Actual source code: ex64.c
petsc-3.4.5 2014-06-29
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_linesearch_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_linesearch_type 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);
62: /* Get physics and time parameters */
63: GetParams(&user);
65: if (user.periodic) {
66: DMDACreate1d(PETSC_COMM_WORLD,DMDA_BOUNDARY_PERIODIC, -4, 3, 1,NULL,&user.da1);
67: DMDACreate1d(PETSC_COMM_WORLD,DMDA_BOUNDARY_PERIODIC, -4, 3, 1,NULL,&user.da1_clone);
68: DMDACreate1d(PETSC_COMM_WORLD,DMDA_BOUNDARY_PERIODIC, -4, 1, 1,NULL,&user.da2);
69: } else {
70: DMDACreate1d(PETSC_COMM_WORLD,DMDA_BOUNDARY_NONE, -4, 3, 1,NULL,&user.da1);
71: DMDACreate1d(PETSC_COMM_WORLD,DMDA_BOUNDARY_NONE, -4, 3, 1,NULL,&user.da1_clone);
72: DMDACreate1d(PETSC_COMM_WORLD,DMDA_BOUNDARY_NONE, -4, 1, 1,NULL,&user.da2);
74: }
75: /* Set Element type (triangular) */
76: DMDASetElementType(user.da1,DMDA_ELEMENT_P1);
77: DMDASetElementType(user.da2,DMDA_ELEMENT_P1);
79: /* Set x and y coordinates */
80: DMDASetUniformCoordinates(user.da1,user.xmin,user.xmax,NULL,NULL,NULL,NULL);
81: DMDASetUniformCoordinates(user.da2,user.xmin,user.xmax,NULL,NULL,NULL,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);
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: DMCreateMatrix(user.da1,MATAIJ,&user.M);
102: /* Get the (usual) mass matrix structure from da2 */
103: DMCreateMatrix(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);
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: SetVariableBounds(user.da1,xl,xu);
116: SNESVISetVariableBounds(snes,xl,xu);
117: SNESSetFromOptions(snes);
118: /*SNESVISetRedundancyCheck(snes,(PetscErrorCode (*)(SNES,IS,IS*,void*))CheckRedundancy,user.da1_clone);*/
119: PetscViewerBinaryOpen(PETSC_COMM_WORLD,"file_out",FILE_MODE_WRITE,&view_out);
120: PetscViewerBinaryOpen(PETSC_COMM_WORLD,"file_p",FILE_MODE_WRITE,&view_p);
121: PetscViewerBinaryOpen(PETSC_COMM_WORLD,"file_q",FILE_MODE_WRITE,&view_q);
122: PetscViewerBinaryOpen(PETSC_COMM_WORLD,"file_psi",FILE_MODE_WRITE,&view_psi);
123: PetscViewerBinaryOpen(PETSC_COMM_WORLD,"file_mat",FILE_MODE_WRITE,&view_mat);
124: /* PetscViewerDrawSetBounds(PETSC_VIEWER_DRAW_(PETSC_COMM_WORLD),5,bounds); */
126: if (user.graphics) {
127: PetscViewerDrawSetBounds(PETSC_VIEWER_DRAW_(PETSC_COMM_WORLD),5,bounds);
129: VecView(x,PETSC_VIEWER_DRAW_(PETSC_COMM_WORLD));
130: }
131: while (t<user.T) {
133: char filename[PETSC_MAX_PATH_LEN];
134: PetscScalar a = 1.0;
135: PetscInt i;
136: PetscViewer view;
139: SNESSetFunction(snes,r,FormFunction,(void*)&user);
140: SNESSetJacobian(snes,J,J,FormJacobian,(void*)&user);
142: DPsi(&user);
143: VecView(user.DPsiv,view_psi);
