Actual source code: ex9.c

  2: static char help[] = "Solves a problem associated to the Brusselator wave model in chemical reactions, illustrating the use of shell matrices.\n\n"
  3:   "The command line options are:\n"
  4:   "  -n <n>, where <n> = block dimension of the 2x2 block matrix.\n"
  5:   "  -L <L>, where <L> = bifurcation parameter.\n"
  6:   "  -alpha <alpha>, -beta <beta>, -delta1 <delta1>,  -delta2 <delta2>,\n"
  7:   "       where <alpha> <beta> <delta1> <delta2> = model parameters.\n\n";

 9:  #include slepceps.h

 11: /*
 12:    This example computes the eigenvalues with largest real part of the 
 13:    following matrix

 15:         A = [ tau1*T+(beta-1)*I     alpha^2*I
 16:                   -beta*I        tau2*T-alpha^2*I ],

 18:    where

 20:         T = tridiag{1,-2,1}
 21:         h = 1/(n+1)
 22:         tau1 = delta1/(h*L)^2
 23:         tau2 = delta2/(h*L)^2
 24:  */


 27: /* 
 28:    Matrix operations
 29: */
 30: PetscErrorCode MatBrussel_Mult(Mat,Vec,Vec);
 31: PetscErrorCode MatBrussel_Shift(PetscScalar*,Mat);
 32: PetscErrorCode MatBrussel_GetDiagonal(Mat,Vec);

 34: typedef struct {
 35:   Mat         T;
 36:   Vec         x1, x2, y1, y2;
 37:   PetscScalar alpha, beta, tau1, tau2, sigma;
 38: } CTX_BRUSSEL;

 42: int main( int argc, char **argv )
 43: {
 44:   Mat                  A;                  /* eigenvalue problem matrix */
 45:   EPS                  eps;                  /* eigenproblem solver context */
 46:   EPSType              type;
 47:   PetscReal            error, tol, re, im;
 48:   PetscScalar          delta1, delta2, L, h, kr, ki, value[3];
 49:   PetscInt             N=30, n, i, col[3], Istart, Iend;
 50:   int                  nev, maxit, its, nconv;
 51:   PetscTruth     FirstBlock=PETSC_FALSE, LastBlock=PETSC_FALSE;
 53:   CTX_BRUSSEL    *ctx;

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

 57:   PetscOptionsGetInt(PETSC_NULL,"-n",&N,PETSC_NULL);
 58:   PetscPrintf(PETSC_COMM_WORLD,"\nBrusselator wave model, n=%d\n\n",N);

 60:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
 61:         Generate the matrix 
 62:      - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */

 64:   /* 
 65:      Create shell matrix context and set default parameters
 66:   */
 67:   PetscNew(CTX_BRUSSEL,&ctx);
 68:   ctx->alpha = 2.0;
 69:   ctx->beta  = 5.45;
 70:   delta1     = 0.008;
 71:   delta2     = 0.004;
 72:   L          = 0.51302;

 74:   /* 
 75:      Look the command line for user-provided parameters
 76:   */
 77:   PetscOptionsGetScalar(PETSC_NULL,"-L",&L,PETSC_NULL);
 78:   PetscOptionsGetScalar(PETSC_NULL,"-alpha",&ctx->alpha,PETSC_NULL);
 79:   PetscOptionsGetScalar(PETSC_NULL,"-beta",&ctx->beta,PETSC_NULL);
 80:   PetscOptionsGetScalar(PETSC_NULL,"-delta1",&delta1,PETSC_NULL);
 81:   PetscOptionsGetScalar(PETSC_NULL,"-delta2",&delta2,PETSC_NULL);

 83:   /* 
 84:      Create matrix T
 85:   */
 86:   MatCreate(PETSC_COMM_WORLD,&ctx->T);
 87:   MatSetSizes(ctx->T,PETSC_DECIDE,PETSC_DECIDE,N,N);
 88:   MatSetFromOptions(ctx->T);
 89: 
 90:   MatGetOwnershipRange(ctx->T,&Istart,&Iend);
 91:   if (Istart==0) FirstBlock=PETSC_TRUE;
 92:   if (Iend==N) LastBlock=PETSC_TRUE;
 93:   value[0]=1.0; value[1]=-2.0; value[2]=1.0;
 94:   for( i=(FirstBlock? Istart+1: Istart); i<(LastBlock? Iend-1: Iend); i++ ) {
 95:     col[0]=i-1; col[1]=i; col[2]=i+1;
 96:     MatSetValues(ctx->T,1,&i,3,col,value,INSERT_VALUES);
 97:   }
 98:   if (LastBlock) {
 99:     i=N-1; col[0]=N-2; col[1]=N-1;
100:     MatSetValues(ctx->T,1,&i,2,col,value,INSERT_VALUES);
101:   }
102:   if (FirstBlock) {
103:     i=0; col[0]=0; col[1]=1; value[0]=-2.0; value[1]=1.0;
104:     MatSetValues(ctx->T,1,&i,2,col,value,INSERT_VALUES);
105:   }

