Actual source code: ex61.c
petsc-3.4.5 2014-06-29
1: static char help[] = "2D coupled Allen-Cahn and Cahn-Hilliard equation for constant mobility and triangular elements. Use periodic boundary condidtions.\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: ./ex61 -ksp_type gmres -snes_vi_monitor -snes_atol 1.e-11 -da_refine 3 -T 0.1 -ksp_monitor_true_residual -pc_type lu -pc_factor_mat_solver_package superlu -snes_converged_reason -ksp_converged_reason -ksp_rtol 1.e-9 -snes_linesearch_monitor -VG 10 -draw_fields 1,3,4 -snes_linesearch_type basic
14: ./ex61 -ksp_type gmres -snes_vi_monitor -snes_atol 1.e-11 -da_refine 4 -T 0.1 -ksp_monitor_true_residual -pc_type sor -snes_converged_reason -ksp_converged_reason -ksp_rtol 1.e-9 -snes_linesearch_monitor -VG 10 -draw_fields 1,3,4 -snes_linesearch_type basic
16: ./ex61 -ksp_type fgmres -snes_vi_monitor -snes_atol 1.e-11 -da_refine 5 -T 0.1 -ksp_monitor_true_residual -snes_converged_reason -ksp_converged_reason -ksp_rtol 1.e-9 -snes_linesearch_monitor -VG 10 -draw_fields 1,3,4 -snes_linesearch_type basic -pc_type mg -pc_mg_galerkin
18: ./ex61 -ksp_type fgmres -snes_vi_monitor -snes_atol 1.e-11 -da_refine 5 -snes_converged_reason -ksp_converged_reason -snes_linesearch_monitor -VG 1 -draw_fields 1,3,4 -pc_type mg -pc_mg_galerkin -log_summary -dt .0000000000001 -mg_coarse_pc_type svd -ksp_monitor_true_residual -ksp_rtol 1.e-9
20: Movie version
21: ./ex61 -ksp_type fgmres -snes_vi_monitor -snes_atol 1.e-11 -da_refine 6 -snes_converged_reason -ksp_converged_reason -snes_linesearch_monitor -VG 10 -draw_fields 1,3,4 -pc_type mg -pc_mg_galerkin -log_summary -dt .000001 -mg_coarse_pc_type redundant -mg_coarse_redundant_pc_type svd -ksp_monitor_true_residual -ksp_rtol 1.e-9 -snes_linesearch_type basic -T .0020
23: */
25: /*
26: Possible additions to the code. At each iteration count the number of solution elements that are at the upper bound and stop the program if large
28: Is the solution at time 0 nonsense? Looks totally different from first time step. Why does cubic line search at beginning screw it up?
30: Add command-line option for constant or degenerate mobility
31: Add command-line option for graphics at each time step
33: Check time-step business; what should it be? How to check that it is good?
34: Make random right hand side forcing function proportional to time step so smaller time steps don't mean more radiation
35: How does the multigrid linear solver work now?
36: What happens when running with degenerate mobility
39: */
41: #include petscsnes.h
42: #include petscdmda.h
44: typedef struct {
45: PetscReal dt,T; /* Time step and end time */
46: PetscReal dtevent; /* time scale of radiation events, roughly one event per dtevent */
47: PetscInt maxevents; /* once this number of events is reached no more events are generated */
48: PetscReal initv; /* initial value of phase variables */
49: PetscReal initeta;
50: PetscBool degenerate; /* use degenerate mobility */
51: PetscReal smallnumber;
52: PetscBool graphics;
53: PetscInt domain;
54: PetscBool radiation;
55: PetscBool voidgrowth; /* use initial conditions for void growth */
56: DM da1,da2;
57: Mat M; /* Jacobian matrix */
58: Mat M_0;
59: Vec q,wv,cv,wi,ci,eta,cvi,DPsiv,DPsii,DPsieta,Pv,Pi,Piv,logcv,logci,logcvi,Riv;
60: Vec phi1,phi2,Phi2D_V,Sv,Si; /* for twodomain modeling */
61: Vec work1,work2,work3,work4;
62: PetscScalar Dv,Di,Evf,Eif,A,kBT,kav,kai,kaeta,Rsurf,Rbulk,L,VG; /* physics parameters */
63: PetscScalar Svr,Sir,cv_eq,ci_eq; /* for twodomain modeling */
64: PetscReal asmallnumber; /* gets added to degenerate mobility */
65: PetscReal xmin,xmax,ymin,ymax;
66: PetscInt Mda, Nda;
67: PetscViewer graphicsfile; /* output of solution at each times step */
68: } AppCtx;
70: PetscErrorCode GetParams(AppCtx*);
71: PetscErrorCode SetRandomVectors(AppCtx*,PetscReal);
72: PetscErrorCode SetVariableBounds(DM,Vec,Vec);
73: PetscErrorCode SetUpMatrices(AppCtx*);
74: PetscErrorCode UpdateMatrices(AppCtx*);
75: PetscErrorCode FormFunction(SNES,Vec,Vec,void*);
76: PetscErrorCode FormJacobian(SNES,Vec,Mat*,Mat*,MatStructure*,void*);
77: PetscErrorCode SetInitialGuess(Vec,AppCtx*);
78: PetscErrorCode Update_q(AppCtx*);
79: PetscErrorCode Update_u(Vec,AppCtx*);
80: PetscErrorCode DPsi(AppCtx*);
81: PetscErrorCode LaplacianFiniteDifference(AppCtx*);
82: PetscErrorCode Llog(Vec,Vec);
83: PetscErrorCode Phi(AppCtx*);
84: PetscErrorCode Phi_read(AppCtx*);
88: int main(int argc, char **argv)
89: {
90: PetscErrorCode ierr;
91: Vec x,r; /* Solution and residual vectors */
92: SNES snes; /* Nonlinear solver context */
93: AppCtx user; /* Application context */
94: Vec xl,xu; /* Upper and lower bounds on variables */
95: Mat J;
96: PetscScalar t=0.0,normq;
97: IS inactiveconstraints;
98: PetscInt ninactiveconstraints,N;
99: SNESConvergedReason reason;
100: char cv_filename[80],eta_filename[80];
101: /*PetscViewer view_out, view_cv,view_eta,view_vtk_cv,view_vtk_eta;*/
102: /*PetscReal bounds[] = {1000.0,-1000.,0.0,1.0,1000.0,-1000.0,0.0,1.0,1000.0,-1000.0}; */
103: /* PetscViewer view_out, view_q, view_psi, view_mat;*/
104: /* PetscViewer view_rand;*/
106: PetscInitialize(&argc,&argv, (char*)0, help);
108: /* Get physics and time parameters */
109: GetParams(&user);
110: /* Create a 1D DA with dof = 5; the whole thing */
111: DMDACreate2d(PETSC_COMM_WORLD,DMDA_BOUNDARY_PERIODIC,DMDA_BOUNDARY_PERIODIC,DMDA_STENCIL_BOX, -3,-3,PETSC_DECIDE,PETSC_DECIDE, 5, 1,NULL,NULL,&user.da1);
113: /* Create a 1D DA with dof = 1; for individual componentes */
