Actual source code: ex61.c
petsc-3.5.4 2015-05-23
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,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,DM_BOUNDARY_PERIODIC,DM_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,DM_BOUNDARY_PERIODIC,DM_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: DMSetMatType(user.da1,MATAIJ);
172: DMCreateMatrix(user.da1,&user.M);
173: /* Get the (usual) mass matrix structure from da2 */
174: DMSetMatType(user.da2,MATAIJ);
175: DMCreateMatrix(user.da2,&user.M_0);
176: SetInitialGuess(x,&user);
177: /* twodomain modeling */
178: if (user.domain) {
179: switch (user.domain) {
180: case 1:
181: Phi(&user);
182: break;
183: case 2:
184: Phi_read(&user);
185: break;
186: }
187: }
189: /* Form the jacobian matrix and M_0 */
190: SetUpMatrices(&user);
191: MatDuplicate(user.M,MAT_DO_NOT_COPY_VALUES,&J);
193: SNESCreate(PETSC_COMM_WORLD,&snes);
194: SNESSetDM(snes,user.da1);
196: SNESSetFunction(snes,r,FormFunction,(void*)&user);
197: SNESSetJacobian(snes,J,J,FormJacobian,(void*)&user);
200: SetVariableBounds(user.da1,xl,xu);
201: SNESVISetVariableBounds(snes,xl,xu);
202: SNESSetTolerances(snes,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT,100,PETSC_DEFAULT);
203: SNESSetFromOptions(snes);
205: /* PetscViewerBinaryOpen(PETSC_COMM_WORLD,"file_rand",FILE_MODE_WRITE,&view_rand);
206: PetscViewerBinaryOpen(PETSC_COMM_WORLD,"file_mat2",FILE_MODE_WRITE,&view_mat);
207: PetscViewerBinaryOpen(PETSC_COMM_WORLD,"file_q",FILE_MODE_WRITE,&view_q);
208: PetscViewerBinaryOpen(PETSC_COMM_WORLD,"file_out",FILE_MODE_WRITE,&view_out);
209: PetscViewerBinaryOpen(PETSC_COMM_WORLD,"file_psi",FILE_MODE_WRITE,&view_psi);*/
211: /*PetscViewerBinaryOpen(PETSC_COMM_WORLD,"file_out",FILE_MODE_WRITE,&view_out);
213: PetscViewerBinaryOpen(PETSC_COMM_WORLD,"file_cv",FILE_MODE_WRITE,&view_cv);
214: PetscViewerBinaryOpen(PETSC_COMM_WORLD,"file_eta",FILE_MODE_WRITE,&view_eta);*/
216: /* PetscViewerDrawSetBounds(PETSC_VIEWER_DRAW_(PETSC_COMM_WORLD),5,bounds); */
217: if (user.graphics) {
218: VecView(x,PETSC_VIEWER_DRAW_(PETSC_COMM_WORLD));
219: }
220: /*
221: if (user.graphicsfile) {
222: DMView(user.da1,user.graphicsfile);
223: VecView(x,user.graphicsfile);
224: }
225: */
226: while (t<user.T) {
227: SNESSetFunction(snes,r,FormFunction,(void*)&user);
228: SNESSetJacobian(snes,J,J,FormJacobian,(void*)&user);
230: SetRandomVectors(&user,t);
231: /* VecView(user.Pv,view_rand);
232: VecView(user.Pi,view_rand);
233: VecView(user.Piv,view_rand);*/
235: DPsi(&user);
236: /* VecView(user.DPsiv,view_psi);
237: VecView(user.DPsii,view_psi);
238: VecView(user.DPsieta,view_psi);*/
240: Update_q(&user);
242: /* VecView(user.q,view_q);*/
243: /* MatView(user.M,view_mat);*/
247: sprintf(cv_filename,"file_cv_%f.vtk",t);
248: sprintf(eta_filename,"file_eta_%f.vtk",t);
249: /* PetscViewerASCIIOpen(PETSC_COMM_WORLD,cv_filename,&view_vtk_cv);
250: PetscViewerASCIIOpen(PETSC_COMM_WORLD,eta_filename,&view_vtk_eta);
251: PetscViewerSetFormat(view_vtk_cv, PETSC_VIEWER_ASCII_VTK);
252: PetscViewerSetFormat(view_vtk_eta, PETSC_VIEWER_ASCII_VTK);
253: DMView(user.da2,view_vtk_cv);
254: DMView(user.da2,view_vtk_eta);
255: VecView(user.cv,view_cv);
256: VecView(user.eta,view_eta);
257: VecView(user.cv,view_vtk_cv);
258: VecView(user.eta,view_vtk_eta);
259: PetscViewerDestroy(&view_vtk_cv);
260: PetscViewerDestroy(&view_vtk_eta);*/
263: VecNorm(user.q,NORM_2,&normq);
264: printf("2-norm of q = %14.12f\n",normq);
265: SNESSolve(snes,NULL,x);
266: SNESGetConvergedReason(snes,&reason);
267: if (reason < 0) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_CONV_FAILED,"Nonlinear solver failed");
268: SNESVIGetInactiveSet(snes,&inactiveconstraints);
269: ISGetSize(inactiveconstraints,&ninactiveconstraints);
270: /* if (ninactiveconstraints < .90*N) SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_SUP,"To many active constraints, model has become non-physical"); */
272: /* VecView(x,view_out);*/
273: if (user.graphics) {
274: VecView(x,PETSC_VIEWER_DRAW_(PETSC_COMM_WORLD));
275: }
276: /* VecView(x,PETSC_VIEWER_BINARY_(PETSC_COMM_WORLD));*/
277: PetscInt its;
278: SNESGetIterationNumber(snes,&its);
279: PetscPrintf(PETSC_COMM_WORLD,"SNESVI solver converged at t = %g in %d iterations\n",t,its);
281: Update_u(x,&user);
282: UpdateMatrices(&user);
283: t = t + user.dt;
284: /*
285: if (user.graphicsfile) {
286: VecView(x,user.graphicsfile);
287: }
288: */
289: }
291: /* PetscViewerDestroy(&view_rand);
292: PetscViewerDestroy(&view_mat);
293: PetscViewerDestroy(&view_q);
294: PetscViewerDestroy(&view_out);
295: PetscViewerDestroy(&view_psi);
