Ejemplo n.º 1
0
int main(int argc,char **argv)
{
  PetscErrorCode ierr;
  AppCtx         ctx;
  TS             ts;
  Vec            tsrhs,U;

  ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
  ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
  ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
  ierr = TSSetType(ts,TSEULER);CHKERRQ(ierr);
  ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
  ierr = VecCreateMPI(PETSC_COMM_WORLD,PETSC_DECIDE,1,&tsrhs);CHKERRQ(ierr);
  ierr = VecCreateMPI(PETSC_COMM_WORLD,PETSC_DECIDE,1,&U);CHKERRQ(ierr);
  ierr = TSSetRHSFunction(ts,tsrhs,TSFunction,&ctx);CHKERRQ(ierr);
  ctx.f = f;

  ierr = SNESCreate(PETSC_COMM_WORLD,&ctx.snes);CHKERRQ(ierr);
  ierr = SNESSetFromOptions(ctx.snes);CHKERRQ(ierr);
  ierr = SNESSetFunction(ctx.snes,NULL,SNESFunction,&ctx);CHKERRQ(ierr);
  ierr = SNESSetJacobian(ctx.snes,NULL,NULL,SNESComputeJacobianDefault,&ctx);CHKERRQ(ierr);
  ctx.F = F;
  ierr = VecCreateMPI(PETSC_COMM_WORLD,PETSC_DECIDE,1,&ctx.V);CHKERRQ(ierr);

  ierr = VecSet(U,1.0);CHKERRQ(ierr);
  ierr = TSSolve(ts,U);CHKERRQ(ierr);

  ierr = VecDestroy(&ctx.V);CHKERRQ(ierr);
  ierr = VecDestroy(&tsrhs);CHKERRQ(ierr);
  ierr = VecDestroy(&U);CHKERRQ(ierr);
  ierr = SNESDestroy(&ctx.snes);CHKERRQ(ierr);
  ierr = TSDestroy(&ts);CHKERRQ(ierr);
  ierr = PetscFinalize();
  return ierr;
}
Ejemplo n.º 2
0
int main(int argc,char **argv)
{
  PetscErrorCode ierr;
  PetscInt       time_steps = 100,steps;
  PetscMPIInt    size;
  Vec            global;
  PetscReal      dt,ftime;
  TS             ts;
  MatStructure   A_structure;
  Mat            A = 0;

  ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
  ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);

  ierr = PetscOptionsGetInt(NULL,"-time",&time_steps,NULL);CHKERRQ(ierr);

  /* set initial conditions */
  ierr = VecCreate(PETSC_COMM_WORLD,&global);CHKERRQ(ierr);
  ierr = VecSetSizes(global,PETSC_DECIDE,3);CHKERRQ(ierr);
  ierr = VecSetFromOptions(global);CHKERRQ(ierr);
  ierr = Initial(global,NULL);CHKERRQ(ierr);

  /* make timestep context */
  ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
  ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
  ierr = TSMonitorSet(ts,Monitor,NULL,NULL);CHKERRQ(ierr);

  dt = 0.1;

  /*
    The user provides the RHS and Jacobian
  */
  ierr = TSSetRHSFunction(ts,NULL,RHSFunction,NULL);CHKERRQ(ierr);
  ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
  ierr = MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,3,3);CHKERRQ(ierr);
  ierr = MatSetFromOptions(A);CHKERRQ(ierr);
  ierr = MatSetUp(A);CHKERRQ(ierr);
  ierr = RHSJacobian(ts,0.0,global,&A,&A,&A_structure,NULL);CHKERRQ(ierr);
  ierr = TSSetRHSJacobian(ts,A,A,RHSJacobian,NULL);CHKERRQ(ierr);

  ierr = TSSetFromOptions(ts);CHKERRQ(ierr);

  ierr = TSSetInitialTimeStep(ts,0.0,dt);CHKERRQ(ierr);
  ierr = TSSetDuration(ts,time_steps,1);CHKERRQ(ierr);
  ierr = TSSetSolution(ts,global);CHKERRQ(ierr);

  ierr = TSSolve(ts,global);CHKERRQ(ierr);
  ierr = TSGetSolveTime(ts,&ftime);CHKERRQ(ierr);
  ierr = TSGetTimeStepNumber(ts,&steps);CHKERRQ(ierr);


  /* free the memories */

  ierr = TSDestroy(&ts);CHKERRQ(ierr);
  ierr = VecDestroy(&global);CHKERRQ(ierr);
  ierr = MatDestroy(&A);CHKERRQ(ierr);

  ierr = PetscFinalize();
  return 0;
}
Ejemplo n.º 3
0
/*
   FormFunctionGradient - Evaluates the function and corresponding gradient.

   Input Parameters:
   tao - the Tao context
   X   - the input vector
   ptr - optional user-defined context, as set by TaoSetObjectiveAndGradientRoutine()

   Output Parameters:
   f   - the newly evaluated function
   G   - the newly evaluated gradient
*/
PetscErrorCode FormFunctionGradient(Tao tao,Vec IC,PetscReal *f,Vec G,void *ctx)
{
  User           user_ptr = (User)ctx;
  TS             ts;
  PetscScalar    *x_ptr,*y_ptr;
  PetscErrorCode ierr;

  ierr = VecCopy(IC,user_ptr->x);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Create timestepping solver context
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
  ierr = TSSetType(ts,TSCN);CHKERRQ(ierr);
  ierr = TSSetIFunction(ts,NULL,IFunction,user_ptr);CHKERRQ(ierr);
  ierr = TSSetIJacobian(ts,user_ptr->A,user_ptr->A,IJacobian,user_ptr);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Set time
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSetTime(ts,0.0);CHKERRQ(ierr);
  ierr = TSSetDuration(ts,PETSC_DEFAULT,0.5);CHKERRQ(ierr);
  ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_MATCHSTEP);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Save trajectory of solution so that TSAdjointSolve() may be used
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSetSaveTrajectory(ts);CHKERRQ(ierr);
 
  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Set runtime options
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSetFromOptions(ts);CHKERRQ(ierr);

  ierr = TSSolve(ts,user_ptr->x);CHKERRQ(ierr);
  ierr = VecGetArray(user_ptr->x,&x_ptr);CHKERRQ(ierr);
  *f   = (x_ptr[0]-user_ptr->x_ob[0])*(x_ptr[0]-user_ptr->x_ob[0])+(x_ptr[1]-user_ptr->x_ob[1])*(x_ptr[1]-user_ptr->x_ob[1]);
  ierr = PetscPrintf(PETSC_COMM_WORLD,"Observed value y_ob=[%f; %f], ODE solution y=[%f;%f], Cost function f=%f\n",(double)user_ptr->x_ob[0],(double)user_ptr->x_ob[1],(double)x_ptr[0],(double)x_ptr[1],(double)(*f));CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Adjoint model starts here
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  /*   Redet initial conditions for the adjoint integration */
  ierr     = VecGetArray(user_ptr->lambda[0],&y_ptr);CHKERRQ(ierr);
  y_ptr[0] = 2.*(x_ptr[0]-user_ptr->x_ob[0]);
  y_ptr[1] = 2.*(x_ptr[1]-user_ptr->x_ob[1]);
  ierr     = VecRestoreArray(user_ptr->lambda[0],&y_ptr);CHKERRQ(ierr);
  ierr     = TSSetCostGradients(ts,1,user_ptr->lambda,NULL);CHKERRQ(ierr);

  ierr = TSAdjointSolve(ts);CHKERRQ(ierr);
  ierr = VecCopy(user_ptr->lambda[0],G);
  ierr = TSDestroy(&ts);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
Ejemplo n.º 4
0
/*
 * This is a modified version of PETSc/src/ts/examples/tutorials/ex15.c
 * to demonstrate how MOOSE interact with an external solver package
 */
PetscErrorCode
externalPETScDiffusionFDMSolve(TS ts, Vec u, PetscReal dt, PetscReal time)
{
  PetscErrorCode ierr;
#if !PETSC_VERSION_LESS_THAN(3, 8, 0)
  PetscInt current_step;
#endif
  DM da;

  PetscFunctionBeginUser;

  ierr = TSGetDM(ts, &da);
  CHKERRQ(ierr);

#if !PETSC_VERSION_LESS_THAN(3, 7, 0)
  PetscOptionsSetValue(NULL, "-ts_monitor", NULL);
  PetscOptionsSetValue(NULL, "-snes_monitor", NULL);
  PetscOptionsSetValue(NULL, "-ksp_monitor", NULL);
#else
  PetscOptionsSetValue("-ts_monitor", NULL);
  PetscOptionsSetValue("-snes_monitor", NULL);
  PetscOptionsSetValue("-ksp_monitor", NULL);
#endif

  /*ierr = TSSetMaxTime(ts,1.0);CHKERRQ(ierr);*/
  ierr = TSSetExactFinalTime(ts, TS_EXACTFINALTIME_STEPOVER);
  CHKERRQ(ierr);

  ierr = TSSetSolution(ts, u);
  CHKERRQ(ierr);
  ierr = TSSetTimeStep(ts, dt);
  CHKERRQ(ierr);
  ierr = TSSetTime(ts, time - dt);
  CHKERRQ(ierr);
#if !PETSC_VERSION_LESS_THAN(3, 8, 0)
  ierr = TSGetStepNumber(ts, &current_step);
  CHKERRQ(ierr);
  ierr = TSSetMaxSteps(ts, current_step + 1);
  CHKERRQ(ierr);
#else
  SETERRQ(PetscObjectComm((PetscObject)ts), PETSC_ERR_SUP, "Require PETSc-3.8.x or higher ");
#endif
  /*  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
   Sets various TS parameters from user options
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSetFromOptions(ts);
  CHKERRQ(ierr);
  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Solve nonlinear system
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSolve(ts, u);
  CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
Ejemplo n.º 5
0
PetscErrorCode RunTest(int nx, int ny, int nz, int loops, double *wt)
{
  Vec            x,f;
  TS             ts;
  AppCtx         _app,*app=&_app;
  double         t1,t2;
  PetscErrorCode ierr;
  PetscFunctionBegin;

  app->nx = nx; app->h[0] = 1./(nx-1);
  app->ny = ny; app->h[1] = 1./(ny-1);
  app->nz = nz; app->h[2] = 1./(nz-1);

  ierr = VecCreate(PETSC_COMM_SELF,&x);CHKERRQ(ierr);
  ierr = VecSetSizes(x,nx*ny*nz,nx*ny*nz);CHKERRQ(ierr);
  ierr = VecSetUp(x);CHKERRQ(ierr);
  ierr = VecDuplicate(x,&f);CHKERRQ(ierr);

  ierr = TSCreate(PETSC_COMM_SELF,&ts);CHKERRQ(ierr);
  ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
  ierr = TSSetType(ts,TSTHETA);CHKERRQ(ierr);
  ierr = TSThetaSetTheta(ts,1.0);CHKERRQ(ierr);
  ierr = TSSetTimeStep(ts,0.01);CHKERRQ(ierr);
  ierr = TSSetTime(ts,0.0);CHKERRQ(ierr);
  ierr = TSSetDuration(ts,10,1.0);CHKERRQ(ierr);

  ierr = TSSetSolution(ts,x);CHKERRQ(ierr);
  ierr = TSSetIFunction(ts,f,FormFunction,app);CHKERRQ(ierr);
  ierr = PetscOptionsSetValue("-snes_mf","1");CHKERRQ(ierr);
  {
    SNES snes;
    KSP  ksp;
    ierr = TSGetSNES(ts,&snes);CHKERRQ(ierr);
    ierr = SNESGetKSP(snes,&ksp);CHKERRQ(ierr);
    ierr = KSPSetType(ksp,KSPCG);CHKERRQ(ierr);
  }
  ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
  ierr = TSSetUp(ts);CHKERRQ(ierr);

  *wt = 1e300;
  while (loops-- > 0) {
    ierr = FormInitial(0.0,x,app);CHKERRQ(ierr);
    ierr = PetscGetTime(&t1);CHKERRQ(ierr);
    ierr = TSSolve(ts,x,PETSC_NULL);CHKERRQ(ierr);
    ierr = PetscGetTime(&t2);CHKERRQ(ierr);
    *wt = PetscMin(*wt,t2-t1);
  }

  ierr = VecDestroy(&x);CHKERRQ(ierr);
  ierr = VecDestroy(&f);CHKERRQ(ierr);
  ierr = TSDestroy(&ts);CHKERRQ(ierr);
  
  PetscFunctionReturn(0);
}
Ejemplo n.º 6
0
int main(int argc,char **argv)
{
  PetscErrorCode ierr;
  AppCtx         ctx;
  TS             ts;
  Vec            tsrhs,U;
  IS             is;
  PetscInt       I;
  PetscMPIInt    rank;

  ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
  ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
  ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
  ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
  ierr = TSSetType(ts,TSEULER);CHKERRQ(ierr);
  ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
  ierr = VecCreateMPI(PETSC_COMM_WORLD,1,PETSC_DETERMINE,&tsrhs);CHKERRQ(ierr);
  ierr = VecCreateMPI(PETSC_COMM_WORLD,1,PETSC_DETERMINE,&U);CHKERRQ(ierr);
  ierr = TSSetRHSFunction(ts,tsrhs,TSFunction,&ctx);CHKERRQ(ierr);
  ctx.f = f;

  ierr = SNESCreate(PETSC_COMM_WORLD,&ctx.snes);CHKERRQ(ierr);
  ierr = SNESSetFromOptions(ctx.snes);CHKERRQ(ierr);
  ierr = SNESSetFunction(ctx.snes,NULL,SNESFunction,&ctx);CHKERRQ(ierr);
  ierr = SNESSetJacobian(ctx.snes,NULL,NULL,SNESComputeJacobianDefault,&ctx);CHKERRQ(ierr);
  ctx.F = F;
  ierr = VecCreateMPI(PETSC_COMM_WORLD,1,PETSC_DETERMINE,&ctx.V);CHKERRQ(ierr);

  /* Create scatters to move between separate U and V representation and UV representation of solution */
  ierr = VecCreateMPI(PETSC_COMM_WORLD,2,PETSC_DETERMINE,&ctx.UV);CHKERRQ(ierr);
  I    = 2*rank;
  ierr = ISCreateGeneral(PETSC_COMM_WORLD,1,&I,PETSC_COPY_VALUES,&is);CHKERRQ(ierr);
  ierr = VecScatterCreateWithData(U,NULL,ctx.UV,is,&ctx.scatterU);CHKERRQ(ierr);
  ierr = ISDestroy(&is);CHKERRQ(ierr);
  I    = 2*rank + 1;
  ierr = ISCreateGeneral(PETSC_COMM_WORLD,1,&I,PETSC_COPY_VALUES,&is);CHKERRQ(ierr);
  ierr = VecScatterCreateWithData(ctx.V,NULL,ctx.UV,is,&ctx.scatterV);CHKERRQ(ierr);
  ierr = ISDestroy(&is);CHKERRQ(ierr);

  ierr = VecSet(U,1.0);CHKERRQ(ierr);
  ierr = TSSolve(ts,U);CHKERRQ(ierr);

  ierr = VecDestroy(&ctx.V);CHKERRQ(ierr);
  ierr = VecDestroy(&ctx.UV);CHKERRQ(ierr);
  ierr = VecScatterDestroy(&ctx.scatterU);CHKERRQ(ierr);
  ierr = VecScatterDestroy(&ctx.scatterV);CHKERRQ(ierr);
  ierr = VecDestroy(&tsrhs);CHKERRQ(ierr);
  ierr = VecDestroy(&U);CHKERRQ(ierr);
  ierr = SNESDestroy(&ctx.snes);CHKERRQ(ierr);
  ierr = TSDestroy(&ts);CHKERRQ(ierr);
  ierr = PetscFinalize();
  return ierr;
}
Ejemplo n.º 7
0
int main(int argc, char **argv)
{
  PetscErrorCode ierr;
  Vec            x;  /* Solution vector */
  TS             ts;   /* Time-stepping context */
  AppCtx         user; /* Application context */
  Mat            J;
  PetscViewer    viewer;

  PetscInitialize(&argc,&argv,"petscopt_ex6", help);

  /* Get physics and time parameters */
  ierr = Parameter_settings(&user);CHKERRQ(ierr);
  /* Create a 2D DA with dof = 1 */
  ierr = DMDACreate2d(PETSC_COMM_WORLD,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,DMDA_STENCIL_STAR,-4,-4,PETSC_DECIDE,PETSC_DECIDE,1,1,NULL,NULL,&user.da);CHKERRQ(ierr);
  /* Set x and y coordinates */
  ierr = DMDASetUniformCoordinates(user.da,user.xmin,user.xmax,user.ymin,user.ymax,NULL,NULL);CHKERRQ(ierr);