114: DMDACreate2d(PETSC_COMM_WORLD,DMDA_BOUNDARY_PERIODIC,DMDA_BOUNDARY_PERIODIC,DMDA_STENCIL_BOX, -3,-3,PETSC_DECIDE,PETSC_DECIDE, 1, 1,NULL,NULL,&user.da2);
117: /* Set Element type (triangular) */
118: DMDASetElementType(user.da1,DMDA_ELEMENT_P1);
119: DMDASetElementType(user.da2,DMDA_ELEMENT_P1);
121: /* Set x and y coordinates */
122: DMDASetUniformCoordinates(user.da1,user.xmin,user.xmax,user.ymin,user.ymax,NULL,NULL);
123: DMDASetUniformCoordinates(user.da2,user.xmin,user.xmax,user.ymin,user.ymax,NULL,NULL);
126: /* Get global vector x from DM (da1) and duplicate vectors r,xl,xu */
127: DMCreateGlobalVector(user.da1,&x);
128: VecGetSize(x,&N);
129: VecDuplicate(x,&r);
130: VecDuplicate(x,&xl);
131: VecDuplicate(x,&xu);
132: VecDuplicate(x,&user.q);
134: /* Get global vector user->wv from da2 and duplicate other vectors */
135: DMCreateGlobalVector(user.da2,&user.wv);
136: VecDuplicate(user.wv,&user.cv);
137: VecDuplicate(user.wv,&user.wi);
138: VecDuplicate(user.wv,&user.ci);
139: VecDuplicate(user.wv,&user.eta);
140: VecDuplicate(user.wv,&user.cvi);
141: VecDuplicate(user.wv,&user.DPsiv);
142: VecDuplicate(user.wv,&user.DPsii);
143: VecDuplicate(user.wv,&user.DPsieta);
144: VecDuplicate(user.wv,&user.Pv);
145: VecDuplicate(user.wv,&user.Pi);
146: VecDuplicate(user.wv,&user.Piv);
147: VecDuplicate(user.wv,&user.logcv);
148: VecDuplicate(user.wv,&user.logci);
149: VecDuplicate(user.wv,&user.logcvi);
150: VecDuplicate(user.wv,&user.work1);
151: VecDuplicate(user.wv,&user.work2);
152: VecDuplicate(user.wv,&user.Riv);
153: VecDuplicate(user.wv,&user.phi1);
154: VecDuplicate(user.wv,&user.phi2);
155: VecDuplicate(user.wv,&user.Phi2D_V);
156: VecDuplicate(user.wv,&user.Sv);
157: VecDuplicate(user.wv,&user.Si);
158: VecDuplicate(user.wv,&user.work3);
159: VecDuplicate(user.wv,&user.work4);
160: /* for twodomain modeling */
161: VecDuplicate(user.wv,&user.phi1);
162: VecDuplicate(user.wv,&user.phi2);
163: VecDuplicate(user.wv,&user.Phi2D_V);
164: VecDuplicate(user.wv,&user.Sv);
165: VecDuplicate(user.wv,&user.Si);
166: VecDuplicate(user.wv,&user.work3);
167: VecDuplicate(user.wv,&user.work4);
170: /* Get Jacobian matrix structure from the da for the entire thing, da1 */
171: DMCreateMatrix(user.da1,MATAIJ,&user.M);
172: /* Get the (usual) mass matrix structure from da2 */
173: DMCreateMatrix(user.da2,MATAIJ,&user.M_0);
174: SetInitialGuess(x,&user);
175: /* twodomain modeling */
176: if (user.domain) {
177: switch (user.domain) {
178: case 1:
179: Phi(&user);
180: break;
181: case 2:
182: Phi_read(&user);
183: break;
184: }
185: }
187: /* Form the jacobian matrix and M_0 */
188: SetUpMatrices(&user);
189: MatDuplicate(user.M,MAT_DO_NOT_COPY_VALUES,&J);
191: SNESCreate(PETSC_COMM_WORLD,&snes);
192: SNESSetDM(snes,user.da1);
194: SNESSetFunction(snes,r,FormFunction,(void*)&user);
195: SNESSetJacobian(snes,J,J,FormJacobian,(void*)&user);
198: SetVariableBounds(user.da1,xl,xu);
199: SNESVISetVariableBounds(snes,xl,xu);
200: SNESSetTolerances(snes,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT,100,PETSC_DEFAULT);
201: SNESSetFromOptions(snes);
203: /* PetscViewerBinaryOpen(PETSC_COMM_WORLD,"file_rand",FILE_MODE_WRITE,&view_rand);
204: PetscViewerBinaryOpen(PETSC_COMM_WORLD,"file_mat2",FILE_MODE_WRITE,&view_mat);
205: PetscViewerBinaryOpen(PETSC_COMM_WORLD,"file_q",FILE_MODE_WRITE,&view_q);
206: PetscViewerBinaryOpen(PETSC_COMM_WORLD,"file_out",FILE_MODE_WRITE,&view_out);
207: PetscViewerBinaryOpen(PETSC_COMM_WORLD,"file_psi",FILE_MODE_WRITE,&view_psi);*/
209: /*PetscViewerBinaryOpen(PETSC_COMM_WORLD,"file_out",FILE_MODE_WRITE,&view_out);
211: PetscViewerBinaryOpen(PETSC_COMM_WORLD,"file_cv",FILE_MODE_WRITE,&view_cv);
212: PetscViewerBinaryOpen(PETSC_COMM_WORLD,"file_eta",FILE_MODE_WRITE,&view_eta);*/
214: /* PetscViewerDrawSetBounds(PETSC_VIEWER_DRAW_(PETSC_COMM_WORLD),5,bounds); */
215: if (user.graphics) {
216: VecView(x,PETSC_VIEWER_DRAW_(PETSC_COMM_WORLD));
217: }
218: /*
219: if (user.graphicsfile) {
220: DMView(user.da1,user.graphicsfile);
221: VecView(x,user.graphicsfile);
222: }
223: */
224: while (t<user.T) {
225: SNESSetFunction(snes,r,FormFunction,(void*)&user);
226: SNESSetJacobian(snes,J,J,FormJacobian,(void*)&user);
228: SetRandomVectors(&user,t);
229: /* VecView(user.Pv,view_rand);
230: VecView(user.Pi,view_rand);
231: VecView(user.Piv,view_rand);*/
233: DPsi(&user);
234: /* VecView(user.DPsiv,view_psi);
235: VecView(user.DPsii,view_psi);
236: VecView(user.DPsieta,view_psi);*/
238: Update_q(&user);
240: /* VecView(user.q,view_q);*/
241: /* MatView(user.M,view_mat);*/
245: sprintf(cv_filename,"file_cv_%f.vtk",t);
246: sprintf(eta_filename,"file_eta_%f.vtk",t);
247: /* PetscViewerASCIIOpen(PETSC_COMM_WORLD,cv_filename,&view_vtk_cv);
248: PetscViewerASCIIOpen(PETSC_COMM_WORLD,eta_filename,&view_vtk_eta);
249: PetscViewerSetFormat(view_vtk_cv, PETSC_VIEWER_ASCII_VTK);
250: PetscViewerSetFormat(view_vtk_eta, PETSC_VIEWER_ASCII_VTK);
251: DMView(user.da2,view_vtk_cv);
252: DMView(user.da2,view_vtk_eta);
253: VecView(user.cv,view_cv);
254: VecView(user.eta,view_eta);
255: VecView(user.cv,view_vtk_cv);
256: VecView(user.eta,view_vtk_eta);
257: PetscViewerDestroy(&view_vtk_cv);
258: PetscViewerDestroy(&view_vtk_eta);*/
261: VecNorm(user.q,NORM_2,&normq);
262: printf("2-norm of q = %14.12f\n",normq);
263: SNESSolve(snes,NULL,x);
264: SNESGetConvergedReason(snes,&reason);
265: if (reason < 0) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_CONV_FAILED,"Nonlinear solver failed");
266: SNESVIGetInactiveSet(snes,&inactiveconstraints);
267: ISGetSize(inactiveconstraints,&ninactiveconstraints);