296: PetscViewerDestroy(&view_out);
298: PetscViewerDestroy(&view_cv);
299: PetscViewerDestroy(&view_eta);*/
301: if (user.graphicsfile) {
302: PetscViewerDestroy(&user.graphicsfile);
303: }
305: VecDestroy(&x);
306: VecDestroy(&r);
307: VecDestroy(&xl);
308: VecDestroy(&xu);
309: VecDestroy(&user.q);
310: VecDestroy(&user.wv);
311: VecDestroy(&user.cv);
312: VecDestroy(&user.wi);
313: VecDestroy(&user.ci);
314: VecDestroy(&user.eta);
315: VecDestroy(&user.cvi);
316: VecDestroy(&user.DPsiv);
317: VecDestroy(&user.DPsii);
318: VecDestroy(&user.DPsieta);
319: VecDestroy(&user.Pv);
320: VecDestroy(&user.Pi);
321: VecDestroy(&user.Piv);
322: VecDestroy(&user.logcv);
323: VecDestroy(&user.logci);
324: VecDestroy(&user.logcvi);
325: VecDestroy(&user.work1);
326: VecDestroy(&user.work2);
327: VecDestroy(&user.Riv);
328: MatDestroy(&user.M);
329: MatDestroy(&user.M_0);
330: DMDestroy(&user.da1);
331: DMDestroy(&user.da2);
334: PetscFinalize();
335: return 0;
336: }
340: PetscErrorCode Update_u(Vec X,AppCtx *user)
341: {
343: PetscInt i,n;
344: PetscScalar *xx,*wv_p,*cv_p,*wi_p,*ci_p,*eta_p;
347: VecGetLocalSize(user->wv,&n);
348: VecGetArray(X,&xx);
349: VecGetArray(user->wv,&wv_p);
350: VecGetArray(user->cv,&cv_p);
351: VecGetArray(user->wi,&wi_p);
352: VecGetArray(user->ci,&ci_p);
353: VecGetArray(user->eta,&eta_p);
356: for (i=0; i<n; i++) {
357: wv_p[i] = xx[5*i];
358: cv_p[i] = xx[5*i+1];
359: wi_p[i] = xx[5*i+2];
360: ci_p[i] = xx[5*i+3];
361: eta_p[i] = xx[5*i+4];
362: }
363: VecRestoreArray(X,&xx);
364: VecRestoreArray(user->wv,&wv_p);
365: VecRestoreArray(user->cv,&cv_p);
366: VecRestoreArray(user->wi,&wi_p);
367: VecRestoreArray(user->ci,&ci_p);
368: VecRestoreArray(user->eta,&eta_p);
369: return(0);
370: }
374: PetscErrorCode Update_q(AppCtx *user)
375: {
377: PetscScalar *q_p,*w1,*w2,max1;
378: PetscInt i,n;
381: VecPointwiseMult(user->Riv,user->eta,user->eta);
382: VecScale(user->Riv,user->Rsurf);
383: VecShift(user->Riv,user->Rbulk);
384: VecPointwiseMult(user->Riv,user->ci,user->Riv);
385: VecPointwiseMult(user->Riv,user->cv,user->Riv);
387: VecCopy(user->Riv,user->work1);
388: if (user->radiation) {
389: VecAXPY(user->work1,-1.0,user->Pv);
390: }
391: if (user->domain) {
392: VecCopy(user->cv,user->work3);
393: VecShift(user->work3,-1.0*user->cv_eq);
394: VecCopy(user->Phi2D_V,user->work4);
395: VecScale(user->work4,-1.0);
396: VecShift(user->work4,1.0);
397: VecPointwiseMult(user->work4,user->work4,user->work3);
398: VecScale(user->work4,user->Svr);
399: VecAXPY(user->work1,300.0,user->work4);
400: }
401: VecScale(user->work1,user->dt);
402: VecAXPY(user->work1,-1.0,user->cv);
403: MatMult(user->M_0,user->work1,user->work2);
405: VecGetArray(user->q,&q_p);
406: VecGetArray(user->work1,&w1);
407: VecGetArray(user->work2,&w2);
408: VecGetLocalSize(user->wv,&n);
409: for (i=0; i<n; i++) q_p[5*i]=w2[i];
411: MatMult(user->M_0,user->DPsiv,user->work1);
412: for (i=0; i<n; i++) q_p[5*i+1]=w1[i];
414: VecCopy(user->Riv,user->work1);
415: if (user->radiation) {
416: VecAXPY(user->work1,-1.0,user->Pi);
417: }
418: if (user->domain) {
419: VecCopy(user->ci,user->work3);
420: VecShift(user->work3,-1.0*user->ci_eq);
421: VecCopy(user->Phi2D_V,user->work4);
422: VecScale(user->work4,-1.0);
423: VecShift(user->work4,1.0);
424: VecPointwiseMult(user->work4,user->work4,user->work3);
425: VecScale(user->work4,user->Sir);
426: VecAXPY(user->work1,300.0,user->work4);
427: }
428: VecScale(user->work1,user->dt);
429: VecAXPY(user->work1,-1.0,user->ci);
430: MatMult(user->M_0,user->work1,user->work2);
431: for (i=0; i<n; i++) q_p[5*i+2]=w2[i];
433: MatMult(user->M_0,user->DPsii,user->work1);
434: for (i=0; i<n; i++) q_p[5*i+3]=w1[i];
436: VecCopy(user->DPsieta,user->work1);
437: VecScale(user->work1,user->L);
438: VecAXPY(user->work1,-1.0/user->dt,user->eta);
439: if (user->radiation) {
440: VecAXPY(user->work1,-1.0,user->Piv);
441: }
442: MatMult(user->M_0,user->work1,user->work2);
443: for (i=0; i<n; i++) q_p[5*i+4]=w2[i];
445: VecRestoreArray(user->q,&q_p);
446: VecRestoreArray(user->work1,&w1);
447: VecRestoreArray(user->work2,&w2);
448: return(0);
449: }
453: PetscErrorCode DPsi(AppCtx *user)
454: {
456: PetscScalar Evf=user->Evf,Eif=user->Eif,kBT=user->kBT,A=user->A;
457: PetscScalar *cv_p,*ci_p,*eta_p,*logcv_p,*logci_p,*logcvi_p,*DPsiv_p,*DPsii_p,*DPsieta_p;
458: PetscInt n,i;
461: VecGetLocalSize(user->cv,&n);
462: VecGetArray(user->cv,&cv_p);
463: VecGetArray(user->ci,&ci_p);
464: VecGetArray(user->eta,&eta_p);
465: VecGetArray(user->logcv,&logcv_p);
466: VecGetArray(user->logci,&logci_p);