  /* Get global vector x from DM  */
  ierr = DMCreateGlobalVector(user.da,&x);CHKERRQ(ierr);

  ierr = ini_bou(x,&user);CHKERRQ(ierr);
  ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"ini_x",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr);
  ierr = VecView(x,viewer);CHKERRQ(ierr);
  ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);

  /* Get Jacobian matrix structure from the da */
  ierr = DMSetMatType(user.da,MATAIJ);CHKERRQ(ierr);
  ierr = DMCreateMatrix(user.da,&J);CHKERRQ(ierr);

  ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
  ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
  ierr = TSSetIFunction(ts,NULL,IFunction,&user);CHKERRQ(ierr);
  ierr = TSSetIJacobian(ts,J,J,IJacobian,&user);CHKERRQ(ierr);
  ierr = TSSetApplicationContext(ts,&user);CHKERRQ(ierr);
  ierr = TSSetDuration(ts,PETSC_DEFAULT,user.tmax);CHKERRQ(ierr);
  ierr = TSSetInitialTimeStep(ts,user.t0,.005);CHKERRQ(ierr);
  ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
  ierr = TSSetPostStep(ts,PostStep);CHKERRQ(ierr);
  ierr = TSSolve(ts,x);CHKERRQ(ierr);

  ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"fin_x",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr);
  ierr = VecView(x,viewer);CHKERRQ(ierr);
  ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);

  ierr = VecDestroy(&x);CHKERRQ(ierr);
  ierr = MatDestroy(&J);CHKERRQ(ierr);
  ierr = DMDestroy(&user.da);CHKERRQ(ierr);
  ierr = TSDestroy(&ts);CHKERRQ(ierr);
  PetscFinalize();
  return 0;
}
Ejemplo n.º 8
0
Archivo: ex9.c Proyecto: 00liujj/petsc
int main(int argc,char **argv)
{
  PetscErrorCode ierr;
  AppCtx         ctx;
  TS             ts;
  Vec            tsrhs,UV;
  IS             is;
  PetscInt       I;
  PetscMPIInt    rank;


  PetscInitialize(&argc,&argv,(char*)0,help);
  ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
  ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
  ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
  ierr = TSSetType(ts,TSROSW);CHKERRQ(ierr);
  ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
  ierr = VecCreateMPI(PETSC_COMM_WORLD,2,PETSC_DETERMINE,&tsrhs);CHKERRQ(ierr);
  ierr = VecCreateMPI(PETSC_COMM_WORLD,2,PETSC_DETERMINE,&UV);CHKERRQ(ierr);
  ierr = TSSetRHSFunction(ts,tsrhs,TSFunctionRHS,&ctx);CHKERRQ(ierr);
  ierr = TSSetIFunction(ts,NULL,TSFunctionI,&ctx);CHKERRQ(ierr);
  ctx.f = f;
  ctx.F = F;

  ierr = VecCreateMPI(PETSC_COMM_WORLD,1,PETSC_DETERMINE,&ctx.U);CHKERRQ(ierr);
  ierr = VecCreateMPI(PETSC_COMM_WORLD,1,PETSC_DETERMINE,&ctx.V);CHKERRQ(ierr);
  ierr = VecCreateMPI(PETSC_COMM_WORLD,1,PETSC_DETERMINE,&ctx.UF);CHKERRQ(ierr);
  ierr = VecCreateMPI(PETSC_COMM_WORLD,1,PETSC_DETERMINE,&ctx.VF);CHKERRQ(ierr);
  I    = 2*rank;
  ierr = ISCreateGeneral(PETSC_COMM_WORLD,1,&I,PETSC_COPY_VALUES,&is);CHKERRQ(ierr);
  ierr = VecScatterCreate(ctx.U,NULL,UV,is,&ctx.scatterU);CHKERRQ(ierr);
  ierr = ISDestroy(&is);CHKERRQ(ierr);
  I    = 2*rank + 1;
  ierr = ISCreateGeneral(PETSC_COMM_WORLD,1,&I,PETSC_COPY_VALUES,&is);CHKERRQ(ierr);
  ierr = VecScatterCreate(ctx.V,NULL,UV,is,&ctx.scatterV);CHKERRQ(ierr);
  ierr = ISDestroy(&is);CHKERRQ(ierr);

  ierr = VecSet(UV,1.0);CHKERRQ(ierr);
  ierr = TSSolve(ts,UV);CHKERRQ(ierr);
  ierr = VecDestroy(&tsrhs);CHKERRQ(ierr);
  ierr = VecDestroy(&UV);CHKERRQ(ierr);
  ierr = VecDestroy(&ctx.U);CHKERRQ(ierr);
  ierr = VecDestroy(&ctx.V);CHKERRQ(ierr);
  ierr = VecDestroy(&ctx.UF);CHKERRQ(ierr);
  ierr = VecDestroy(&ctx.VF);CHKERRQ(ierr);
  ierr = VecScatterDestroy(&ctx.scatterU);CHKERRQ(ierr);
  ierr = VecScatterDestroy(&ctx.scatterV);CHKERRQ(ierr);
  ierr = TSDestroy(&ts);CHKERRQ(ierr);
  PetscFinalize();
  return 0;
}
Ejemplo n.º 9
0
int main(int argc, char **argv)
{
  PetscErrorCode ierr;
  Vec            x;  /* Solution vector */
  TS             ts;   /* Time-stepping context */
  AppCtx         user; /* Application context */
  PetscViewer    viewer;

  PetscInitialize(&argc,&argv,"petscopt_ex7", help);

  /* Get physics and time parameters */
  ierr = Parameter_settings(&user);CHKERRQ(ierr);
  /* Create a 2D DA with dof = 1 */
  ierr = DMDACreate2d(PETSC_COMM_WORLD,user.bx,user.by,DMDA_STENCIL_STAR,-4,-4,PETSC_DECIDE,PETSC_DECIDE,1,user.st_width,NULL,NULL,&user.da);CHKERRQ(ierr);
  /* Set x and y coordinates */
  ierr = DMDASetUniformCoordinates(user.da,user.xmin,user.xmax,user.ymin,user.ymax,0,0);CHKERRQ(ierr);
  ierr = DMDASetCoordinateName(user.da,0,"X - the angle");
  ierr = DMDASetCoordinateName(user.da,1,"Y - the speed");

  /* Get global vector x from DM  */
  ierr = DMCreateGlobalVector(user.da,&x);CHKERRQ(ierr);

  ierr = ini_bou(x,&user);CHKERRQ(ierr);
  ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"ini_x",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr);
  ierr = VecView(x,viewer);CHKERRQ(ierr);
  ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);

  ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
  ierr = TSSetDM(ts,user.da);CHKERRQ(ierr);
  ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
  ierr = TSSetType(ts,TSARKIMEX);CHKERRQ(ierr);
  ierr = TSSetIFunction(ts,NULL,IFunction,&user);CHKERRQ(ierr);
  /*  ierr = TSSetIJacobian(ts,NULL,NULL,IJacobian,&user);CHKERRQ(ierr);  */
  ierr = TSSetApplicationContext(ts,&user);CHKERRQ(ierr);
  ierr = TSSetInitialTimeStep(ts,0.0,.005);CHKERRQ(ierr);
  ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
  ierr = TSSetPostStep(ts,PostStep);CHKERRQ(ierr);
  ierr = TSSolve(ts,x);CHKERRQ(ierr);

  ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"fin_x",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr);
  ierr = VecView(x,viewer);CHKERRQ(ierr);
  ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);

  ierr = VecDestroy(&x);CHKERRQ(ierr);
  ierr = DMDestroy(&user.da);CHKERRQ(ierr);
  ierr = TSDestroy(&ts);CHKERRQ(ierr);
  PetscFinalize();
  return 0;
}
Ejemplo n.º 10
0
int main(int argc,char **argv)
{
  TS             ts;
  SNES           snes;
  SNESLineSearch linesearch;
  Vec            x;
  AppCtx         ctx;
  PetscErrorCode ierr;
  DM             da;

  ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
  ierr = SetFromOptions(&ctx);CHKERRQ(ierr);
  ierr = TSCreate(PETSC_COMM_WORLD, &ts);CHKERRQ(ierr);
  ierr = TSSetType(ts,TSCN);CHKERRQ(ierr);
  ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
  ierr = TSSetIFunction(ts, NULL, FormIFunction, &ctx);CHKERRQ(ierr);
  ierr = DMDACreate2d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,-4,-4,PETSC_DECIDE,PETSC_DECIDE,N_SPECIES,1,NULL,NULL,&da);CHKERRQ(ierr);
  ierr = DMDASetUniformCoordinates(da, 0.0, 1.0, 0.0, 1.0, 0.0, 1.0);CHKERRQ(ierr);
  ierr = DMDASetFieldName(da,0,"species A");CHKERRQ(ierr);
  ierr = DMDASetFieldName(da,1,"species B");CHKERRQ(ierr);
  ierr = DMDASetFieldName(da,2,"species C");CHKERRQ(ierr);
  ierr = DMSetApplicationContext(da,&ctx);CHKERRQ(ierr);
  ierr = DMCreateGlobalVector(da,&x);CHKERRQ(ierr);
  ierr = FormInitialGuess(da, &ctx, x);CHKERRQ(ierr);

  ierr = TSSetDM(ts, da);CHKERRQ(ierr);
  ierr = TSSetDuration(ts,10000,1000.0);CHKERRQ(ierr);
  ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_STEPOVER);CHKERRQ(ierr);
  ierr = TSSetInitialTimeStep(ts,0.0,1.0);CHKERRQ(ierr);
  ierr = TSSetSolution(ts,x);CHKERRQ(ierr);
  ierr = TSSetFromOptions(ts);CHKERRQ(ierr);

  ierr = TSGetSNES(ts,&snes);CHKERRQ(ierr);
  ierr = SNESGetLineSearch(snes,&linesearch);CHKERRQ(ierr);
  ierr = SNESLineSearchSetPostCheck(linesearch, ReactingFlowPostCheck, (void*)&ctx);CHKERRQ(ierr);
  ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
  ierr = TSSolve(ts,x);CHKERRQ(ierr);

  ierr = VecDestroy(&x);CHKERRQ(ierr);
  ierr = TSDestroy(&ts);CHKERRQ(ierr);
  ierr = DMDestroy(&da);CHKERRQ(ierr);
  ierr = PetscFinalize();
  PetscFunctionReturn(0);
}
Ejemplo n.º 11
0
int main(int argc, char **argv) {
  
  PetscInitialize( &argc, &argv, (char*)0, 0);

  Grid g = DecomposeGrid( CartesianGrid(N, N) );

  std::cout << g.cells().size() << std::endl;

  Vec u,r;
  u = CreateGhostedVector(g);

  VecDuplicate(u, &r);
  double dt = 1.0 / (N*(fabs(a)+fabs(b)));
  
  // Pocatecni podminka
  VecSet(u, 0.0);
  
  MyContext ctx;
  ctx.gptr = &g;
 
  double t = 0;
  
  TS ts;
  TSCreate(PETSC_COMM_WORLD, &ts);
  TSSetProblemType(ts, TS_NONLINEAR);
  TSSetSolution(ts, u);
  TSSetRHSFunction(ts, NULL, CalculateRHS, &ctx);
  TSSetType(ts, TSEULER);
  TSSetInitialTimeStep(ts, 0.0, dt);
  TSSetDuration(ts, 10000000, tEnd);
  TSSetExactFinalTime(ts, TS_EXACTFINALTIME_MATCHSTEP);
  TSSetFromOptions(ts);
  
  TSSolve(ts, u);

  Save(u, "u.dat");
  
  VecDestroy(&r);
  VecDestroy(&u);
  PetscFinalize();

  return 0;
}
Ejemplo n.º 12
0
int main(int argc,char **argv)
{
  TS                     ts;
  Vec                    x,c;
  PetscErrorCode         ierr;
  DM                     da;

  PetscInitialize(&argc,&argv,(char *)0,help);
  ierr = TSCreate(PETSC_COMM_WORLD, &ts);CHKERRQ(ierr);
  ierr = TSSetType(ts,TSCN);CHKERRQ(ierr);
  ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
  ierr = DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE,DMDA_STENCIL_STAR,-4,-4,PETSC_DECIDE,PETSC_DECIDE,1,1,PETSC_NULL,PETSC_NULL,&da);CHKERRQ(ierr);
  ierr = DMDASetUniformCoordinates(da, 0.0, 1.0, 0.0, 1.0, 0.0, 1.0);CHKERRQ(ierr);

  ierr = DMDASetFieldName(da,0,"Heat");CHKERRQ(ierr);
  ierr = DMCreateGlobalVector(da,&x);CHKERRQ(ierr);
  ierr = FormInitialGuess(da,PETSC_NULL,x);CHKERRQ(ierr);
  ierr = DMDATSSetIFunctionLocal(da,INSERT_VALUES,(PetscErrorCode (*)(DMDALocalInfo*,PetscReal,void*,void*,void*,void*))FormIFunctionLocal,PETSC_NULL);CHKERRQ(ierr);

  /* set up the coefficient */
  ierr = DMGetNamedGlobalVector(da,"coefficient",&c);CHKERRQ(ierr);
  ierr = FormDiffusionCoefficient(da,PETSC_NULL,c);CHKERRQ(ierr);
  ierr = DMRestoreNamedGlobalVector(da,"coefficient",&c);CHKERRQ(ierr);

  ierr = DMCoarsenHookAdd(da,PETSC_NULL,CoefficientRestrictHook,ts);CHKERRQ(ierr);
  ierr = DMSubDomainHookAdd(da,PETSC_NULL,CoefficientSubDomainRestrictHook,ts);CHKERRQ(ierr);

  ierr = TSSetDM(ts, da);CHKERRQ(ierr);
  ierr = TSSetDuration(ts,10000,1000.0);CHKERRQ(ierr);
  ierr = TSSetInitialTimeStep(ts,0.0,0.05);CHKERRQ(ierr);
  ierr = TSSetSolution(ts,x);CHKERRQ(ierr);
  ierr = TSSetFromOptions(ts);CHKERRQ(ierr);

  ierr = TSSolve(ts,x);CHKERRQ(ierr);

  ierr = VecDestroy(&x);CHKERRQ(ierr);
  ierr = TSDestroy(&ts);CHKERRQ(ierr);
  ierr = DMDestroy(&da);CHKERRQ(ierr);
  ierr = PetscFinalize();