268: /* if (ninactiveconstraints < .90*N) SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_SUP,"To many active constraints, model has become non-physical"); */
270: /* VecView(x,view_out);*/
271: if (user.graphics) {
272: VecView(x,PETSC_VIEWER_DRAW_(PETSC_COMM_WORLD));
273: }
274: /* VecView(x,PETSC_VIEWER_BINARY_(PETSC_COMM_WORLD));*/
275: PetscInt its;
276: SNESGetIterationNumber(snes,&its);
277: PetscPrintf(PETSC_COMM_WORLD,"SNESVI solver converged at t = %g in %d iterations\n",t,its);
279: Update_u(x,&user);
280: UpdateMatrices(&user);
281: t = t + user.dt;
282: /*
283: if (user.graphicsfile) {
284: VecView(x,user.graphicsfile);
285: }
286: */
287: }
289: /* PetscViewerDestroy(&view_rand);
290: PetscViewerDestroy(&view_mat);
291: PetscViewerDestroy(&view_q);
292: PetscViewerDestroy(&view_out);
293: PetscViewerDestroy(&view_psi);
294: PetscViewerDestroy(&view_out);
296: PetscViewerDestroy(&view_cv);
297: PetscViewerDestroy(&view_eta);*/
299: if (user.graphicsfile) {
300: PetscViewerDestroy(&user.graphicsfile);
301: }
303: VecDestroy(&x);
304: VecDestroy(&r);
305: VecDestroy(&xl);
306: VecDestroy(&xu);
307: VecDestroy(&user.q);
308: VecDestroy(&user.wv);
309: VecDestroy(&user.cv);
310: VecDestroy(&user.wi);
311: VecDestroy(&user.ci);
312: VecDestroy(&user.eta);
313: VecDestroy(&user.cvi);
314: VecDestroy(&user.DPsiv);
315: VecDestroy(&user.DPsii);
316: VecDestroy(&user.DPsieta);
317: VecDestroy(&user.Pv);
318: VecDestroy(&user.Pi);
319: VecDestroy(&user.Piv);
320: VecDestroy(&user.logcv);
321: VecDestroy(&user.logci);
322: VecDestroy(&user.logcvi);
323: VecDestroy(&user.work1);
324: VecDestroy(&user.work2);
325: VecDestroy(&user.Riv);
326: MatDestroy(&user.M);
327: MatDestroy(&user.M_0);
328: DMDestroy(&user.da1);
329: DMDestroy(&user.da2);
332: PetscFinalize();
333: return 0;
334: }
338: PetscErrorCode Update_u(Vec X,AppCtx *user)
339: {
341: PetscInt i,n;
342: PetscScalar *xx,*wv_p,*cv_p,*wi_p,*ci_p,*eta_p;
345: VecGetLocalSize(user->wv,&n);
346: VecGetArray(X,&xx);
347: VecGetArray(user->wv,&wv_p);
348: VecGetArray(user->cv,&cv_p);
349: VecGetArray(user->wi,&wi_p);
350: VecGetArray(user->ci,&ci_p);
351: VecGetArray(user->eta,&eta_p);
354: for (i=0; i<n; i++) {
355: wv_p[i] = xx[5*i];
356: cv_p[i] = xx[5*i+1];
357: wi_p[i] = xx[5*i+2];
358: ci_p[i] = xx[5*i+3];
359: eta_p[i] = xx[5*i+4];
360: }
361: VecRestoreArray(X,&xx);
362: VecRestoreArray(user->wv,&wv_p);
363: VecRestoreArray(user->cv,&cv_p);
364: VecRestoreArray(user->wi,&wi_p);
365: VecRestoreArray(user->ci,&ci_p);
366: VecRestoreArray(user->eta,&eta_p);
367: return(0);
368: }
372: PetscErrorCode Update_q(AppCtx *user)
373: {
375: PetscScalar *q_p,*w1,*w2,max1;
376: PetscInt i,n;
379: VecPointwiseMult(user->Riv,user->eta,user->eta);
380: VecScale(user->Riv,user->Rsurf);
381: VecShift(user->Riv,user->Rbulk);
382: VecPointwiseMult(user->Riv,user->ci,user->Riv);
383: VecPointwiseMult(user->Riv,user->cv,user->Riv);
385: VecCopy(user->Riv,user->work1);
386: if (user->radiation) {
387: VecAXPY(user->work1,-1.0,user->Pv);
388: }
389: if (user->domain) {
390: VecCopy(user->cv,user->work3);
391: VecShift(user->work3,-1.0*user->cv_eq);
392: VecCopy(user->Phi2D_V,user->work4);
393: VecScale(user->work4,-1.0);
394: VecShift(user->work4,1.0);
395: VecPointwiseMult(user->work4,user->work4,user->work3);
396: VecScale(user->work4,user->Svr);
397: VecAXPY(user->work1,300.0,user->work4);
398: }
399: VecScale(user->work1,user->dt);
400: VecAXPY(user->work1,-1.0,user->cv);
401: MatMult(user->M_0,user->work1,user->work2);
403: VecGetArray(user->q,&q_p);
404: VecGetArray(user->work1,&w1);
405: VecGetArray(user->work2,&w2);
406: VecGetLocalSize(user->wv,&n);
407: for (i=0; i<n; i++) q_p[5*i]=w2[i];
409: MatMult(user->M_0,user->DPsiv,user->work1);
410: for (i=0; i<n; i++) q_p[5*i+1]=w1[i];
412: VecCopy(user->Riv,user->work1);
413: if (user->radiation) {
414: VecAXPY(user->work1,-1.0,user->Pi);
415: }
416: if (user->domain) {
417: VecCopy(user->ci,user->work3);
418: VecShift(user->work3,-1.0*user->ci_eq);
419: VecCopy(user->Phi2D_V,user->work4);
420: VecScale(user->work4,-1.0);
421: VecShift(user->work4,1.0);
422: VecPointwiseMult(user->work4,user->work4,user->work3);
423: VecScale(user->work4,user->Sir);
424: VecAXPY(user->work1,300.0,user->work4);
425: }
426: VecScale(user->work1,user->dt);
427: VecAXPY(user->work1,-1.0,user->ci);
428: MatMult(user->M_0,user->work1,user->work2);
429: for (i=0; i<n; i++) q_p[5*i+2]=w2[i];
431: MatMult(user->M_0,user->DPsii,user->work1);
432: for (i=0; i<n; i++) q_p[5*i+3]=w1[i];
434: VecCopy(user->DPsieta,user->work1);
435: VecScale(user->work1,user->L);
436: VecAXPY(user->work1,-1.0/user->dt,user->eta);
437: if (user->radiation) {
438: VecAXPY(user->work1,-1.0,user->Piv);
439: }
440: MatMult(user->M_0,user->work1,user->work2);
441: for (i=0; i<n; i++) q_p[5*i+4]=w2[i];
443: VecRestoreArray(user->q,&q_p);
444: VecRestoreArray(user->work1,&w1);
445: VecRestoreArray(user->work2,&w2);
446: return(0);
447: }
451: PetscErrorCode DPsi(AppCtx *user)
452: {
454: PetscScalar Evf=user->Evf,Eif=user->Eif,kBT=user->kBT,A=user->A;
455: PetscScalar *cv_p,*ci_p,*eta_p,*logcv_p,*logci_p,*logcvi_p,*DPsiv_p,*DPsii_p,*DPsieta_p;
456: PetscInt n,i;
459: VecGetLocalSize(user->cv,&n);
460: VecGetArray(user->cv,&cv_p);
461: VecGetArray(user->ci,&ci_p);
462: VecGetArray(user->eta,&eta_p);
463: VecGetArray(user->logcv,&logcv_p);
464: VecGetArray(user->logci,&logci_p);
465: VecGetArray(user->logcvi,&logcvi_p);
466: VecGetArray(user->DPsiv,&DPsiv_p);
467: VecGetArray(user->DPsii,&DPsii_p);
468: VecGetArray(user->DPsieta,&DPsieta_p);