467: VecGetArray(user->logcvi,&logcvi_p);
468: VecGetArray(user->DPsiv,&DPsiv_p);
469: VecGetArray(user->DPsii,&DPsii_p);
470: VecGetArray(user->DPsieta,&DPsieta_p);
472: Llog(user->cv,user->logcv);
474: Llog(user->ci,user->logci);
477: VecCopy(user->cv,user->cvi);
478: VecAXPY(user->cvi,1.0,user->ci);
479: VecScale(user->cvi,-1.0);
480: VecShift(user->cvi,1.0);
481: Llog(user->cvi,user->logcvi);
483: for (i=0; i<n; i++) {
484: 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);
485: 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];
487: 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]);
488: }
490: VecRestoreArray(user->cv,&cv_p);
491: VecRestoreArray(user->ci,&ci_p);
492: VecRestoreArray(user->eta,&eta_p);
493: VecRestoreArray(user->logcv,&logcv_p);
494: VecRestoreArray(user->logci,&logci_p);
495: VecRestoreArray(user->logcvi,&logcvi_p);
496: VecRestoreArray(user->DPsiv,&DPsiv_p);
497: VecRestoreArray(user->DPsii,&DPsii_p);
498: VecRestoreArray(user->DPsieta,&DPsieta_p);
499: return(0);
500: }
505: PetscErrorCode Llog(Vec X, Vec Y)
506: {
508: PetscScalar *x,*y;
509: PetscInt n,i;
512: VecGetArray(X,&x);
513: VecGetArray(Y,&y);
514: VecGetLocalSize(X,&n);
515: for (i=0; i<n; i++) {
516: if (x[i] < 1.0e-12) y[i] = log(1.0e-12);
517: else y[i] = log(x[i]);
518: }
519: return(0);
520: }
525: PetscErrorCode SetInitialGuess(Vec X,AppCtx *user)
526: {
528: PetscInt n,i,Mda,Nda;
529: PetscScalar *xx,*cv_p,*ci_p,*wv_p,*wi_p,*eta;
531: /* needed for the void growth case */
532: 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;
533: PetscInt nele,nen,idx[3];
534: const PetscInt *ele;
535: PetscScalar x[3],y[3];
536: Vec coords;
537: const PetscScalar *_coords;
538: PetscViewer view;
539: PetscScalar xwidth = user->xmax - user->xmin;
542: VecGetLocalSize(X,&n);
544: if (user->voidgrowth) {
545: DMDAGetInfo(user->da2,NULL,&Mda,&Nda,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL);
546: DMGetCoordinatesLocal(user->da2,&coords);
547: VecGetArrayRead(coords,&_coords);
549: h = (user->xmax-user->xmin)/Mda;
550: xmid = (user->xmax + user->xmin)/2.0;
551: ymid = (user->ymax + user->ymin)/2.0;
552: lambda = 4.0*h;
554: DMDAGetElements(user->da2,&nele,&nen,&ele);
555: for (i=0; i < nele; i++) {
556: idx[0] = ele[3*i]; idx[1] = ele[3*i+1]; idx[2] = ele[3*i+2];
558: x[0] = _coords[2*idx[0]]; y[0] = _coords[2*idx[0]+1];
559: x[1] = _coords[2*idx[1]]; y[1] = _coords[2*idx[1]+1];
560: x[2] = _coords[2*idx[2]]; y[2] = _coords[2*idx[2]+1];
562: PetscInt k;
563: PetscScalar vals_cv[3],vals_ci[3],vals_eta[3],s,hhr,r;
564: for (k=0; k < 3; k++) {
565: s = PetscSqrtScalar((x[k] - xmid)*(x[k] - xmid) + (y[k] - ymid)*(y[k] - ymid));
566: if (s < xwidth*(5.0/64.0)) {
567: vals_cv[k] = cv_v;
568: vals_ci[k] = ci_v;
569: vals_eta[k] = eta_v;
570: } else if (s>= xwidth*(5.0/64.0) && s<= xwidth*(7.0/64.0)) {
571: /* r = (s - xwidth*(6.0/64.0))/(0.5*lambda); */
572: r = (s - xwidth*(6.0/64.0))/(xwidth/64.0);
573: hhr = 0.25*(-r*r*r + 3*r + 2);
574: vals_cv[k] = cv_m + (1.0 - hhr)*(cv_v - cv_m);
575: vals_ci[k] = ci_m + (1.0 - hhr)*(ci_v - ci_m);
576: vals_eta[k] = eta_m + (1.0 - hhr)*(eta_v - eta_m);
577: } else {
578: vals_cv[k] = cv_m;
579: vals_ci[k] = ci_m;
580: vals_eta[k] = eta_m;
581: }
582: }
583: VecSetValuesLocal(user->cv,3,idx,vals_cv,INSERT_VALUES);
584: VecSetValuesLocal(user->ci,3,idx,vals_ci,INSERT_VALUES);
585: VecSetValuesLocal(user->eta,3,idx,vals_eta,INSERT_VALUES);
586: }
587: VecAssemblyBegin(user->cv);
588: VecAssemblyEnd(user->cv);
589: VecAssemblyBegin(user->ci);
590: VecAssemblyEnd(user->ci);
591: VecAssemblyBegin(user->eta);
592: VecAssemblyEnd(user->eta);
594: DMDARestoreElements(user->da2,&nele,&nen,&ele);
595: VecRestoreArrayRead(coords,&_coords);
597: PetscViewerBinaryOpen(PETSC_COMM_WORLD,"file_initial",FILE_MODE_WRITE,&view);
598: VecView(user->cv,view);
599: VecView(user->ci,view);
600: VecView(user->eta,view);
601: PetscViewerDestroy(&view);
602: } else {
603: /* VecSet(user->cv,user->initv); */
604: /* VecSet(user->ci,user->initv); */
605: VecSet(user->cv,.05);
606: VecSet(user->ci,.05);
607: VecSet(user->eta,user->initeta);
608: }
610: DPsi(user);
611: VecCopy(user->DPsiv,user->wv);
612: VecCopy(user->DPsii,user->wi);
614: VecGetArray(X,&xx);
615: VecGetArray(user->cv,&cv_p);
616: VecGetArray(user->ci,&ci_p);
617: VecGetArray(user->wv,&wv_p);
618: VecGetArray(user->wi,&wi_p);
619: VecGetArray(user->eta,&eta);
620: for (i=0; i<n/5; i++) {
621: xx[5*i] =wv_p[i];
622: xx[5*i+1]=cv_p[i];
623: xx[5*i+2]=wi_p[i];
624: xx[5*i+3]=ci_p[i];
625: xx[5*i+4]=eta[i];
626: }
628: /* VecView(user->wv,view);