  PetscFunctionReturn(0);
}
Ejemplo n.º 13
0
int main(int argc,char **argv)
{
  TS             ts;                 /* timestepping context */
  PetscErrorCode ierr;
  PetscViewer    viewer;

  ierr = PetscInitialize(&argc,&argv,NULL,help);if (ierr) return ierr;
  ierr = PetscDLLibraryAppend(PETSC_COMM_WORLD,&PetscDLLibrariesLoaded,"advection-diffusion-reaction/ex1");CHKERRQ(ierr);
  ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
  ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"advection-diffusion-reaction/binaryoutput",FILE_MODE_READ,&viewer);CHKERRQ(ierr);
  ierr = TSLoad(ts,viewer);CHKERRQ(ierr);
  ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
  /* ierr = PetscFPTView(0);CHKERRQ(ierr); */
  ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
  ierr = TSSetUp(ts);CHKERRQ(ierr);
  ierr = TSView(ts,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
  ierr = TSSolve(ts,NULL);CHKERRQ(ierr);
  ierr = TSDestroy(&ts);CHKERRQ(ierr);
  ierr = PetscFinalize();
  return ierr;
}
Ejemplo n.º 14
0
Archivo: ex45.c Proyecto: petsc/petsc
int main(int argc, char **argv)
{
    AppCtx         ctx;
    DM             dm;
    TS             ts;
    Vec            u, r;
    PetscReal      t       = 0.0;
    PetscReal      L2error = 0.0;
    PetscErrorCode ierr;

    ierr = PetscInitialize(&argc, &argv, NULL, help);
    CHKERRQ(ierr);
    ierr = ProcessOptions(PETSC_COMM_WORLD, &ctx);
    CHKERRQ(ierr);
    ierr = CreateMesh(PETSC_COMM_WORLD, &dm, &ctx);
    CHKERRQ(ierr);
    ierr = DMSetApplicationContext(dm, &ctx);
    CHKERRQ(ierr);
    ierr = PetscMalloc1(1, &ctx.exactFuncs);
    CHKERRQ(ierr);
    ierr = SetupDiscretization(dm, &ctx);
    CHKERRQ(ierr);

    ierr = DMCreateGlobalVector(dm, &u);
    CHKERRQ(ierr);
    ierr = PetscObjectSetName((PetscObject) u, "temperature");
    CHKERRQ(ierr);
    ierr = VecDuplicate(u, &r);
    CHKERRQ(ierr);

    ierr = TSCreate(PETSC_COMM_WORLD, &ts);
    CHKERRQ(ierr);
    ierr = TSSetDM(ts, dm);
    CHKERRQ(ierr);
    ierr = DMTSSetBoundaryLocal(dm, DMPlexTSComputeBoundary, &ctx);
    CHKERRQ(ierr);
    ierr = DMTSSetIFunctionLocal(dm, DMPlexTSComputeIFunctionFEM, &ctx);
    CHKERRQ(ierr);
    ierr = DMTSSetIJacobianLocal(dm, DMPlexTSComputeIJacobianFEM, &ctx);
    CHKERRQ(ierr);
    ierr = TSSetExactFinalTime(ts, TS_EXACTFINALTIME_STEPOVER);
    CHKERRQ(ierr);
    ierr = TSSetFromOptions(ts);
    CHKERRQ(ierr);

    ierr = DMProjectFunction(dm, t, ctx.exactFuncs, NULL, INSERT_ALL_VALUES, u);
    CHKERRQ(ierr);
    ierr = TSSolve(ts, u);
    CHKERRQ(ierr);

    ierr = TSGetTime(ts, &t);
    CHKERRQ(ierr);
    ierr = DMComputeL2Diff(dm, t, ctx.exactFuncs, NULL, u, &L2error);
    CHKERRQ(ierr);
    if (L2error < 1.0e-11) {
        ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: < 1.0e-11\n");
        CHKERRQ(ierr);
    }
    else                   {
        ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: %g\n", L2error);
        CHKERRQ(ierr);
    }
    ierr = VecViewFromOptions(u, NULL, "-sol_vec_view");
    CHKERRQ(ierr);

    ierr = VecDestroy(&u);
    CHKERRQ(ierr);
    ierr = VecDestroy(&r);
    CHKERRQ(ierr);
    ierr = TSDestroy(&ts);
    CHKERRQ(ierr);
    ierr = DMDestroy(&dm);
    CHKERRQ(ierr);
    ierr = PetscFree(ctx.exactFuncs);
    CHKERRQ(ierr);
    ierr = PetscFinalize();
    return ierr;
}
Ejemplo n.º 15
0
Archivo: ex1adj.c Proyecto: petsc/petsc
int main(int argc,char **argv)
{
  TS             ts;            /* ODE integrator */
  Vec            U;             /* solution will be stored here */
  Mat            A;             /* Jacobian matrix */
  Mat            Ap;            /* dfdp */
  PetscErrorCode ierr;
  PetscMPIInt    size;
  PetscInt       n = 2;
  PetscScalar    *u,*v;
  AppCtx         app;
  PetscInt       direction[1];
  PetscBool      terminate[1];
  Vec            lambda[2],mu[2];
  PetscReal      tend;

  FILE           *f;
  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Initialize program
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
  ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
  if (size > 1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"Only for sequential runs");
  app.mode = 1;
  app.lambda1 = 2.75;
  app.lambda2 = 0.36;
  tend = 0.125;
  ierr = PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"ex1adj options","");CHKERRQ(ierr);
  {
    ierr = PetscOptionsReal("-lambda1","","",app.lambda1,&app.lambda1,NULL);CHKERRQ(ierr);
    ierr = PetscOptionsReal("-lambda2","","",app.lambda2,&app.lambda2,NULL);CHKERRQ(ierr);
    ierr = PetscOptionsReal("-tend","","",tend,&tend,NULL);CHKERRQ(ierr);
  }
  ierr = PetscOptionsEnd();CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Create necessary matrix and vectors
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
  ierr = MatSetSizes(A,n,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr);
  ierr = MatSetType(A,MATDENSE);CHKERRQ(ierr);
  ierr = MatSetFromOptions(A);CHKERRQ(ierr);
  ierr = MatSetUp(A);CHKERRQ(ierr);

  ierr = MatCreateVecs(A,&U,NULL);CHKERRQ(ierr);

  ierr = MatCreate(PETSC_COMM_WORLD,&Ap);CHKERRQ(ierr);
  ierr = MatSetSizes(Ap,n,1,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr);
  ierr = MatSetType(Ap,MATDENSE);CHKERRQ(ierr);
  ierr = MatSetFromOptions(Ap);CHKERRQ(ierr);
  ierr = MatSetUp(Ap);CHKERRQ(ierr);
  ierr = MatZeroEntries(Ap);CHKERRQ(ierr); /* initialize to zeros */

  ierr = VecGetArray(U,&u);CHKERRQ(ierr);
  u[0] = 0;
  u[1] = 1;
  ierr = VecRestoreArray(U,&u);CHKERRQ(ierr);
  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Create timestepping solver context
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
  ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
  ierr = TSSetType(ts,TSCN);CHKERRQ(ierr);
  ierr = TSSetIFunction(ts,NULL,(TSIFunction)IFunction,&app);CHKERRQ(ierr);
  ierr = TSSetIJacobian(ts,A,A,(TSIJacobian)IJacobian,&app);CHKERRQ(ierr);
  ierr = TSSetRHSJacobianP(ts,Ap,RHSJacobianP,&app);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Set initial conditions
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSetSolution(ts,U);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Save trajectory of solution so that TSAdjointSolve() may be used
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSetSaveTrajectory(ts);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Set solver options
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSetMaxTime(ts,tend);CHKERRQ(ierr);
  ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_MATCHSTEP);CHKERRQ(ierr);
  ierr = TSSetTimeStep(ts,1./256.);CHKERRQ(ierr);
  ierr = TSSetFromOptions(ts);CHKERRQ(ierr);

  /* Set directions and terminate flags for the two events */
  direction[0] = 0;
  terminate[0] = PETSC_FALSE;
  ierr = TSSetEventHandler(ts,1,direction,terminate,EventFunction,PostEventFunction,(void*)&app);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Run timestepping solver
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSolve(ts,U);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Adjoint model starts here
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = MatCreateVecs(A,&lambda[0],NULL);CHKERRQ(ierr);
  ierr = MatCreateVecs(A,&lambda[1],NULL);CHKERRQ(ierr);
  /*   Set initial conditions for the adjoint integration */
  ierr = VecZeroEntries(lambda[0]);CHKERRQ(ierr);
  ierr = VecZeroEntries(lambda[1]);CHKERRQ(ierr);
  ierr = VecGetArray(lambda[0],&u);CHKERRQ(ierr);
  u[0] = 1.;
  ierr = VecRestoreArray(lambda[0],&u);CHKERRQ(ierr);
  ierr = VecGetArray(lambda[1],&u);CHKERRQ(ierr);
  u[1] = 1.;
  ierr = VecRestoreArray(lambda[1],&u);CHKERRQ(ierr);

  ierr = MatCreateVecs(Ap,&mu[0],NULL);CHKERRQ(ierr);
  ierr = MatCreateVecs(Ap,&mu[1],NULL);CHKERRQ(ierr);
  ierr = VecZeroEntries(mu[0]);CHKERRQ(ierr);
  ierr = VecZeroEntries(mu[1]);CHKERRQ(ierr);
  ierr = TSSetCostGradients(ts,2,lambda,mu);CHKERRQ(ierr);

  ierr = TSAdjointSolve(ts);CHKERRQ(ierr);

  /*
  ierr = VecView(lambda[0],PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
  ierr = VecView(lambda[1],PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
  ierr = VecView(mu[0],PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
  ierr = VecView(mu[1],PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
  */
  ierr = VecGetArray(mu[0],&u);CHKERRQ(ierr);
  ierr = VecGetArray(mu[1],&v);CHKERRQ(ierr);
  f = fopen("adj_mu.out", "a");
  ierr = PetscFPrintf(PETSC_COMM_WORLD,f,"%20.15lf %20.15lf %20.15lf\n",tend,u[0],v[0]);CHKERRQ(ierr);
  ierr = VecRestoreArray(mu[0],&u);CHKERRQ(ierr);
  ierr = VecRestoreArray(mu[1],&v);CHKERRQ(ierr);
  fclose(f);
  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Free work space.  All PETSc objects should be destroyed when they are no longer needed.
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = MatDestroy(&A);CHKERRQ(ierr);
  ierr = VecDestroy(&U);CHKERRQ(ierr);
  ierr = TSDestroy(&ts);CHKERRQ(ierr);

  ierr = MatDestroy(&Ap);CHKERRQ(ierr);
  ierr = VecDestroy(&lambda[0]);CHKERRQ(ierr);
  ierr = VecDestroy(&lambda[1]);CHKERRQ(ierr);
  ierr = VecDestroy(&mu[0]);CHKERRQ(ierr);
  ierr = VecDestroy(&mu[1]);CHKERRQ(ierr);
  ierr = PetscFinalize();
  return ierr;
}
Ejemplo n.º 16
0
int main(int argc,char **argv)
{
  TS             ts;            /* ODE integrator */
  Vec            U;             /* solution will be stored here */
  Mat            A;             /* Jacobian matrix */
  Mat            Jacp;          /* Jacobian matrix */
  PetscErrorCode ierr;
  PetscMPIInt    size;
  PetscInt       n = 2;
  AppCtx         ctx;
  PetscScalar    *u;
  PetscReal      du[2] = {0.0,0.0};
  PetscBool      ensemble = PETSC_FALSE,flg1,flg2;
  PetscReal      ftime;
  PetscInt       steps;
  PetscScalar    *x_ptr,*y_ptr;
  Vec            lambda[1],q,mu[1];

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Initialize program
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
  ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
  if (size > 1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"Only for sequential runs");

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Create necessary matrix and vectors
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
  ierr = MatSetSizes(A,n,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr);
  ierr = MatSetType(A,MATDENSE);CHKERRQ(ierr);
  ierr = MatSetFromOptions(A);CHKERRQ(ierr);
  ierr = MatSetUp(A);CHKERRQ(ierr);

  ierr = MatCreateVecs(A,&U,NULL);CHKERRQ(ierr);

  ierr = MatCreate(PETSC_COMM_WORLD,&Jacp);CHKERRQ(ierr);
  ierr = MatSetSizes(Jacp,PETSC_DECIDE,PETSC_DECIDE,2,1);CHKERRQ(ierr);
  ierr = MatSetFromOptions(Jacp);CHKERRQ(ierr);
  ierr = MatSetUp(Jacp);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Set runtime options
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"Swing equation options","");CHKERRQ(ierr);
  {
    ctx.beta    = 2;
    ctx.c       = 10000.0;
    ctx.u_s     = 1.0;
    ctx.omega_s = 1.0;
    ctx.omega_b = 120.0*PETSC_PI;
    ctx.H       = 5.0;
    ierr        = PetscOptionsScalar("-Inertia","","",ctx.H,&ctx.H,NULL);CHKERRQ(ierr);
    ctx.D       = 5.0;
    ierr        = PetscOptionsScalar("-D","","",ctx.D,&ctx.D,NULL);CHKERRQ(ierr);
    ctx.E       = 1.1378;
    ctx.V       = 1.0;
    ctx.X       = 0.545;
    ctx.Pmax    = ctx.E*ctx.V/ctx.X;;
    ierr        = PetscOptionsScalar("-Pmax","","",ctx.Pmax,&ctx.Pmax,NULL);CHKERRQ(ierr);
    ctx.Pm      = 1.1;
    ierr        = PetscOptionsScalar("-Pm","","",ctx.Pm,&ctx.Pm,NULL);CHKERRQ(ierr);
    ctx.tf      = 0.1;
    ctx.tcl     = 0.2;
    ierr        = PetscOptionsReal("-tf","Time to start fault","",ctx.tf,&ctx.tf,NULL);CHKERRQ(ierr);
    ierr        = PetscOptionsReal("-tcl","Time to end fault","",ctx.tcl,&ctx.tcl,NULL);CHKERRQ(ierr);
    ierr        = PetscOptionsBool("-ensemble","Run ensemble of different initial conditions","",ensemble,&ensemble,NULL);CHKERRQ(ierr);
    if (ensemble) {
      ctx.tf      = -1;
      ctx.tcl     = -1;
    }

    ierr = VecGetArray(U,&u);CHKERRQ(ierr);
    u[0] = PetscAsinScalar(ctx.Pm/ctx.Pmax);
    u[1] = 1.0;
    ierr = PetscOptionsRealArray("-u","Initial solution","",u,&n,&flg1);CHKERRQ(ierr);
    n    = 2;
    ierr = PetscOptionsRealArray("-du","Perturbation in initial solution","",du,&n,&flg2);CHKERRQ(ierr);
    u[0] += du[0];
    u[1] += du[1];
    ierr = VecRestoreArray(U,&u);CHKERRQ(ierr);
    if (flg1 || flg2) {
      ctx.tf      = -1;
      ctx.tcl     = -1;
    }
  }
  ierr = PetscOptionsEnd();CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Create timestepping solver context
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
  ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
  ierr = TSSetType(ts,TSRK);CHKERRQ(ierr);
  ierr = TSSetRHSFunction(ts,NULL,(TSRHSFunction)RHSFunction,&ctx);CHKERRQ(ierr);
  ierr = TSSetRHSJacobian(ts,A,A,(TSRHSJacobian)RHSJacobian,&ctx);CHKERRQ(ierr);
  ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_MATCHSTEP);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Set initial conditions
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSetSolution(ts,U);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Save trajectory of solution so that TSAdjointSolve() may be used
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSetSaveTrajectory(ts);CHKERRQ(ierr);

  ierr = MatCreateVecs(A,&lambda[0],NULL);CHKERRQ(ierr);
  /*   Set initial conditions for the adjoint integration */
  ierr = VecGetArray(lambda[0],&y_ptr);CHKERRQ(ierr);
  y_ptr[0] = 0.0; y_ptr[1] = 0.0;
  ierr = VecRestoreArray(lambda[0],&y_ptr);CHKERRQ(ierr);

  ierr = MatCreateVecs(Jacp,&mu[0],NULL);CHKERRQ(ierr);
  ierr = VecGetArray(mu[0],&x_ptr);CHKERRQ(ierr);
  x_ptr[0] = -1.0;
  ierr = VecRestoreArray(mu[0],&x_ptr);CHKERRQ(ierr);
  ierr = TSSetCostGradients(ts,1,lambda,mu);CHKERRQ(ierr);
  ierr = TSSetCostIntegrand(ts,1,(PetscErrorCode (*)(TS,PetscReal,Vec,Vec,void*))CostIntegrand,
                                        (PetscErrorCode (*)(TS,PetscReal,Vec,Vec*,void*))DRDYFunction,
                                        (PetscErrorCode (*)(TS,PetscReal,Vec,Vec*,void*))DRDPFunction,PETSC_TRUE,&ctx);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Set solver options
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSetDuration(ts,PETSC_DEFAULT,10.0);CHKERRQ(ierr);
  ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_STEPOVER);CHKERRQ(ierr);
  ierr = TSSetInitialTimeStep(ts,0.0,.01);CHKERRQ(ierr);
  ierr = TSSetFromOptions(ts);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Solve nonlinear system
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  if (ensemble) {
    for (du[1] = -2.5; du[1] <= .01; du[1] += .1) {
      ierr = VecGetArray(U,&u);CHKERRQ(ierr);
      u[0] = PetscAsinScalar(ctx.Pm/ctx.Pmax);
      u[1] = ctx.omega_s;
      u[0] += du[0];
      u[1] += du[1];
      ierr = VecRestoreArray(U,&u);CHKERRQ(ierr);
      ierr = TSSetInitialTimeStep(ts,0.0,.01);CHKERRQ(ierr);
      ierr = TSSolve(ts,U);CHKERRQ(ierr);
    }
  } else {
    ierr = TSSolve(ts,U);CHKERRQ(ierr);
  }
  ierr = VecView(U,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
  ierr = TSGetSolveTime(ts,&ftime);CHKERRQ(ierr);
  ierr = TSGetTimeStepNumber(ts,&steps);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Adjoint model starts here
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  /*   Set initial conditions for the adjoint integration */
  ierr = VecGetArray(lambda[0],&y_ptr);CHKERRQ(ierr);
  y_ptr[0] = 0.0; y_ptr[1] = 0.0;
  ierr = VecRestoreArray(lambda[0],&y_ptr);CHKERRQ(ierr);

  ierr = VecGetArray(mu[0],&x_ptr);CHKERRQ(ierr);
  x_ptr[0] = -1.0;
  ierr = VecRestoreArray(mu[0],&x_ptr);CHKERRQ(ierr);