470: Llog(user->cv,user->logcv);
472: Llog(user->ci,user->logci);
475: VecCopy(user->cv,user->cvi);
476: VecAXPY(user->cvi,1.0,user->ci);
477: VecScale(user->cvi,-1.0);
478: VecShift(user->cvi,1.0);
479: Llog(user->cvi,user->logcvi);
481: for (i=0; i<n; i++) {
482: DPsiv_p[i] = (eta_p[i]-1.0)*(eta_p[i]-1.0)*(Evf + kBT*(logcv_p[i] - logcvi_p[i])) + eta_p[i]*eta_p[i]*2*A*(cv_p[i]-1);
483: DPsii_p[i] = (eta_p[i]-1.0)*(eta_p[i]-1.0)*(Eif + kBT*(logci_p[i] - logcvi_p[i])) + eta_p[i]*eta_p[i]*2*A*ci_p[i];
485: DPsieta_p[i] = 2.0*(eta_p[i]-1.0)*(Evf*cv_p[i] + Eif*ci_p[i] + kBT*(cv_p[i]* logcv_p[i] + ci_p[i]* logci_p[i] + (1-cv_p[i]-ci_p[i])*logcvi_p[i])) + 2.0*eta_p[i]*A*((cv_p[i]-1.0)*(cv_p[i]-1.0) + ci_p[i]*ci_p[i]);
486: }
488: VecRestoreArray(user->cv,&cv_p);
489: VecRestoreArray(user->ci,&ci_p);
490: VecRestoreArray(user->eta,&eta_p);
491: VecRestoreArray(user->logcv,&logcv_p);
492: VecRestoreArray(user->logci,&logci_p);
493: VecRestoreArray(user->logcvi,&logcvi_p);
494: VecRestoreArray(user->DPsiv,&DPsiv_p);
495: VecRestoreArray(user->DPsii,&DPsii_p);
496: VecRestoreArray(user->DPsieta,&DPsieta_p);
497: return(0);
498: }
503: PetscErrorCode Llog(Vec X, Vec Y)
504: {
506: PetscScalar *x,*y;
507: PetscInt n,i;
510: VecGetArray(X,&x);
511: VecGetArray(Y,&y);
512: VecGetLocalSize(X,&n);
513: for (i=0; i<n; i++) {
514: if (x[i] < 1.0e-12) y[i] = log(1.0e-12);
515: else y[i] = log(x[i]);
516: }
517: return(0);
518: }
523: PetscErrorCode SetInitialGuess(Vec X,AppCtx *user)
524: {
526: PetscInt n,i,Mda,Nda;
527: PetscScalar *xx,*cv_p,*ci_p,*wv_p,*wi_p,*eta;
529: /* needed for the void growth case */
530: PetscScalar xmid,ymid,cv_v=1.0,cv_m=0.122,ci_v=0.0,ci_m=.00069,eta_v=1.0,eta_m=0.0,h,lambda;
531: PetscInt nele,nen,idx[3];
532: const PetscInt *ele;
533: PetscScalar x[3],y[3];
534: Vec coords;
535: const PetscScalar *_coords;
536: PetscViewer view;
537: PetscScalar xwidth = user->xmax - user->xmin;
540: VecGetLocalSize(X,&n);
542: if (user->voidgrowth) {
543: DMDAGetInfo(user->da2,NULL,&Mda,&Nda,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL);
544: DMGetCoordinatesLocal(user->da2,&coords);
545: VecGetArrayRead(coords,&_coords);
547: h = (user->xmax-user->xmin)/Mda;
548: xmid = (user->xmax + user->xmin)/2.0;
549: ymid = (user->ymax + user->ymin)/2.0;
550: lambda = 4.0*h;
552: DMDAGetElements(user->da2,&nele,&nen,&ele);
553: for (i=0; i < nele; i++) {
554: idx[0] = ele[3*i]; idx[1] = ele[3*i+1]; idx[2] = ele[3*i+2];
556: x[0] = _coords[2*idx[0]]; y[0] = _coords[2*idx[0]+1];
557: x[1] = _coords[2*idx[1]]; y[1] = _coords[2*idx[1]+1];
558: x[2] = _coords[2*idx[2]]; y[2] = _coords[2*idx[2]+1];
560: PetscInt k;
561: PetscScalar vals_cv[3],vals_ci[3],vals_eta[3],s,hhr,r;
562: for (k=0; k < 3; k++) {
563: s = PetscSqrtScalar((x[k] - xmid)*(x[k] - xmid) + (y[k] - ymid)*(y[k] - ymid));
564: if (s < xwidth*(5.0/64.0)) {
565: vals_cv[k] = cv_v;
566: vals_ci[k] = ci_v;
567: vals_eta[k] = eta_v;
568: } else if (s>= xwidth*(5.0/64.0) && s<= xwidth*(7.0/64.0)) {
569: /* r = (s - xwidth*(6.0/64.0))/(0.5*lambda); */
570: r = (s - xwidth*(6.0/64.0))/(xwidth/64.0);
571: hhr = 0.25*(-r*r*r + 3*r + 2);
572: vals_cv[k] = cv_m + (1.0 - hhr)*(cv_v - cv_m);
573: vals_ci[k] = ci_m + (1.0 - hhr)*(ci_v - ci_m);
574: vals_eta[k] = eta_m + (1.0 - hhr)*(eta_v - eta_m);
575: } else {
576: vals_cv[k] = cv_m;
577: vals_ci[k] = ci_m;
578: vals_eta[k] = eta_m;
579: }
580: }
581: VecSetValuesLocal(user->cv,3,idx,vals_cv,INSERT_VALUES);
582: VecSetValuesLocal(user->ci,3,idx,vals_ci,INSERT_VALUES);
583: VecSetValuesLocal(user->eta,3,idx,vals_eta,INSERT_VALUES);
584: }
585: VecAssemblyBegin(user->cv);
586: VecAssemblyEnd(user->cv);
587: VecAssemblyBegin(user->ci);
588: VecAssemblyEnd(user->ci);
589: VecAssemblyBegin(user->eta);
590: VecAssemblyEnd(user->eta);
592: DMDARestoreElements(user->da2,&nele,&nen,&ele);
593: VecRestoreArrayRead(coords,&_coords);
595: PetscViewerBinaryOpen(PETSC_COMM_WORLD,"file_initial",FILE_MODE_WRITE,&view);
596: VecView(user->cv,view);
597: VecView(user->ci,view);
598: VecView(user->eta,view);
599: PetscViewerDestroy(&view);
600: } else {
601: /* VecSet(user->cv,user->initv); */
602: /* VecSet(user->ci,user->initv); */
603: VecSet(user->cv,.05);
604: VecSet(user->ci,.05);
605: VecSet(user->eta,user->initeta);
606: }
608: DPsi(user);
609: VecCopy(user->DPsiv,user->wv);
610: VecCopy(user->DPsii,user->wi);
612: VecGetArray(X,&xx);
613: VecGetArray(user->cv,&cv_p);
614: VecGetArray(user->ci,&ci_p);
615: VecGetArray(user->wv,&wv_p);
616: VecGetArray(user->wi,&wi_p);
617: VecGetArray(user->eta,&eta);
618: for (i=0; i<n/5; i++) {
619: xx[5*i] =wv_p[i];
620: xx[5*i+1]=cv_p[i];
621: xx[5*i+2]=wi_p[i];
622: xx[5*i+3]=ci_p[i];
623: xx[5*i+4]=eta[i];
624: }
626: /* VecView(user->wv,view);
627: VecView(user->cv,view);
628: VecView(user->wi,view);
629: VecView(user->ci,view);
630: PetscViewerDestroy(&view);*/
632: VecRestoreArray(X,&xx);
633: VecRestoreArray(user->cv,&cv_p);
634: VecRestoreArray(user->ci,&ci_p);
635: VecRestoreArray(user->wv,&wv_p);
636: VecRestoreArray(user->wi,&wi_p);
637: VecRestoreArray(user->eta,&eta);
638: return(0);
639: }
641: typedef struct {
642: PetscReal dt,x,y,strength;
643: } RandomValues;
648: PetscErrorCode SetRandomVectors(AppCtx *user,PetscReal t)
649: {
650: PetscErrorCode ierr;
651: static RandomValues *randomvalues = 0;
652: static PetscInt randindex = 0,n; /* indicates how far into the randomvalues we have currently used */
653: static PetscReal randtime = 0; /* indicates time of last radiation event */
654: PetscInt i,j,M,N,cnt = 0;