629: VecView(user->cv,view);
630: VecView(user->wi,view);
631: VecView(user->ci,view);
632: PetscViewerDestroy(&view);*/
634: VecRestoreArray(X,&xx);
635: VecRestoreArray(user->cv,&cv_p);
636: VecRestoreArray(user->ci,&ci_p);
637: VecRestoreArray(user->wv,&wv_p);
638: VecRestoreArray(user->wi,&wi_p);
639: VecRestoreArray(user->eta,&eta);
640: return(0);
641: }
643: typedef struct {
644: PetscReal dt,x,y,strength;
645: } RandomValues;
650: PetscErrorCode SetRandomVectors(AppCtx *user,PetscReal t)
651: {
652: PetscErrorCode ierr;
653: static RandomValues *randomvalues = 0;
654: static PetscInt randindex = 0,n; /* indicates how far into the randomvalues we have currently used */
655: static PetscReal randtime = 0; /* indicates time of last radiation event */
656: PetscInt i,j,M,N,cnt = 0;
657: PetscInt xs,ys,xm,ym;
660: if (!randomvalues) {
661: PetscViewer viewer;
662: char filename[PETSC_MAX_PATH_LEN];
663: PetscBool flg;
664: PetscInt seed;
666: PetscOptionsGetInt(NULL,"-random_seed",&seed,&flg);
667: if (flg) {
668: sprintf(filename,"ex61.random.%d",(int)seed);
669: } else {
670: PetscStrcpy(filename,"ex61.random");
671: }
672: PetscViewerBinaryOpen(PETSC_COMM_WORLD,filename,FILE_MODE_READ,&viewer);
673: PetscViewerBinaryRead(viewer,&n,1,PETSC_INT);
674: PetscMalloc1(n,&randomvalues);
675: PetscViewerBinaryRead(viewer,randomvalues,4*n,PETSC_DOUBLE);
676: for (i=0; i<n; i++) randomvalues[i].dt = randomvalues[i].dt*user->dtevent;
677: PetscViewerDestroy(&viewer);
678: }
679: user->maxevents = PetscMin(user->maxevents,n);
681: VecSet(user->Pv,0.0);
682: DMDAGetInfo(user->da1,0,&M,&N,0,0,0,0,0,0,0,0,0,0);
683: DMDAGetGhostCorners(user->da1,&xs,&ys,0,&xm,&ym,0);
684: while (user->maxevents > randindex && randtime + randomvalues[randindex].dt < t + user->dt) { /* radiation event has occured since last time step */
685: i = ((PetscInt) (randomvalues[randindex].x*M)) - xs;
686: j = ((PetscInt) (randomvalues[randindex].y*N)) - ys;
687: if (i >= 0 && i < xm && j >= 0 && j < ym) { /* point is on this process */
688: /* need to make sure eta at the given point is not great than .8 */
689: VecSetValueLocal(user->Pv,i + 1 + xm*(j + 1), randomvalues[randindex].strength*user->VG,INSERT_VALUES);
690: }
691: randtime += randomvalues[randindex++].dt;
692: cnt++;
693: }
694: PetscPrintf(PETSC_COMM_WORLD,"Number of radiation events %d\n",cnt);
695: VecAssemblyBegin(user->Pv);
696: VecAssemblyEnd(user->Pv);
698: VecCopy(user->Pv,user->Pi);
699: VecScale(user->Pi,0.9);
700: VecPointwiseMult(user->Piv,user->Pi,user->Pv);
701: return(0);
702: }
706: PetscErrorCode FormFunction(SNES snes,Vec X,Vec F,void *ctx)
707: {
709: AppCtx *user=(AppCtx*)ctx;
712: MatMultAdd(user->M,X,user->q,F);
713: return(0);
714: }
718: PetscErrorCode FormJacobian(SNES snes,Vec X,Mat J,Mat B,void *ctx)
719: {
721: AppCtx *user=(AppCtx*)ctx;
724: MatCopy(user->M,J,*flg);
725: MatAssemblyBegin(J,MAT_FINAL_ASSEMBLY);
726: MatAssemblyEnd(J,MAT_FINAL_ASSEMBLY);
727: return(0);
728: }
732: PetscErrorCode SetVariableBounds(DM da,Vec xl,Vec xu)
733: {
735: PetscScalar ***l,***u;
736: PetscInt xs,xm,ys,ym;
737: PetscInt j,i;
740: DMDAVecGetArrayDOF(da,xl,&l);
741: DMDAVecGetArrayDOF(da,xu,&u);
743: DMDAGetCorners(da,&xs,&ys,NULL,&xm,&ym,NULL);
745: for (j=ys; j<ys+ym; j++) {
746: for (i=xs; i < xs+xm; i++) {
747: l[j][i][0] = -PETSC_INFINITY;
748: l[j][i][1] = 0.0;
749: l[j][i][2] = -PETSC_INFINITY;
750: l[j][i][3] = 0.0;
751: l[j][i][4] = 0.0;
752: u[j][i][0] = PETSC_INFINITY;
753: u[j][i][1] = 1.0;
754: u[j][i][2] = PETSC_INFINITY;
755: u[j][i][3] = 1.0;
756: u[j][i][4] = 1.0;
757: }
758: }
761: DMDAVecRestoreArrayDOF(da,xl,&l);
762: DMDAVecRestoreArrayDOF(da,xu,&u);
763: return(0);
764: }
768: PetscErrorCode GetParams(AppCtx *user)
769: {
771: PetscBool flg,graphicsfile = PETSC_FALSE;
774: /* Set default parameters */
775: user->xmin = 0.0; user->xmax = 128.0;
776: user->ymin = 0.0; user->ymax = 128.0;
777: user->Dv = 1.0;
778: user->Di = 4.0;
779: user->Evf = 0.8;
780: user->Eif = 1.2;
781: user->A = 1.0;
782: user->kBT = 0.11;
783: user->kav = 1.0;
784: user->kai = 1.0;
785: user->kaeta = 1.0;
786: user->Rsurf = 10.0;
787: user->Rbulk = 1.0;
788: user->VG = 100.0;
789: user->L = 10.0;
791: user->T = 1.0e-2;
792: user->dt = 1.0e-4;
793: user->initv = .00069;
794: user->initeta = 0.0;
795: user->degenerate = PETSC_FALSE;
796: user->maxevents = 10;
797: user->graphics = PETSC_TRUE;
799: /* multidomain modeling */
800: user->domain = 1;
801: user->Svr = 0.5;
802: user->Sir = 0.5;
803: user->cv_eq = 6.9e-4;
804: user->ci_eq = 6.9e-4;
805: /* void growth */
806: user->voidgrowth = PETSC_FALSE;
