Actual source code: ex64.c
1: static char help[] = "1D coupled Allen-Cahn and Cahn-Hilliard equation for constant mobility. Only c_v and eta are considered.\n\
2: Runtime options include:\n\
3: -xmin <xmin>\n\
4: -xmax <xmax>\n\
5: -ymin <ymin>\n\
6: -T <T>, where <T> is the end time for the time domain simulation\n\
7: -dt <dt>,where <dt> is the step size for the numerical integration\n\
8: -gamma <gamma>\n\
9: -theta_c <theta_c>\n\n";
11: /*
12: ./ex63 -ksp_type fgmres -snes_vi_monitor -snes_atol 1.e-11 -snes_converged_reason -ksp_converged_reason -snes_ls_monitor -VG 10000000 -draw_fields 1,3,4 -pc_type mg -pc_mg_galerkin -log_summary -dt .000001 -mg_coarse_pc_type svd -ksp_monitor_true_residual -ksp_rtol 1.e-9 -snes_ls basic -T .0020 -P_casc .0005 -snes_monitor_solution -da_refine 10
13: */
15: #include petscsnes.h
16: #include petscdmda.h
18: typedef struct{
19: PetscReal dt,T; /* Time step and end time */
20: DM da1,da1_clone,da2;
21: Mat M; /* Jacobian matrix */
22: Mat M_0;
23: Vec q,wv,cv,eta,DPsiv,DPsieta,logcv,logcv2;
24: Vec work1,work2;
25: PetscScalar Mv,L,kaeta,kav,Evf,A,B,cv0,Sv;
26: PetscReal xmin,xmax;
27: PetscInt nx;
28: PetscBool graphics;
29: PetscBool periodic;
30: PetscBool lumpedmass;
31: }AppCtx;
33: PetscErrorCode GetParams(AppCtx*);
34: PetscErrorCode SetVariableBounds(DM,Vec,Vec);
35: PetscErrorCode SetUpMatrices(AppCtx*);
36: PetscErrorCode FormFunction(SNES,Vec,Vec,void*);
37: PetscErrorCode FormJacobian(SNES,Vec,Mat*,Mat*,MatStructure*,void*);
38: PetscErrorCode SetInitialGuess(Vec,AppCtx*);
39: PetscErrorCode Update_q(AppCtx*);
40: PetscErrorCode Update_u(Vec,AppCtx*);
41: PetscErrorCode DPsi(AppCtx*);
42: PetscErrorCode Llog(Vec,Vec);
43: PetscErrorCode CheckRedundancy(SNES,IS,IS*,DM);
47: int main(int argc, char **argv)
48: {
50: Vec x,r; /* solution and residual vectors */
51: SNES snes; /* Nonlinear solver context */
52: AppCtx user; /* Application context */
53: Vec xl,xu; /* Upper and lower bounds on variables */
54: Mat J;
55: PetscScalar t=0.0;
56: PetscViewer view_out, view_p, view_q, view_psi, view_mat;
57: PetscReal bounds[] = {1000.0,-1000.,0.0,1.0,1000.0,-1000.0,0.0,1.0,1000.0,-1000.0};
60: PetscInitialize(&argc,&argv, (char*)0, help);
61:
62: /* Get physics and time parameters */
63: GetParams(&user);
65: if (user.periodic) {
66: DMDACreate1d(PETSC_COMM_WORLD,DMDA_BOUNDARY_PERIODIC, -4, 3, 1,PETSC_NULL,&user.da1);
67: DMDACreate1d(PETSC_COMM_WORLD,DMDA_BOUNDARY_PERIODIC, -4, 3, 1,PETSC_NULL,&user.da1_clone);