655: PetscInt xs,ys,xm,ym;
658: if (!randomvalues) {
659: PetscViewer viewer;
660: char filename[PETSC_MAX_PATH_LEN];
661: PetscBool flg;
662: PetscInt seed;
664: PetscOptionsGetInt(NULL,"-random_seed",&seed,&flg);
665: if (flg) {
666: sprintf(filename,"ex61.random.%d",(int)seed);
667: } else {
668: PetscStrcpy(filename,"ex61.random");
669: }
670: PetscViewerBinaryOpen(PETSC_COMM_WORLD,filename,FILE_MODE_READ,&viewer);
671: PetscViewerBinaryRead(viewer,&n,1,PETSC_INT);
672: PetscMalloc(n*sizeof(RandomValues),&randomvalues);
673: PetscViewerBinaryRead(viewer,randomvalues,4*n,PETSC_DOUBLE);
674: for (i=0; i<n; i++) randomvalues[i].dt = randomvalues[i].dt*user->dtevent;
675: PetscViewerDestroy(&viewer);
676: }
677: user->maxevents = PetscMin(user->maxevents,n);
679: VecSet(user->Pv,0.0);
680: DMDAGetInfo(user->da1,0,&M,&N,0,0,0,0,0,0,0,0,0,0);
681: DMDAGetGhostCorners(user->da1,&xs,&ys,0,&xm,&ym,0);
682: while (user->maxevents > randindex && randtime + randomvalues[randindex].dt < t + user->dt) { /* radiation event has occured since last time step */
683: i = ((PetscInt) (randomvalues[randindex].x*M)) - xs;
684: j = ((PetscInt) (randomvalues[randindex].y*N)) - ys;
685: if (i >= 0 && i < xm && j >= 0 && j < ym) { /* point is on this process */
686: /* need to make sure eta at the given point is not great than .8 */
687: VecSetValueLocal(user->Pv,i + 1 + xm*(j + 1), randomvalues[randindex].strength*user->VG,INSERT_VALUES);
688: }
689: randtime += randomvalues[randindex++].dt;
690: cnt++;
691: }
692: PetscPrintf(PETSC_COMM_WORLD,"Number of radiation events %d\n",cnt);
693: VecAssemblyBegin(user->Pv);
694: VecAssemblyEnd(user->Pv);
696: VecCopy(user->Pv,user->Pi);
697: VecScale(user->Pi,0.9);
698: VecPointwiseMult(user->Piv,user->Pi,user->Pv);
699: return(0);
700: }
704: PetscErrorCode FormFunction(SNES snes,Vec X,Vec F,void *ctx)
705: {
707: AppCtx *user=(AppCtx*)ctx;
710: MatMultAdd(user->M,X,user->q,F);
711: return(0);
712: }
716: PetscErrorCode FormJacobian(SNES snes,Vec X,Mat *J,Mat *B,MatStructure *flg,void *ctx)
717: {
719: AppCtx *user=(AppCtx*)ctx;
722: *flg = SAME_NONZERO_PATTERN;
723: MatCopy(user->M,*J,*flg);
724: MatAssemblyBegin(*J,MAT_FINAL_ASSEMBLY);
725: MatAssemblyEnd(*J,MAT_FINAL_ASSEMBLY);
726: return(0);
727: }
731: PetscErrorCode SetVariableBounds(DM da,Vec xl,Vec xu)
732: {
734: PetscScalar ***l,***u;
735: PetscInt xs,xm,ys,ym;
736: PetscInt j,i;
739: DMDAVecGetArrayDOF(da,xl,&l);
740: DMDAVecGetArrayDOF(da,xu,&u);
742: DMDAGetCorners(da,&xs,&ys,NULL,&xm,&ym,NULL);
744: for (j=ys; j<ys+ym; j++) {
745: for (i=xs; i < xs+xm; i++) {
746: l[j][i][0] = -SNES_VI_INF;
747: l[j][i][1] = 0.0;
748: l[j][i][2] = -SNES_VI_INF;
749: l[j][i][3] = 0.0;
750: l[j][i][4] = 0.0;
751: u[j][i][0] = SNES_VI_INF;
752: u[j][i][1] = 1.0;
753: u[j][i][2] = SNES_VI_INF;
754: u[j][i][3] = 1.0;
755: u[j][i][4] = 1.0;
756: }
757: }
760: DMDAVecRestoreArrayDOF(da,xl,&l);
761: DMDAVecRestoreArrayDOF(da,xu,&u);
762: return(0);
763: }
767: PetscErrorCode GetParams(AppCtx *user)
768: {
770: PetscBool flg,graphicsfile = PETSC_FALSE;
773: /* Set default parameters */
774: user->xmin = 0.0; user->xmax = 128.0;
775: user->ymin = 0.0; user->ymax = 128.0;
776: user->Dv = 1.0;
777: user->Di = 4.0;
778: user->Evf = 0.8;
779: user->Eif = 1.2;
780: user->A = 1.0;
781: user->kBT = 0.11;
782: user->kav = 1.0;
783: user->kai = 1.0;
784: user->kaeta = 1.0;
785: user->Rsurf = 10.0;
786: user->Rbulk = 1.0;
787: user->VG = 100.0;
788: user->L = 10.0;
790: user->T = 1.0e-2;
791: user->dt = 1.0e-4;
792: user->initv = .00069;
793: user->initeta = 0.0;
794: user->degenerate = PETSC_FALSE;
795: user->maxevents = 10;
796: user->graphics = PETSC_TRUE;
798: /* multidomain modeling */
799: user->domain = 1;
800: user->Svr = 0.5;
801: user->Sir = 0.5;
802: user->cv_eq = 6.9e-4;
803: user->ci_eq = 6.9e-4;
804: /* void growth */
805: user->voidgrowth = PETSC_FALSE;
807: user->radiation = PETSC_FALSE;
809: /* degenerate mobility */
810: user->smallnumber = 1.0e-3;
812: PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"Coupled Cahn-Hillard/Allen-Cahn Equations","Phasefield");
813: PetscOptionsInt("-domain","Number of domains (0=one domain, 1=two domains, 2=multidomain\n","None",user->domain,&user->domain,&flg);
815: PetscOptionsReal("-Dv","Vacancy Diffusivity\n","None",user->Dv,&user->Dv,&flg);
816: PetscOptionsReal("-Di","Interstitial Diffusivity\n","None",user->Di,&user->Di,&flg);
817: PetscOptionsReal("-Evf","Vacancy Formation Energy\n","None",user->Evf,&user->Evf,&flg);
818: PetscOptionsReal("-Eif","Interstitial Formation energy\n","None",user->Eif,&user->Eif,&flg);
819: PetscOptionsReal("-A","???","None",user->A,&user->A,&flg);
820: PetscOptionsReal("-kBT","Boltzmann's Constant times the Absolute Temperature","None",user->kBT,&user->kBT,&flg);
821: PetscOptionsReal("-kav","???","None",user->kav,&user->kav,&flg);
822: PetscOptionsReal("-kai","???","None",user->kai,&user->kai,&flg);
823: PetscOptionsReal("-kaeta","???","None",user->kaeta,&user->kaeta,&flg);
824: PetscOptionsReal("-Rsurf","???","None",user->Rsurf,&user->Rsurf,&flg);
825: PetscOptionsReal("-Rbulk","???","None",user->Rbulk,&user->Rbulk,&flg);
826: PetscOptionsReal("-VG","Maximum increase in vacancy (or interstitial) concentration due to a cascade event","None",user->VG,&user->VG,&flg);
827: PetscOptionsReal("-L","???","None",user->L,&user->L,&flg);
829: PetscOptionsReal("-initv","Initial solution of Cv and Ci","None",user->initv,&user->initv,&flg);
830: PetscOptionsReal("-initeta","Initial solution of Eta","None",user->initeta,&user->initeta,&flg);