808: user->radiation = PETSC_FALSE;
810: /* degenerate mobility */
811: user->smallnumber = 1.0e-3;
813: PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"Coupled Cahn-Hillard/Allen-Cahn Equations","Phasefield");
814: PetscOptionsInt("-domain","Number of domains (0=one domain, 1=two domains, 2=multidomain\n","None",user->domain,&user->domain,&flg);
816: PetscOptionsReal("-Dv","Vacancy Diffusivity\n","None",user->Dv,&user->Dv,&flg);
817: PetscOptionsReal("-Di","Interstitial Diffusivity\n","None",user->Di,&user->Di,&flg);
818: PetscOptionsReal("-Evf","Vacancy Formation Energy\n","None",user->Evf,&user->Evf,&flg);
819: PetscOptionsReal("-Eif","Interstitial Formation energy\n","None",user->Eif,&user->Eif,&flg);
820: PetscOptionsReal("-A","???","None",user->A,&user->A,&flg);
821: PetscOptionsReal("-kBT","Boltzmann's Constant times the Absolute Temperature","None",user->kBT,&user->kBT,&flg);
822: PetscOptionsReal("-kav","???","None",user->kav,&user->kav,&flg);
823: PetscOptionsReal("-kai","???","None",user->kai,&user->kai,&flg);
824: PetscOptionsReal("-kaeta","???","None",user->kaeta,&user->kaeta,&flg);
825: PetscOptionsReal("-Rsurf","???","None",user->Rsurf,&user->Rsurf,&flg);
826: PetscOptionsReal("-Rbulk","???","None",user->Rbulk,&user->Rbulk,&flg);
827: PetscOptionsReal("-VG","Maximum increase in vacancy (or interstitial) concentration due to a cascade event","None",user->VG,&user->VG,&flg);
828: PetscOptionsReal("-L","???","None",user->L,&user->L,&flg);
830: PetscOptionsReal("-initv","Initial solution of Cv and Ci","None",user->initv,&user->initv,&flg);
831: PetscOptionsReal("-initeta","Initial solution of Eta","None",user->initeta,&user->initeta,&flg);
832: PetscOptionsBool("-degenerate","Run with degenerate mobility\n","None",user->degenerate,&user->degenerate,&flg);
833: PetscOptionsReal("-smallnumber","Small number added to degenerate mobility\n","None",user->smallnumber,&user->smallnumber,&flg);
835: PetscOptionsBool("-voidgrowth","Use initial conditions for void growth\n","None",user->voidgrowth,&user->voidgrowth,&flg);
836: PetscOptionsBool("-radiation","Use initial conditions for void growth\n","None",user->radiation,&user->radiation,&flg);
837: PetscOptionsReal("-xmin","Lower X coordinate of domain\n","None",user->xmin,&user->xmin,&flg);
838: PetscOptionsReal("-xmax","Upper X coordinate of domain\n","None",user->xmax,&user->xmax,&flg);
839: PetscOptionsReal("-T","Total runtime\n","None",user->T,&user->T,&flg);
840: PetscOptionsReal("-dt","Time step\n","None",user->dt,&user->dt,&flg);
842: user->dtevent = user->dt;
844: PetscOptionsReal("-dtevent","Average time between random events\n","None",user->dtevent,&user->dtevent,&flg);
845: PetscOptionsInt("-maxevents","Maximum random events allowed\n","None",user->maxevents,&user->maxevents,&flg);
847: PetscOptionsBool("-graphics","Contour plot solutions at each timestep\n","None",user->graphics,&user->graphics,&flg);
848: PetscOptionsBool("-graphicsfile","Save solution at each timestep\n","None",graphicsfile,&graphicsfile,&flg);
849: if (graphicsfile) {
850: PetscViewerBinaryOpen(PETSC_COMM_WORLD,"ex61.data",FILE_MODE_WRITE,&user->graphicsfile);
851: }
852: PetscOptionsEnd();
853: return(0);
854: }
859: PetscErrorCode SetUpMatrices(AppCtx *user)
860: {
862: PetscInt nele,nen,i,n;
863: const PetscInt *ele;
864: PetscScalar dt=user->dt,hx,hy;
866: PetscInt idx[3];
867: PetscScalar eM_0[3][3],eM_2_even[3][3],eM_2_odd[3][3];
868: PetscScalar cv_sum, ci_sum;
869: Mat M =user->M;
870: Mat M_0=user->M_0;
871: PetscInt Mda=user->Mda, Nda=user->Nda;
872: PetscScalar *cv_p,*ci_p;
873: /* newly added */
874: Vec cvlocal,cilocal;
877: /* MatSetOption(M,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);
878: MatSetOption(M_0,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);*/
880: /* new stuff */
881: DMGetLocalVector(user->da2,&cvlocal);
882: DMGetLocalVector(user->da2,&cilocal);
883: DMGlobalToLocalBegin(user->da2,user->cv,INSERT_VALUES,cvlocal);
884: DMGlobalToLocalEnd(user->da2,user->cv,INSERT_VALUES,cvlocal);
885: DMGlobalToLocalBegin(user->da2,user->ci,INSERT_VALUES,cilocal);
886: DMGlobalToLocalEnd(user->da2,user->ci,INSERT_VALUES,cilocal);
887: /* old stuff */
888: /*
889: VecGetArray(user->cv,&cv_p);
890: VecGetArray(user->ci,&ci_p);
891: */
892: /* new stuff */
893: VecGetArray(cvlocal,&cv_p);
894: VecGetArray(cilocal,&ci_p);
896: MatGetLocalSize(M,&n,NULL);
897: DMDAGetInfo(user->da1,NULL,&Mda,&Nda,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL);
898: hx = (user->xmax-user->xmin)/Mda;
899: hy = (user->ymax-user->ymin)/Nda;