  /*   Set RHS JacobianP */
  ierr = TSAdjointSetRHSJacobian(ts,Jacp,RHSJacobianP,&ctx);CHKERRQ(ierr);

  ierr = TSAdjointSolve(ts);CHKERRQ(ierr);

  ierr = PetscPrintf(PETSC_COMM_WORLD,"\n sensitivity wrt initial conditions: d[Psi(tf)]/d[phi0]  d[Psi(tf)]/d[omega0]\n");CHKERRQ(ierr);
  ierr = VecView(lambda[0],PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
  ierr = VecView(mu[0],PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
  ierr = TSGetCostIntegral(ts,&q);CHKERRQ(ierr);
  ierr = VecView(q,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
  ierr = VecGetArray(q,&x_ptr);CHKERRQ(ierr);
  ierr = PetscPrintf(PETSC_COMM_WORLD,"\n cost function=%g\n",(double)(x_ptr[0]-ctx.Pm));CHKERRQ(ierr);
  ierr = VecRestoreArray(q,&x_ptr);CHKERRQ(ierr);

  ierr = ComputeSensiP(lambda[0],mu[0],&ctx);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Free work space.  All PETSc objects should be destroyed when they are no longer needed.
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = MatDestroy(&A);CHKERRQ(ierr);
  ierr = MatDestroy(&Jacp);CHKERRQ(ierr);
  ierr = VecDestroy(&U);CHKERRQ(ierr);
  ierr = VecDestroy(&lambda[0]);CHKERRQ(ierr);
  ierr = VecDestroy(&mu[0]);CHKERRQ(ierr);
  ierr = TSDestroy(&ts);CHKERRQ(ierr);
  ierr = PetscFinalize();
  return(0);
}
Ejemplo n.º 17
0
int main(int argc, char **argv)
{
  MPI_Comm          comm;
  PetscMPIInt       rank;
  PetscErrorCode    ierr;
  User              user;
  PetscLogDouble       v1, v2;
  PetscInt          nplot = 0;
  char              filename1[2048], fileName[2048];
  PetscBool         set = PETSC_FALSE;
  PetscInt          steps_output;

  ierr = PetscInitialize(&argc, &argv, (char*) 0, help);CHKERRQ(ierr);
  comm = PETSC_COMM_WORLD;
  ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
  ierr = PetscNew(&user);CHKERRQ(ierr);
  ierr = PetscNew(&user->algebra);CHKERRQ(ierr);
  ierr = PetscNew(&user->model);CHKERRQ(ierr);
  ierr = PetscNew(&user->model->physics);CHKERRQ(ierr);

  Algebra   algebra = user->algebra;

  ierr = LoadOptions(comm, user);CHKERRQ(ierr);
  ierr = PetscTime(&v1);CHKERRQ(ierr);
  ierr = CreateMesh(comm, user);CHKERRQ(ierr);
  ierr = PetscTime(&v2);CHKERRQ(ierr);
  ierr = PetscPrintf(PETSC_COMM_WORLD,
		       "Read and Distribute mesh takes %f sec \n", v2 - v1);CHKERRQ(ierr);
  ierr = SetUpLocalSpace(user);CHKERRQ(ierr); //Set up the dofs of each element
  ierr = ConstructGeometryFVM(&user->facegeom, &user->cellgeom, user);CHKERRQ(ierr);

  ierr = LimiterSetup(user);CHKERRQ(ierr);

  if(user->output_solution){
  // the output file options
    ierr = PetscOptionsBegin(PETSC_COMM_WORLD,0,"Options for output solution",0);CHKERRQ(ierr);
    ierr = PetscOptionsString("-solutionfile", "solution file", "AeroSim.c", filename1,filename1, 2048, &set);CHKERRQ(ierr);
    if(!set){SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_NULL,"please use option -solutionfile to specify solution file name \n");}
    ierr = PetscOptionsInt("-steps_output", "the number of time steps between two outputs", "", steps_output, &steps_output, &set);CHKERRQ(ierr);
    if(!set){ steps_output = 1;}
    ierr = PetscOptionsEnd();CHKERRQ(ierr);
  }

  if (user->TimeIntegralMethod == EXPLICITMETHOD) {
    if(user->myownexplicitmethod){
      ierr = PetscPrintf(PETSC_COMM_WORLD,"Using the fully explicit method based on my own routing\n");CHKERRQ(ierr);
      user->current_time = user->initial_time;
      user->current_step = 1;
      ierr = DMCreateGlobalVector(user->dm, &algebra->solution);CHKERRQ(ierr);
      ierr = PetscObjectSetName((PetscObject) algebra->solution, "solution");CHKERRQ(ierr);
      ierr = SetInitialCondition(user->dm, algebra->solution, user);CHKERRQ(ierr);
      ierr = VecDuplicate(algebra->solution, &algebra->fn);CHKERRQ(ierr);
      ierr = VecDuplicate(algebra->solution, &algebra->oldsolution);CHKERRQ(ierr);
      if(user->Explicit_RK2){
        ierr = PetscPrintf(PETSC_COMM_WORLD,"Use the second order Runge Kutta method \n");CHKERRQ(ierr);
      }else{
        ierr = PetscPrintf(PETSC_COMM_WORLD,"Use the first order forward Euler method \n");CHKERRQ(ierr);
      }
      nplot = 0; //the plot step
      while(user->current_time < (user->final_time - 0.05 * user->dt)){
        user->current_time = user->current_time + user->dt;

        ierr = FormTimeStepFunction(user, algebra, algebra->solution, algebra->fn);CHKERRQ(ierr);
        PetscReal fnnorm;
        ierr = VecNorm(algebra->fn,NORM_INFINITY,&fnnorm);CHKERRQ(ierr);
        if(0){
          PetscViewer    viewer;
          ierr = OutputVTK(user->dm, "function.vtk", &viewer);CHKERRQ(ierr);
          ierr = VecView(algebra->fn, viewer);CHKERRQ(ierr);
          ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
          ierr = PetscPrintf(PETSC_COMM_WORLD,"Step %D at time %g with founction norm = %g \n",
                                user->current_step, user->current_time, fnnorm);CHKERRQ(ierr);
          //break;
        }
        if(user->Explicit_RK2){
          ierr = VecCopy(algebra->solution, algebra->oldsolution);CHKERRQ(ierr);//U^n
          ierr = VecAXPY(algebra->solution, user->dt, algebra->fn);CHKERRQ(ierr);//U^{(1)}
          ierr = FormTimeStepFunction(user, algebra, algebra->solution, algebra->fn);CHKERRQ(ierr);//f(U^{(1)})
          ierr = VecAXPY(algebra->solution, 1.0, algebra->oldsolution);CHKERRQ(ierr);//U^n + U^{(1)}
          ierr = VecAXPY(algebra->solution, user->dt, algebra->fn);CHKERRQ(ierr);// + dt*f(U^{(1)})
          ierr = VecScale(algebra->solution, 0.5);CHKERRQ(ierr);
        }else{
          ierr = VecCopy(algebra->solution, algebra->oldsolution);CHKERRQ(ierr);
          ierr = VecAXPY(algebra->solution, user->dt, algebra->fn);CHKERRQ(ierr);
        }

        {// Monitor the solution and function norms
          PetscReal         norm;
          PetscLogDouble    space =0;
          PetscInt          size;

          ierr = VecNorm(algebra->solution,NORM_INFINITY,&norm);CHKERRQ(ierr);
          ierr = VecGetSize(algebra->solution, &size);CHKERRQ(ierr);
          norm = norm/size;
          if (norm>1.e5) {
            SETERRQ2(PETSC_COMM_WORLD, PETSC_ERR_LIB,
            "The norm of the solution is: %f (current time: %f). The explicit method is going to DIVERGE!!!", norm, user->current_time);
          }
          if (user->current_step%10==0) {
            ierr = PetscPrintf(PETSC_COMM_WORLD,"Step %D at time %g with solution norm = %g and founction norm = %g \n",
                                user->current_step, user->current_time, norm, fnnorm);CHKERRQ(ierr);
          }
          ierr =  PetscMallocGetCurrentUsage(&space);CHKERRQ(ierr);
//          if (user->current_step%10==0) {
//            ierr =  PetscPrintf(PETSC_COMM_WORLD,"Current space PetscMalloc()ed %g M\n",
//                                 space/(1024*1024));CHKERRQ(ierr);
//          }
        }

        { // Monitor the difference of two steps' solution
          PetscReal         norm;
          ierr = VecAXPY(algebra->oldsolution, -1, algebra->solution);CHKERRQ(ierr);
          ierr = VecNorm(algebra->oldsolution,NORM_INFINITY,&norm);CHKERRQ(ierr);
          if (user->current_step%10==0) {
            ierr = PetscPrintf(PETSC_COMM_WORLD,"Step %D at time %g with ||u_k-u_{k-1}|| = %g \n",
                              user->current_step, user->current_time, norm);CHKERRQ(ierr);
          }
          if((norm<1.e-6)||(user->current_step > user->max_time_its)) break;
        }

        // output the solution
        if (user->output_solution && (user->current_step%steps_output==0)){
          PetscViewer    viewer;

          // update file name for the current time step
          ierr = PetscSNPrintf(fileName, sizeof(fileName),"%s_%d.vtk",filename1, nplot);CHKERRQ(ierr);
          ierr = PetscPrintf(PETSC_COMM_WORLD,"Outputing solution %s (current time %f)\n", fileName, user->current_time);CHKERRQ(ierr);
          ierr = OutputVTK(user->dm, fileName, &viewer);CHKERRQ(ierr);
          ierr = VecView(algebra->solution, viewer);CHKERRQ(ierr);
          ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
          nplot++;
        }

        user->current_step++;

      }
      ierr = VecDestroy(&algebra->fn);CHKERRQ(ierr);
    }else{
      PetscReal         ftime;
      TS                ts;
      TSConvergedReason reason;
      PetscInt          nsteps;

      ierr = PetscPrintf(PETSC_COMM_WORLD,"Using the fully explicit method based on the PETSC TS routing\n");CHKERRQ(ierr);
      ierr = DMCreateGlobalVector(user->dm, &algebra->solution);CHKERRQ(ierr);
      ierr = PetscObjectSetName((PetscObject) algebra->solution, "solution");CHKERRQ(ierr);
      ierr = SetInitialCondition(user->dm, algebra->solution, user);CHKERRQ(ierr);
      ierr = TSCreate(comm, &ts);CHKERRQ(ierr);
      ierr = TSSetType(ts, TSEULER);CHKERRQ(ierr);
      ierr = TSSetDM(ts, user->dm);CHKERRQ(ierr);
      ierr = TSMonitorSet(ts,TSMonitorFunctionError,&user,NULL);CHKERRQ(ierr);
      ierr = TSSetRHSFunction(ts, NULL, MyRHSFunction, user);CHKERRQ(ierr);
      ierr = TSSetDuration(ts, 1000, user->final_time);CHKERRQ(ierr);
      ierr = TSSetInitialTimeStep(ts, user->initial_time, user->dt);CHKERRQ(ierr);
      ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
      ierr = TSSolve(ts, algebra->solution);CHKERRQ(ierr);
      ierr = TSGetSolveTime(ts, &ftime);CHKERRQ(ierr);
      ierr = TSGetTimeStepNumber(ts, &nsteps);CHKERRQ(ierr);
      ierr = TSGetConvergedReason(ts, &reason);CHKERRQ(ierr);
      ierr = PetscPrintf(PETSC_COMM_WORLD,"%s at time %g after %D steps\n",TSConvergedReasons[reason],ftime,nsteps);CHKERRQ(ierr);
      ierr = TSDestroy(&ts);CHKERRQ(ierr);
    }

    if(user->benchmark_couette) {
      ierr = DMCreateGlobalVector(user->dm, &algebra->exactsolution);CHKERRQ(ierr);
      ierr = ComputeExactSolution(user->dm, user->final_time, algebra->exactsolution, user);CHKERRQ(ierr);
    }

    if (user->output_solution){
      PetscViewer    viewer;
      ierr = OutputVTK(user->dm, "solution.vtk", &viewer);CHKERRQ(ierr);
      ierr = VecView(algebra->solution, viewer);CHKERRQ(ierr);
      ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
    }

    if(user->benchmark_couette) {
      PetscViewer    viewer;
      PetscReal      norm;

      ierr = OutputVTK(user->dm, "exact_solution.vtk", &viewer);CHKERRQ(ierr);
      ierr = VecView(algebra->exactsolution, viewer);CHKERRQ(ierr);
      ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);

      ierr = VecAXPY(algebra->exactsolution, -1, algebra->solution);CHKERRQ(ierr);
      ierr = VecNorm(algebra->exactsolution,NORM_INFINITY,&norm);CHKERRQ(ierr);
      ierr = PetscPrintf(PETSC_COMM_WORLD,"Final time at %f, Error: ||u_k-u|| = %g \n", user->final_time, norm);CHKERRQ(ierr);

      ierr = OutputVTK(user->dm, "Error.vtk", &viewer);CHKERRQ(ierr);
      ierr = VecView(algebra->exactsolution, viewer);CHKERRQ(ierr);
      ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
    }

    ierr = VecDestroy(&algebra->solution);CHKERRQ(ierr);
    ierr = VecDestroy(&algebra->oldsolution);CHKERRQ(ierr);
    ierr = DMDestroy(&user->dm);CHKERRQ(ierr);
  } else if (user->TimeIntegralMethod == IMPLICITMETHOD) {
    ierr = PetscPrintf(PETSC_COMM_WORLD,"Using the fully implicit method\n");CHKERRQ(ierr);
    ierr =  SNESCreate(comm,&user->snes);CHKERRQ(ierr);
    ierr =  SNESSetDM(user->snes,user->dm);CHKERRQ(ierr);

    ierr = DMCreateGlobalVector(user->dm, &algebra->solution);CHKERRQ(ierr);
    ierr = VecDuplicate(algebra->solution, &algebra->oldsolution);CHKERRQ(ierr);
    ierr = VecDuplicate(algebra->solution, &algebra->f);CHKERRQ(ierr);
    ierr = VecDuplicate(algebra->solution, &algebra->fn);CHKERRQ(ierr);
    ierr = VecDuplicate(algebra->solution, &algebra->oldfn);CHKERRQ(ierr);

    ierr = PetscObjectSetName((PetscObject) algebra->solution, "solution");CHKERRQ(ierr);
    ierr = SetInitialCondition(user->dm, algebra->solution, user);CHKERRQ(ierr);

    ierr = DMSetMatType(user->dm, MATAIJ);CHKERRQ(ierr);
//    ierr = DMCreateMatrix(user->dm, &algebra->A);CHKERRQ(ierr);
    ierr = DMCreateMatrix(user->dm, &algebra->J);CHKERRQ(ierr);
    if (user->JdiffP) {
     /*Set up the preconditioner matrix*/
     ierr = DMCreateMatrix(user->dm, &algebra->P);CHKERRQ(ierr);
    }else{
     algebra->P = algebra->J;
    }

    ierr = MatSetOption(algebra->J, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);CHKERRQ(ierr);

    /*set nonlinear function */
    ierr =  SNESSetFunction(user->snes, algebra->f, FormFunction, (void*)user);CHKERRQ(ierr);
    /* compute Jacobian */
    ierr =  SNESSetJacobian(user->snes, algebra->J, algebra->P, FormJacobian, (void*)user);CHKERRQ(ierr);

    ierr = SNESSetFromOptions(user->snes);CHKERRQ(ierr);

    /* do the solve */
    if (user->timestep == TIMESTEP_STEADY_STATE) {
      ierr = SolveSteadyState(user);CHKERRQ(ierr);
    } else {
      ierr = SolveTimeDependent(user);CHKERRQ(ierr);
    }

    if (user->output_solution){
      PetscViewer    viewer;
      ierr = OutputVTK(user->dm, "solution.vtk", &viewer);CHKERRQ(ierr);
      ierr = VecView(algebra->solution, viewer);CHKERRQ(ierr);
      ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
    }

    if(user->benchmark_couette) {
      PetscViewer    viewer;
      PetscReal      norm;

      ierr = OutputVTK(user->dm, "exact_solution.vtk", &viewer);CHKERRQ(ierr);
      ierr = VecView(algebra->exactsolution, viewer);CHKERRQ(ierr);
      ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);

      ierr = VecAXPY(algebra->exactsolution, -1, algebra->solution);CHKERRQ(ierr);
      ierr = VecNorm(algebra->exactsolution,NORM_INFINITY,&norm);CHKERRQ(ierr);
      ierr = PetscPrintf(PETSC_COMM_WORLD,"Error: ||u_k-u|| = %g \n", norm);CHKERRQ(ierr);

      ierr = OutputVTK(user->dm, "Error.vtk", &viewer);CHKERRQ(ierr);
      ierr = VecView(algebra->exactsolution, viewer);CHKERRQ(ierr);
      ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
    }

    ierr = VecDestroy(&algebra->solution);CHKERRQ(ierr);
    ierr = VecDestroy(&algebra->f);CHKERRQ(ierr);
    ierr = VecDestroy(&algebra->oldsolution);CHKERRQ(ierr);
    ierr = VecDestroy(&algebra->fn);CHKERRQ(ierr);
    ierr = VecDestroy(&algebra->oldfn);CHKERRQ(ierr);

    ierr = SNESDestroy(&user->snes);CHKERRQ(ierr);
    ierr = DMDestroy(&user->dm);CHKERRQ(ierr);

