Subversion Repositories slepc-dev

static char help[] = "Solves a problem associated to the Brusselator wave model in chemical reactions, illustrating the use of shell matrices.\n\n"

  "The command line options are:\n\n"

  "  -n <n>, where <n> = block dimension of the 2x2 block matrix.\n"

  "  -L <L>, where <L> = bifurcation parameter.\n"

  "  -alpha <alpha>, -beta <beta>, -delta1 <delta1>,  -delta2 <delta2>,\n"

  "       where <alpha> <beta> <delta1> <delta2> = model parameters.\n\n";

#include "slepceps.h"

/*

   This example computes the eigenvalues with largest real part of the

   following matrix

        A = [ tau1*T+(beta-1)*I     alpha^2*I

                  -beta*I        tau2*T-alpha^2*I ],

   where

        T = tridiag{1,-2,1}

        h = 1/(n+1)

        tau1 = delta1/(h*L)^2

        tau2 = delta2/(h*L)^2

 */

/*

   Matrix operations

*/

extern int MatBrussel_Mult(Mat,Vec,Vec);

extern int MatBrussel_Shift(PetscScalar*,Mat);

extern int MatBrussel_GetDiagonal(Mat,Vec);

typedef struct {

  Mat         T;

  Vec         x1, x2, y1, y2;

  PetscScalar alpha, beta, tau1, tau2, sigma;

} CTX_BRUSSEL;

#undef __FUNCT__

#define __FUNCT__ "main"

int main( int argc, char **argv )

{

  Mat         A;               /* eigenvalue problem matrix */

  EPS         eps;             /* eigenproblem solver context */

  EPSType     type;

  PetscReal   error, tol, re, im;

  PetscScalar delta1, delta2, L, h, kr, ki, value[3];

  PetscInt    N=30, n, i, col[3], Istart, Iend, FirstBlock=0, LastBlock=0;

  int         nev, ierr, maxit, its, nconv;

  CTX_BRUSSEL *ctx;

  SlepcInitialize(&argc,&argv,(char*)0,help);

  ierr = PetscOptionsGetInt(PETSC_NULL,"-n",&N,PETSC_NULL);CHKERRQ(ierr);

  ierr = PetscPrintf(PETSC_COMM_WORLD,"\nBrusselator wave model, n=%d\n\n",N);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

        Generate the matrix

     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */

  /*

     Create shell matrix context and set default parameters

  */

  ierr = PetscNew(CTX_BRUSSEL,&ctx);CHKERRQ(ierr);

  ctx->alpha = 2.0;

  ctx->beta  = 5.45;

  delta1     = 0.008;

  delta2     = 0.004;

  L          = 0.51302;

  /*

     Look the command line for user-provided parameters

  */

  ierr = PetscOptionsGetScalar(PETSC_NULL,"-L",&L,PETSC_NULL);CHKERRQ(ierr);

  ierr = PetscOptionsGetScalar(PETSC_NULL,"-alpha",&ctx->alpha,PETSC_NULL);CHKERRQ(ierr);

  ierr = PetscOptionsGetScalar(PETSC_NULL,"-beta",&ctx->beta,PETSC_NULL);CHKERRQ(ierr);

  ierr = PetscOptionsGetScalar(PETSC_NULL,"-delta1",&delta1,PETSC_NULL);CHKERRQ(ierr);

  ierr = PetscOptionsGetScalar(PETSC_NULL,"-delta2",&delta2,PETSC_NULL);CHKERRQ(ierr);

  /*

     Create matrix T

  */

  ierr = MatCreate(PETSC_COMM_WORLD,&ctx->T);CHKERRQ(ierr);

  ierr = MatSetSizes(ctx->T,PETSC_DECIDE,PETSC_DECIDE,N,N);CHKERRQ(ierr);

  ierr = MatSetFromOptions(ctx->T);CHKERRQ(ierr);

  ierr = MatGetOwnershipRange(ctx->T,&Istart,&Iend);CHKERRQ(ierr);

  if (Istart==0) FirstBlock=PETSC_TRUE;

  if (Iend==N) LastBlock=PETSC_TRUE;

  value[0]=1.0; value[1]=-2.0; value[2]=1.0;

  for( i=(FirstBlock? Istart+1: Istart); i<(LastBlock? Iend-1: Iend); i++ ) {

    col[0]=i-1; col[1]=i; col[2]=i+1;

    ierr = MatSetValues(ctx->T,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr);