144: VecView(user.DPsieta,view_psi);
146: Update_q(&user);
147: VecView(user.q,view_q);
148: MatView(user.M,view_mat);
150: SNESSolve(snes,NULL,x);
151: VecView(x,view_out);
154: if (user.graphics) {
155: VecView(x,PETSC_VIEWER_DRAW_(PETSC_COMM_WORLD));
156: }
158: PetscInt its;
159: SNESGetIterationNumber(snes,&its);
160: PetscPrintf(PETSC_COMM_WORLD,"SNESVI solver converged at t = %5.4g in %d iterations\n",t,its);
162: Update_u(x,&user);
164: for (i=0; i < (int)(user.T/a) ; i++) {
165: if (t/a > i - user.dt/a && t/a < i + user.dt/a) {
166: sprintf(filename,"output_%f",t);
167: PetscViewerBinaryOpen(PETSC_COMM_WORLD,filename,FILE_MODE_WRITE,&view);
168: VecView(user.cv,view);
169: VecView(user.eta,view);
170: PetscViewerDestroy(&view);
171: }
172: }
174: t = t + user.dt;
176: }
179: PetscViewerDestroy(&view_out);
180: PetscViewerDestroy(&view_p);
181: PetscViewerDestroy(&view_q);
182: PetscViewerDestroy(&view_psi);
183: PetscViewerDestroy(&view_mat);
184: VecDestroy(&x);
185: VecDestroy(&r);
186: VecDestroy(&xl);
187: VecDestroy(&xu);
188: VecDestroy(&user.q);
189: VecDestroy(&user.wv);
190: VecDestroy(&user.cv);
191: VecDestroy(&user.eta);
192: VecDestroy(&user.DPsiv);
193: VecDestroy(&user.DPsieta);
194: VecDestroy(&user.logcv);
195: VecDestroy(&user.logcv2);
196: VecDestroy(&user.work1);
197: VecDestroy(&user.work2);
198: MatDestroy(&user.M);
199: MatDestroy(&user.M_0);
200: DMDestroy(&user.da1);
201: DMDestroy(&user.da1_clone);
202: DMDestroy(&user.da2);
203: SNESDestroy(&snes);
204: PetscFinalize();
205: return 0;
206: }
210: PetscErrorCode Update_u(Vec X,AppCtx *user)
211: {
213: PetscInt i,n;
214: PetscScalar *xx,*wv_p,*cv_p,*eta_p;
217: VecGetLocalSize(user->wv,&n);
219: VecGetArray(X,&xx);
220: VecGetArray(user->wv,&wv_p);
221: VecGetArray(user->cv,&cv_p);
222: VecGetArray(user->eta,&eta_p);
225: for (i=0; i<n; i++) {
226: wv_p[i] = xx[3*i];
227: cv_p[i] = xx[3*i+1];
228: eta_p[i] = xx[3*i+2];
229: }
230: VecRestoreArray(X,&xx);
231: VecRestoreArray(user->wv,&wv_p);
232: VecRestoreArray(user->cv,&cv_p);
233: VecRestoreArray(user->eta,&eta_p);
234: return(0);
235: }
239: PetscErrorCode Update_q(AppCtx *user)
240: {
242: PetscScalar *q_p, *w1, *w2;
243: PetscInt n,i;
246: VecGetArray(user->q,&q_p);
247: VecGetArray(user->work1,&w1);
248: VecGetArray(user->work2,&w2);
249: VecGetLocalSize(user->wv,&n);
251: MatMult(user->M_0,user->cv,user->work1);
252: VecScale(user->work1,-1.0);
253: for (i=0; i<n; i++) q_p[3*i]=w1[i];
255: MatMult(user->M_0,user->DPsiv,user->work1);
256: for (i=0; i<n; i++) q_p[3*i+1]=w1[i];
258: VecCopy(user->DPsieta,user->work1);
259: VecScale(user->work1,user->L*user->dt);
260: VecAXPY(user->work1,-1.0,user->eta);