68: DMDACreate1d(PETSC_COMM_WORLD,DMDA_BOUNDARY_PERIODIC, -4, 1, 1,PETSC_NULL,&user.da2);
69: } else {
70: DMDACreate1d(PETSC_COMM_WORLD,DMDA_BOUNDARY_NONE, -4, 3, 1,PETSC_NULL,&user.da1);
71: DMDACreate1d(PETSC_COMM_WORLD,DMDA_BOUNDARY_NONE, -4, 3, 1,PETSC_NULL,&user.da1_clone);
72: DMDACreate1d(PETSC_COMM_WORLD,DMDA_BOUNDARY_NONE, -4, 1, 1,PETSC_NULL,&user.da2);
74: }
75: /* Set Element type (triangular) */
76: DMDASetElementType(user.da1,DMDA_ELEMENT_P1);
77: DMDASetElementType(user.da2,DMDA_ELEMENT_P1);
78:
79: /* Set x and y coordinates */
80: DMDASetUniformCoordinates(user.da1,user.xmin,user.xmax,PETSC_NULL,PETSC_NULL,PETSC_NULL,PETSC_NULL);
81: DMDASetUniformCoordinates(user.da2,user.xmin,user.xmax,PETSC_NULL,PETSC_NULL,PETSC_NULL,PETSC_NULL);
82: /* Get global vector x from DM (da1) and duplicate vectors r,xl,xu */
83: DMCreateGlobalVector(user.da1,&x);
84: VecDuplicate(x,&r);
85: VecDuplicate(x,&xl);
86: VecDuplicate(x,&xu);
87: VecDuplicate(x,&user.q);
88:
89: /* Get global vector user->wv from da2 and duplicate other vectors */
90: DMCreateGlobalVector(user.da2,&user.wv);
91: VecDuplicate(user.wv,&user.cv);
92: VecDuplicate(user.wv,&user.eta);
93: VecDuplicate(user.wv,&user.DPsiv);
94: VecDuplicate(user.wv,&user.DPsieta);
95: VecDuplicate(user.wv,&user.logcv);
96: VecDuplicate(user.wv,&user.logcv2);
97: VecDuplicate(user.wv,&user.work1);
98: VecDuplicate(user.wv,&user.work2);
100: /* Get Jacobian matrix structure from the da for the entire thing, da1 */
101: DMGetMatrix(user.da1,MATAIJ,&user.M);
102: /* Get the (usual) mass matrix structure from da2 */
103: DMGetMatrix(user.da2,MATAIJ,&user.M_0);
104: /* Form the jacobian matrix and M_0 */
105: SetUpMatrices(&user);
106: SetInitialGuess(x,&user);
107: MatDuplicate(user.M,MAT_DO_NOT_COPY_VALUES,&J);
108:
109: SNESCreate(PETSC_COMM_WORLD,&snes);
110: SNESSetDM(snes,user.da1);
112: SNESSetFunction(snes,r,FormFunction,(void*)&user);
113: SNESSetJacobian(snes,J,J,FormJacobian,(void*)&user);
115: SNESSetType(snes,SNESVI);
116: SNESSetFromOptions(snes);
117: SetVariableBounds(user.da1,xl,xu);
118: //SNESVISetRedundancyCheck(snes,(PetscErrorCode (*)(SNES,IS,IS*,void*))CheckRedundancy,user.da1_clone);
119: SNESVISetVariableBounds(snes,xl,xu);
120: PetscViewerBinaryOpen(PETSC_COMM_WORLD,"file_out",FILE_MODE_WRITE,&view_out);
121: PetscViewerBinaryOpen(PETSC_COMM_WORLD,"file_p",FILE_MODE_WRITE,&view_p);
122: PetscViewerBinaryOpen(PETSC_COMM_WORLD,"file_q",FILE_MODE_WRITE,&view_q);
123: PetscViewerBinaryOpen(PETSC_COMM_WORLD,"file_psi",FILE_MODE_WRITE,&view_psi);