  }

  if (LastBlock) {

    i=N-1; col[0]=N-2; col[1]=N-1;

    ierr = MatSetValues(ctx->T,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);

  }

  if (FirstBlock) {

    i=0; col[0]=0; col[1]=1; value[0]=-2.0; value[1]=1.0;

    ierr = MatSetValues(ctx->T,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);

  }

  ierr = MatAssemblyBegin(ctx->T,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);

  ierr = MatAssemblyEnd(ctx->T,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);

  ierr = MatGetLocalSize(ctx->T,&n,PETSC_NULL);CHKERRQ(ierr);

  /*

     Fill the remaining information in the shell matrix context

     and create auxiliary vectors

  */

  h = 1.0 / (double)(N+1);

  ctx->tau1 = delta1 / ((h*L)*(h*L));

  ctx->tau2 = delta2 / ((h*L)*(h*L));

  ctx->sigma = 0.0;

  ierr = VecCreateMPIWithArray(PETSC_COMM_WORLD,n,PETSC_DECIDE,PETSC_NULL,&ctx->x1);CHKERRQ(ierr);

  ierr = VecCreateMPIWithArray(PETSC_COMM_WORLD,n,PETSC_DECIDE,PETSC_NULL,&ctx->x2);CHKERRQ(ierr);

  ierr = VecCreateMPIWithArray(PETSC_COMM_WORLD,n,PETSC_DECIDE,PETSC_NULL,&ctx->y1);CHKERRQ(ierr);

  ierr = VecCreateMPIWithArray(PETSC_COMM_WORLD,n,PETSC_DECIDE,PETSC_NULL,&ctx->y2);CHKERRQ(ierr);

  /*

     Create the shell matrix

  */

  ierr = MatCreateShell(PETSC_COMM_WORLD,2*n,2*n,2*N,2*N,(void*)ctx,&A);CHKERRQ(ierr);

  ierr = MatShellSetOperation(A,MATOP_MULT,(void(*)())MatBrussel_Mult);CHKERRQ(ierr);

  ierr = MatShellSetOperation(A,MATOP_SHIFT,(void(*)())MatBrussel_Shift);CHKERRQ(ierr);

  ierr = MatShellSetOperation(A,MATOP_GET_DIAGONAL,(void(*)())MatBrussel_GetDiagonal);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

                Create the eigensolver and set various options

     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */

  /*

     Create eigensolver context

  */

  ierr = EPSCreate(PETSC_COMM_WORLD,&eps);CHKERRQ(ierr);

  /*

     Set operators. In this case, it is a standard eigenvalue problem

  */

  ierr = EPSSetOperators(eps,A,PETSC_NULL);CHKERRQ(ierr);

  ierr = EPSSetProblemType(eps,EPS_NHEP);CHKERRQ(ierr);

  /*

     Force to use ARPACK if it is installed and ask for the rightmost eigenvalues

  */

#if defined(SLEPC_HAVE_ARPACK)

  ierr = EPSSetType(eps,EPSARPACK);CHKERRQ(ierr);

#else

  ierr = EPSSetType(eps, EPSLAPACK);CHKERRQ(ierr);

#endif

  ierr = EPSSetWhichEigenpairs(eps,EPS_LARGEST_REAL);CHKERRQ(ierr);

  /*

     Set other solver options at runtime

  */

  ierr = EPSSetFromOptions(eps);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

