Actual source code: ex2.c

petsc-3.12.1 2019-10-22
Report Typos and Errors

  2: static char help[] = "Reaction Equation from Chemistry\n";

  4: /*

  6:      Page 6, An example from Atomospheric Chemistry

  8:                  u_1_t =
  9:                  u_2_t =
 10:                  u_3_t =
 11:                  u_4_t =

 13:   -ts_monitor_lg_error -ts_monitor_lg_solution  -ts_view -ts_max_time 2.e4

 15: */


 18: /*
 19:    Include "petscts.h" so that we can use TS solvers.  Note that this
 20:    file automatically includes:
 21:      petscsys.h       - base PETSc routines   petscvec.h - vectors
 22:      petscmat.h - matrices
 23:      petscis.h     - index sets            petscksp.h - Krylov subspace methods
 24:      petscviewer.h - viewers               petscpc.h  - preconditioners
 25:      petscksp.h   - linear solvers
 26: */

 28: #include <petscts.h>

 30: typedef struct {
 31:   PetscScalar k1,k2,k3;
 32:   PetscScalar sigma2;
 33:   Vec         initialsolution;
 34: } AppCtx;

 36: PetscScalar k1(AppCtx *ctx,PetscReal t)
 37: {
 38:   PetscReal th    = t/3600.0;
 39:   PetscReal barth = th - 24.0*PetscFloorReal(th/24.0);
 40:   if (((((PetscInt)th) % 24) < 4) || ((((PetscInt)th) % 24) >= 20)) return(1.0e-40);
 41:   else return(ctx->k1*PetscExpReal(7.0*PetscPowReal(PetscSinReal(.0625*PETSC_PI*(barth - 4.0)),.2)));
 42: }

 44: static PetscErrorCode IFunction(TS ts,PetscReal t,Vec U,Vec Udot,Vec F,AppCtx *ctx)
 45: {
 46:   PetscErrorCode    ierr;
 47:   PetscScalar       *f;
 48:   const PetscScalar *u,*udot;

 51:   VecGetArrayRead(U,&u);
 52:   VecGetArrayRead(Udot,&udot);
 53:   VecGetArray(F,&f);
 54:   f[0] = udot[0] - k1(ctx,t)*u[2] + ctx->k2*u[0];
 55:   f[1] = udot[1] - k1(ctx,t)*u[2] + ctx->k3*u[1]*u[3] - ctx->sigma2;
 56:   f[2] = udot[2] - ctx->k3*u[1]*u[3] + k1(ctx,t)*u[2];
 57:   f[3] = udot[3] - ctx->k2*u[0] + ctx->k3*u[1]*u[3];
 58:   VecRestoreArrayRead(U,&u);
 59:   VecRestoreArrayRead(Udot,&udot);
 60:   VecRestoreArray(F,&f);
 61:   return(0);
 62: }

 64: static PetscErrorCode IJacobian(TS ts,PetscReal t,Vec U,Vec Udot,PetscReal a,Mat A,Mat B,AppCtx *ctx)
 65: {
 66:   PetscErrorCode    ierr;
 67:   PetscInt          rowcol[] = {0,1,2,3};
 68:   PetscScalar       J[4][4];
 69:   const PetscScalar *u,*udot;

 72:   VecGetArrayRead(U,&u);
 73:   VecGetArrayRead(Udot,&udot);
 74:   J[0][0] = a + ctx->k2;   J[0][1] = 0.0;                J[0][2] = -k1(ctx,t);       J[0][3] = 0.0;
 75:   J[1][0] = 0.0;           J[1][1] = a + ctx->k3*u[3];   J[1][2] = -k1(ctx,t);       J[1][3] = ctx->k3*u[1];
 76:   J[2][0] = 0.0;           J[2][1] = -ctx->k3*u[3];      J[2][2] = a + k1(ctx,t);    J[2][3] =  -ctx->k3*u[1];
 77:   J[3][0] =  -ctx->k2;     J[3][1] = ctx->k3*u[3];       J[3][2] = 0.0;              J[3][3] = a + ctx->k3*u[1];
 78:   MatSetValues(B,4,rowcol,4,rowcol,&J[0][0],INSERT_VALUES);
 79:   VecRestoreArrayRead(U,&u);
 80:   VecRestoreArrayRead(Udot,&udot);