124: PetscViewerBinaryOpen(PETSC_COMM_WORLD,"file_mat",FILE_MODE_WRITE,&view_mat);
125: /* PetscViewerDrawSetBounds(PETSC_VIEWER_DRAW_(PETSC_COMM_WORLD),5,bounds); */
127: if (user.graphics) {
128: PetscViewerDrawSetBounds(PETSC_VIEWER_DRAW_(PETSC_COMM_WORLD),5,bounds);
130: VecView(x,PETSC_VIEWER_DRAW_(PETSC_COMM_WORLD));
131: }
132: while(t<user.T) {
134: char filename[PETSC_MAX_PATH_LEN];
135: PetscScalar a = 1.0;
136: PetscInt i;
137: PetscViewer view;
140: SNESSetFunction(snes,r,FormFunction,(void*)&user);
141: SNESSetJacobian(snes,J,J,FormJacobian,(void*)&user);
143: DPsi(&user);
144: VecView(user.DPsiv,view_psi);
145: VecView(user.DPsieta,view_psi);
147: Update_q(&user);
148: VecView(user.q,view_q);
149: MatView(user.M,view_mat);
151: SNESSolve(snes,PETSC_NULL,x);
152: VecView(x,view_out);
155: if (user.graphics) {
156: VecView(x,PETSC_VIEWER_DRAW_(PETSC_COMM_WORLD));
157: }
158:
159: PetscInt its;
160: SNESGetIterationNumber(snes,&its);
161: PetscPrintf(PETSC_COMM_WORLD,"SNESVI solver converged at t = %5.4g in %d iterations\n",t,its);
163: Update_u(x,&user);
165: for (i=0; i < (int)(user.T/a) ; i++) {
166: if (t/a > i - user.dt/a && t/a < i + user.dt/a) {
167: sprintf(filename,"output_%f",t);
168: PetscViewerBinaryOpen(PETSC_COMM_WORLD,filename,FILE_MODE_WRITE,&view);
169: VecView(user.cv,view);
170: VecView(user.eta,view);
171: PetscViewerDestroy(&view);
172: }
173:
174: }
176: t = t + user.dt;
177:
178: }
180:
181: PetscViewerDestroy(&view_out);
182: PetscViewerDestroy(&view_p);
183: PetscViewerDestroy(&view_q);
184: PetscViewerDestroy(&view_psi);
185: PetscViewerDestroy(&view_mat);
186: VecDestroy(&x);
187: VecDestroy(&r);
188: VecDestroy(&xl);
189: VecDestroy(&xu);
190: VecDestroy(&user.q);
191: VecDestroy(&user.wv);
192: VecDestroy(&user.cv);
193: VecDestroy(&user.eta);
194: VecDestroy(&user.DPsiv);
195: VecDestroy(&user.DPsieta);
196: VecDestroy(&user.logcv);
197: VecDestroy(&user.logcv2);
198: VecDestroy(&user.work1);
199: VecDestroy(&user.work2);
200: MatDestroy(&user.M);
201: MatDestroy(&user.M_0);
202: DMDestroy(&user.da1);
203: DMDestroy(&user.da1_clone);
204: DMDestroy(&user.da2);
205: SNESDestroy(&snes);
206: PetscFinalize();
207: return 0;
208: }
212: PetscErrorCode Update_u(Vec X,AppCtx *user)
213: {
215: PetscInt i,n;
216: PetscScalar *xx,*wv_p,*cv_p,*eta_p;
217:
219: VecGetLocalSize(user->wv,&n);
220:
221: VecGetArray(X,&xx);
222: VecGetArray(user->wv,&wv_p);
223: VecGetArray(user->cv,&cv_p);
224: VecGetArray(user->eta,&eta_p);
225:
226:
227: for(i=0;i<n;i++) {
228: wv_p[i] = xx[3*i];