                      Solve the eigensystem

     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */

  ierr = EPSSolve(eps);CHKERRQ(ierr);

  ierr = EPSGetIterationNumber(eps, &its);CHKERRQ(ierr);

  ierr = PetscPrintf(PETSC_COMM_WORLD," Number of iterations of the method: %d\n",its);CHKERRQ(ierr);

  /*

     Optional: Get some information from the solver and display it

  */

  ierr = EPSGetType(eps,&type);CHKERRQ(ierr);

  ierr = PetscPrintf(PETSC_COMM_WORLD," Solution method: %s\n\n",type);CHKERRQ(ierr);

  ierr = EPSGetDimensions(eps,&nev,PETSC_NULL);CHKERRQ(ierr);

  ierr = PetscPrintf(PETSC_COMM_WORLD," Number of requested eigenvalues: %d\n",nev);CHKERRQ(ierr);

  ierr = EPSGetTolerances(eps,&tol,&maxit);CHKERRQ(ierr);

  ierr = PetscPrintf(PETSC_COMM_WORLD," Stopping condition: tol=%.4g, maxit=%d\n",tol,maxit);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

                    Display solution and clean up

     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */

  /*

     Get number of converged eigenpairs

  */

  ierr = EPSGetConverged(eps,&nconv);CHKERRQ(ierr);

  ierr = PetscPrintf(PETSC_COMM_WORLD," Number of converged approximate eigenpairs: %d\n\n",nconv);CHKERRQ(ierr);

  if (nconv>0) {

    /*

       Display eigenvalues and relative errors

    */

    ierr = PetscPrintf(PETSC_COMM_WORLD,

         "           k             ||Ax-kx||/||kx||\n"

         "  --------------------- ------------------\n" );CHKERRQ(ierr);

    for( i=0; i<nconv; i++ ) {

      /*

         Get converged eigenpairs: i-th eigenvalue is stored in kr (real part) and

         ki (imaginary part)

      */

      ierr = EPSGetEigenpair(eps,i,&kr,&ki,PETSC_NULL,PETSC_NULL);CHKERRQ(ierr);

      /*

         Compute the relative error associated to each eigenpair

      */

      ierr = EPSComputeRelativeError(eps,i,&error);CHKERRQ(ierr);

#if defined(PETSC_USE_COMPLEX)

      re = PetscRealPart(kr);

      im = PetscImaginaryPart(kr);

#else

      re = kr;

      im = ki;

#endif

      if( im != 0.0 ) {

        ierr = PetscPrintf(PETSC_COMM_WORLD," % 6f %+6f i",re,im);CHKERRQ(ierr);

      } else {

        ierr = PetscPrintf(PETSC_COMM_WORLD,"       % 6f      ",re); CHKERRQ(ierr);

      }

      ierr = PetscPrintf(PETSC_COMM_WORLD," % 12f\n",error);CHKERRQ(ierr);

    }

    ierr = PetscPrintf(PETSC_COMM_WORLD,"\n" );CHKERRQ(ierr);

  }

  /*

     Free work space

  */

  ierr = EPSDestroy(eps);CHKERRQ(ierr);

  ierr = MatDestroy(A);CHKERRQ(ierr);

  ierr = MatDestroy(ctx->T);CHKERRQ(ierr);

  ierr = VecDestroy(ctx->x1);CHKERRQ(ierr);

  ierr = VecDestroy(ctx->x2);CHKERRQ(ierr);

  ierr = VecDestroy(ctx->y1);CHKERRQ(ierr);

  ierr = VecDestroy(ctx->y2);CHKERRQ(ierr);

  ierr = PetscFree(ctx);CHKERRQ(ierr);

  ierr = SlepcFinalize();CHKERRQ(ierr);

  return 0;

}

#undef __FUNC__

#define __FUNC__ "MatBrussel_Mult"

int MatBrussel_Mult(Mat A,Vec x,Vec y)

{

  int         ierr;

  PetscInt    n;

  PetscScalar *px, *py;

