Actual source code: ex4.c
petsc-3.5.4 2015-05-23
2: static char help[] = "Chemo-taxis Problems from Mathematical Biology.\n";
4: /*
5: Page 18, Chemo-taxis Problems from Mathematical Biology
7: rho_t =
8: c_t =
10: Further discusson on Page 134 and in 2d on Page 409
11: */
13: /*
15: Include "petscdmda.h" so that we can use distributed arrays (DMDAs).
16: Include "petscts.h" so that we can use SNES solvers. Note that this
17: file automatically includes:
18: petscsys.h - base PETSc routines petscvec.h - vectors
19: petscmat.h - matrices
20: petscis.h - index sets petscksp.h - Krylov subspace methods
21: petscviewer.h - viewers petscpc.h - preconditioners
22: petscksp.h - linear solvers
23: */
24: #include <petscdm.h>
25: #include <petscdmda.h>
26: #include <petscts.h>
28: typedef struct {
29: PetscScalar rho,c;
30: } Field;
32: typedef struct {
33: PetscScalar epsilon,delta,alpha,beta,gamma,kappa,lambda,mu,cstar;
34: PetscBool upwind;
35: } AppCtx;
37: /*
38: User-defined routines
39: */
40: extern PetscErrorCode IFunction(TS,PetscReal,Vec,Vec,Vec,void*),InitialConditions(DM,Vec);
44: int main(int argc,char **argv)
45: {
46: TS ts; /* nonlinear solver */
47: Vec U; /* solution, residual vectors */
49: DM da;
50: AppCtx appctx;
52: /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
53: Initialize program
54: - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
55: PetscInitialize(&argc,&argv,(char*)0,help);
57: appctx.epsilon = 1.0e-3;
58: appctx.delta = 1.0;
59: appctx.alpha = 10.0;
60: appctx.beta = 4.0;
61: appctx.gamma = 1.0;
62: appctx.kappa = .75;
63: appctx.lambda = 1.0;
64: appctx.mu = 100.;
65: appctx.cstar = .2;
66: appctx.upwind = PETSC_TRUE;
68: PetscOptionsGetScalar(NULL,"-delta",&appctx.delta,NULL);
69: PetscOptionsGetBool(NULL,"-upwind",&appctx.upwind,NULL);
71: /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
72: Create distributed array (DMDA) to manage parallel grid and vectors
73: - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
74: DMDACreate1d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE,-8,2,1,NULL,&da);
75: DMDASetFieldName(da,0,"rho");
76: DMDASetFieldName(da,1,"c");
78: /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
79: Extract global vectors from DMDA; then duplicate for remaining
80: vectors that are the same types
81: - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
82: DMCreateGlobalVector(da,&U);
84: /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
85: Create timestepping solver context
86: - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
87: TSCreate(PETSC_COMM_WORLD,&ts);
88: TSSetType(ts,TSROSW);
89: TSSetDM(ts,da);
90: TSSetProblemType(ts,TS_NONLINEAR);
91: TSSetIFunction(ts,NULL,IFunction,&appctx);
94: /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
95: Set initial conditions
96: - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
97: InitialConditions(da,U);
98: TSSetSolution(ts,U);
100: /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
101: Set solver options
102: - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
103: TSSetInitialTimeStep(ts,0.0,.0001);
104: TSSetDuration(ts,PETSC_DEFAULT,1.0);
105: TSSetFromOptions(ts);
107: /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
108: Solve nonlinear system
109: - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
110: TSSolve(ts,U);
112: /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
113: Free work space. All PETSc objects should be destroyed when they
114: are no longer needed.
115: - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
116: VecDestroy(&U);
117: TSDestroy(&ts);
118: DMDestroy(&da);
120: PetscFinalize();
121: return(0);
122: }
123: /* ------------------------------------------------------------------- */
126: /*
127: IFunction - Evaluates nonlinear function, F(U).