229: cv_p[i] = xx[3*i+1];
230: eta_p[i] = xx[3*i+2];
231: }
232: VecRestoreArray(X,&xx);
233: VecRestoreArray(user->wv,&wv_p);
234: VecRestoreArray(user->cv,&cv_p);
235: VecRestoreArray(user->eta,&eta_p);
236:
237: return(0);
238: }
242: PetscErrorCode Update_q(AppCtx *user)
243: {
245: PetscScalar *q_p, *w1, *w2;
246: PetscInt n,i;
249:
250: VecGetArray(user->q,&q_p);
251: VecGetArray(user->work1,&w1);
252: VecGetArray(user->work2,&w2);
253: VecGetLocalSize(user->wv,&n);
255: MatMult(user->M_0,user->cv,user->work1);
256: VecScale(user->work1,-1.0);
257: for (i=0;i<n;i++) {
258: q_p[3*i]=w1[i];
259: }
261: MatMult(user->M_0,user->DPsiv,user->work1);
262: for (i=0;i<n;i++) {
263: q_p[3*i+1]=w1[i];
264: }
266: VecCopy(user->DPsieta,user->work1);
267: VecScale(user->work1,user->L*user->dt);
268: VecAXPY(user->work1,-1.0,user->eta);
269: MatMult(user->M_0,user->work1,user->work2);
270: for (i=0;i<n;i++) {
271: q_p[3*i+2]=w2[i];
272: }
274: VecRestoreArray(user->q,&q_p);
275: VecRestoreArray(user->work1,&w1);
276: VecRestoreArray(user->work2,&w2);
277:
278: return(0);
279: }
283: PetscErrorCode DPsi(AppCtx* user)
284: {
285: PetscErrorCode ierr;
286: PetscScalar Evf=user->Evf,A=user->A,B=user->B,cv0=user->cv0;
287: PetscScalar *cv_p,*eta_p,*logcv_p,*logcv2_p,*DPsiv_p,*DPsieta_p;
288: PetscInt n,i;
292: VecGetLocalSize(user->cv,&n);
293: VecGetArray(user->cv,&cv_p);
294: VecGetArray(user->eta,&eta_p);
295: VecGetArray(user->logcv,&logcv_p);
296: VecGetArray(user->logcv2,&logcv2_p);
297: VecGetArray(user->DPsiv,&DPsiv_p);
298: VecGetArray(user->DPsieta,&DPsieta_p);
300: Llog(user->cv,user->logcv);
302: VecCopy(user->cv,user->work1);
303: VecScale(user->work1,-1.0);
304: VecShift(user->work1,1.0);
305: Llog(user->work1,user->logcv2);
307: for (i=0;i<n;i++)
308: {
309: DPsiv_p[i] = (eta_p[i]-1.0)*(eta_p[i]-1.0)*(eta_p[i]+1.0)*(eta_p[i]+1.0)*( Evf + logcv_p[i] - logcv2_p[i]) - 2.0*A*(cv_p[i] - cv0)*eta_p[i]*(eta_p[i]+2.0)*(eta_p[i]-1.0)*(eta_p[i]-1.0) + 2.0*B*(cv_p[i] - 1.0)*eta_p[i]*eta_p[i];
310:
311: DPsieta_p[i] = 4.0*eta_p[i]*(eta_p[i]-1.0)*(eta_p[i]+1.0)*(Evf*cv_p[i] + cv_p[i]*logcv_p[i] + (1.0-cv_p[i])*logcv2_p[i] ) - A*(cv_p[i] - cv0)*(cv_p[i] - cv0)*(4.0*eta_p[i]*eta_p[i]*eta_p[i] - 6.0*eta_p[i] + 2.0) + 2.0*B*(cv_p[i]-1.0)*(cv_p[i]-1.0)*eta_p[i];
312:
313: }
315: VecRestoreArray(user->cv,&cv_p);
316: VecRestoreArray(user->eta,&eta_p);
317: VecGetArray(user->logcv,&logcv_p);
318: VecGetArray(user->logcv2,&logcv2_p);
319: VecRestoreArray(user->DPsiv,&DPsiv_p);
320: VecRestoreArray(user->DPsieta,&DPsieta_p);