901: eM_0[0][0]=eM_0[1][1]=eM_0[2][2]=hx*hy/12.0;
902: 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;
904: eM_2_odd[0][0] = 1.0;
905: eM_2_odd[1][1] = eM_2_odd[2][2] = 0.5;
906: eM_2_odd[0][1] = eM_2_odd[0][2] = eM_2_odd[1][0]= eM_2_odd[2][0] = -0.5;
907: eM_2_odd[1][2] = eM_2_odd[2][1] = 0.0;
909: eM_2_even[0][0] = 1.0;
910: eM_2_even[1][1] = eM_2_even[2][2] = 0.5;
911: eM_2_even[0][1] = eM_2_even[0][2] = eM_2_even[1][0]= eM_2_even[2][0] = -0.5;
912: eM_2_even[1][2] = eM_2_even[2][1] = 0.0;
914: /* eM_2_even[1][1] = 1.0;
915: eM_2_even[0][0] = eM_2_even[2][2] = 0.5;
916: eM_2_even[0][1] = eM_2_even[1][0] = eM_2_even[1][2] = eM_2_even[2][1] = -0.5;
917: eM_2_even[0][2] = eM_2_even[2][0] = 0.0;
918: */
920: /* for (k=0;k < Mda*Nda*2;k++) { */
921: DMDAGetElements(user->da1,&nele,&nen,&ele);
922: for (i=0; i < nele; i++) {
923: /*
924: idx[0] = connect[k*3];
925: idx[1] = connect[k*3+1];
926: idx[2] = connect[k*3+2];
927: */
928: idx[0] = ele[3*i];
929: idx[1] = ele[3*i+1];
930: idx[2] = ele[3*i+2];
932: PetscInt row,cols[6],r,row_M_0,cols3[3];
933: PetscScalar vals[6],vals_M_0[3],vals3[3];
935: for (r=0; r<3; r++) {
936: /* row_M_0 = connect[k*3+r]; */
937: row_M_0 = idx[r];
939: vals_M_0[0]=eM_0[r][0];
940: vals_M_0[1]=eM_0[r][1];
941: vals_M_0[2]=eM_0[r][2];
944: MatSetValuesLocal(M_0,1,&row_M_0,3,idx,vals_M_0,ADD_VALUES);
946: if (user->degenerate) {
947: cv_sum = (cv_p[idx[0]] + cv_p[idx[1]] + cv_p[idx[2]])*user->Dv/(3.0*user->kBT);
948: ci_sum = (ci_p[idx[0]] + ci_p[idx[1]] + ci_p[idx[2]])*user->Di/(3.0*user->kBT);
949: } else {
950: cv_sum = user->initv*user->Dv/user->kBT;
951: ci_sum = user->initv*user->Di/user->kBT;
952: }
956: row = 5*idx[r];
957: cols[0] = 5*idx[0]; vals[0] = dt*eM_2_odd[r][0]*cv_sum;
958: cols[1] = 5*idx[1]; vals[1] = dt*eM_2_odd[r][1]*cv_sum;
959: cols[2] = 5*idx[2]; vals[2] = dt*eM_2_odd[r][2]*cv_sum;
960: cols[3] = 5*idx[0]+1; vals[3] = eM_0[r][0];
961: cols[4] = 5*idx[1]+1; vals[4] = eM_0[r][1];
962: cols[5] = 5*idx[2]+1; vals[5] = eM_0[r][2];
965: MatSetValuesLocal(M,1,&row,6,cols,vals,ADD_VALUES);
968: row = 5*idx[r]+1;
969: cols[0] = 5*idx[0]; vals[0] = -1.0*eM_0[r][0];
970: cols[1] = 5*idx[1]; vals[1] = -1.0*eM_0[r][1];
971: cols[2] = 5*idx[2]; vals[2] = -1.0*eM_0[r][2];
972: cols[3] = 5*idx[0]+1; vals[3] = user->kav*eM_2_odd[r][0];
973: cols[4] = 5*idx[1]+1; vals[4] = user->kav*eM_2_odd[r][1];
974: cols[5] = 5*idx[2]+1; vals[5] = user->kav*eM_2_odd[r][2];
976: MatSetValuesLocal(M,1,&row,6,cols,vals,ADD_VALUES);
978: row = 5*idx[r]+2;
979: cols[0] = 5*idx[0]+2; vals[0] = dt*eM_2_odd[r][0]*ci_sum;
980: cols[1] = 5*idx[1]+2; vals[1] = dt*eM_2_odd[r][1]*ci_sum;
981: cols[2] = 5*idx[2]+2; vals[2] = dt*eM_2_odd[r][2]*ci_sum;
982: cols[3] = 5*idx[0]+3; vals[3] = eM_0[r][0];
983: cols[4] = 5*idx[1]+3; vals[4] = eM_0[r][1];
984: cols[5] = 5*idx[2]+3; vals[5] = eM_0[r][2];
986: MatSetValuesLocal(M,1,&row,6,cols,vals,ADD_VALUES);
989: row = 5*idx[r]+3;
990: cols[0] = 5*idx[0]+2; vals[0] = -1.0*eM_0[r][0];
991: cols[1] = 5*idx[1]+2; vals[1] = -1.0*eM_0[r][1];
992: cols[2] = 5*idx[2]+2; vals[2] = -1.0*eM_0[r][2];
993: cols[3] = 5*idx[0]+3; vals[3] = user->kai*eM_2_odd[r][0];
994: cols[4] = 5*idx[1]+3; vals[4] = user->kai*eM_2_odd[r][1];
995: cols[5] = 5*idx[2]+3; vals[5] = user->kai*eM_2_odd[r][2];
997: MatSetValuesLocal(M,1,&row,6,cols,vals,ADD_VALUES);
1000: row = 5*idx[r]+4;
1001: /*
1002: cols3[0] = 5*idx[0]+4; vals3[0] = eM_0[r][0]/dt + user->L*user->kaeta*dt*eM_2_odd[r][0];
1003: cols3[1] = 5*idx[1]+4; vals3[1] = eM_0[r][1]/dt + user->L*user->kaeta*dt*eM_2_odd[r][1];
1004: cols3[2] = 5*idx[2]+4; vals3[2] = eM_0[r][2]/dt + user->L*user->kaeta*dt*eM_2_odd[r][2];
1005: */
1006: cols3[0] = 5*idx[0]+4; vals3[0] = (eM_0[r][0]/dt + user->L*user->kaeta*eM_2_odd[r][0]);
1007: cols3[1] = 5*idx[1]+4; vals3[1] = (eM_0[r][1]/dt + user->L*user->kaeta*eM_2_odd[r][1]);
1008: cols3[2] = 5*idx[2]+4; vals3[2] = (eM_0[r][2]/dt + user->L*user->kaeta*eM_2_odd[r][2]);
1010: MatSetValuesLocal(M,1,&row,3,cols3,vals3,ADD_VALUES);
1012: }
1013: }
1015: /* new */
1016: VecRestoreArray(cvlocal,&cv_p);
1017: VecRestoreArray(cilocal,&ci_p);
1018: DMRestoreLocalVector(user->da2,&cvlocal);
1019: DMRestoreLocalVector(user->da2,&cilocal);
1020: /* old */
1021: /*
1022: VecRestoreArray(user->cv,&cv_p);
1023: VecRestoreArray(user->ci,&ci_p);
1024: */
1025: MatAssemblyBegin(M_0,MAT_FINAL_ASSEMBLY);
1026: MatAssemblyEnd(M_0,MAT_FINAL_ASSEMBLY);
1028: MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);
1029: MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);
1031: DMDARestoreElements(user->da1,&nele,&nen,&ele);