 82:   MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);
 83:   MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);
 84:   if (A != B) {
 85:     MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);
 86:     MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);
 87:   }
 88:   return(0);
 89: }

 91: static PetscErrorCode Solution(TS ts,PetscReal t,Vec U,AppCtx *ctx)
 92: {

 96:   VecCopy(ctx->initialsolution,U);
 97:   if (t > 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Solution not given");
 98:   return(0);
 99: }

101: int main(int argc,char **argv)
102: {
103:   TS             ts;            /* ODE integrator */
104:   Vec            U;             /* solution */
105:   Mat            A;             /* Jacobian matrix */
107:   PetscMPIInt    size;
108:   PetscInt       n = 4;
109:   AppCtx         ctx;
110:   PetscScalar    *u;

112:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
113:      Initialize program
114:      - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
115:   PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
116:   MPI_Comm_size(PETSC_COMM_WORLD,&size);
117:   if (size > 1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"Only for sequential runs");

119:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
120:     Create necessary matrix and vectors
121:     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
122:   MatCreate(PETSC_COMM_WORLD,&A);
123:   MatSetSizes(A,n,n,PETSC_DETERMINE,PETSC_DETERMINE);
124:   MatSetFromOptions(A);
125:   MatSetUp(A);

127:   MatCreateVecs(A,&U,NULL);

129:   ctx.k1     = 1.0e-5;
130:   ctx.k2     = 1.0e5;
131:   ctx.k3     = 1.0e-16;
132:   ctx.sigma2 = 1.0e6;

134:   VecDuplicate(U,&ctx.initialsolution);
135:   VecGetArray(ctx.initialsolution,&u);
136:   u[0] = 0.0;
137:   u[1] = 1.3e8;
138:   u[2] = 5.0e11;
139:   u[3] = 8.0e11;
140:   VecRestoreArray(ctx.initialsolution,&u);

142:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
143:      Create timestepping solver context
144:      - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
145:   TSCreate(PETSC_COMM_WORLD,&ts);
146:   TSSetProblemType(ts,TS_NONLINEAR);
147:   TSSetType(ts,TSROSW);
148:   TSSetIFunction(ts,NULL,(TSIFunction) IFunction,&ctx);
149:   TSSetIJacobian(ts,A,A,(TSIJacobian)IJacobian,&ctx);

151:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
152:      Set initial conditions
153:    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
154:   Solution(ts,0,U,&ctx);
155:   TSSetTime(ts,4.0*3600);
156:   TSSetTimeStep(ts,1.0);
157:   TSSetSolution(ts,U);

159:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
160:      Set solver options
161:    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
162:   TSSetMaxTime(ts,518400.0);
163:   TSSetExactFinalTime(ts,TS_EXACTFINALTIME_STEPOVER);
164:   TSSetMaxStepRejections(ts,100);
165:   TSSetMaxSNESFailures(ts,-1); /* unlimited */
166:   TSSetFromOptions(ts);

168:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
169:      Solve nonlinear system
170:      - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
171:   TSSolve(ts,U);

173:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
174:      Free work space.  All PETSc objects should be destroyed when they
175:      are no longer needed.
176:    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
177:   VecDestroy(&ctx.initialsolution);
178:   MatDestroy(&A);
179:   VecDestroy(&U);
180:   TSDestroy(&ts);

182:   PetscFinalize();
183:   return ierr;
184: }


187: /*TEST

189:    test:
190:      args: -ts_view -ts_max_time 2.e4
191:      timeoutfactor: 15
192:      requires: !single

194: TEST*/