dolfin team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

Thanks, I've applied the patch.

--
Anders


On Wed, Dec 02, 2009 at 09:41:46PM +0100, Marie Rognes wrote:
> Anders Logg wrote:
> >On Wed, Dec 02, 2009 at 08:53:12PM +0100, Marie Rognes wrote:
> >>A patch for setting slepc problem types. (Hopefully. Depending on
> >>how well 'bzr send' worked.)
> >>
> >
> >It didn't work. Try again. :-)
>
> Trying manually: see attachment.
>

> # Bazaar merge directive format 2 (Bazaar 0.90)
> # revision_id: meg@xxxxxxxxx-20091202194945-arvlq614lkei4419
> # target_branch: bzr+ssh://bazaar.launchpad.net/~dolfin-\
> #   core/dolfin/main/
> # testament_sha1: 674ec601229653a601f274286db5e8439142f0fd
> # timestamp: 2009-12-02 21:40:21 +0100
> # base_revision_id: logg@xxxxxxxxx-20091202095634-mhvgsb6ooni710jo
> #
> # Begin patch
> === modified file 'demo/la/eigensolver/python/demo.py'
> --- demo/la/eigensolver/python/demo.py	2009-10-09 09:28:03 +0000
> +++ demo/la/eigensolver/python/demo.py	2009-12-02 19:49:45 +0000
> @@ -1,4 +1,6 @@
> -"This simple program illustrates the use of the SLEPc eigenvalue solver."
> +"""
> +This program illustrates the use of the SLEPc eigenvalue solver for
> +both standard and generalized eigenvalue problems."""
>
>  __author__ = "Kristian B. Oelgaard (k.b.oelgaard@xxxxxxxxxx)"
>  __date__ = "2007-11-28 -- 2009-10-09"
> @@ -6,6 +8,7 @@
>  __license__  = "GNU LGPL Version 2.1"
>
>  # Modified by Anders Logg, 2008.
> +# Modified by Marie Rognes, 2009.
>
>  from dolfin import *
>  import numpy
> @@ -14,7 +17,7 @@
>  if not has_la_backend("PETSc"):
>      print "DOLFIN has not been configured with PETSc. Exiting."
>      exit()
> -
> +
>  if not has_slepc():
>      print "DOLFIN has not been configured with SLEPc. Exiting."
>      exit()
> @@ -23,23 +26,49 @@
>  parameters["linear_algebra_backend"] = "PETSc"
>
>  # Build stiftness matrix
> -mesh = UnitSquare(64, 64)
> +mesh = UnitSquare(4, 4)
>  V = FunctionSpace(mesh, "CG", 1)
>  v = TestFunction(V)
>  u = TrialFunction(V)
>  A = PETScMatrix()
>  assemble(dot(grad(v), grad(u))*dx, tensor=A)
>
> -# Compute the first n eigenvalues
> -n = 10
> +# Build mass matrix
> +M = PETScMatrix()
> +assemble(v*u*dx, tensor=M)
> +
> +# Compute the n largest eigenvalues of A x = \lambda x
> +n = 3
>  esolver = SLEPcEigenSolver()
> -esolver.parameters["spectrum"] = "largest magnitude"
>  esolver.solve(A, n)
>
> -print "Eigenvalue solver converged in %d iterations" % (esolver.get_iteration_number(),)
> -
>  # Display eigenvalues
>  for i in range(n):
>      lr, lc, r_vec, c_vec = esolver.get_eigenpair(i)
>      print "Eigenvalue " + str(i) + ": " + str(lr)
>      print "Eigenvector " + str(i) + ": " + str(r_vec.array())
> +
> +# Compute the eigenvalues close to 10 of A x = \lambda M x
> +print
> +print "Computing eigenvalues of generalized problem"
> +esolver = SLEPcEigenSolver()
> +esolver.parameters["solver"] = "krylov-schur"
> +esolver.parameters["spectral_transform"] = "shift-and-invert"
> +esolver.parameters["spectral_shift"] = 10.0
> +esolver.solve(A, M, n)
> +
> +m = esolver.get_number_converged()
> +print "Number of converged eigenvalues: %d" % m
> +for i in range(m):
> +    r, c = esolver.get_eigenvalue(i)
> +    print "Real(Eigenvalue) " + str(i) + ": " + str(r)
> +
> +
> +# Test a different eigensolver type
> +print
> +print "Testing lanczos eigenvalue solver (not converging)"
> +esolver = SLEPcEigenSolver()
> +esolver.parameters["problem_type"] = "hermitian"