107:   MatAssemblyBegin(ctx->T,MAT_FINAL_ASSEMBLY);
108:   MatAssemblyEnd(ctx->T,MAT_FINAL_ASSEMBLY);
109:   MatGetLocalSize(ctx->T,&n,PETSC_NULL);

111:   /* 
112:      Fill the remaining information in the shell matrix context
113:      and create auxiliary vectors
114:   */
115:   h = 1.0 / (double)(N+1);
116:   ctx->tau1 = delta1 / ((h*L)*(h*L));
117:   ctx->tau2 = delta2 / ((h*L)*(h*L));
118:   ctx->sigma = 0.0;
119:   VecCreateMPIWithArray(PETSC_COMM_WORLD,n,PETSC_DECIDE,PETSC_NULL,&ctx->x1);
120:   VecCreateMPIWithArray(PETSC_COMM_WORLD,n,PETSC_DECIDE,PETSC_NULL,&ctx->x2);
121:   VecCreateMPIWithArray(PETSC_COMM_WORLD,n,PETSC_DECIDE,PETSC_NULL,&ctx->y1);
122:   VecCreateMPIWithArray(PETSC_COMM_WORLD,n,PETSC_DECIDE,PETSC_NULL,&ctx->y2);

124:   /* 
125:      Create the shell matrix
126:   */
127:   MatCreateShell(PETSC_COMM_WORLD,2*n,2*n,2*N,2*N,(void*)ctx,&A);
128:   MatShellSetOperation(A,MATOP_MULT,(void(*)())MatBrussel_Mult);
129:   MatShellSetOperation(A,MATOP_SHIFT,(void(*)())MatBrussel_Shift);
130:   MatShellSetOperation(A,MATOP_GET_DIAGONAL,(void(*)())MatBrussel_GetDiagonal);

132:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
133:                 Create the eigensolver and set various options
134:      - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */

136:   /* 
137:      Create eigensolver context
138:   */
139:   EPSCreate(PETSC_COMM_WORLD,&eps);

141:   /* 
142:      Set operators. In this case, it is a standard eigenvalue problem
143:   */
144:   EPSSetOperators(eps,A,PETSC_NULL);
145:   EPSSetProblemType(eps,EPS_NHEP);

147:   /*
148:      Ask for the rightmost eigenvalues
149:   */
150:   EPSSetWhichEigenpairs(eps,EPS_LARGEST_REAL);

152:   /*
153:      Set other solver options at runtime
154:   */
155:   EPSSetFromOptions(eps);

157:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
158:                       Solve the eigensystem
159:      - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */

161:   EPSSolve(eps);
162:   EPSGetIterationNumber(eps, &its);
163:   PetscPrintf(PETSC_COMM_WORLD," Number of iterations of the method: %d\n",its);
164: 
165:   /*
166:      Optional: Get some information from the solver and display it
167:   */
168:   EPSGetType(eps,&type);
169:   PetscPrintf(PETSC_COMM_WORLD," Solution method: %s\n\n",type);
170:   EPSGetDimensions(eps,&nev,PETSC_NULL);
171:   PetscPrintf(PETSC_COMM_WORLD," Number of requested eigenvalues: %d\n",nev);
172:   EPSGetTolerances(eps,&tol,&maxit);
173:   PetscPrintf(PETSC_COMM_WORLD," Stopping condition: tol=%.4g, maxit=%d\n",tol,maxit);

175:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
176:                     Display solution and clean up
177:      - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */

179:   /* 
180:      Get number of converged eigenpairs
181:   */
182:   EPSGetConverged(eps,&nconv);
183:   PetscPrintf(PETSC_COMM_WORLD," Number of converged approximate eigenpairs: %d\n\n",nconv);

185:   if (nconv>0) {
186:     /*
187:        Display eigenvalues and relative errors
188:     */
189:     PetscPrintf(PETSC_COMM_WORLD,
190:          "           k             ||Ax-kx||/||kx||\n"
191:          "  --------------------- ------------------\n" );
192:     for( i=0; i<nconv; i++ ) {
193:       /* 
194:          Get converged eigenpairs: i-th eigenvalue is stored in kr (real part) and
195:          ki (imaginary part)
196:       */
197:       EPSGetEigenpair(eps,i,&kr,&ki,PETSC_NULL,PETSC_NULL);