  CTX_BRUSSEL *ctx;

  ierr = MatShellGetContext(A,(void**)&ctx);CHKERRQ(ierr);

  ierr = MatGetLocalSize(ctx->T,&n,PETSC_NULL);CHKERRQ(ierr);

  ierr = VecGetArray(x,&px);CHKERRQ(ierr);

  ierr = VecGetArray(y,&py);CHKERRQ(ierr);

  ierr = VecPlaceArray(ctx->x1,px);CHKERRQ(ierr);

  ierr = VecPlaceArray(ctx->x2,px+n);CHKERRQ(ierr);

  ierr = VecPlaceArray(ctx->y1,py);CHKERRQ(ierr);

  ierr = VecPlaceArray(ctx->y2,py+n);CHKERRQ(ierr);

  ierr = MatMult(ctx->T,ctx->x1,ctx->y1);CHKERRQ(ierr);

  ierr = VecScale(ctx->y1,ctx->tau1);CHKERRQ(ierr);

  ierr = VecAXPY(ctx->y1,ctx->beta - 1.0 + ctx->sigma,ctx->x1);CHKERRQ(ierr);

  ierr = VecAXPY(ctx->y1,ctx->alpha * ctx->alpha,ctx->x2);CHKERRQ(ierr);

  ierr = MatMult(ctx->T,ctx->x2,ctx->y2);CHKERRQ(ierr);

  ierr = VecScale(ctx->y2,ctx->tau2);CHKERRQ(ierr);

  ierr = VecAXPY(ctx->y2,-ctx->beta,ctx->x1);CHKERRQ(ierr);

  ierr = VecAXPY(ctx->y2,-ctx->alpha * ctx->alpha + ctx->sigma,ctx->x2);CHKERRQ(ierr);

  ierr = VecRestoreArray(x,&px);CHKERRQ(ierr);

  ierr = VecRestoreArray(y,&py);CHKERRQ(ierr);

  ierr = VecResetArray(ctx->x1);CHKERRQ(ierr);

  ierr = VecResetArray(ctx->x2);CHKERRQ(ierr);

  ierr = VecResetArray(ctx->y1);CHKERRQ(ierr);

  ierr = VecResetArray(ctx->y2);CHKERRQ(ierr);

  return 0;

}

#undef __FUNCT__

#define __FUNCT__ "MatBrussel_Shift"

int MatBrussel_Shift( PetscScalar* a, Mat Y )

{

  CTX_BRUSSEL *ctx;

  int         ierr;

  ierr = MatShellGetContext( Y, (void**)&ctx ); CHKERRQ(ierr);

  ctx->sigma += *a;

  PetscFunctionReturn(0);

}

#undef __FUNC__

#define __FUNC__ "MatBrussel_GetDiagonal"

int MatBrussel_GetDiagonal(Mat A,Vec diag)

{

  Vec         d1, d2;

  int         ierr;

  PetscInt    n;

  PetscScalar *pd;

  MPI_Comm    comm;

  CTX_BRUSSEL *ctx;

  ierr = MatShellGetContext(A,(void**)&ctx);CHKERRQ(ierr);

  ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr);

  ierr = MatGetLocalSize(ctx->T,&n,PETSC_NULL);CHKERRQ(ierr);

  ierr = VecGetArray(diag,&pd);CHKERRQ(ierr);

  ierr = VecCreateMPIWithArray(comm,n,PETSC_DECIDE,pd,&d1);CHKERRQ(ierr);

  ierr = VecCreateMPIWithArray(comm,n,PETSC_DECIDE,pd+n,&d2);CHKERRQ(ierr);

  ierr = VecSet(d1,-2.0*ctx->tau1 + ctx->beta - 1.0 + ctx->sigma);CHKERRQ(ierr);

  ierr = VecSet(d2,-2.0*ctx->tau2 - ctx->alpha*ctx->alpha + ctx->sigma);CHKERRQ(ierr);

  ierr = VecDestroy(d1);CHKERRQ(ierr);

  ierr = VecDestroy(d2);CHKERRQ(ierr);

  ierr = VecRestoreArray(diag,&pd);CHKERRQ(ierr);

  return 0;

}