831: PetscOptionsBool("-degenerate","Run with degenerate mobility\n","None",user->degenerate,&user->degenerate,&flg);
832: PetscOptionsReal("-smallnumber","Small number added to degenerate mobility\n","None",user->smallnumber,&user->smallnumber,&flg);
834: PetscOptionsBool("-voidgrowth","Use initial conditions for void growth\n","None",user->voidgrowth,&user->voidgrowth,&flg);
835: PetscOptionsBool("-radiation","Use initial conditions for void growth\n","None",user->radiation,&user->radiation,&flg);
836: PetscOptionsReal("-xmin","Lower X coordinate of domain\n","None",user->xmin,&user->xmin,&flg);
837: PetscOptionsReal("-xmax","Upper X coordinate of domain\n","None",user->xmax,&user->xmax,&flg);
838: PetscOptionsReal("-T","Total runtime\n","None",user->T,&user->T,&flg);
839: PetscOptionsReal("-dt","Time step\n","None",user->dt,&user->dt,&flg);
841: user->dtevent = user->dt;
843: PetscOptionsReal("-dtevent","Average time between random events\n","None",user->dtevent,&user->dtevent,&flg);
844: PetscOptionsInt("-maxevents","Maximum random events allowed\n","None",user->maxevents,&user->maxevents,&flg);
846: PetscOptionsBool("-graphics","Contour plot solutions at each timestep\n","None",user->graphics,&user->graphics,&flg);
847: PetscOptionsBool("-graphicsfile","Save solution at each timestep\n","None",graphicsfile,&graphicsfile,&flg);
848: if (graphicsfile) {
849: PetscViewerBinaryOpen(PETSC_COMM_WORLD,"ex61.data",FILE_MODE_WRITE,&user->graphicsfile);
850: }
851: PetscOptionsEnd();
852: return(0);
853: }
858: PetscErrorCode SetUpMatrices(AppCtx *user)
859: {
861: PetscInt nele,nen,i,n;
862: const PetscInt *ele;
863: PetscScalar dt=user->dt,hx,hy;
865: PetscInt idx[3];
866: PetscScalar eM_0[3][3],eM_2_even[3][3],eM_2_odd[3][3];
867: PetscScalar cv_sum, ci_sum;
868: Mat M =user->M;
869: Mat M_0=user->M_0;
870: PetscInt Mda=user->Mda, Nda=user->Nda;
871: PetscScalar *cv_p,*ci_p;
872: /* newly added */
873: Vec cvlocal,cilocal;
876: /* MatSetOption(M,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);
877: MatSetOption(M_0,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);*/
879: /* new stuff */
880: DMGetLocalVector(user->da2,&cvlocal);
881: DMGetLocalVector(user->da2,&cilocal);
882: DMGlobalToLocalBegin(user->da2,user->cv,INSERT_VALUES,cvlocal);
883: DMGlobalToLocalEnd(user->da2,user->cv,INSERT_VALUES,cvlocal);
884: DMGlobalToLocalBegin(user->da2,user->ci,INSERT_VALUES,cilocal);
885: DMGlobalToLocalEnd(user->da2,user->ci,INSERT_VALUES,cilocal);
886: /* old stuff */
887: /*
888: VecGetArray(user->cv,&cv_p);
889: VecGetArray(user->ci,&ci_p);
890: */
891: /* new stuff */
892: VecGetArray(cvlocal,&cv_p);
893: VecGetArray(cilocal,&ci_p);
895: MatGetLocalSize(M,&n,NULL);
896: DMDAGetInfo(user->da1,NULL,&Mda,&Nda,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL);
897: hx = (user->xmax-user->xmin)/Mda;
898: hy = (user->ymax-user->ymin)/Nda;
900: eM_0[0][0]=eM_0[1][1]=eM_0[2][2]=hx*hy/12.0;
901: eM_0[0][1]=eM_0[0][2]=eM_0[1][0]=eM_0[1][2]=eM_0[2][0]=eM_0[2][1]=hx*hy/24.0;
903: eM_2_odd[0][0] = 1.0;
904: eM_2_odd[1][1] = eM_2_odd[2][2] = 0.5;
905: eM_2_odd[0][1] = eM_2_odd[0][2] = eM_2_odd[1][0]= eM_2_odd[2][0] = -0.5;
906: eM_2_odd[1][2] = eM_2_odd[2][1] = 0.0;
908: eM_2_even[0][0] = 1.0;
909: eM_2_even[1][1] = eM_2_even[2][2] = 0.5;
910: eM_2_even[0][1] = eM_2_even[0][2] = eM_2_even[1][0]= eM_2_even[2][0] = -0.5;
911: eM_2_even[1][2] = eM_2_even[2][1] = 0.0;
913: /* eM_2_even[1][1] = 1.0;
914: eM_2_even[0][0] = eM_2_even[2][2] = 0.5;
915: eM_2_even[0][1] = eM_2_even[1][0] = eM_2_even[1][2] = eM_2_even[2][1] = -0.5;
916: eM_2_even[0][2] = eM_2_even[2][0] = 0.0;
917: */
919: /* for (k=0;k < Mda*Nda*2;k++) { */
920: DMDAGetElements(user->da1,&nele,&nen,&ele);
921: for (i=0; i < nele; i++) {
922: /*
923: idx[0] = connect[k*3];
924: idx[1] = connect[k*3+1];
925: idx[2] = connect[k*3+2];
926: */
927: idx[0] = ele[3*i];
928: idx[1] = ele[3*i+1];
929: idx[2] = ele[3*i+2];
931: PetscInt row,cols[6],r,row_M_0,cols3[3];
932: PetscScalar vals[6],vals_M_0[3],vals3[3];
934: for (r=0; r<3; r++) {
935: /* row_M_0 = connect[k*3+r]; */
936: row_M_0 = idx[r];
938: vals_M_0[0]=eM_0[r][0];
939: vals_M_0[1]=eM_0[r][1];
940: vals_M_0[2]=eM_0[r][2];
943: MatSetValuesLocal(M_0,1,&row_M_0,3,idx,vals_M_0,ADD_VALUES);
945: if (user->degenerate) {
946: cv_sum = (cv_p[idx[0]] + cv_p[idx[1]] + cv_p[idx[2]])*user->Dv/(3.0*user->kBT);
947: ci_sum = (ci_p[idx[0]] + ci_p[idx[1]] + ci_p[idx[2]])*user->Di/(3.0*user->kBT);
948: } else {
949: cv_sum = user->initv*user->Dv/user->kBT;
950: ci_sum = user->initv*user->Di/user->kBT;
951: }
955: row = 5*idx[r];
956: cols[0] = 5*idx[0]; vals[0] = dt*eM_2_odd[r][0]*cv_sum;
957: cols[1] = 5*idx[1]; vals[1] = dt*eM_2_odd[r][1]*cv_sum;
958: cols[2] = 5*idx[2]; vals[2] = dt*eM_2_odd[r][2]*cv_sum;
959: cols[3] = 5*idx[0]+1; vals[3] = eM_0[r][0];
960: cols[4] = 5*idx[1]+1; vals[4] = eM_0[r][1];
961: cols[5] = 5*idx[2]+1; vals[5] = eM_0[r][2];
964: MatSetValuesLocal(M,1,&row,6,cols,vals,ADD_VALUES);
967: row = 5*idx[r]+1;
968: cols[0] = 5*idx[0]; vals[0] = -1.0*eM_0[r][0];
969: cols[1] = 5*idx[1]; vals[1] = -1.0*eM_0[r][1];
970: cols[2] = 5*idx[2]; vals[2] = -1.0*eM_0[r][2];
971: cols[3] = 5*idx[0]+1; vals[3] = user->kav*eM_2_odd[r][0];
972: cols[4] = 5*idx[1]+1; vals[4] = user->kav*eM_2_odd[r][1];
973: cols[5] = 5*idx[2]+1; vals[5] = user->kav*eM_2_odd[r][2];
975: MatSetValuesLocal(M,1,&row,6,cols,vals,ADD_VALUES);
977: row = 5*idx[r]+2;
978: cols[0] = 5*idx[0]+2; vals[0] = dt*eM_2_odd[r][0]*ci_sum;
979: cols[1] = 5*idx[1]+2; vals[1] = dt*eM_2_odd[r][1]*ci_sum;