  } else {
    SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"WRONG option for the time integral method. Using the option '-time_integral_method 0 or 1'");
  }

  ierr = VecDestroy(&user->cellgeom);CHKERRQ(ierr);
  ierr = VecDestroy(&user->facegeom);CHKERRQ(ierr);
  ierr = DMDestroy(&user->dmGrad);CHKERRQ(ierr);

  ierr = PetscFunctionListDestroy(&LimitList);CHKERRQ(ierr);
  ierr = PetscFree(user->model->physics);CHKERRQ(ierr);
  ierr = PetscFree(user->algebra);CHKERRQ(ierr);
  ierr = PetscFree(user->model);CHKERRQ(ierr);
  ierr = PetscFree(user);CHKERRQ(ierr);

  {
    PetscLogDouble    space =0;
    ierr =  PetscMallocGetCurrentUsage(&space);CHKERRQ(ierr);
    ierr =  PetscPrintf(PETSC_COMM_WORLD,"Unfreed space at the End %g M\n", space/(1024*1024));CHKERRQ(ierr);
  }

  ierr = PetscFinalize();
  return(0);
}
Ejemplo n.º 18
0
Archivo: ex2.c Proyecto: fengyuqi/petsc
int main(int argc,char **argv)
{
  TS             ts;            /* ODE integrator */
  Vec            U;             /* solution will be stored here */
  Mat            A;             /* Jacobian matrix */
  PetscErrorCode ierr;
  PetscMPIInt    size;
  PetscInt       n = 2;
  AppCtx         ctx;
  PetscScalar    *u;
  PetscReal      du[2] = {0.0,0.0};
  PetscBool      ensemble = PETSC_FALSE,flg1,flg2;

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Initialize program
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
  ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
  if (size > 1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"Only for sequential runs");

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Create necessary matrix and vectors
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
  ierr = MatSetSizes(A,n,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr);
  ierr = MatSetType(A,MATDENSE);CHKERRQ(ierr);
  ierr = MatSetFromOptions(A);CHKERRQ(ierr);
  ierr = MatSetUp(A);CHKERRQ(ierr);

  ierr = MatCreateVecs(A,&U,NULL);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Set runtime options
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"Swing equation options","");CHKERRQ(ierr);
  {
    ctx.omega_s = 2.0*PETSC_PI*60.0;
    ctx.H       = 5.0;
    ierr        = PetscOptionsScalar("-Inertia","","",ctx.H,&ctx.H,NULL);CHKERRQ(ierr);
    ctx.D       = 5.0;
    ierr        = PetscOptionsScalar("-D","","",ctx.D,&ctx.D,NULL);CHKERRQ(ierr);
    ctx.E       = 1.1378;
    ctx.V       = 1.0;
    ctx.X       = 0.545;
    ctx.Pmax    = ctx.E*ctx.V/ctx.X;;
    ierr        = PetscOptionsScalar("-Pmax","","",ctx.Pmax,&ctx.Pmax,NULL);CHKERRQ(ierr);
    ctx.Pm      = 0.9;
    ierr        = PetscOptionsScalar("-Pm","","",ctx.Pm,&ctx.Pm,NULL);CHKERRQ(ierr);
    ctx.tf      = 1.0;
    ctx.tcl     = 1.05;
    ierr        = PetscOptionsReal("-tf","Time to start fault","",ctx.tf,&ctx.tf,NULL);CHKERRQ(ierr);
    ierr        = PetscOptionsReal("-tcl","Time to end fault","",ctx.tcl,&ctx.tcl,NULL);CHKERRQ(ierr);
    ierr        = PetscOptionsBool("-ensemble","Run ensemble of different initial conditions","",ensemble,&ensemble,NULL);CHKERRQ(ierr);
    if (ensemble) {
      ctx.tf      = -1;
      ctx.tcl     = -1;
    }

    ierr = VecGetArray(U,&u);CHKERRQ(ierr);
    u[0] = PetscAsinScalar(ctx.Pm/ctx.Pmax);
    u[1] = 1.0;
    ierr = PetscOptionsRealArray("-u","Initial solution","",u,&n,&flg1);CHKERRQ(ierr);
    n    = 2;
    ierr = PetscOptionsRealArray("-du","Perturbation in initial solution","",du,&n,&flg2);CHKERRQ(ierr);
    u[0] += du[0];
    u[1] += du[1];
    ierr = VecRestoreArray(U,&u);CHKERRQ(ierr);
    if (flg1 || flg2) {
      ctx.tf      = -1;
      ctx.tcl     = -1;
    }
  }
  ierr = PetscOptionsEnd();CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Create timestepping solver context
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
  ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
  ierr = TSSetType(ts,TSROSW);CHKERRQ(ierr);
  ierr = TSSetIFunction(ts,NULL,(TSIFunction) IFunction,&ctx);CHKERRQ(ierr);
  ierr = TSSetIJacobian(ts,A,A,(TSIJacobian)IJacobian,&ctx);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Set initial conditions
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSetSolution(ts,U);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Set solver options
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSetDuration(ts,100000,35.0);CHKERRQ(ierr);
  ierr = TSSetInitialTimeStep(ts,0.0,.01);CHKERRQ(ierr);
  ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
  /* ierr = TSSetPostStep(ts,PostStep);CHKERRQ(ierr);  */


  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Solve nonlinear system
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  if (ensemble) {
    for (du[1] = -2.5; du[1] <= .01; du[1] += .1) {
      ierr = VecGetArray(U,&u);CHKERRQ(ierr);
      u[0] = PetscAsinScalar(ctx.Pm/ctx.Pmax);
      u[1] = ctx.omega_s;
      u[0] += du[0];
      u[1] += du[1];
      ierr = VecRestoreArray(U,&u);CHKERRQ(ierr);
      ierr = TSSetInitialTimeStep(ts,0.0,.01);CHKERRQ(ierr);
      ierr = TSSolve(ts,U);CHKERRQ(ierr);
    }
  } else {
    ierr = TSSolve(ts,U);CHKERRQ(ierr);
  }
  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Free work space.  All PETSc objects should be destroyed when they are no longer needed.
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = MatDestroy(&A);CHKERRQ(ierr);
  ierr = VecDestroy(&U);CHKERRQ(ierr);
  ierr = TSDestroy(&ts);CHKERRQ(ierr);

  ierr = PetscFinalize();
  return(0);
}
Ejemplo n.º 19
0
int main(int argc,char **argv)
{
  PetscErrorCode ierr;
  DM             da;                   /* structured grid topology object */
  TS             ts;                   /* time-stepping object (contains snes) */
  SNES           snes;                 /* Newton solver object */
  Vec            X,residual;           /* solution, residual */
  Mat            J;                    /* Jacobian matrix */
  PetscInt       Mx,My,fsteps,steps;
  ISColoring     iscoloring;
  PetscReal      tstart,tend,ftime,secperday=3600.0*24.0,Y0;
  PetscBool      fdflg = PETSC_FALSE, mfileflg = PETSC_FALSE, optflg = PETSC_FALSE;
  char           mfile[PETSC_MAX_PATH_LEN] = "out.m";
  MatFDColoring  matfdcoloring;
  PorousCtx      user;                 /* user-defined work context */

  PetscInitialize(&argc,&argv,(char *)0,help);

  ierr = DMDACreate2d(PETSC_COMM_WORLD,
             DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE, // correct for zero Dirichlet
             DMDA_STENCIL_STAR, // nonlinear diffusion but diffusivity
                                //   depends on soln W not grad W
             -21,-21,           // default to 20x20 grid but override with
                                //   -da_grid_x, -da_grid_y (or -da_refine)
             PETSC_DECIDE,PETSC_DECIDE, // num of procs in each dim
             2,                 // dof = 2:  node = (W,Y)
                                //        or node = (P,dPsqr)
                                //        or node = (ddxE,ddyN)
             1,                 // s = 1 (stencil extends out one cell)
             PETSC_NULL,PETSC_NULL, // no specify proc decomposition
             &da);CHKERRQ(ierr);
  ierr = DMSetApplicationContext(da,&user);CHKERRQ(ierr);

  /* get Vecs and Mats for this grid */
  ierr = DMCreateGlobalVector(da,&X);CHKERRQ(ierr);
  ierr = VecDuplicate(X,&residual);CHKERRQ(ierr);
  ierr = VecDuplicate(X,&user.geom);CHKERRQ(ierr);
  ierr = DMGetMatrix(da,MATAIJ,&J);CHKERRQ(ierr);

  /* set up contexts */
  tstart   = 10.0 * secperday; /* 10 days in seconds */
  tend     = 30.0 * secperday;
  steps    = 20;
  Y0       = 1.0;              /* initial value of Y, for computing initial
                                  value of P; note Ymin = 0.1 is different */
  user.da = da;
  ierr = DefaultContext(&user);CHKERRQ(ierr);

  ierr = PetscOptionsBegin(PETSC_COMM_WORLD,
           "","options to (W,P)-space better hydrology model alt","");CHKERRQ(ierr);
  {
    ierr = PetscOptionsReal("-alt_sigma","nonlinear power","",
                            user.sigma,&user.sigma,PETSC_NULL);CHKERRQ(ierr);
    ierr = PetscOptionsReal("-alt_Ymin",
                            "min capacity thickness (esp. in pressure computation)","",
                            user.Ymin,&user.Ymin,PETSC_NULL);CHKERRQ(ierr);
    ierr = PetscOptionsReal("-alt_Wmin",
                            "min water amount (esp. in pressure computation)","",
                            user.Wmin,&user.Wmin,PETSC_NULL);CHKERRQ(ierr);
    ierr = PetscOptionsReal("-alt_Y0",
                            "constant initial capacity thickness","",
                            Y0,&Y0,PETSC_NULL);CHKERRQ(ierr);
    ierr = PetscOptionsReal("-alt_Cmelt",
                            "additional coefficient for amount of melt","",
                            user.Cmelt,&user.Cmelt,PETSC_NULL);CHKERRQ(ierr);
    ierr = PetscOptionsReal("-alt_Creep",
                            "creep closure coefficient","",
                            user.Creep,&user.Creep,PETSC_NULL);CHKERRQ(ierr);
    ierr = PetscOptionsReal("-alt_L","half-width of square region in meters","",
                            user.L,&user.L,PETSC_NULL);CHKERRQ(ierr);
    ierr = PetscOptionsReal("-alt_tstart_days","start time in days","",
                            tstart/secperday,&tstart,&optflg);CHKERRQ(ierr);
    if (optflg) { tstart *= secperday; }
    ierr = PetscOptionsReal("-alt_tend_days","end time in days","",
                            tend/secperday,&tend,&optflg);CHKERRQ(ierr);
    if (optflg) { tend *= secperday; }
    ierr = PetscOptionsInt("-alt_steps","number of timesteps to take","",
                           steps,&steps,PETSC_NULL);CHKERRQ(ierr);
    ierr = PetscOptionsBool("-alt_converge_check",
                            "run silent and check for convergence",
                            "",user.run_silent,&user.run_silent,PETSC_NULL);
                            CHKERRQ(ierr);
    ierr = PetscOptionsString("-mfile",
                            "name of Matlab file to write results","",
                            mfile,mfile,PETSC_MAX_PATH_LEN,&mfileflg);
                            CHKERRQ(ierr);
  }
  ierr = PetscOptionsEnd();CHKERRQ(ierr);

  /* fix remaining parameters */
  ierr = DerivedConstants(&user);CHKERRQ(ierr);
  ierr = VecStrideSet(user.geom,0,user.H0);CHKERRQ(ierr);  /* H(x,y) = H0 */
  ierr = VecStrideSet(user.geom,1,0.0);CHKERRQ(ierr);      /* b(x,y) = 0  */
  ierr = DMDASetUniformCoordinates(da,  // square domain
              -user.L, user.L, -user.L, user.L, 0.0, 1.0);CHKERRQ(ierr);
  ierr = DMDAGetInfo(da,PETSC_IGNORE,&Mx,&My,
            PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,
            PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,
            PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE);CHKERRQ(ierr);
  user.dx = 2.0 * user.L / (Mx-1);
  user.dy = 2.0 * user.L / (My-1);

  /* setup TS = timestepping object */
  ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
  ierr = TSSetType(ts,TSCN);CHKERRQ(ierr);
  ierr = TSSetRHSFunction(ts,residual,RHSFunction,&user);CHKERRQ(ierr);

  /* use coloring to compute rhs Jacobian efficiently */
  ierr = PetscOptionsGetBool(PETSC_NULL,"-fd",&fdflg,PETSC_NULL);CHKERRQ(ierr);
  if (fdflg){
    ierr = DMGetColoring(da,IS_COLORING_GLOBAL,MATAIJ,&iscoloring);CHKERRQ(ierr);
    ierr = MatFDColoringCreate(J,iscoloring,&matfdcoloring);CHKERRQ(ierr);
    ierr = MatFDColoringSetFromOptions(matfdcoloring);CHKERRQ(ierr);
    ierr = ISColoringDestroy(&iscoloring);CHKERRQ(ierr);
    ierr = MatFDColoringSetFunction(matfdcoloring,
             (PetscErrorCode (*)(void))RHSFunction,&user);CHKERRQ(ierr);
    ierr = TSSetRHSJacobian(ts,J,J,TSDefaultComputeJacobianColor,
             matfdcoloring);CHKERRQ(ierr);
  } else { /* default case */
    ierr = TSSetRHSJacobian(ts,J,J,RHSJacobian,&user);CHKERRQ(ierr);
  }

  /* set initial state:  W = barenblatt, P = pi (W/Y0)^sigma */
  ierr = InitialState(da,&user,tstart,Y0,X);CHKERRQ(ierr);

  /* set up times for time-stepping */
  ierr = TSSetInitialTimeStep(ts,tstart,
           (tend - tstart) / (PetscReal)steps);CHKERRQ(ierr);
  ierr = TSSetDuration(ts,steps,tend);CHKERRQ(ierr);
  ierr = TSSetExactFinalTime(ts,PETSC_TRUE);CHKERRQ(ierr);
  ierr = TSMonitorSet(ts,MyTSMonitor,&user,PETSC_NULL);CHKERRQ(ierr);

  /* Set SNESVI type and supply upper and lower bounds. */
  ierr = TSGetSNES(ts,&snes);CHKERRQ(ierr);
  ierr = SNESVISetComputeVariableBounds(snes,FormPositivityBounds);
        CHKERRQ(ierr);

  /* ask user to finalize settings */
  ierr = TSSetFromOptions(ts);CHKERRQ(ierr);

  /* report on setup */
  if (!user.run_silent) {
    ierr = PetscPrintf(PETSC_COMM_WORLD,
      "setup done: square       side length = %.3f km\n"
      "            grid               Mx,My = %d,%d\n"
      "            spacing            dx,dy = %.3f,%.3f m\n"
      "            times     tstart:dt:tend = %.3f:%.3f:%.3f days\n",
      2.0 * user.L / 1000.0, Mx, My, user.dx, user.dy,
      tstart / secperday, (tend-tstart)/(steps*secperday), tend / secperday);
      CHKERRQ(ierr);
  }
  if (mfileflg) {
    if (!user.run_silent) {
      ierr = PetscPrintf(PETSC_COMM_WORLD,
        "writing initial W,P and geometry H,b to Matlab file %s ...\n",
        mfile);CHKERRQ(ierr);
    }
    ierr = print2vecmatlab(da,X,"W_init","P_init",mfile,PETSC_FALSE);CHKERRQ(ierr);
    ierr = print2vecmatlab(da,user.geom,"H","b",mfile,PETSC_TRUE);CHKERRQ(ierr);
  }

  /* run time-stepping with implicit steps  */
  ierr = TSSolve(ts,X,&ftime);CHKERRQ(ierr);