199:       /*
200:          Compute the relative error associated to each eigenpair
201:       */
202:       EPSComputeRelativeError(eps,i,&error);

204: #if defined(PETSC_USE_COMPLEX)
205:       re = PetscRealPart(kr);
206:       im = PetscImaginaryPart(kr);
207: #else
208:       re = kr;
209:       im = ki;
210: #endif
211:       if( im != 0.0 ) {
212:         PetscPrintf(PETSC_COMM_WORLD," % 6f %+6f i",re,im);
213:       } else {
214:         PetscPrintf(PETSC_COMM_WORLD,"       % 6f      ",re);
215:       }
216:       PetscPrintf(PETSC_COMM_WORLD," % 12g\n",error);
217:     }
218:     PetscPrintf(PETSC_COMM_WORLD,"\n" );
219:   }
220: 
221:   /* 
222:      Free work space
223:   */
224:   EPSDestroy(eps);
225:   MatDestroy(A);
226:   MatDestroy(ctx->T);
227:   VecDestroy(ctx->x1);
228:   VecDestroy(ctx->x2);
229:   VecDestroy(ctx->y1);
230:   VecDestroy(ctx->y2);
231:   PetscFree(ctx);
232:   SlepcFinalize();
233:   return 0;
234: }

238: PetscErrorCode MatBrussel_Mult(Mat A,Vec x,Vec y)
239: {
241:   PetscInt       n;
242:   PetscScalar    *px, *py;
243:   CTX_BRUSSEL    *ctx;

246:   MatShellGetContext(A,(void**)&ctx);
247:   MatGetLocalSize(ctx->T,&n,PETSC_NULL);
248:   VecGetArray(x,&px);
249:   VecGetArray(y,&py);
250:   VecPlaceArray(ctx->x1,px);
251:   VecPlaceArray(ctx->x2,px+n);
252:   VecPlaceArray(ctx->y1,py);
253:   VecPlaceArray(ctx->y2,py+n);

255:   MatMult(ctx->T,ctx->x1,ctx->y1);
256:   VecScale(ctx->y1,ctx->tau1);
257:   VecAXPY(ctx->y1,ctx->beta - 1.0 + ctx->sigma,ctx->x1);
258:   VecAXPY(ctx->y1,ctx->alpha * ctx->alpha,ctx->x2);

260:   MatMult(ctx->T,ctx->x2,ctx->y2);
261:   VecScale(ctx->y2,ctx->tau2);
262:   VecAXPY(ctx->y2,-ctx->beta,ctx->x1);
263:   VecAXPY(ctx->y2,-ctx->alpha * ctx->alpha + ctx->sigma,ctx->x2);

265:   VecRestoreArray(x,&px);
266:   VecRestoreArray(y,&py);
267:   VecResetArray(ctx->x1);
268:   VecResetArray(ctx->x2);
269:   VecResetArray(ctx->y1);
270:   VecResetArray(ctx->y2);
271:   return(0);
272: }

276: PetscErrorCode MatBrussel_Shift( PetscScalar* a, Mat Y )
277: {
278:   CTX_BRUSSEL    *ctx;

282:   MatShellGetContext( Y, (void**)&ctx );
283:   ctx->sigma += *a;
284:   return(0);
285: }

289: int MatBrussel_GetDiagonal(Mat A,Vec diag)
290: {
291:   Vec            d1, d2;
293:   PetscInt       n;
294:   PetscScalar    *pd;
295:   MPI_Comm       comm;
296:   CTX_BRUSSEL    *ctx;

299:   MatShellGetContext(A,(void**)&ctx);
300:   PetscObjectGetComm((PetscObject)A,&comm);
301:   MatGetLocalSize(ctx->T,&n,PETSC_NULL);
302:   VecGetArray(diag,&pd);
303:   VecCreateMPIWithArray(comm,n,PETSC_DECIDE,pd,&d1);
304:   VecCreateMPIWithArray(comm,n,PETSC_DECIDE,pd+n,&d2);

306:   VecSet(d1,-2.0*ctx->tau1 + ctx->beta - 1.0 + ctx->sigma);
307:   VecSet(d2,-2.0*ctx->tau2 - ctx->alpha*ctx->alpha + ctx->sigma);

309:   VecDestroy(d1);
310:   VecDestroy(d2);
311:   VecRestoreArray(diag,&pd);
312:   return(0);
313: }