323: return(0);
325: }
330: PetscErrorCode Llog(Vec X, Vec Y)
331: {
332: PetscErrorCode ierr;
333: PetscScalar *x,*y;
334: PetscInt n,i;
337:
338: VecGetArray(X,&x);
339: VecGetArray(Y,&y);
340: VecGetLocalSize(X,&n);
341: for (i=0;i<n;i++) {
342: if (x[i] < 1.0e-12) {
343: y[i] = log(1.0e-12);
344: }
345: else {
346: y[i] = log(x[i]);
347: }
348: }
349:
350: return(0);
351: }
355: PetscErrorCode SetInitialGuess(Vec X,AppCtx* user)
356: {
357: PetscErrorCode ierr;
360: PetscInt n,i,Mda;
361: PetscScalar *xx,*cv_p,*wv_p,*eta_p;
362: PetscViewer view_out;
363: /* needed for the void growth case */
364: PetscScalar xmid,cv_v=1.0,cv_m=user->Sv*user->cv0,eta_v=1.0,eta_m=0.0,h,lambda;
365: PetscInt nele,nen,idx[2];
366: const PetscInt *ele;
367: PetscScalar x[2];
368: Vec coords;
369: const PetscScalar *_coords;
370: PetscScalar xwidth = user->xmax - user->xmin;
374: VecGetLocalSize(X,&n);
375:
376:
377: DMDAGetInfo(user->da2,PETSC_NULL,&Mda,PETSC_NULL,PETSC_NULL,PETSC_NULL,PETSC_NULL,PETSC_NULL,PETSC_NULL,PETSC_NULL,PETSC_NULL,PETSC_NULL,PETSC_NULL,PETSC_NULL);
378: DMDAGetGhostedCoordinates(user->da2,&coords);
379: VecGetArrayRead(coords,&_coords);
381: if (user->periodic) {
382: h = (user->xmax-user->xmin)/Mda;
383: } else {
384: h = (user->xmax-user->xmin)/(Mda-1.0);
385: }
387: xmid = (user->xmax + user->xmin)/2.0;
388: lambda = 4.0*h;
389:
390: DMDAGetElements(user->da2,&nele,&nen,&ele);
391: for (i=0;i < nele; i++) {
392: idx[0] = ele[2*i]; idx[1] = ele[2*i+1];
393:
394: x[0] = _coords[idx[0]];
395: x[1] = _coords[idx[1]];
396:
397:
398: PetscInt k;
399: PetscScalar vals_DDcv[2],vals_cv[2],vals_eta[2],s,hhr,r;
400: for (k=0; k < 2 ; k++) {
401: s = PetscAbs(x[k] - xmid);
402: if (s <= xwidth*(5.0/64.0)) {
403: vals_cv[k] = cv_v;
404: vals_eta[k] = eta_v;
405: vals_DDcv[k] = 0.0;
406: } else if (s> xwidth*(5.0/64.0) && s<= xwidth*(7.0/64.0) ) {
407: //r = (s - xwidth*(6.0/64.0) )/(0.5*lambda);
408: r = (s - xwidth*(6.0/64.0) )/(xwidth/64.0);
409: hhr = 0.25*(-r*r*r + 3*r + 2);
410: vals_cv[k] = cv_m + (1.0 - hhr)*(cv_v - cv_m);
411: vals_eta[k] = eta_m + (1.0 - hhr)*(eta_v - eta_m);
412: vals_DDcv[k] = (cv_v - cv_m)*r*6.0/(lambda*lambda);
413: } else {
414: vals_cv[k] = cv_m;
415: vals_eta[k] = eta_m;
416: vals_DDcv[k] = 0.0;
417: }
418: }
419:
420: VecSetValuesLocal(user->cv,2,idx,vals_cv,INSERT_VALUES);
421: VecSetValuesLocal(user->eta,2,idx,vals_eta,INSERT_VALUES);
422: VecSetValuesLocal(user->work2,2,idx,vals_DDcv,INSERT_VALUES);
423:
424: VecAssemblyBegin(user->cv);