> +esolver.parameters["solver"] = "lanczos"
> +esolver.solve(M)
> +
>
> === modified file 'dolfin/la/SLEPcEigenSolver.cpp'
> --- dolfin/la/SLEPcEigenSolver.cpp	2009-10-12 18:07:27 +0000
> +++ dolfin/la/SLEPcEigenSolver.cpp	2009-12-02 19:49:45 +0000
> @@ -6,7 +6,7 @@
>  // Modified by Marie Rognes, 2009.
>  //
>  // First added:  2005-08-31
> -// Last changed: 2009-10-12
> +// Last changed: 2009-12-02
>
>  #ifdef HAS_SLEPC
>
> @@ -142,9 +142,6 @@
>    const uint nn = static_cast<int>(n);
>    EPSSetDimensions(eps, nn, PETSC_DECIDE, PETSC_DECIDE);
>
> -  // Set algorithm type (Hermitian matrix)
> -  //EPSSetProblemType(eps, EPS_NHEP);
> -
>    // Set parameters from PETSc parameter database
>    EPSSetFromOptions(eps);
>
> @@ -175,6 +172,7 @@
>  //-----------------------------------------------------------------------------
>  void SLEPcEigenSolver::read_parameters()
>  {
> +  set_problem_type(parameters["problem_type"]);
>    set_spectrum(parameters["spectrum"]);
>    set_solver(parameters["solver"]);
>    set_tolerance(parameters["tolerance"], parameters["maximum_iterations"]);
> @@ -184,6 +182,23 @@
>  }
>  //-----------------------------------------------------------------------------
>
> +void SLEPcEigenSolver::set_problem_type(std::string type)
> +{
> +  // Do nothing if default type is specified
> +  if (type == "default")
> +    return;
> +
> +  if (type == "hermitian")
> +    EPSSetProblemType(eps, EPS_HEP);
> +  else if (type == "non_hermitian")
> +    EPSSetProblemType(eps, EPS_NHEP);
> +  else if (type == "gen_hermitian")
> +    EPSSetProblemType(eps, EPS_GHEP);
> +  else if (type == "gen_non_hermitian")
> +    EPSSetProblemType(eps, EPS_GNHEP);
> +  else
> +    error("Unknown problem type: \"%s\".", type.c_str());
> +}
>
>  void SLEPcEigenSolver::set_spectral_transform(std::string transform,
>                                                double shift)
> @@ -202,7 +217,6 @@
>      error("Unknown transform: \"%s\".", transform.c_str());
>  }
>
> -
>  void SLEPcEigenSolver::set_spectrum(std::string spectrum)
>  {
>    // Do nothing if default type is specified
> @@ -235,7 +249,10 @@
>    if (solver == "default")
>      return;
>
> -  // Choose solver
> +  // Choose solver.
> +
> +  // (Note that lanczos will give PETSc error unless problem_type is
> +  // set to 'hermitian' or 'gen_hermitian')
>    if (solver == "power")
>      EPSSetType(eps, EPSPOWER);
>    else if (solver == "subspace")
>
> === modified file 'dolfin/la/SLEPcEigenSolver.h'
> --- dolfin/la/SLEPcEigenSolver.h	2009-10-12 18:07:27 +0000
> +++ dolfin/la/SLEPcEigenSolver.h	2009-12-02 19:49:45 +0000
> @@ -6,7 +6,7 @@
>  // Modified by Marie Rognes, 2009.
>  //
>  // First added:  2005-08-31
> -// Last changed: 2009-10-12
> +// Last changed: 2009-12-02
>
>  #ifndef __SLEPC_EIGEN_SOLVER_H
>  #define __SLEPC_EIGEN_SOLVER_H
> @@ -112,6 +112,7 @@
>      {
>        Parameters p("slepc_eigenvalue_solver");
>
> +      p.add("problem_type",       "default");
>        p.add("spectrum",           "largest magnitude");
>        p.add("solver",             "krylov-schur");
>        p.add("tolerance",          1e-15);
> @@ -130,6 +131,9 @@
>      /// Callback for changes in parameter values
>      void read_parameters();
>
> +    // Set problem type (used for SLEPc internals)
> +    void set_problem_type(std::string type);
> +
>      // Set spectral transform
>      void set_spectral_transform(std::string transform, double shift);
>
>
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