  /* make a report on run and final state */
  ierr = TSGetTimeStepNumber(ts,&fsteps);CHKERRQ(ierr);
  if ((!user.run_silent) && (ftime != tend)) {
    ierr = PetscPrintf(PETSC_COMM_WORLD,
    "***WARNING3***:  reported final time wrong:  ftime(=%.12e) != tend(=%.12e) (days)\n",
    ftime / secperday, tend / secperday);CHKERRQ(ierr); }
  if ((!user.run_silent) && (fsteps != steps)) {
    ierr = PetscPrintf(PETSC_COMM_WORLD,
    "***WARNING4***:  reported number of steps wrong:  fsteps(=%D) != steps(=%D)\n",
    fsteps, steps);CHKERRQ(ierr); }

  if (mfileflg) {
    if (!user.run_silent) {
      ierr = PetscPrintf(PETSC_COMM_WORLD,
        "writing final fields to %s ...\n",mfile);CHKERRQ(ierr);
    }
    ierr = print2vecmatlab(da,X,"W_final","P_final",mfile,PETSC_TRUE);CHKERRQ(ierr);
    ierr = printfigurematlab(da,2,"W_init","W_final",mfile,PETSC_TRUE);CHKERRQ(ierr);
    ierr = printfigurematlab(da,3,"P_init","P_final",mfile,PETSC_TRUE);CHKERRQ(ierr);
  }

  if (user.run_silent) {
    ierr = PetscPrintf(PETSC_COMM_WORLD, "%6d  %6d  %9.3f  %.12e\n",
                       Mx, My, (tend-tstart)/secperday, user.maxrnorm);CHKERRQ(ierr);
  }

  /* Free work space.  */
  ierr = MatDestroy(&J);CHKERRQ(ierr);
  if (fdflg) { ierr = MatFDColoringDestroy(&matfdcoloring);CHKERRQ(ierr); }
  ierr = VecDestroy(&X);CHKERRQ(ierr);
  ierr = VecDestroy(&user.geom);CHKERRQ(ierr);
  ierr = VecDestroy(&residual);CHKERRQ(ierr);
  ierr = TSDestroy(&ts);CHKERRQ(ierr);
  ierr = DMDestroy(&da);CHKERRQ(ierr);

  ierr = PetscFinalize();CHKERRQ(ierr);

  PetscFunctionReturn((PetscInt)(user.not_converged_warning));
}
Ejemplo n.º 20
0
int main(int argc,char **argv)
{
  TS                ts;         /* time integrator */
  TSAdapt           adapt;
  Vec               X;          /* solution vector */
  Mat               J;          /* Jacobian matrix */
  PetscInt          steps,maxsteps,ncells,xs,xm,i;
  PetscErrorCode    ierr;
  PetscReal         ftime,dt;
  char              chemfile[PETSC_MAX_PATH_LEN] = "chem.inp",thermofile[PETSC_MAX_PATH_LEN] = "therm.dat";
  struct _User      user;
  TSConvergedReason reason;
  PetscBool         showsolutions = PETSC_FALSE;
  char              **snames,*names;
  Vec               lambda;     /* used with TSAdjoint for sensitivities */

  ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
  ierr = PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"Chemistry solver options","");CHKERRQ(ierr);
  ierr = PetscOptionsString("-chem","CHEMKIN input file","",chemfile,chemfile,sizeof(chemfile),NULL);CHKERRQ(ierr);
  ierr = PetscOptionsString("-thermo","NASA thermo input file","",thermofile,thermofile,sizeof(thermofile),NULL);CHKERRQ(ierr);
  user.pressure = 1.01325e5;    /* Pascal */
  ierr = PetscOptionsReal("-pressure","Pressure of reaction [Pa]","",user.pressure,&user.pressure,NULL);CHKERRQ(ierr);
  user.Tini   = 1550;
  ierr = PetscOptionsReal("-Tini","Initial temperature [K]","",user.Tini,&user.Tini,NULL);CHKERRQ(ierr);
  user.diffus = 100;
  ierr = PetscOptionsReal("-diffus","Diffusion constant","",user.diffus,&user.diffus,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsBool("-draw_solution","Plot the solution for each cell","",showsolutions,&showsolutions,NULL);CHKERRQ(ierr);
  user.diffusion = PETSC_TRUE;
  ierr = PetscOptionsBool("-diffusion","Have diffusion","",user.diffusion,&user.diffusion,NULL);CHKERRQ(ierr);
  user.reactions = PETSC_TRUE;
  ierr = PetscOptionsBool("-reactions","Have reactions","",user.reactions,&user.reactions,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsEnd();CHKERRQ(ierr);

  ierr = TC_initChem(chemfile, thermofile, 0, 1.0);TCCHKERRQ(ierr);
  user.Nspec = TC_getNspec();
  user.Nreac = TC_getNreac();

  ierr    = DMDACreate1d(PETSC_COMM_WORLD,DM_BOUNDARY_PERIODIC,-1,user.Nspec+1,1,NULL,&user.dm);CHKERRQ(ierr);
  ierr    = DMDAGetInfo(user.dm,NULL,&ncells,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL);CHKERRQ(ierr);
  user.dx = 1.0/ncells;  /* Set the coordinates of the cell centers; note final ghost cell is at x coordinate 1.0 */
  ierr    = DMDASetUniformCoordinates(user.dm,0.0,1.0,0.0,1.0,0.0,1.0);CHKERRQ(ierr);

  /* set the names of each field in the DMDA based on the species name */
  ierr = PetscMalloc1((user.Nspec+1)*LENGTHOFSPECNAME,&names);CHKERRQ(ierr);
  ierr = PetscStrcpy(names,"Temp");CHKERRQ(ierr);
  TC_getSnames(user.Nspec,names+LENGTHOFSPECNAME);CHKERRQ(ierr);
  ierr = PetscMalloc1((user.Nspec+2),&snames);CHKERRQ(ierr);
  for (i=0; i<user.Nspec+1; i++) snames[i] = names+i*LENGTHOFSPECNAME;
  snames[user.Nspec+1] = NULL;
  ierr = DMDASetFieldNames(user.dm,(const char * const *)snames);CHKERRQ(ierr);
  ierr = PetscFree(snames);CHKERRQ(ierr);
  ierr = PetscFree(names);CHKERRQ(ierr);


  ierr = DMCreateMatrix(user.dm,&J);CHKERRQ(ierr);
  ierr = DMCreateGlobalVector(user.dm,&X);CHKERRQ(ierr);

  ierr = PetscMalloc3(user.Nspec+1,&user.tchemwork,PetscSqr(user.Nspec+1),&user.Jdense,user.Nspec+1,&user.rows);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Create timestepping solver context
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
  ierr = TSSetDM(ts,user.dm);CHKERRQ(ierr);
  ierr = TSSetType(ts,TSARKIMEX);CHKERRQ(ierr);
  ierr = TSARKIMEXSetFullyImplicit(ts,PETSC_TRUE);CHKERRQ(ierr);
  ierr = TSARKIMEXSetType(ts,TSARKIMEX4);CHKERRQ(ierr);
  ierr = TSSetRHSFunction(ts,NULL,FormRHSFunction,&user);CHKERRQ(ierr);
  ierr = TSSetRHSJacobian(ts,J,J,FormRHSJacobian,&user);CHKERRQ(ierr);

  ftime    = 1.0;
  maxsteps = 10000;
  ierr     = TSSetDuration(ts,maxsteps,ftime);CHKERRQ(ierr);
  ierr     = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_STEPOVER);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Set initial conditions
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = FormInitialSolution(ts,X,&user);CHKERRQ(ierr);
  ierr = TSSetSolution(ts,X);CHKERRQ(ierr);
  dt   = 1e-10;                 /* Initial time step */
  ierr = TSSetInitialTimeStep(ts,0.0,dt);CHKERRQ(ierr);
  ierr = TSGetAdapt(ts,&adapt);CHKERRQ(ierr);
  ierr = TSAdaptSetStepLimits(adapt,1e-12,1e-4);CHKERRQ(ierr); /* Also available with -ts_adapt_dt_min/-ts_adapt_dt_max */
  ierr = TSSetMaxSNESFailures(ts,-1);CHKERRQ(ierr);            /* Retry step an unlimited number of times */


  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Pass information to graphical monitoring routine
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  if (showsolutions) {
    ierr = DMDAGetCorners(user.dm,&xs,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr);
    for (i=xs;i<xs+xm;i++) {
      ierr = MonitorCell(ts,&user,i);CHKERRQ(ierr);
    }
  }

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Set runtime options
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSetFromOptions(ts);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Set final conditions for sensitivities
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = DMCreateGlobalVector(user.dm,&lambda);CHKERRQ(ierr);
  ierr = TSSetCostGradients(ts,1,&lambda,NULL);CHKERRQ(ierr);
  ierr = VecSetValue(lambda,0,1.0,INSERT_VALUES);CHKERRQ(ierr);
  ierr = VecAssemblyBegin(lambda);CHKERRQ(ierr);
  ierr = VecAssemblyEnd(lambda);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Solve ODE
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSolve(ts,X);CHKERRQ(ierr);
  ierr = TSGetSolveTime(ts,&ftime);CHKERRQ(ierr);
  ierr = TSGetTimeStepNumber(ts,&steps);CHKERRQ(ierr);
  ierr = TSGetConvergedReason(ts,&reason);CHKERRQ(ierr);
  ierr = PetscPrintf(PETSC_COMM_WORLD,"%s at time %g after %D steps\n",TSConvergedReasons[reason],(double)ftime,steps);CHKERRQ(ierr);

  {
    Vec                max;
    const char * const *names;
    PetscInt           i;
    const PetscReal    *bmax;

    ierr = TSMonitorEnvelopeGetBounds(ts,&max,NULL);CHKERRQ(ierr);
    if (max) {
      ierr = TSMonitorLGGetVariableNames(ts,&names);CHKERRQ(ierr);
      if (names) {
        ierr = VecGetArrayRead(max,&bmax);CHKERRQ(ierr);
        ierr = PetscPrintf(PETSC_COMM_SELF,"Species - maximum mass fraction\n");CHKERRQ(ierr);
        for (i=1; i<user.Nspec; i++) {
          if (bmax[i] > .01) {ierr = PetscPrintf(PETSC_COMM_SELF,"%s %g\n",names[i],bmax[i]);CHKERRQ(ierr);}
        }
        ierr = VecRestoreArrayRead(max,&bmax);CHKERRQ(ierr);
      }
    }
  }

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Free work space.
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  TC_reset();
  ierr = DMDestroy(&user.dm);CHKERRQ(ierr);
  ierr = MatDestroy(&J);CHKERRQ(ierr);
  ierr = VecDestroy(&X);CHKERRQ(ierr);
  ierr = VecDestroy(&lambda);CHKERRQ(ierr);
  ierr = TSDestroy(&ts);CHKERRQ(ierr);
  ierr = PetscFree3(user.tchemwork,user.Jdense,user.rows);CHKERRQ(ierr);
  ierr = PetscFinalize();
  return ierr;
}
Ejemplo n.º 21
0
int main(int argc,char **argv)
{
  TS             ts;            /* ODE integrator */
  Vec            Y;             /* solution will be stored here */
  Mat            A;             /* Jacobian matrix */
  PetscErrorCode ierr;
  PetscMPIInt    size;
  PetscInt       n = 6;
  PetscScalar    *y;
 
  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Initialize program
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
  ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
  if (size > 1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"Only for sequential runs");

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Create necessary matrix and vectors
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
  ierr = MatSetSizes(A,n,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr);
  ierr = MatSetFromOptions(A);CHKERRQ(ierr);
  ierr = MatSetUp(A);CHKERRQ(ierr);

  ierr = MatCreateVecs(A,&Y,PETSC_NULL);CHKERRQ(ierr);

  ierr = VecGetArray(Y,&y);CHKERRQ(ierr);
  y[0] = 0.0;
  y[1] = 3.0;
  y[2] = y[1];
  y[3] = 6.0;
  y[4] = 0.0;
  y[5] = 0.0;
  ierr = VecRestoreArray(Y,&y);CHKERRQ(ierr);
  
  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Create timestepping solver context
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
  ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
  ierr = TSSetType(ts,TSARKIMEX);CHKERRQ(ierr);
  ierr = TSSetEquationType(ts,TS_EQ_DAE_IMPLICIT_INDEX1);CHKERRQ(ierr);
  ierr = TSARKIMEXSetFullyImplicit(ts,PETSC_TRUE);CHKERRQ(ierr);
  /*ierr = TSSetType(ts,TSROSW);CHKERRQ(ierr);*/
  ierr = TSSetIFunction(ts,PETSC_NULL,IFunctionImplicit,PETSC_NULL);CHKERRQ(ierr);
  ierr = TSSetIJacobian(ts,A,A,IJacobianImplicit,PETSC_NULL);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Set initial conditions
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSetSolution(ts,Y);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Set solver options
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSetDuration(ts,100000,0.15);CHKERRQ(ierr);
  ierr = TSSetInitialTimeStep(ts,0.0,.001);CHKERRQ(ierr);
  ierr = TSSetFromOptions(ts);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Do Time stepping
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSolve(ts,Y);CHKERRQ(ierr);
  
  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Free work space.  All PETSc objects should be destroyed when they are no longer needed.
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = MatDestroy(&A);CHKERRQ(ierr);
  ierr = VecDestroy(&Y);CHKERRQ(ierr);
  ierr = TSDestroy(&ts);CHKERRQ(ierr);

  ierr = PetscFinalize();
  return(0);
}
Ejemplo n.º 22
0
int main(int argc,char **argv)
{
  TS             ts;            /* ODE integrator */
  Vec            U;             /* solution will be stored here */
  Mat            A;             /* Jacobian matrix */
  PetscErrorCode ierr;
  PetscMPIInt    rank;
  PetscInt       n = 2;
  PetscScalar    *u;
  PetscInt       direction=-1;
  PetscBool      terminate=PETSC_FALSE;
  TSAdapt        adapt;

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Initialize program
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
  ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Create necessary matrix and vectors
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
  ierr = MatSetSizes(A,n,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr);
  ierr = MatSetType(A,MATDENSE);CHKERRQ(ierr);
  ierr = MatSetFromOptions(A);CHKERRQ(ierr);
  ierr = MatSetUp(A);CHKERRQ(ierr);

  ierr = MatCreateVecs(A,&U,NULL);CHKERRQ(ierr);

  ierr = VecGetArray(U,&u);CHKERRQ(ierr);
  u[0] = 1.0*rank;
  u[1] = 20.0;
  ierr = VecRestoreArray(U,&u);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Create timestepping solver context
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
  ierr = TSSetSaveTrajectory(ts);CHKERRQ(ierr);
  ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
  ierr = TSSetType(ts,TSROSW);CHKERRQ(ierr);
  ierr = TSSetIFunction(ts,NULL,(TSIFunction) IFunction,NULL);CHKERRQ(ierr);
  ierr = TSSetIJacobian(ts,A,A,(TSIJacobian)IJacobian,NULL);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Set initial conditions
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSetSolution(ts,U);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Set solver options
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSetDuration(ts,1000,30.0);CHKERRQ(ierr);
  ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_STEPOVER);CHKERRQ(ierr);
  ierr = TSSetInitialTimeStep(ts,0.0,0.1);CHKERRQ(ierr);

  ierr = TSSetEventHandler(ts,1,&direction,&terminate,EventFunction,PostEventFunction,NULL);CHKERRQ(ierr);

  /* The adapative time step controller could take very large timesteps resulting in
     the same event occuring multiple times in the same interval. A maximum step size
     limit is enforced here to avoid this issue.
  */
  ierr = TSGetAdapt(ts,&adapt);CHKERRQ(ierr);
  ierr = TSAdaptSetStepLimits(adapt,0.0,0.5);CHKERRQ(ierr);

  ierr = TSSetFromOptions(ts);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Run timestepping solver
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSolve(ts,U);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Free work space.  All PETSc objects should be destroyed when they are no longer needed.
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = MatDestroy(&A);CHKERRQ(ierr);
  ierr = VecDestroy(&U);CHKERRQ(ierr);
  ierr = TSDestroy(&ts);CHKERRQ(ierr);

  ierr = PetscFinalize();
  return ierr;
}
Ejemplo n.º 23
0
int main(int argc,char **argv)
{
  TS             ts;                   /* nonlinear solver */
  Vec            u,r;                  /* solution, residual vector */
  Mat            J;                    /* Jacobian matrix */
  PetscInt       steps,maxsteps = 1000;     /* iterations for convergence */
  PetscErrorCode ierr;
  DM             da;
  PetscReal      ftime,dt;
  AppCtx         user;              /* user-defined work context */

  PetscInitialize(&argc,&argv,(char*)0,help);
  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Create distributed array (DMDA) to manage parallel grid and vectors
  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE,DMDA_STENCIL_STAR,-8,-8,PETSC_DECIDE,PETSC_DECIDE,
                      1,1,NULL,NULL,&da);CHKERRQ(ierr);