129: Input Parameters:
130: . ts - the TS context
131: . U - input vector
132: . ptr - optional user-defined context, as set by SNESSetFunction()
134: Output Parameter:
135: . F - function vector
136: */
137: PetscErrorCode IFunction(TS ts,PetscReal ftime,Vec U,Vec Udot,Vec F,void *ptr)
138: {
139: AppCtx *appctx = (AppCtx*)ptr;
140: DM da;
142: PetscInt i,Mx,xs,xm;
143: PetscReal hx,sx;
144: PetscScalar rho,c,rhoxx,cxx,cx,rhox,kcxrhox;
145: Field *u,*f,*udot;
146: Vec localU;
149: TSGetDM(ts,&da);
150: DMGetLocalVector(da,&localU);
151: DMDAGetInfo(da,PETSC_IGNORE,&Mx,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE);
153: hx = 1.0/(PetscReal)(Mx-1); sx = 1.0/(hx*hx);
155: /*
156: Scatter ghost points to local vector,using the 2-step process
157: DMGlobalToLocalBegin(),DMGlobalToLocalEnd().
158: By placing code between these two statements, computations can be
159: done while messages are in transition.
160: */
161: DMGlobalToLocalBegin(da,U,INSERT_VALUES,localU);
162: DMGlobalToLocalEnd(da,U,INSERT_VALUES,localU);
164: /*
165: Get pointers to vector data
166: */
167: DMDAVecGetArray(da,localU,&u);
168: DMDAVecGetArray(da,Udot,&udot);
169: DMDAVecGetArray(da,F,&f);
171: /*
172: Get local grid boundaries
173: */
174: DMDAGetCorners(da,&xs,NULL,NULL,&xm,NULL,NULL);
176: if (!xs) {
177: f[0].rho = udot[0].rho; /* u[0].rho - 0.0; */
178: f[0].c = udot[0].c; /* u[0].c - 1.0; */
179: xs++;
180: xm--;
181: }
182: if (xs+xm == Mx) {
183: f[Mx-1].rho = udot[Mx-1].rho; /* u[Mx-1].rho - 1.0; */
184: f[Mx-1].c = udot[Mx-1].c; /* u[Mx-1].c - 0.0; */
185: xm--;
186: }
188: /*
189: Compute function over the locally owned part of the grid
190: */
191: for (i=xs; i<xs+xm; i++) {
192: rho = u[i].rho;
193: rhoxx = (-2.0*rho + u[i-1].rho + u[i+1].rho)*sx;
194: c = u[i].c;
195: cxx = (-2.0*c + u[i-1].c + u[i+1].c)*sx;
197: if (!appctx->upwind) {
198: rhox = .5*(u[i+1].rho - u[i-1].rho)/hx;
199: cx = .5*(u[i+1].c - u[i-1].c)/hx;
200: kcxrhox = appctx->kappa*(cxx*rho + cx*rhox);
201: } else {
202: kcxrhox = appctx->kappa*((u[i+1].c - u[i].c)*u[i+1].rho - (u[i].c - u[i-1].c)*u[i].rho)*sx;
203: }
205: f[i].rho = udot[i].rho - appctx->epsilon*rhoxx + kcxrhox - appctx->mu*PetscAbsScalar(rho)*(1.0 - rho)*PetscMax(0,PetscRealPart(c - appctx->cstar)) + appctx->beta*rho;
206: f[i].c = udot[i].c - appctx->delta*cxx + appctx->lambda*c + appctx->alpha*rho*c/(appctx->gamma + c);
207: }
209: /*
210: Restore vectors
211: */
212: DMDAVecRestoreArray(da,localU,&u);
213: DMDAVecRestoreArray(da,Udot,&udot);
214: DMDAVecRestoreArray(da,F,&f);
215: DMRestoreLocalVector(da,&localU);
216: return(0);
217: }
219: /* ------------------------------------------------------------------- */
222: PetscErrorCode InitialConditions(DM da,Vec U)
223: {
225: PetscInt i,xs,xm,Mx;
226: Field *u;
227: PetscReal hx,x;
230: DMDAGetInfo(da,PETSC_IGNORE,&Mx,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE);
232: hx = 1.0/(PetscReal)(Mx-1);
234: /*
235: Get pointers to vector data
236: */
237: DMDAVecGetArray(da,U,&u);
239: /*
240: Get local grid boundaries
241: */
242: DMDAGetCorners(da,&xs,NULL,NULL,&xm,NULL,NULL);
244: /*
245: Compute function over the locally owned part of the grid
246: */
247: for (i=xs; i<xs+xm; i++) {
248: x = i*hx;
249: if (x < 1.0) u[i].rho = 0.0;
250: else u[i].rho = 1.0;
251: u[i].c = PetscCosReal(.5*PETSC_PI*x);
252: }
254: /*
255: Restore vectors
256: */
257: DMDAVecRestoreArray(da,U,&u);
258: return(0);
259: }