1032: return(0);
1033: }
1038: PetscErrorCode UpdateMatrices(AppCtx *user)
1039: {
1041: PetscInt i,n,Mda,Nda,nele,nen;
1042: const PetscInt *ele;
1044: PetscInt idx[3];
1045: PetscScalar eM_2_odd[3][3],eM_2_even[3][3],h,dt=user->dt;
1046: Mat M=user->M;
1047: PetscScalar *cv_p,*ci_p,cv_sum,ci_sum;
1048: /* newly added */
1049: Vec cvlocal,cilocal;
1052: MatGetLocalSize(M,&n,NULL);
1054: /* new stuff */
1055: DMGetLocalVector(user->da2,&cvlocal);
1056: DMGetLocalVector(user->da2,&cilocal);
1057: DMGlobalToLocalBegin(user->da2,user->cv,INSERT_VALUES,cvlocal);
1058: DMGlobalToLocalEnd(user->da2,user->cv,INSERT_VALUES,cvlocal);
1059: DMGlobalToLocalBegin(user->da2,user->ci,INSERT_VALUES,cilocal);
1060: DMGlobalToLocalEnd(user->da2,user->ci,INSERT_VALUES,cilocal);
1061: /* new stuff */
1062: VecGetArray(cvlocal,&cv_p);
1063: VecGetArray(cilocal,&ci_p);
1065: /* old stuff */
1066: /*
1067: VecGetArray(user->cv,&cv_p);
1068: VecGetArray(user->ci,&ci_p);
1069: */
1070: DMDAGetInfo(user->da1,NULL,&Mda,&Nda,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL);
1074: h = (user->xmax-user->xmin)/Mda;
1076: DMDAGetElements(user->da1,&nele,&nen,&ele);
1078: for (i=0; i < nele; i++) {
1079: /*
1080: idx[0] = connect[k*3];
1081: idx[1] = connect[k*3+1];
1082: idx[2] = connect[k*3+2];
1083: */
1084: idx[0] = ele[3*i];
1085: idx[1] = ele[3*i+1];
1086: idx[2] = ele[3*i+2];
1088: PetscInt r,row,cols[3];
1089: PetscScalar vals[3];
1090: for (r=0; r<3; r++) {
1091: row = 5*idx[r];
1092: cols[0] = 5*idx[0]; vals[0] = 0.0;
1093: cols[1] = 5*idx[1]; vals[1] = 0.0;
1094: cols[2] = 5*idx[2]; vals[2] = 0.0;
1096: /* Insert values in matrix M for 1st dof */
1097: MatSetValuesLocal(M,1,&row,3,cols,vals,INSERT_VALUES);
1099: row = 5*idx[r]+2;
1100: cols[0] = 5*idx[0]+2; vals[0] = 0.0;
1101: cols[1] = 5*idx[1]+2; vals[1] = 0.0;
1102: cols[2] = 5*idx[2]+2; vals[2] = 0.0;
1104: /* Insert values in matrix M for 3nd dof */
1105: MatSetValuesLocal(M,1,&row,3,cols,vals,INSERT_VALUES);
1106: }
1107: }
1109: MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);
1110: MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);
1112: eM_2_odd[0][0] = 1.0;
1113: eM_2_odd[1][1] = eM_2_odd[2][2] = 0.5;
1114: eM_2_odd[0][1] = eM_2_odd[0][2] = eM_2_odd[1][0]= eM_2_odd[2][0] = -0.5;
1115: eM_2_odd[1][2] = eM_2_odd[2][1] = 0.0;
1117: eM_2_even[0][0] = 1.0;
1118: eM_2_even[1][1] = eM_2_even[2][2] = 0.5;
1119: eM_2_even[0][1] = eM_2_even[0][2] = eM_2_even[1][0]= eM_2_even[2][0] = -0.5;
1120: eM_2_even[1][2] = eM_2_even[2][1] = 0.0;
1122: /*
1123: eM_2_even[1][1] = 1.0;
1124: eM_2_even[0][0] = eM_2_even[2][2] = 0.5;
1125: eM_2_even[0][1] = eM_2_even[1][0] = eM_2_even[1][2] = eM_2_even[2][1] = -0.5;
1126: eM_2_even[0][2] = eM_2_even[2][0] = 0.0;
1127: */
1129: /* Get local element info */
1130: /* for (k=0;k < Mda*Nda*2;k++) { */
1131: for (i=0; i < nele; i++) {
1132: /*
1133: idx[0] = connect[k*3];
1134: idx[1] = connect[k*3+1];
1135: idx[2] = connect[k*3+2];
1136: */
1137: idx[0] = ele[3*i];
1138: idx[1] = ele[3*i+1];
1139: idx[2] = ele[3*i+2];
1141: PetscInt row,cols[3],r;
1142: PetscScalar vals[3];
1144: for (r=0; r<3; r++) {
1146: if (user->degenerate) {
1147: printf("smallnumber = %14.12f\n",user->smallnumber);
1148: cv_sum = (user->smallnumber + cv_p[idx[0]] + cv_p[idx[1]] + cv_p[idx[2]])*user->Dv/(3.0*user->kBT);
1149: ci_sum = (user->smallnumber + ci_p[idx[0]] + ci_p[idx[1]] + ci_p[idx[2]])*user->Di/(3.0*user->kBT);
1150: } else {
1151: cv_sum = user->initv*user->Dv/(user->kBT);
1152: ci_sum = user->initv*user->Di/user->kBT;
1153: }
1155: row = 5*idx[r];
1156: cols[0] = 5*idx[0]; vals[0] = dt*eM_2_odd[r][0]*cv_sum;
1157: cols[1] = 5*idx[1]; vals[1] = dt*eM_2_odd[r][1]*cv_sum;
1158: cols[2] = 5*idx[2]; vals[2] = dt*eM_2_odd[r][2]*cv_sum;
1160: /* Insert values in matrix M for 1st dof */
1161: MatSetValuesLocal(M,1,&row,3,cols,vals,ADD_VALUES);
1163: row = 5*idx[r]+2;
1164: cols[0] = 5*idx[0]+2; vals[0] = dt*eM_2_odd[r][0]*ci_sum;
1165: cols[1] = 5*idx[1]+2; vals[1] = dt*eM_2_odd[r][1]*ci_sum;
1166: cols[2] = 5*idx[2]+2; vals[2] = dt*eM_2_odd[r][2]*ci_sum;
1168: MatSetValuesLocal(M,1,&row,3,cols,vals,ADD_VALUES);
1169: }
1170: }
1172: /* new stuff */
1173: VecRestoreArray(cvlocal,&cv_p);
1174: VecRestoreArray(cilocal,&ci_p);
1175: DMRestoreLocalVector(user->da2,&cvlocal);
1176: DMRestoreLocalVector(user->da2,&cilocal);
1177: /* old stuff */
1178: /*
1179: VecRestoreArray(user->cv,&cv_p);
1180: VecRestoreArray(user->ci,&ci_p);
1181: */
1183: MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);
1184: MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);