425: VecAssemblyEnd(user->cv);
426: VecAssemblyBegin(user->eta);
427: VecAssemblyEnd(user->eta);
428: VecAssemblyBegin(user->work2);
429: VecAssemblyEnd(user->work2);
430:
431: DMDARestoreElements(user->da2,&nele,&nen,&ele);
432: VecRestoreArrayRead(coords,&_coords);
433: }
435: DPsi(user);
436: VecCopy(user->DPsiv,user->wv);
437: VecAXPY(user->wv,-2.0*user->kav,user->work2);
439: VecGetArray(X,&xx);
440: VecGetArray(user->wv,&wv_p);
441: VecGetArray(user->cv,&cv_p);
442: VecGetArray(user->eta,&eta_p);
444: for (i=0;i<n/3;i++)
445: {
446: xx[3*i]=wv_p[i];
447: xx[3*i+1]=cv_p[i];
448: xx[3*i+2]=eta_p[i];
449: }
451: PetscViewerBinaryOpen(PETSC_COMM_WORLD,"file_initial",FILE_MODE_WRITE,&view_out);
452: VecView(user->wv,view_out);
453: VecView(user->cv,view_out);
454: VecView(user->eta,view_out);
455: PetscViewerDestroy(&view_out);
457: VecRestoreArray(X,&xx);
458: VecRestoreArray(user->wv,&wv_p);
459: VecRestoreArray(user->cv,&cv_p);
460: VecRestoreArray(user->eta,&eta_p);
461: return(0);
462: }
466: PetscErrorCode FormFunction(SNES snes,Vec X,Vec F,void* ctx)
467: {
469: AppCtx *user=(AppCtx*)ctx;
470:
472: MatMultAdd(user->M,X,user->q,F);
473: return(0);
474: }
478: PetscErrorCode FormJacobian(SNES snes,Vec X,Mat *J,Mat *B,MatStructure *flg,void *ctx)
479: {
481: AppCtx *user=(AppCtx*)ctx;
482:
484: *flg = SAME_NONZERO_PATTERN;
485: MatCopy(user->M,*J,*flg);
486: MatAssemblyBegin(*J,MAT_FINAL_ASSEMBLY);
487: MatAssemblyEnd(*J,MAT_FINAL_ASSEMBLY);
488: return(0);
489: }
492: PetscErrorCode SetVariableBounds(DM da,Vec xl,Vec xu)
493: {
495: PetscScalar **l,**u;
496: PetscInt xs,xm;
497: PetscInt i;
498:
500: DMDAVecGetArrayDOF(da,xl,&l);
501: DMDAVecGetArrayDOF(da,xu,&u);
502:
503: DMDAGetCorners(da,&xs,PETSC_NULL,PETSC_NULL,&xm,PETSC_NULL,PETSC_NULL);
504:
505:
506: for(i=xs; i < xs+xm;i++) {
507: l[i][0] = -SNES_VI_INF;
508: l[i][1] = 0.0;
509: l[i][2] = 0.0;
510: u[i][0] = SNES_VI_INF;
511: u[i][1] = 1.0;
512: u[i][2] = 1.0;
513: }
514:
515: DMDAVecRestoreArrayDOF(da,xl,&l);
516: DMDAVecRestoreArrayDOF(da,xu,&u);
517: return(0);
518: }
522: PetscErrorCode GetParams(AppCtx* user)
523: {
525: PetscBool flg;
526:
528:
529: /* Set default parameters */
530: user->xmin = 0.0; user->xmax = 128.0;
531: user->Mv = 1.0;
532: user->L = 1.0;
533: user->kaeta = 1.0;
534: user->kav = 0.5;
535: user->Evf = 9.09;
536: user->A = 9.09;
537: user->B = 9.09;
538: user->cv0 = 1.13e-4;
539: user->Sv = 500.0;
540: user->dt = 1.0e-5;
541: user->T = 1.0e-2;
542: user->graphics = PETSC_TRUE;
543: user->periodic = PETSC_FALSE;
