices inside the assemble_mass()
> >>>> function. How exactly should I do that?
> >>>>
> >>> See the constrain_element_* calls in the example codes.  They're
> >>> usually important in the context of hanging node constraints, but the
> >>> periodic boundary constraints work the same way.  (and any
> >>> DirichletBoundaries work nearly the same way, if you're currently
> >>> using penalty Dirichlet BCs and want to switch)
> >>> ---
> >>> Roy
> >>>
> >>
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> >
> >
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