1185: return(0);
1186: }
1192: PetscErrorCode Phi(AppCtx *user)
1193: {
1194: PetscErrorCode ierr;
1195: PetscScalar xmid, xqu, lambda, h,x[3],y[3];
1196: Vec coords;
1197: const PetscScalar *_coords;
1198: PetscInt nele,nen,i,idx[3],Mda,Nda;
1199: const PetscInt *ele;
1200: PetscViewer view;
1203: DMDAGetInfo(user->da1,NULL,&Mda,&Nda,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL);
1204: DMGetCoordinatesLocal(user->da2,&coords);
1205: VecGetArrayRead(coords,&_coords);
1207: h = (user->xmax - user->xmin)/Mda;
1208: xmid = (user->xmin + user->xmax)/2.0;
1209: xqu = (user->xmin + xmid)/2.0;
1210: lambda = 4.0*h;
1213: DMDAGetElements(user->da2,&nele,&nen,&ele);
1214: for (i=0; i < nele; i++) {
1215: idx[0] = ele[3*i]; idx[1] = ele[3*i+1]; idx[2] = ele[3*i+2];
1216: /* printf("idx[0]=%d,idx[1]=%d,idx[2]=%d\n",idx[0],idx[1],idx[2]); */
1218: x[0] = _coords[2*idx[0]]; y[0] = _coords[2*idx[0]+1];
1219: x[1] = _coords[2*idx[1]]; y[1] = _coords[2*idx[1]+1];
1220: x[2] = _coords[2*idx[2]]; y[2] = _coords[2*idx[2]+1];
1222: /*printf("x[0]=%f,x[1]=%f,x[2]=%f\n",x[0],x[1],x[2]);*/
1223: /*printf("y[0]=%f,y[1]=%f,y[2]=%f\n",y[0],y[1],y[2]);*/
1225: PetscScalar vals1[3],vals2[3],dist1,dist2,s1,r,hhr,xc1,xc2;
1226: PetscInt k;
1228: xc1 = user->xmin;
1229: xc2 = xmid;
1231: /*VecSet(user->phi1,0.0);*/
1232: for (k=0; k < 3; k++) {
1233: if (x[k]-xqu > 0) s1 = (x[k] - xqu);
1234: else s1 = -(x[k] - xqu);
1236: if (x[k] - xc1 > 0) dist1 = (x[k] - xc1);
1237: else dist1 = -(x[k] - xc1);
1239: if (x[k] - xc2 > 0) dist2 = (x[k] - xc2);
1240: else dist2 = -(x[k] - xc2);
1242: if (dist1 <= 0.5*lambda) {
1243: r = (x[k]-xc1)/(0.5*lambda);
1244: hhr = 0.25*(-r*r*r + 3.0*r + 2.0);
1245: vals1[k] = hhr;
1246: } else if (dist2 <= 0.5*lambda) {
1247: r = (x[k]-xc2)/(0.5*lambda);
1248: hhr = 0.25*(-r*r*r + 3.0*r + 2.0);
1249: vals1[k] = 1.0 - hhr;
1250: } else if (s1 <= xqu - 2.0*h) vals1[k] = 1.0;
1251: /*else if (abs(x[k]-(user->xmax-h)) < 0.1*h) {*/
1252: else if ((user->xmax-h)-x[k] < 0.1*h) vals1[k] = .15625;
1253: else vals1[k] = 0.0;
1254: }
1256: VecSetValuesLocal(user->phi1,3,idx,vals1,INSERT_VALUES);
1258: xc1 = xmid;
1259: xc2 = user->xmax;
1261: /*VecSet(user->phi2,0.0);*/
1262: for (k=0;k < 3; k++) {
1263: /*
1264: s1 = abs(x[k] - (xqu+xmid));
1265: dist1 = abs(x[k] - xc1);
1266: dist2 = abs(x[k] - xc2);
1267: */
1268: if (x[k]-(xqu + xmid) > 0) s1 = (x[k] - (xqu + xmid));
1269: else s1 = -(x[k] - (xqu + xmid));
1271: if (x[k] - xc1 > 0) dist1 = (x[k] - xc1);
1272: else dist1 = -(x[k] - xc1);
1274: if (x[k] - xc2 > 0) dist2 = (x[k] - xc2);
1275: else dist2 = -(x[k] - xc2);
1277: if (dist1 <= 0.5*lambda) {
1278: r = (x[k]-xc1)/(0.5*lambda);
1279: hhr = 0.25*(-r*r*r + 3.0*r + 2.0);
1280: vals2[k] = hhr;
1281: } else if (dist2 <= 0.5*lambda) {
1282: r = -(x[k]-xc2)/(0.5*lambda);
1283: hhr = 0.25*(-r*r*r + 3.0*r + 2.0);
1284: vals2[k] = hhr;
1285: } else if (s1 <= xqu - 2.0*h) vals2[k] = 1.0;
1286: else if (x[k]-(user->xmin) < 0.1*h) vals2[k] = 0.5;
1287: else if ((x[k]-(user->xmin+h)) < 0.1*h) vals2[k] = .15625;
1288: else vals2[k] = 0.0;
1290: }
1292: VecSetValuesLocal(user->phi2,3,idx,vals2,INSERT_VALUES);
1293: /*
1294: for (k=0;k < 3; k++) {
1295: vals_sum[k] = vals1[k]*vals1[k] + vals2[k]*vals2[k];
1296: }
1297: */
1298: /*VecSetValuesLocal(user->Phi2D_V,3,idx,vals_sum,INSERT_VALUES);*/
1300: }
1302: VecAssemblyBegin(user->phi1);
1303: VecAssemblyEnd(user->phi1);
1304: VecAssemblyBegin(user->phi2);
1305: VecAssemblyEnd(user->phi2);
1306: PetscViewerBinaryOpen(PETSC_COMM_WORLD,"file_phi",FILE_MODE_WRITE,&view);
1308: VecView(user->phi1,view);
1309: VecView(user->phi2,view);
1312: /*VecView(user->phi1,0);*/
1313: /*VecView(user->phi2,0);*/
1315: VecPointwiseMult(user->phi1,user->phi1,user->phi1);
1316: VecPointwiseMult(user->phi2,user->phi2,user->phi2);
1317: VecView(user->phi1,view);
1318: VecView(user->phi2,view);
1320: VecCopy(user->phi1,user->Phi2D_V);
1321: VecAXPY(user->Phi2D_V,1.0,user->phi2);
1322: /*VecView(user->Phi2D_V,0);*/
1324: VecView(user->Phi2D_V,view);
1325: PetscViewerDestroy(&view);
1326: /* VecNorm(user->Phi2D_V,NORM_INFINITY,&max1);*/
1327: /*VecMin(user->Phi2D_V,&loc1,&min1);*/
1328: /*printf("norm phi = %f, min phi = %f\n",max1,min1);*/
1329: return(0);
1330: }
1334: PetscErrorCode Phi_read(AppCtx *user)
1335: {
1337: PetscReal *values;
1338: PetscViewer viewer;
1341: VecGetArray(user->Phi2D_V,&values);
1342: PetscViewerBinaryOpen(PETSC_COMM_WORLD,"phi3",FILE_MODE_READ,&viewer);
1343: PetscViewerBinaryRead(viewer,values,16384,PETSC_DOUBLE);
1344: PetscViewerDestroy(&viewer);
1345: return(0);
1346: }