261: MatMult(user->M_0,user->work1,user->work2);
262: for (i=0; i<n; i++) q_p[3*i+2]=w2[i];
264: VecRestoreArray(user->q,&q_p);
265: VecRestoreArray(user->work1,&w1);
266: VecRestoreArray(user->work2,&w2);
267: return(0);
268: }
272: PetscErrorCode DPsi(AppCtx *user)
273: {
275: PetscScalar Evf=user->Evf,A=user->A,B=user->B,cv0=user->cv0;
276: PetscScalar *cv_p,*eta_p,*logcv_p,*logcv2_p,*DPsiv_p,*DPsieta_p;
277: PetscInt n,i;
280: VecGetLocalSize(user->cv,&n);
281: VecGetArray(user->cv,&cv_p);
282: VecGetArray(user->eta,&eta_p);
283: VecGetArray(user->logcv,&logcv_p);
284: VecGetArray(user->logcv2,&logcv2_p);
285: VecGetArray(user->DPsiv,&DPsiv_p);
286: VecGetArray(user->DPsieta,&DPsieta_p);
288: Llog(user->cv,user->logcv);
290: VecCopy(user->cv,user->work1);
291: VecScale(user->work1,-1.0);
292: VecShift(user->work1,1.0);
293: Llog(user->work1,user->logcv2);
295: for (i=0; i<n; i++)
296: {
297: 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];
299: 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];
301: }
303: VecRestoreArray(user->cv,&cv_p);
304: VecRestoreArray(user->eta,&eta_p);
305: VecGetArray(user->logcv,&logcv_p);
306: VecGetArray(user->logcv2,&logcv2_p);
307: VecRestoreArray(user->DPsiv,&DPsiv_p);
308: VecRestoreArray(user->DPsieta,&DPsieta_p);
309: return(0);
311: }
316: PetscErrorCode Llog(Vec X, Vec Y)
317: {
319: PetscScalar *x,*y;
320: PetscInt n,i;
323: VecGetArray(X,&x);
324: VecGetArray(Y,&y);
325: VecGetLocalSize(X,&n);
326: for (i=0; i<n; i++) {
327: if (x[i] < 1.0e-12) y[i] = log(1.0e-12);
328: else y[i] = log(x[i]);
329: }
330: return(0);
331: }
335: PetscErrorCode SetInitialGuess(Vec X,AppCtx *user)
336: {
339: PetscInt n,i,Mda;
340: PetscScalar *xx,*cv_p,*wv_p,*eta_p;
341: PetscViewer view_out;
343: /* needed for the void growth case */
344: PetscScalar xmid,cv_v=1.0,cv_m=user->Sv*user->cv0,eta_v=1.0,eta_m=0.0,h,lambda;
345: PetscInt nele,nen,idx[2];
346: const PetscInt *ele;
347: PetscScalar x[2];
348: Vec coords;
349: const PetscScalar *_coords;
350: PetscScalar xwidth = user->xmax - user->xmin;
353: VecGetLocalSize(X,&n);
355: DMDAGetInfo(user->da2,NULL,&Mda,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL);
356: DMGetCoordinatesLocal(user->da2,&coords);
357: VecGetArrayRead(coords,&_coords);
359: if (user->periodic) h = (user->xmax-user->xmin)/Mda;
360: else h = (user->xmax-user->xmin)/(Mda-1.0);
362: xmid = (user->xmax + user->xmin)/2.0;
363: lambda = 4.0*h;
365: DMDAGetElements(user->da2,&nele,&nen,&ele);
366: for (i=0; i < nele; i++) {
367: idx[0] = ele[2*i]; idx[1] = ele[2*i+1];
369: x[0] = _coords[idx[0]];
370: x[1] = _coords[idx[1]];
373: PetscInt k;
374: PetscScalar vals_DDcv[2],vals_cv[2],vals_eta[2],s,hhr,r;