  /*  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Extract global vectors from DMDA;
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = DMCreateGlobalVector(da,&u);CHKERRQ(ierr);
  ierr = VecDuplicate(u,&r);CHKERRQ(ierr);

  /* Initialize user application context */
  user.c = -30.0;

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Create timestepping solver context
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
  ierr = TSSetDM(ts,da);CHKERRQ(ierr);
  ierr = TSSetType(ts,TSBEULER);CHKERRQ(ierr);
  ierr = TSSetRHSFunction(ts,r,RHSFunction,&user);CHKERRQ(ierr);

  /* Set Jacobian */
  ierr = DMCreateMatrix(da,MATAIJ,&J);CHKERRQ(ierr);
  ierr = TSSetRHSJacobian(ts,J,J,RHSJacobian,NULL);CHKERRQ(ierr);

  ftime = 1.0;
  ierr  = TSSetDuration(ts,maxsteps,ftime);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Set initial conditions
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = FormInitialSolution(da,u,&user);CHKERRQ(ierr);
  dt   = .01;
  ierr = TSSetInitialTimeStep(ts,0.0,dt);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Set runtime options
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSetFromOptions(ts);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Solve nonlinear system
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSolve(ts,u);CHKERRQ(ierr);
  ierr = TSGetSolveTime(ts,&ftime);CHKERRQ(ierr);
  ierr = TSGetTimeStepNumber(ts,&steps);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Free work space.
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = MatDestroy(&J);CHKERRQ(ierr);
  ierr = VecDestroy(&u);CHKERRQ(ierr);
  ierr = VecDestroy(&r);CHKERRQ(ierr);
  ierr = TSDestroy(&ts);CHKERRQ(ierr);
  ierr = DMDestroy(&da);CHKERRQ(ierr);

  ierr = PetscFinalize();
  PetscFunctionReturn(0);
}
Ejemplo n.º 24
0
int main(int argc,char **argv)
{
  AppCtx         appctx;                 /* user-defined application context */
  PetscErrorCode ierr;
  PetscInt       i, xs, xm, ind, j, lenglob;
  PetscReal      x, *wrk_ptr1, *wrk_ptr2;
  MatNullSpace   nsp;
  PetscMPIInt    size;

   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Initialize program and set problem parameters
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  PetscFunctionBegin;

  ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;

  /*initialize parameters */
  appctx.param.N    = 10;  /* order of the spectral element */
  appctx.param.E    = 10;  /* number of elements */
  appctx.param.L    = 4.0;  /* length of the domain */
  appctx.param.mu   = 0.01; /* diffusion coefficient */
  appctx.initial_dt = 5e-3;
  appctx.param.steps = PETSC_MAX_INT;
  appctx.param.Tend  = 4;

  ierr = PetscOptionsGetInt(NULL,NULL,"-N",&appctx.param.N,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsGetInt(NULL,NULL,"-E",&appctx.param.E,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsGetReal(NULL,NULL,"-Tend",&appctx.param.Tend,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsGetReal(NULL,NULL,"-mu",&appctx.param.mu,NULL);CHKERRQ(ierr);
  appctx.param.Le = appctx.param.L/appctx.param.E;

  ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
  if (appctx.param.E % size) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"Number of elements must be divisible by number of processes");

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Create GLL data structures
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = PetscGLLCreate(appctx.param.N,PETSCGLL_VIA_LINEARALGEBRA,&appctx.SEMop.gll);CHKERRQ(ierr);
  lenglob  = appctx.param.E*(appctx.param.N-1);

  /*
     Create distributed array (DMDA) to manage parallel grid and vectors
     and to set up the ghost point communication pattern.  There are E*(Nl-1)+1
     total grid values spread equally among all the processors, except first and last
  */

  ierr = DMDACreate1d(PETSC_COMM_WORLD,DM_BOUNDARY_PERIODIC,lenglob,1,1,NULL,&appctx.da);CHKERRQ(ierr);
  ierr = DMSetFromOptions(appctx.da);CHKERRQ(ierr);
  ierr = DMSetUp(appctx.da);CHKERRQ(ierr);
 
  /*
     Extract global and local vectors from DMDA; we use these to store the
     approximate solution.  Then duplicate these for remaining vectors that
     have the same types.
  */

  ierr = DMCreateGlobalVector(appctx.da,&appctx.dat.curr_sol);CHKERRQ(ierr);
  ierr = VecDuplicate(appctx.dat.curr_sol,&appctx.SEMop.grid);CHKERRQ(ierr);
  ierr = VecDuplicate(appctx.dat.curr_sol,&appctx.SEMop.mass);CHKERRQ(ierr);

  ierr = DMDAGetCorners(appctx.da,&xs,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr);
  ierr = DMDAVecGetArray(appctx.da,appctx.SEMop.grid,&wrk_ptr1);CHKERRQ(ierr);
  ierr = DMDAVecGetArray(appctx.da,appctx.SEMop.mass,&wrk_ptr2);CHKERRQ(ierr);
  
  /* Compute function over the locally owned part of the grid */
  
    xs=xs/(appctx.param.N-1);
    xm=xm/(appctx.param.N-1);
  
  /* 
     Build total grid and mass over entire mesh (multi-elemental) 
  */ 

  for (i=xs; i<xs+xm; i++) {
    for (j=0; j<appctx.param.N-1; j++) {
      x = (appctx.param.Le/2.0)*(appctx.SEMop.gll.nodes[j]+1.0)+appctx.param.Le*i; 
      ind=i*(appctx.param.N-1)+j;
      wrk_ptr1[ind]=x;
      wrk_ptr2[ind]=.5*appctx.param.Le*appctx.SEMop.gll.weights[j];
      if (j==0) wrk_ptr2[ind]+=.5*appctx.param.Le*appctx.SEMop.gll.weights[j];
    } 
  }
  ierr = DMDAVecRestoreArray(appctx.da,appctx.SEMop.grid,&wrk_ptr1);CHKERRQ(ierr);
  ierr = DMDAVecRestoreArray(appctx.da,appctx.SEMop.mass,&wrk_ptr2);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
   Create matrix data structure; set matrix evaluation routine.
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = DMSetMatrixPreallocateOnly(appctx.da, PETSC_TRUE);CHKERRQ(ierr);
  ierr = DMCreateMatrix(appctx.da,&appctx.SEMop.stiff);CHKERRQ(ierr);
  ierr = DMCreateMatrix(appctx.da,&appctx.SEMop.grad);CHKERRQ(ierr);
  /*
   For linear problems with a time-dependent f(u,t) in the equation
   u_t = f(u,t), the user provides the discretized right-hand-side
   as a time-dependent matrix.
   */
  ierr = RHSMatrixLaplaciangllDM(appctx.ts,0.0,appctx.dat.curr_sol,appctx.SEMop.stiff,appctx.SEMop.stiff,&appctx);CHKERRQ(ierr);
  ierr = RHSMatrixAdvectiongllDM(appctx.ts,0.0,appctx.dat.curr_sol,appctx.SEMop.grad,appctx.SEMop.grad,&appctx);CHKERRQ(ierr);
   /*
       For linear problems with a time-dependent f(u,t) in the equation
       u_t = f(u,t), the user provides the discretized right-hand-side
       as a time-dependent matrix.
    */
  
  ierr = MatDuplicate(appctx.SEMop.stiff,MAT_COPY_VALUES,&appctx.SEMop.keptstiff);CHKERRQ(ierr);

  /* attach the null space to the matrix, this probably is not needed but does no harm */
  ierr = MatNullSpaceCreate(PETSC_COMM_WORLD,PETSC_TRUE,0,NULL,&nsp);CHKERRQ(ierr);
  ierr = MatSetNullSpace(appctx.SEMop.stiff,nsp);CHKERRQ(ierr);
  ierr = MatSetNullSpace(appctx.SEMop.keptstiff,nsp);CHKERRQ(ierr);  
  ierr = MatNullSpaceTest(nsp,appctx.SEMop.stiff,NULL);CHKERRQ(ierr);
  ierr = MatNullSpaceDestroy(&nsp);CHKERRQ(ierr);
  /* attach the null space to the matrix, this probably is not needed but does no harm */
  ierr = MatNullSpaceCreate(PETSC_COMM_WORLD,PETSC_TRUE,0,NULL,&nsp);CHKERRQ(ierr);
  ierr = MatSetNullSpace(appctx.SEMop.grad,nsp);CHKERRQ(ierr);
  ierr = MatNullSpaceTest(nsp,appctx.SEMop.grad,NULL);CHKERRQ(ierr);
  ierr = MatNullSpaceDestroy(&nsp);CHKERRQ(ierr);

  /* Create the TS solver that solves the ODE and its adjoint; set its options */
  ierr = TSCreate(PETSC_COMM_WORLD,&appctx.ts);CHKERRQ(ierr);
  ierr = TSSetProblemType(appctx.ts,TS_NONLINEAR);CHKERRQ(ierr);
  ierr = TSSetType(appctx.ts,TSRK);CHKERRQ(ierr);
  ierr = TSSetDM(appctx.ts,appctx.da);CHKERRQ(ierr);
  ierr = TSSetTime(appctx.ts,0.0);CHKERRQ(ierr);
  ierr = TSSetTimeStep(appctx.ts,appctx.initial_dt);CHKERRQ(ierr);
  ierr = TSSetMaxSteps(appctx.ts,appctx.param.steps);CHKERRQ(ierr);
  ierr = TSSetMaxTime(appctx.ts,appctx.param.Tend);CHKERRQ(ierr);
  ierr = TSSetExactFinalTime(appctx.ts,TS_EXACTFINALTIME_MATCHSTEP);CHKERRQ(ierr);
  ierr = TSSetTolerances(appctx.ts,1e-7,NULL,1e-7,NULL);CHKERRQ(ierr);
  ierr = TSSetSaveTrajectory(appctx.ts);CHKERRQ(ierr);
  ierr = TSSetFromOptions(appctx.ts);CHKERRQ(ierr);
  ierr = TSSetRHSFunction(appctx.ts,NULL,RHSFunction,&appctx);CHKERRQ(ierr);
  ierr = TSSetRHSJacobian(appctx.ts,appctx.SEMop.stiff,appctx.SEMop.stiff,RHSJacobian,&appctx);CHKERRQ(ierr);

  /* Set Initial conditions for the problem  */
  ierr = TrueSolution(appctx.ts,0,appctx.dat.curr_sol,&appctx);CHKERRQ(ierr);

  ierr = TSSetSolutionFunction(appctx.ts,(PetscErrorCode (*)(TS,PetscReal,Vec,void *))TrueSolution,&appctx);CHKERRQ(ierr);
  ierr = TSSetTime(appctx.ts,0.0);CHKERRQ(ierr);
  ierr = TSSetStepNumber(appctx.ts,0);CHKERRQ(ierr);

  ierr = TSSolve(appctx.ts,appctx.dat.curr_sol);CHKERRQ(ierr);

  ierr = MatDestroy(&appctx.SEMop.stiff);CHKERRQ(ierr);
  ierr = MatDestroy(&appctx.SEMop.keptstiff);CHKERRQ(ierr);
  ierr = MatDestroy(&appctx.SEMop.grad);CHKERRQ(ierr);
  ierr = VecDestroy(&appctx.SEMop.grid);CHKERRQ(ierr);
  ierr = VecDestroy(&appctx.SEMop.mass);CHKERRQ(ierr);
  ierr = VecDestroy(&appctx.dat.curr_sol);CHKERRQ(ierr);
  ierr = PetscGLLDestroy(&appctx.SEMop.gll);CHKERRQ(ierr);
  ierr = DMDestroy(&appctx.da);CHKERRQ(ierr);
  ierr = TSDestroy(&appctx.ts);CHKERRQ(ierr);

  /*
     Always call PetscFinalize() before exiting a program.  This routine
       - finalizes the PETSc libraries as well as MPI
       - provides summary and diagnostic information if certain runtime
         options are chosen (e.g., -log_summary).
  */
    ierr = PetscFinalize();
    return ierr;
}
Ejemplo n.º 25
0
int main(int argc,char **argv)
{
  TS                ts;         /* time integrator */
  SNES              snes;       /* nonlinear solver */
  SNESLineSearch    linesearch; /* line search */
  Vec               X;          /* solution, residual vectors */
  Mat               J;          /* Jacobian matrix */
  PetscInt          steps,maxsteps,mx;
  PetscErrorCode    ierr;
  DM                da;
  PetscReal         ftime,dt;
  struct _User      user;       /* user-defined work context */
  TSConvergedReason reason;

  PetscInitialize(&argc,&argv,(char*)0,help);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Create distributed array (DMDA) to manage parallel grid and vectors
  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = DMDACreate1d(PETSC_COMM_WORLD,DMDA_BOUNDARY_NONE,-11,2,2,NULL,&da);CHKERRQ(ierr);

  /*  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Extract global vectors from DMDA;
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = DMCreateGlobalVector(da,&X);CHKERRQ(ierr);

  /* Initialize user application context */
  ierr = PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"Advection-reaction options","");
  {
    user.a[0] = 1;           ierr = PetscOptionsReal("-a0","Advection rate 0","",user.a[0],&user.a[0],NULL);CHKERRQ(ierr);
    user.a[1] = 0;           ierr = PetscOptionsReal("-a1","Advection rate 1","",user.a[1],&user.a[1],NULL);CHKERRQ(ierr);
    user.k[0] = 1e6;         ierr = PetscOptionsReal("-k0","Reaction rate 0","",user.k[0],&user.k[0],NULL);CHKERRQ(ierr);
    user.k[1] = 2*user.k[0]; ierr = PetscOptionsReal("-k1","Reaction rate 1","",user.k[1],&user.k[1],NULL);CHKERRQ(ierr);
    user.s[0] = 0;           ierr = PetscOptionsReal("-s0","Source 0","",user.s[0],&user.s[0],NULL);CHKERRQ(ierr);
    user.s[1] = 1;           ierr = PetscOptionsReal("-s1","Source 1","",user.s[1],&user.s[1],NULL);CHKERRQ(ierr);
  }
  ierr = PetscOptionsEnd();CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Create timestepping solver context
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
  ierr = TSSetDM(ts,da);CHKERRQ(ierr);
  ierr = TSSetType(ts,TSARKIMEX);CHKERRQ(ierr);
  ierr = TSSetRHSFunction(ts,NULL,FormRHSFunction,&user);CHKERRQ(ierr);
  ierr = TSSetIFunction(ts,NULL,FormIFunction,&user);CHKERRQ(ierr);
  ierr = DMCreateMatrix(da,MATAIJ,&J);CHKERRQ(ierr);
  ierr = TSSetIJacobian(ts,J,J,FormIJacobian,&user);CHKERRQ(ierr);

  /* A line search in the nonlinear solve can fail due to ill-conditioning unless an absolute tolerance is set. Since
   * this problem is linear, we deactivate the line search. For a linear problem, it is usually recommended to also use
   * SNESSetType(snes,SNESKSPONLY). */
  ierr = TSGetSNES(ts,&snes);CHKERRQ(ierr);
  ierr = SNESGetLineSearch(snes,&linesearch);CHKERRQ(ierr);
  ierr = SNESLineSearchSetType(linesearch,SNESLINESEARCHBASIC);CHKERRQ(ierr);

  ftime    = 1.0;
  maxsteps = 10000;
  ierr     = TSSetDuration(ts,maxsteps,ftime);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Set initial conditions
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = FormInitialSolution(ts,X,&user);CHKERRQ(ierr);
  ierr = TSSetSolution(ts,X);CHKERRQ(ierr);
  ierr = VecGetSize(X,&mx);CHKERRQ(ierr);
  dt   = .1 * PetscMax(user.a[0],user.a[1]) / mx; /* Advective CFL, I don't know why it needs so much safety factor. */
  ierr = TSSetInitialTimeStep(ts,0.0,dt);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Set runtime options
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSetFromOptions(ts);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Solve nonlinear system
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSolve(ts,X);CHKERRQ(ierr);
  ierr = TSGetSolveTime(ts,&ftime);CHKERRQ(ierr);
  ierr = TSGetTimeStepNumber(ts,&steps);CHKERRQ(ierr);
  ierr = TSGetConvergedReason(ts,&reason);CHKERRQ(ierr);
  ierr = PetscPrintf(PETSC_COMM_WORLD,"%s at time %G after %D steps\n",TSConvergedReasons[reason],ftime,steps);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Free work space.
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = MatDestroy(&J);CHKERRQ(ierr);
  ierr = VecDestroy(&X);CHKERRQ(ierr);
  ierr = TSDestroy(&ts);CHKERRQ(ierr);
  ierr = DMDestroy(&da);CHKERRQ(ierr);
  ierr = PetscFinalize();
  return 0;
}
Ejemplo n.º 26
0
int main(int argc,char **argv)
{
  TS             ts;            /* nonlinear solver */
  Vec            x;             /* solution, residual vectors */
  Mat            A;             /* Jacobian matrix */
  PetscInt       steps;
  PetscReal      ftime   = 0.5;
  PetscBool      monitor = PETSC_FALSE;
  PetscScalar    *x_ptr;
  PetscMPIInt    size;
  struct _n_User user;
  PetscErrorCode ierr;