980: cols[2] = 5*idx[2]+2; vals[2] = dt*eM_2_odd[r][2]*ci_sum;
981: cols[3] = 5*idx[0]+3; vals[3] = eM_0[r][0];
982: cols[4] = 5*idx[1]+3; vals[4] = eM_0[r][1];
983: cols[5] = 5*idx[2]+3; vals[5] = eM_0[r][2];
985: MatSetValuesLocal(M,1,&row,6,cols,vals,ADD_VALUES);
988: row = 5*idx[r]+3;
989: cols[0] = 5*idx[0]+2; vals[0] = -1.0*eM_0[r][0];
990: cols[1] = 5*idx[1]+2; vals[1] = -1.0*eM_0[r][1];
991: cols[2] = 5*idx[2]+2; vals[2] = -1.0*eM_0[r][2];
992: cols[3] = 5*idx[0]+3; vals[3] = user->kai*eM_2_odd[r][0];
993: cols[4] = 5*idx[1]+3; vals[4] = user->kai*eM_2_odd[r][1];
994: cols[5] = 5*idx[2]+3; vals[5] = user->kai*eM_2_odd[r][2];
996: MatSetValuesLocal(M,1,&row,6,cols,vals,ADD_VALUES);
999: row = 5*idx[r]+4;
1000: /*
1001: cols3[0] = 5*idx[0]+4; vals3[0] = eM_0[r][0]/dt + user->L*user->kaeta*dt*eM_2_odd[r][0];
1002: cols3[1] = 5*idx[1]+4; vals3[1] = eM_0[r][1]/dt + user->L*user->kaeta*dt*eM_2_odd[r][1];
1003: cols3[2] = 5*idx[2]+4; vals3[2] = eM_0[r][2]/dt + user->L*user->kaeta*dt*eM_2_odd[r][2];
1004: */
1005: cols3[0] = 5*idx[0]+4; vals3[0] = (eM_0[r][0]/dt + user->L*user->kaeta*eM_2_odd[r][0]);
1006: cols3[1] = 5*idx[1]+4; vals3[1] = (eM_0[r][1]/dt + user->L*user->kaeta*eM_2_odd[r][1]);
1007: cols3[2] = 5*idx[2]+4; vals3[2] = (eM_0[r][2]/dt + user->L*user->kaeta*eM_2_odd[r][2]);
1009: MatSetValuesLocal(M,1,&row,3,cols3,vals3,ADD_VALUES);
1011: }
1012: }
1014: /* new */
1015: VecRestoreArray(cvlocal,&cv_p);
1016: VecRestoreArray(cilocal,&ci_p);
1017: DMRestoreLocalVector(user->da2,&cvlocal);
1018: DMRestoreLocalVector(user->da2,&cilocal);
1019: /* old */
1020: /*
1021: VecRestoreArray(user->cv,&cv_p);
1022: VecRestoreArray(user->ci,&ci_p);
1023: */
1024: MatAssemblyBegin(M_0,MAT_FINAL_ASSEMBLY);
1025: MatAssemblyEnd(M_0,MAT_FINAL_ASSEMBLY);
1027: MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);
1028: MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);
1030: DMDARestoreElements(user->da1,&nele,&nen,&ele);
1031: return(0);
1032: }
1037: PetscErrorCode UpdateMatrices(AppCtx *user)
1038: {
1040: PetscInt i,n,Mda,Nda,nele,nen;
1041: const PetscInt *ele;
1043: PetscInt idx[3];
1044: PetscScalar eM_2_odd[3][3],eM_2_even[3][3],h,dt=user->dt;
1045: Mat M=user->M;
1046: PetscScalar *cv_p,*ci_p,cv_sum,ci_sum;
1047: /* newly added */
1048: Vec cvlocal,cilocal;
1051: MatGetLocalSize(M,&n,NULL);
1053: /* new stuff */
1054: DMGetLocalVector(user->da2,&cvlocal);
1055: DMGetLocalVector(user->da2,&cilocal);
1056: DMGlobalToLocalBegin(user->da2,user->cv,INSERT_VALUES,cvlocal);
1057: DMGlobalToLocalEnd(user->da2,user->cv,INSERT_VALUES,cvlocal);
1058: DMGlobalToLocalBegin(user->da2,user->ci,INSERT_VALUES,cilocal);
1059: DMGlobalToLocalEnd(user->da2,user->ci,INSERT_VALUES,cilocal);
1060: /* new stuff */
1061: VecGetArray(cvlocal,&cv_p);
1062: VecGetArray(cilocal,&ci_p);
1064: /* old stuff */
1065: /*
1066: VecGetArray(user->cv,&cv_p);
1067: VecGetArray(user->ci,&ci_p);
1068: */
1069: DMDAGetInfo(user->da1,NULL,&Mda,&Nda,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL);
1073: h = (user->xmax-user->xmin)/Mda;
1075: DMDAGetElements(user->da1,&nele,&nen,&ele);
1077: for (i=0; i < nele; i++) {
1078: /*
1079: idx[0] = connect[k*3];
1080: idx[1] = connect[k*3+1];
1081: idx[2] = connect[k*3+2];
1082: */
1083: idx[0] = ele[3*i];
1084: idx[1] = ele[3*i+1];
1085: idx[2] = ele[3*i+2];
1087: PetscInt r,row,cols[3];
1088: PetscScalar vals[3];
1089: for (r=0; r<3; r++) {
1090: row = 5*idx[r];
1091: cols[0] = 5*idx[0]; vals[0] = 0.0;
1092: cols[1] = 5*idx[1]; vals[1] = 0.0;
1093: cols[2] = 5*idx[2]; vals[2] = 0.0;
1095: /* Insert values in matrix M for 1st dof */
1096: MatSetValuesLocal(M,1,&row,3,cols,vals,INSERT_VALUES);
1098: row = 5*idx[r]+2;
1099: cols[0] = 5*idx[0]+2; vals[0] = 0.0;
1100: cols[1] = 5*idx[1]+2; vals[1] = 0.0;
1101: cols[2] = 5*idx[2]+2; vals[2] = 0.0;
1103: /* Insert values in matrix M for 3nd dof */
1104: MatSetValuesLocal(M,1,&row,3,cols,vals,INSERT_VALUES);
1105: }
1106: }
1108: MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);
1109: MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);
1111: eM_2_odd[0][0] = 1.0;
1112: eM_2_odd[1][1] = eM_2_odd[2][2] = 0.5;
1113: eM_2_odd[0][1] = eM_2_odd[0][2] = eM_2_odd[1][0]= eM_2_odd[2][0] = -0.5;
1114: eM_2_odd[1][2] = eM_2_odd[2][1] = 0.0;
1116: eM_2_even[0][0] = 1.0;
1117: eM_2_even[1][1] = eM_2_even[2][2] = 0.5;
1118: eM_2_even[0][1] = eM_2_even[0][2] = eM_2_even[1][0]= eM_2_even[2][0] = -0.5;
1119: eM_2_even[1][2] = eM_2_even[2][1] = 0.0;
1121: /*
1122: eM_2_even[1][1] = 1.0;
1123: eM_2_even[0][0] = eM_2_even[2][2] = 0.5;
1124: eM_2_even[0][1] = eM_2_even[1][0] = eM_2_even[1][2] = eM_2_even[2][1] = -0.5;
1125: eM_2_even[0][2] = eM_2_even[2][0] = 0.0;
1126: */
1128: /* Get local element info */
1129: /* for (k=0;k < Mda*Nda*2;k++) { */
1130: for (i=0; i < nele; i++) {
1131: /*
1132: idx[0] = connect[k*3];
1133: idx[1] = connect[k*3+1];
1134: idx[2] = connect[k*3+2];
1135: */
1136: idx[0] = ele[3*i];
1137: idx[1] = ele[3*i+1];
1138: idx[2] = ele[3*i+2];
1140: PetscInt row,cols[3],r;
1141: PetscScalar vals[3];
1143: for (r=0; r<3; r++) {
1145: if (user->degenerate) {
1146: printf("smallnumber = %14.12f\n",user->smallnumber);
1147: cv_sum = (user->smallnumber + cv_p[idx[0]] + cv_p[idx[1]] + cv_p[idx[2]])*user->Dv/(3.0*user->kBT);
1148: ci_sum = (user->smallnumber + ci_p[idx[0]] + ci_p[idx[1]] + ci_p[idx[2]])*user->Di/(3.0*user->kBT);
1149: } else {
1150: cv_sum = user->initv*user->Dv/(user->kBT);
1151: ci_sum = user->initv*user->Di/user->kBT;
1152: }
1154: row = 5*idx[r];
1155: cols[0] = 5*idx[0]; vals[0] = dt*eM_2_odd[r][0]*cv_sum;