375: for (k=0; k < 2; k++) {
376: s = PetscAbs(x[k] - xmid);
377: if (s <= xwidth*(5.0/64.0)) {
378: vals_cv[k] = cv_v;
379: vals_eta[k] = eta_v;
380: vals_DDcv[k] = 0.0;
381: } else if (s> xwidth*(5.0/64.0) && s<= xwidth*(7.0/64.0)) {
382: /*r = (s - xwidth*(6.0/64.0))/(0.5*lambda);*/
383: r = (s - xwidth*(6.0/64.0))/(xwidth/64.0);
384: hhr = 0.25*(-r*r*r + 3*r + 2);
385: vals_cv[k] = cv_m + (1.0 - hhr)*(cv_v - cv_m);
386: vals_eta[k] = eta_m + (1.0 - hhr)*(eta_v - eta_m);
387: vals_DDcv[k] = (cv_v - cv_m)*r*6.0/(lambda*lambda);
388: } else {
389: vals_cv[k] = cv_m;
390: vals_eta[k] = eta_m;
391: vals_DDcv[k] = 0.0;
392: }
393: }
395: VecSetValuesLocal(user->cv,2,idx,vals_cv,INSERT_VALUES);
396: VecSetValuesLocal(user->eta,2,idx,vals_eta,INSERT_VALUES);
397: VecSetValuesLocal(user->work2,2,idx,vals_DDcv,INSERT_VALUES);
399: }
400: DMDARestoreElements(user->da2,&nele,&nen,&ele);
401: VecRestoreArrayRead(coords,&_coords);
403: VecAssemblyBegin(user->cv);
404: VecAssemblyEnd(user->cv);
405: VecAssemblyBegin(user->eta);
406: VecAssemblyEnd(user->eta);
407: VecAssemblyBegin(user->work2);
408: VecAssemblyEnd(user->work2);
410: DPsi(user);
411: VecCopy(user->DPsiv,user->wv);
412: VecAXPY(user->wv,-2.0*user->kav,user->work2);
414: VecGetArray(X,&xx);
415: VecGetArray(user->wv,&wv_p);
416: VecGetArray(user->cv,&cv_p);
417: VecGetArray(user->eta,&eta_p);
419: for (i=0; i<n/3; i++) {
420: xx[3*i] =wv_p[i];
421: xx[3*i+1]=cv_p[i];
422: xx[3*i+2]=eta_p[i];
423: }
425: PetscViewerBinaryOpen(PETSC_COMM_WORLD,"file_initial",FILE_MODE_WRITE,&view_out);
426: VecView(user->wv,view_out);
427: VecView(user->cv,view_out);
428: VecView(user->eta,view_out);
429: PetscViewerDestroy(&view_out);
431: VecRestoreArray(X,&xx);
432: VecRestoreArray(user->wv,&wv_p);
433: VecRestoreArray(user->cv,&cv_p);
434: VecRestoreArray(user->eta,&eta_p);
435: return(0);
436: }
440: PetscErrorCode FormFunction(SNES snes,Vec X,Vec F,void *ctx)
441: {
443: AppCtx *user=(AppCtx*)ctx;
446: MatMultAdd(user->M,X,user->q,F);
447: return(0);
448: }
452: PetscErrorCode FormJacobian(SNES snes,Vec X,Mat *J,Mat *B,MatStructure *flg,void *ctx)
453: {
455: AppCtx *user=(AppCtx*)ctx;
458: *flg = SAME_NONZERO_PATTERN;
459: MatCopy(user->M,*J,*flg);
460: MatAssemblyBegin(*J,MAT_FINAL_ASSEMBLY);
461: MatAssemblyEnd(*J,MAT_FINAL_ASSEMBLY);
462: return(0);
463: }
466: PetscErrorCode SetVariableBounds(DM da,Vec xl,Vec xu)
467: {
469: PetscScalar **l,**u;
470: PetscInt xs,xm;
471: PetscInt i;
474: DMDAVecGetArrayDOF(da,xl,&l);
475: DMDAVecGetArrayDOF(da,xu,&u);
477: DMDAGetCorners(da,&xs,NULL,NULL,&xm,NULL,NULL);
480: for (i=xs; i < xs+xm; i++) {
481: l[i][0] = -SNES_VI_INF;
482: l[i][1] = 0.0;
483: l[i][2] = 0.0;
484: u[i][0] = SNES_VI_INF;