544: user->lumpedmass = PETSC_FALSE;
545:
546: PetscOptionsGetReal(PETSC_NULL,"-xmin",&user->xmin,&flg);
547: PetscOptionsGetReal(PETSC_NULL,"-xmax",&user->xmax,&flg);
548: PetscOptionsGetReal(PETSC_NULL,"-T",&user->T,&flg);
549: PetscOptionsGetReal(PETSC_NULL,"-dt",&user->dt,&flg);
550: PetscOptionsBool("-graphics","Contour plot solutions at each timestep\n","None",user->graphics,&user->graphics,&flg);
551: PetscOptionsBool("-periodic","Use periodic boundary conditions\n","None",user->periodic,&user->periodic,&flg);
552: PetscOptionsBool("-lumpedmass","Use lumped mass matrix\n","None",user->lumpedmass,&user->lumpedmass,&flg);
553:
554: return(0);
555: }
560: PetscErrorCode SetUpMatrices(AppCtx* user)
561: {
562: PetscErrorCode ierr;
563: PetscInt nele,nen,i,n;
564: const PetscInt *ele;
565: PetscScalar dt=user->dt,h;
566:
567: PetscInt idx[2];
568: PetscScalar eM_0[2][2],eM_2[2][2];
569: Mat M=user->M;
570: Mat M_0=user->M_0;
571: PetscInt Mda;
573:
577: MatGetLocalSize(M,&n,PETSC_NULL);
578: DMDAGetInfo(user->da1,PETSC_NULL,&Mda,PETSC_NULL,PETSC_NULL,PETSC_NULL,PETSC_NULL,PETSC_NULL,PETSC_NULL,PETSC_NULL,PETSC_NULL,PETSC_NULL,PETSC_NULL,PETSC_NULL);
580: if (user->periodic) {
581: h = (user->xmax-user->xmin)/Mda;
582: } else {
583: h = (user->xmax-user->xmin)/(Mda-1.0);
584: }
585: if (user->lumpedmass) {
586: eM_0[0][0] = h/2.0;
587: eM_0[1][1] = h/2.0;
588: eM_0[0][1] = eM_0[1][0] = 0.0;
589: } else {
590: eM_0[0][0]=eM_0[1][1]=h/3.0;
591: eM_0[0][1]=eM_0[1][0]=h/6.0;
592: }
593: eM_2[0][0]=eM_2[1][1]=1.0/h;
594: eM_2[0][1]=eM_2[1][0]=-1.0/h;
596: /* Get local element info */
597: DMDAGetElements(user->da1,&nele,&nen,&ele);
598: for(i=0;i < nele;i++) {
599:
600: idx[0] = ele[2*i]; idx[1] = ele[2*i+1];
603: PetscInt row,cols[4],r,row_M_0,cols2[2];
604: PetscScalar vals[4],vals_M_0[2],vals2[2];
606: for(r=0;r<2;r++) {
607: row_M_0 = idx[r];
608: vals_M_0[0]=eM_0[r][0];
609: vals_M_0[1]=eM_0[r][1];
610: MatSetValuesLocal(M_0,1,&row_M_0,2,idx,vals_M_0,ADD_VALUES);
612: row = 3*idx[r];
613: cols[0] = 3*idx[0]; vals[0] = dt*eM_2[r][0]*user->Mv;
614: cols[1] = 3*idx[1]; vals[1] = dt*eM_2[r][1]*user->Mv;
615: cols[2] = 3*idx[0]+1; vals[2] = eM_0[r][0];
616: cols[3] = 3*idx[1]+1; vals[3] = eM_0[r][1];
617:
618: /* Insert values in matrix M for 1st dof */
619: MatSetValuesLocal(M,1,&row,4,cols,vals,ADD_VALUES);
620:
621: row = 3*idx[r]+1;
622: cols[0] = 3*idx[0]; vals[0] = -eM_0[r][0];
623: cols[1] = 3*idx[1]; vals[1] = -eM_0[r][1];
624: cols[2] = 3*idx[0]+1; vals[2] = 2.0*user->kav*eM_2[r][0];