1156: cols[1] = 5*idx[1]; vals[1] = dt*eM_2_odd[r][1]*cv_sum;
1157: cols[2] = 5*idx[2]; vals[2] = dt*eM_2_odd[r][2]*cv_sum;
1159: /* Insert values in matrix M for 1st dof */
1160: MatSetValuesLocal(M,1,&row,3,cols,vals,ADD_VALUES);
1162: row = 5*idx[r]+2;
1163: cols[0] = 5*idx[0]+2; vals[0] = dt*eM_2_odd[r][0]*ci_sum;
1164: cols[1] = 5*idx[1]+2; vals[1] = dt*eM_2_odd[r][1]*ci_sum;
1165: cols[2] = 5*idx[2]+2; vals[2] = dt*eM_2_odd[r][2]*ci_sum;
1167: MatSetValuesLocal(M,1,&row,3,cols,vals,ADD_VALUES);
1168: }
1169: }
1171: /* new stuff */
1172: VecRestoreArray(cvlocal,&cv_p);
1173: VecRestoreArray(cilocal,&ci_p);
1174: DMRestoreLocalVector(user->da2,&cvlocal);
1175: DMRestoreLocalVector(user->da2,&cilocal);
1176: /* old stuff */
1177: /*
1178: VecRestoreArray(user->cv,&cv_p);
1179: VecRestoreArray(user->ci,&ci_p);
1180: */
1182: MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);
1183: MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);
1184: return(0);
1185: }
1191: PetscErrorCode Phi(AppCtx *user)
1192: {
1193: PetscErrorCode ierr;
1194: PetscScalar xmid, xqu, lambda, h,x[3],y[3];
1195: Vec coords;
1196: const PetscScalar *_coords;
1197: PetscInt nele,nen,i,idx[3],Mda,Nda;
1198: const PetscInt *ele;
1199: PetscViewer view;
1202: DMDAGetInfo(user->da1,NULL,&Mda,&Nda,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL);
1203: DMGetCoordinatesLocal(user->da2,&coords);
1204: VecGetArrayRead(coords,&_coords);
1206: h = (user->xmax - user->xmin)/Mda;
1207: xmid = (user->xmin + user->xmax)/2.0;
1208: xqu = (user->xmin + xmid)/2.0;
1209: lambda = 4.0*h;
1212: DMDAGetElements(user->da2,&nele,&nen,&ele);
1213: for (i=0; i < nele; i++) {
1214: idx[0] = ele[3*i]; idx[1] = ele[3*i+1]; idx[2] = ele[3*i+2];
1215: /* printf("idx[0]=%d,idx[1]=%d,idx[2]=%d\n",idx[0],idx[1],idx[2]); */
1217: x[0] = _coords[2*idx[0]]; y[0] = _coords[2*idx[0]+1];
1218: x[1] = _coords[2*idx[1]]; y[1] = _coords[2*idx[1]+1];
1219: x[2] = _coords[2*idx[2]]; y[2] = _coords[2*idx[2]+1];
1221: /*printf("x[0]=%f,x[1]=%f,x[2]=%f\n",x[0],x[1],x[2]);*/
1222: /*printf("y[0]=%f,y[1]=%f,y[2]=%f\n",y[0],y[1],y[2]);*/
1224: PetscScalar vals1[3],vals2[3],dist1,dist2,s1,r,hhr,xc1,xc2;
1225: PetscInt k;
1227: xc1 = user->xmin;
1228: xc2 = xmid;
1230: /*VecSet(user->phi1,0.0);*/
1231: for (k=0; k < 3; k++) {
1232: if (x[k]-xqu > 0) s1 = (x[k] - xqu);
1233: else s1 = -(x[k] - xqu);
1235: if (x[k] - xc1 > 0) dist1 = (x[k] - xc1);
1236: else dist1 = -(x[k] - xc1);
1238: if (x[k] - xc2 > 0) dist2 = (x[k] - xc2);
1239: else dist2 = -(x[k] - xc2);
1241: if (dist1 <= 0.5*lambda) {
1242: r = (x[k]-xc1)/(0.5*lambda);
1243: hhr = 0.25*(-r*r*r + 3.0*r + 2.0);
1244: vals1[k] = hhr;
1245: } else if (dist2 <= 0.5*lambda) {
1246: r = (x[k]-xc2)/(0.5*lambda);
1247: hhr = 0.25*(-r*r*r + 3.0*r + 2.0);
1248: vals1[k] = 1.0 - hhr;
1249: } else if (s1 <= xqu - 2.0*h) vals1[k] = 1.0;
1250: /*else if (abs(x[k]-(user->xmax-h)) < 0.1*h) {*/
1251: else if ((user->xmax-h)-x[k] < 0.1*h) vals1[k] = .15625;
1252: else vals1[k] = 0.0;
1253: }
1255: VecSetValuesLocal(user->phi1,3,idx,vals1,INSERT_VALUES);
1257: xc1 = xmid;
1258: xc2 = user->xmax;
1260: /*VecSet(user->phi2,0.0);*/
1261: for (k=0;k < 3; k++) {
1262: /*
1263: s1 = abs(x[k] - (xqu+xmid));
1264: dist1 = abs(x[k] - xc1);
1265: dist2 = abs(x[k] - xc2);
1266: */
1267: if (x[k]-(xqu + xmid) > 0) s1 = (x[k] - (xqu + xmid));
1268: else s1 = -(x[k] - (xqu + xmid));
1270: if (x[k] - xc1 > 0) dist1 = (x[k] - xc1);
1271: else dist1 = -(x[k] - xc1);
1273: if (x[k] - xc2 > 0) dist2 = (x[k] - xc2);
1274: else dist2 = -(x[k] - xc2);
1276: if (dist1 <= 0.5*lambda) {
1277: r = (x[k]-xc1)/(0.5*lambda);
1278: hhr = 0.25*(-r*r*r + 3.0*r + 2.0);
1279: vals2[k] = hhr;
1280: } else if (dist2 <= 0.5*lambda) {
1281: r = -(x[k]-xc2)/(0.5*lambda);
1282: hhr = 0.25*(-r*r*r + 3.0*r + 2.0);
1283: vals2[k] = hhr;
1284: } else if (s1 <= xqu - 2.0*h) vals2[k] = 1.0;
1285: else if (x[k]-(user->xmin) < 0.1*h) vals2[k] = 0.5;
1286: else if ((x[k]-(user->xmin+h)) < 0.1*h) vals2[k] = .15625;
1287: else vals2[k] = 0.0;
1289: }
1291: VecSetValuesLocal(user->phi2,3,idx,vals2,INSERT_VALUES);
1292: /*
1293: for (k=0;k < 3; k++) {
1294: vals_sum[k] = vals1[k]*vals1[k] + vals2[k]*vals2[k];
1295: }
1296: */
1297: /*VecSetValuesLocal(user->Phi2D_V,3,idx,vals_sum,INSERT_VALUES);*/
1299: }
1301: VecAssemblyBegin(user->phi1);
1302: VecAssemblyEnd(user->phi1);
1303: VecAssemblyBegin(user->phi2);
1304: VecAssemblyEnd(user->phi2);
1305: PetscViewerBinaryOpen(PETSC_COMM_WORLD,"file_phi",FILE_MODE_WRITE,&view);
1307: VecView(user->phi1,view);
1308: VecView(user->phi2,view);
1311: /*VecView(user->phi1,0);*/
1312: /*VecView(user->phi2,0);*/
1314: VecPointwiseMult(user->phi1,user->phi1,user->phi1);
1315: VecPointwiseMult(user->phi2,user->phi2,user->phi2);
1316: VecView(user->phi1,view);
1317: VecView(user->phi2,view);
1319: VecCopy(user->phi1,user->Phi2D_V);
1320: VecAXPY(user->Phi2D_V,1.0,user->phi2);
1321: /*VecView(user->Phi2D_V,0);*/
1323: VecView(user->Phi2D_V,view);
1324: PetscViewerDestroy(&view);
1325: /* VecNorm(user->Phi2D_V,NORM_INFINITY,&max1);*/
1326: /*VecMin(user->Phi2D_V,&loc1,&min1);*/
1327: /*printf("norm phi = %f, min phi = %f\n",max1,min1);*/
1328: return(0);
1329: }
1333: PetscErrorCode Phi_read(AppCtx *user)
1334: {
1336: PetscReal *values;
1337: PetscViewer viewer;
1340: VecGetArray(user->Phi2D_V,&values);
1341: PetscViewerBinaryOpen(PETSC_COMM_WORLD,"phi3",FILE_MODE_READ,&viewer);
1342: PetscViewerBinaryRead(viewer,values,16384,PETSC_DOUBLE);
1343: PetscViewerDestroy(&viewer);
1344: return(0);
1345: }