485: u[i][1] = 1.0;
486: u[i][2] = 1.0;
487: }
489: DMDAVecRestoreArrayDOF(da,xl,&l);
490: DMDAVecRestoreArrayDOF(da,xu,&u);
491: return(0);
492: }
496: PetscErrorCode GetParams(AppCtx *user)
497: {
499: PetscBool flg;
502: /* Set default parameters */
503: user->xmin = 0.0; user->xmax = 128.0;
504: user->Mv = 1.0;
505: user->L = 1.0;
506: user->kaeta = 1.0;
507: user->kav = 0.5;
508: user->Evf = 9.09;
509: user->A = 9.09;
510: user->B = 9.09;
511: user->cv0 = 1.13e-4;
512: user->Sv = 500.0;
513: user->dt = 1.0e-5;
514: user->T = 1.0e-2;
515: user->graphics = PETSC_TRUE;
516: user->periodic = PETSC_FALSE;
517: user->lumpedmass = PETSC_FALSE;
519: PetscOptionsGetReal(NULL,"-xmin",&user->xmin,&flg);
520: PetscOptionsGetReal(NULL,"-xmax",&user->xmax,&flg);
521: PetscOptionsGetReal(NULL,"-T",&user->T,&flg);
522: PetscOptionsGetReal(NULL,"-dt",&user->dt,&flg);
523: PetscOptionsBool("-graphics","Contour plot solutions at each timestep\n","None",user->graphics,&user->graphics,&flg);
524: PetscOptionsBool("-periodic","Use periodic boundary conditions\n","None",user->periodic,&user->periodic,&flg);
525: PetscOptionsBool("-lumpedmass","Use lumped mass matrix\n","None",user->lumpedmass,&user->lumpedmass,&flg);
526: return(0);
527: }
532: PetscErrorCode SetUpMatrices(AppCtx *user)
533: {
535: PetscInt nele,nen,i,n;
536: const PetscInt *ele;
537: PetscScalar dt=user->dt,h;
539: PetscInt idx[2];
540: PetscScalar eM_0[2][2],eM_2[2][2];
541: Mat M =user->M;
542: Mat M_0=user->M_0;
543: PetscInt Mda;
547: MatGetLocalSize(M,&n,NULL);
548: DMDAGetInfo(user->da1,NULL,&Mda,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL);
550: if (user->periodic) h = (user->xmax-user->xmin)/Mda;
551: else h = (user->xmax-user->xmin)/(Mda-1.0);
553: if (user->lumpedmass) {
554: eM_0[0][0] = h/2.0;
555: eM_0[1][1] = h/2.0;
556: eM_0[0][1] = eM_0[1][0] = 0.0;
557: } else {
558: eM_0[0][0]=eM_0[1][1]=h/3.0;
559: eM_0[0][1]=eM_0[1][0]=h/6.0;
560: }
561: eM_2[0][0]=eM_2[1][1]=1.0/h;
562: eM_2[0][1]=eM_2[1][0]=-1.0/h;
564: /* Get local element info */
565: DMDAGetElements(user->da1,&nele,&nen,&ele);
566: for (i=0; i < nele; i++) {
568: idx[0] = ele[2*i]; idx[1] = ele[2*i+1];
570: PetscInt row,cols[4],r,row_M_0,cols2[2];
571: PetscScalar vals[4],vals_M_0[2],vals2[2];
573: for (r=0; r<2; r++) {
574: row_M_0 = idx[r];
575: vals_M_0[0]=eM_0[r][0];
576: vals_M_0[1]=eM_0[r][1];
578: MatSetValuesLocal(M_0,1,&row_M_0,2,idx,vals_M_0,ADD_VALUES);
580: row = 3*idx[r];
581: cols[0] = 3*idx[0]; vals[0] = dt*eM_2[r][0]*user->Mv;
582: cols[1] = 3*idx[1]; vals[1] = dt*eM_2[r][1]*user->Mv;
583: cols[2] = 3*idx[0]+1; vals[2] = eM_0[r][0];
584: cols[3] = 3*idx[1]+1; vals[3] = eM_0[r][1];