625: cols[3] = 3*idx[1]+1; vals[3] = 2.0*user->kav*eM_2[r][1];
627: /* Insert values in matrix M for 2nd dof */
628: MatSetValuesLocal(M,1,&row,4,cols,vals,ADD_VALUES);
629:
630:
631: row = 3*idx[r]+2;
632: cols2[0] = 3*idx[0]+2; vals2[0] = eM_0[r][0] + user->dt*2.0*user->L*user->kaeta*eM_2[r][0];
633: cols2[1] = 3*idx[1]+2; vals2[1] = eM_0[r][1] + user->dt*2.0*user->L*user->kaeta*eM_2[r][1];
634: MatSetValuesLocal(M,1,&row,2,cols2,vals2,ADD_VALUES);
635: }
636: }
638: MatAssemblyBegin(M_0,MAT_FINAL_ASSEMBLY);
639: MatAssemblyEnd(M_0,MAT_FINAL_ASSEMBLY);
640:
641: MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);
642: MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);
643:
644: DMDARestoreElements(user->da1,&nele,&nen,&ele);
645:
646:
647: return(0);
648: }
652: PetscErrorCode CheckRedundancy(SNES snes, IS act, IS *outact, DM da)
653: {
655: PetscScalar **uin,**uout;
656: Vec UIN, UOUT;
657: PetscInt xs,xm,*outindex;
658: const PetscInt *index;
659: PetscInt k,i,l,n,M,cnt=0;
660:
662: DMDAGetInfo(da,0,&M,0,0,0,0,0,0,0,0,0,0,0);
663: DMGetGlobalVector(da,&UIN);
664: VecSet(UIN,0.0);
665: DMGetLocalVector(da,&UOUT);
666: DMDAVecGetArrayDOF(da,UIN,&uin);
667: ISGetIndices(act,&index);
668: ISGetLocalSize(act,&n);
669: for (k=0;k<n;k++){
670: l = index[k]%5;
671: i = index[k]/5;
672: uin[i][l]=1.0;
673: }
674: printf("Number of active constraints before applying redundancy %d\n",n);
675: ISRestoreIndices(act,&index);
676: DMDAVecRestoreArrayDOF(da,UIN,&uin);
677: DMGlobalToLocalBegin(da,UIN,INSERT_VALUES,UOUT);
678: DMGlobalToLocalEnd(da,UIN,INSERT_VALUES,UOUT);
679: DMDAVecGetArrayDOF(da,UOUT,&uout);
680:
681: DMDAGetCorners(da,&xs,PETSC_NULL,PETSC_NULL,&xm,PETSC_NULL,PETSC_NULL);
683: for(i=xs; i < xs+xm;i++) {
684: if (uout[i-1][1] && uout[i][1] && uout[i+1][1])
685: uout[i][0] = 1.0;
686: if (uout[i-1][3] && uout[i][3] && uout[i+1][3])
687: uout[i][2] = 1.0;
688: }
690: for(i=xs; i < xs+xm;i++) {
691: for(l=0;l<5;l++) {
692: if (uout[i][l])
693: cnt++;
694: }
695: }
697: printf("Number of active constraints after applying redundancy %d\n",cnt);
698:
700: PetscMalloc(cnt*sizeof(PetscInt),&outindex);
701: cnt = 0;
702:
703: for(i=xs; i < xs+xm;i++) {
704: for(l=0;l<5;l++) {
705: if (uout[i][l])
706: outindex[cnt++] = 5*(i)+l;
707: }
708: }
709:
710:
711: ISCreateGeneral(PETSC_COMM_WORLD,cnt,outindex,PETSC_OWN_POINTER,outact);
712: DMDAVecRestoreArrayDOF(da,UOUT,&uout);
713: DMRestoreGlobalVector(da,&UIN);
714: DMRestoreLocalVector(da,&UOUT);
715: return(0);
716: }