586: /* Insert values in matrix M for 1st dof */
587: MatSetValuesLocal(M,1,&row,4,cols,vals,ADD_VALUES);
589: row = 3*idx[r]+1;
590: cols[0] = 3*idx[0]; vals[0] = -eM_0[r][0];
591: cols[1] = 3*idx[1]; vals[1] = -eM_0[r][1];
592: cols[2] = 3*idx[0]+1; vals[2] = 2.0*user->kav*eM_2[r][0];
593: cols[3] = 3*idx[1]+1; vals[3] = 2.0*user->kav*eM_2[r][1];
595: /* Insert values in matrix M for 2nd dof */
596: MatSetValuesLocal(M,1,&row,4,cols,vals,ADD_VALUES);
599: row = 3*idx[r]+2;
600: cols2[0] = 3*idx[0]+2; vals2[0] = eM_0[r][0] + user->dt*2.0*user->L*user->kaeta*eM_2[r][0];
601: cols2[1] = 3*idx[1]+2; vals2[1] = eM_0[r][1] + user->dt*2.0*user->L*user->kaeta*eM_2[r][1];
603: MatSetValuesLocal(M,1,&row,2,cols2,vals2,ADD_VALUES);
604: }
605: }
607: MatAssemblyBegin(M_0,MAT_FINAL_ASSEMBLY);
608: MatAssemblyEnd(M_0,MAT_FINAL_ASSEMBLY);
610: MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);
611: MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);
613: DMDARestoreElements(user->da1,&nele,&nen,&ele);
614: return(0);
615: }
619: PetscErrorCode CheckRedundancy(SNES snes, IS act, IS *outact, DM da)
620: {
622: PetscScalar **uin,**uout;
623: Vec UIN, UOUT;
624: PetscInt xs,xm,*outindex;
625: const PetscInt *index;
626: PetscInt k,i,l,n,M,cnt=0;
629: DMDAGetInfo(da,0,&M,0,0,0,0,0,0,0,0,0,0,0);
630: DMGetGlobalVector(da,&UIN);
631: VecSet(UIN,0.0);
632: DMGetLocalVector(da,&UOUT);
633: DMDAVecGetArrayDOF(da,UIN,&uin);
634: ISGetIndices(act,&index);
635: ISGetLocalSize(act,&n);
636: for (k=0; k<n; k++) {
637: l = index[k]%5;
638: i = index[k]/5;
640: uin[i][l]=1.0;
641: }
642: printf("Number of active constraints before applying redundancy %d\n",n);
643: ISRestoreIndices(act,&index);
644: DMDAVecRestoreArrayDOF(da,UIN,&uin);
645: DMGlobalToLocalBegin(da,UIN,INSERT_VALUES,UOUT);
646: DMGlobalToLocalEnd(da,UIN,INSERT_VALUES,UOUT);
647: DMDAVecGetArrayDOF(da,UOUT,&uout);
649: DMDAGetCorners(da,&xs,NULL,NULL,&xm,NULL,NULL);
651: for (i=xs; i < xs+xm;i++) {
652: if (uout[i-1][1] && uout[i][1] && uout[i+1][1]) uout[i][0] = 1.0;
653: if (uout[i-1][3] && uout[i][3] && uout[i+1][3]) uout[i][2] = 1.0;
654: }
656: for (i=xs; i < xs+xm; i++) {
657: for (l=0; l < 5; l++) {
658: if (uout[i][l]) cnt++;
659: }
660: }
662: printf("Number of active constraints after applying redundancy %d\n",cnt);
664: PetscMalloc(cnt*sizeof(PetscInt),&outindex);
665: cnt = 0;
667: for (i=xs; i < xs+xm;i++) {
668: for (l=0;l<5;l++) {
669: if (uout[i][l]) outindex[cnt++] = 5*(i)+l;
670: }
671: }
674: ISCreateGeneral(PETSC_COMM_WORLD,cnt,outindex,PETSC_OWN_POINTER,outact);
675: DMDAVecRestoreArrayDOF(da,UOUT,&uout);
676: DMRestoreGlobalVector(da,&UIN);
677: DMRestoreLocalVector(da,&UOUT);
678: return(0);
679: }