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Initialize program
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  PetscInitialize(&argc,&argv,NULL,help);

  ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
  if (size != 1) SETERRQ(PETSC_COMM_SELF,1,"This is a uniprocessor example only!");

  ierr = RegisterMyARK2();CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Set runtime options
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */

  user.next_output = 0.0;
  ierr = PetscOptionsGetBool(NULL,"-monitor",&monitor,NULL);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Create necessary matrix and vectors, solve same ODE on every process
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
  ierr = MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,2,2);CHKERRQ(ierr);
  ierr = MatSetFromOptions(A);CHKERRQ(ierr);
  ierr = MatSetUp(A);CHKERRQ(ierr);
  ierr = MatCreateVecs(A,&x,NULL);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Create timestepping solver context
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
  ierr = TSSetType(ts,TSBEULER);CHKERRQ(ierr);
  ierr = TSSetIFunction(ts,NULL,IFunction,&user);CHKERRQ(ierr);
  ierr = TSSetIJacobian(ts,A,A,IJacobian,&user);CHKERRQ(ierr);
  ierr = TSSetDuration(ts,PETSC_DEFAULT,ftime);CHKERRQ(ierr);
  if (monitor) {
    ierr = TSMonitorSet(ts,Monitor,&user,NULL);CHKERRQ(ierr);
  }

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Set initial conditions
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = VecGetArray(x,&x_ptr);CHKERRQ(ierr);
  x_ptr[0] = -2;   x_ptr[1] = -2.355301397608119909925287735864250951918;
  ierr = VecRestoreArray(x,&x_ptr);CHKERRQ(ierr);
  ierr = TSSetInitialTimeStep(ts,0.0,.001);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Set runtime options
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSetFromOptions(ts);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Solve nonlinear system
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSolve(ts,x);CHKERRQ(ierr);
  ierr = TSGetSolveTime(ts,&ftime);CHKERRQ(ierr);
  ierr = TSGetTimeStepNumber(ts,&steps);CHKERRQ(ierr);
  ierr = PetscPrintf(PETSC_COMM_WORLD,"steps %D, ftime %g\n",steps,(double)ftime);CHKERRQ(ierr);
  ierr = VecView(x,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Free work space.  All PETSc objects should be destroyed when they
     are no longer needed.
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = MatDestroy(&A);CHKERRQ(ierr);
  ierr = VecDestroy(&x);CHKERRQ(ierr);
  ierr = TSDestroy(&ts);CHKERRQ(ierr);

  ierr = PetscFinalize();
  PetscFunctionReturn(0);
}
Ejemplo n.º 27
0
int main(int argc, char **argv)
{
  TS                ts;
  Vec               x; /*solution vector*/
  Mat               A; /*Jacobian*/
  PetscInt          steps,maxsteps,mx;
  PetscErrorCode    ierr;
  PetscReal         ftime;
  AppCtx      user;       /* user-defined work context */

  PetscInitialize(&argc,&argv,NULL,help);

  /* Initialize user application context */
  ierr = PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"Allen-Cahn equation","");
  user.param = 9e-4;
  user.xleft = -1.;
  user.xright = 2.;
  user.mx = 400;
  ierr = PetscOptionsReal("-eps","parameter","",user.param,&user.param,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsEnd();CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
   Set runtime options
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  /*
   * ierr = PetscOptionsGetBool(NULL,"-monitor",&monitor,NULL);CHKERRQ(ierr);
   */
  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
   Create necessary matrix and vectors, solve same ODE on every process
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
  ierr = MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,user.mx,user.mx);CHKERRQ(ierr);
  ierr = MatSetFromOptions(A);CHKERRQ(ierr);
  ierr = MatSetUp(A);CHKERRQ(ierr);
  ierr = MatGetVecs(A,&x,NULL);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
   Create time stepping solver context
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
  ierr = TSSetType(ts,TSEIMEX);CHKERRQ(ierr);
  ierr = TSSetRHSFunction(ts,NULL,RHSFunction,&user);CHKERRQ(ierr);
  ierr = TSSetIFunction(ts,NULL,FormIFunction,&user);CHKERRQ(ierr);
  ierr = TSSetIJacobian(ts,A,A,FormIJacobian,&user);CHKERRQ(ierr);
  ftime = 142;
  maxsteps = 100000;
  ierr = TSSetDuration(ts,maxsteps,ftime);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
   Set initial conditions
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = FormInitialSolution(ts,x,&user);CHKERRQ(ierr);
  ierr = TSSetSolution(ts,x);CHKERRQ(ierr);
  ierr = VecGetSize(x,&mx);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
   Set runtime options
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSetFromOptions(ts);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
   Solve nonlinear system
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSolve(ts,x);CHKERRQ(ierr);
  ierr = TSGetTime(ts,&ftime);CHKERRQ(ierr);
  ierr = TSGetTimeStepNumber(ts,&steps);CHKERRQ(ierr);
  ierr = PetscPrintf(PETSC_COMM_WORLD,"eps %g, steps %D, ftime %g\n",(double)user.param,steps,(double)ftime);CHKERRQ(ierr);
  /*   ierr = VecView(x,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);*/

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
   Free work space.
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = MatDestroy(&A);CHKERRQ(ierr);
  ierr = VecDestroy(&x);CHKERRQ(ierr);
  ierr = TSDestroy(&ts);CHKERRQ(ierr);
  ierr = PetscFinalize();
  PetscFunctionReturn(0);
}
Ejemplo n.º 28
0
int main(int argc,char **argv)
{
  TS             ts;                   /* nonlinear solver */
  Vec            u,r;                  /* solution, residual vectors */
  Mat            J,Jmf = PETSC_NULL;   /* Jacobian matrices */
  PetscInt       maxsteps = 1000;      /* iterations for convergence */
  PetscErrorCode ierr;
  DM             da;
  PetscReal      dt;
  AppCtx         user;              /* user-defined work context */
  SNES           snes;
  PetscInt       Jtype; /* Jacobian type
                            0: user provide Jacobian;
                            1: slow finite difference;
                            2: fd with coloring; */

  PetscInitialize(&argc,&argv,(char *)0,help);
  /* Initialize user application context */
  user.da            = PETSC_NULL;
  user.nstencilpts   = 5;
  user.c             = -30.0;
  user.boundary      = 0; /* 0: Drichlet BC; 1: Neumann BC */
  user.viewJacobian  = PETSC_FALSE;
  ierr = PetscOptionsGetInt(PETSC_NULL,"-nstencilpts",&user.nstencilpts,PETSC_NULL);CHKERRQ(ierr);
  ierr = PetscOptionsGetInt(PETSC_NULL,"-boundary",&user.boundary,PETSC_NULL);CHKERRQ(ierr);
  ierr = PetscOptionsHasName(PETSC_NULL,"-viewJacobian",&user.viewJacobian);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Create distributed array (DMDA) to manage parallel grid and vectors
  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  if (user.nstencilpts == 5){
    ierr = DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE,DMDA_STENCIL_STAR,-11,-11,PETSC_DECIDE,PETSC_DECIDE,1,1,PETSC_NULL,PETSC_NULL,&da);CHKERRQ(ierr);
  } else if (user.nstencilpts == 9){
    ierr = DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE,DMDA_STENCIL_BOX,-11,-11,PETSC_DECIDE,PETSC_DECIDE,1,1,PETSC_NULL,PETSC_NULL,&da);CHKERRQ(ierr);
  } else {
    SETERRQ1(PETSC_COMM_WORLD,PETSC_ERR_SUP,"nstencilpts %d is not supported",user.nstencilpts);
  }
  user.da = da;

  /*  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Extract global vectors from DMDA;
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = DMCreateGlobalVector(da,&u);CHKERRQ(ierr);
  ierr = VecDuplicate(u,&r);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Create timestepping solver context
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
  ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
  ierr = TSSetType(ts,TSBEULER);CHKERRQ(ierr);
  ierr = TSSetDM(ts,da);CHKERRQ(ierr);
  ierr = TSSetIFunction(ts,r,FormIFunction,&user);CHKERRQ(ierr);
  ierr = TSSetDuration(ts,maxsteps,1.0);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Set initial conditions
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = FormInitialSolution(u,&user);CHKERRQ(ierr);
  ierr = TSSetSolution(ts,u);CHKERRQ(ierr);
  dt   = .01;
  ierr = TSSetInitialTimeStep(ts,0.0,dt);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
   Set Jacobian evaluation routine
  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = DMCreateMatrix(da,MATAIJ,&J);CHKERRQ(ierr);
  Jtype = 0;
  ierr = PetscOptionsGetInt(PETSC_NULL, "-Jtype",&Jtype,PETSC_NULL);CHKERRQ(ierr);
  if (Jtype == 0){ /* use user provided Jacobian evaluation routine */
    if (user.nstencilpts != 5) SETERRQ1(PETSC_COMM_WORLD,PETSC_ERR_SUP,"user Jacobian routine FormIJacobian() does not support nstencilpts=%D",user.nstencilpts);
    ierr = TSSetIJacobian(ts,J,J,FormIJacobian,&user);CHKERRQ(ierr);
  } else { /* use finite difference Jacobian J as preconditioner and '-snes_mf_operator' for Mat*vec */
    ierr = TSGetSNES(ts,&snes);CHKERRQ(ierr);
    ierr = MatCreateSNESMF(snes,&Jmf);CHKERRQ(ierr);
    if (Jtype == 1){ /* slow finite difference J; */
      ierr = SNESSetJacobian(snes,Jmf,J,SNESDefaultComputeJacobian,PETSC_NULL);CHKERRQ(ierr);
    } else if (Jtype == 2){ /* Use coloring to compute  finite difference J efficiently */
      ierr = SNESSetJacobian(snes,Jmf,J,SNESDefaultComputeJacobianColor,0);CHKERRQ(ierr);
    } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Jtype is not supported");
  }

  /*  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
   Sets various TS parameters from user options
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSetFromOptions(ts);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Solve nonlinear system
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSolve(ts,u);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Free work space.
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = MatDestroy(&J);CHKERRQ(ierr);
  ierr = MatDestroy(&Jmf);CHKERRQ(ierr);
  ierr = VecDestroy(&u);CHKERRQ(ierr);
  ierr = VecDestroy(&r);CHKERRQ(ierr);
  ierr = TSDestroy(&ts);CHKERRQ(ierr);
  ierr = DMDestroy(&da);CHKERRQ(ierr);

  ierr = PetscFinalize();
  PetscFunctionReturn(0);
}
Ejemplo n.º 29
0
int main(int argc,char **argv)
{
  TS             ts;            /* ODE integrator */
  Vec            U;             /* solution will be stored here */
  Mat            A;             /* Jacobian matrix */
  PetscErrorCode ierr;
  PetscMPIInt    size;
  PetscInt       n = 3;
  AppCtx         ctx;
  PetscScalar    *u;

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Initialize program
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
  ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
  if (size > 1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"Only for sequential runs");

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Create necessary matrix and vectors
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
  ierr = MatSetSizes(A,n,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr);
  ierr = MatSetFromOptions(A);CHKERRQ(ierr);
  ierr = MatSetUp(A);CHKERRQ(ierr);

  ierr = MatGetVecs(A,&U,NULL);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Set runtime options
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"Reaction options","");CHKERRQ(ierr);
  {
    ctx.k = .9;
    ierr  = PetscOptionsScalar("-k","Reaction coefficient","",ctx.k,&ctx.k,NULL);CHKERRQ(ierr);
    ierr  = VecDuplicate(U,&ctx.initialsolution);CHKERRQ(ierr);
    ierr  = VecGetArray(ctx.initialsolution,&u);CHKERRQ(ierr);
    u[0]  = 1;
    u[1]  = .7;
    u[2]  = 0;
    ierr  = VecRestoreArray(ctx.initialsolution,&u);CHKERRQ(ierr);
    ierr  = PetscOptionsVec("-initial","Initial values","",ctx.initialsolution,NULL);CHKERRQ(ierr);
  }
  ierr = PetscOptionsEnd();CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Create timestepping solver context
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
  ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
  ierr = TSSetType(ts,TSROSW);CHKERRQ(ierr);
  ierr = TSSetIFunction(ts,NULL,(TSIFunction) IFunction,&ctx);CHKERRQ(ierr);
  ierr = TSSetIJacobian(ts,A,A,(TSIJacobian)IJacobian,&ctx);CHKERRQ(ierr);
  ierr = TSSetSolutionFunction(ts,(TSSolutionFunction)Solution,&ctx);CHKERRQ(ierr);

  {
    DM   dm;
    void *ptr;
    ierr = TSGetDM(ts,&dm);CHKERRQ(ierr);
    ierr = PetscDLSym(NULL,"IFunctionView",&ptr);CHKERRQ(ierr);
    ierr = PetscDLSym(NULL,"IFunctionLoad",&ptr);CHKERRQ(ierr);
    ierr = DMTSSetIFunctionSerialize(dm,(PetscErrorCode (*)(void*,PetscViewer))IFunctionView,(PetscErrorCode (*)(void**,PetscViewer))IFunctionLoad);CHKERRQ(ierr);
    ierr = DMTSSetIJacobianSerialize(dm,(PetscErrorCode (*)(void*,PetscViewer))IFunctionView,(PetscErrorCode (*)(void**,PetscViewer))IFunctionLoad);CHKERRQ(ierr);
  }

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Set initial conditions
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = Solution(ts,0,U,&ctx);CHKERRQ(ierr);
  ierr = TSSetSolution(ts,U);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Set solver options
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSetDuration(ts,1000,20.0);CHKERRQ(ierr);
  ierr = TSSetInitialTimeStep(ts,0.0,.001);CHKERRQ(ierr);
  ierr = TSSetFromOptions(ts);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Solve nonlinear system
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSolve(ts,U);CHKERRQ(ierr);

  ierr = TSView(ts,PETSC_VIEWER_BINARY_WORLD);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Free work space.  All PETSc objects should be destroyed when they are no longer needed.
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = VecDestroy(&ctx.initialsolution);CHKERRQ(ierr);
  ierr = MatDestroy(&A);CHKERRQ(ierr);
  ierr = VecDestroy(&U);CHKERRQ(ierr);
  ierr = TSDestroy(&ts);CHKERRQ(ierr);

  ierr = PetscFinalize();
  return(0);
}
Ejemplo n.º 30
0
Archivo: ex4.c Proyecto: fengyuqi/petsc
int main(int argc,char **argv)
{
  TS             ts;                  /* nonlinear solver */
  Vec            U;                   /* solution, residual vectors */
  PetscErrorCode ierr;
  DM             da;
  AppCtx         appctx;

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Initialize program
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  PetscInitialize(&argc,&argv,(char*)0,help);

  appctx.epsilon = 1.0e-3;
  appctx.delta   = 1.0;
  appctx.alpha   = 10.0;
  appctx.beta    = 4.0;
  appctx.gamma   = 1.0;
  appctx.kappa   = .75;
  appctx.lambda  = 1.0;
  appctx.mu      = 100.;
  appctx.cstar   = .2;
  appctx.upwind  = PETSC_TRUE;

  ierr = PetscOptionsGetScalar(NULL,"-delta",&appctx.delta,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsGetBool(NULL,"-upwind",&appctx.upwind,NULL);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Create distributed array (DMDA) to manage parallel grid and vectors
  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = DMDACreate1d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE,-8,2,1,NULL,&da);CHKERRQ(ierr);
  ierr = DMDASetFieldName(da,0,"rho");CHKERRQ(ierr);
  ierr = DMDASetFieldName(da,1,"c");CHKERRQ(ierr);

  /*  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Extract global vectors from DMDA; then duplicate for remaining
     vectors that are the same types
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = DMCreateGlobalVector(da,&U);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Create timestepping solver context
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
  ierr = TSSetType(ts,TSROSW);CHKERRQ(ierr);
  ierr = TSSetDM(ts,da);CHKERRQ(ierr);
  ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
  ierr = TSSetIFunction(ts,NULL,IFunction,&appctx);CHKERRQ(ierr);


  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Set initial conditions
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = InitialConditions(da,U);CHKERRQ(ierr);
  ierr = TSSetSolution(ts,U);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Set solver options
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSetInitialTimeStep(ts,0.0,.0001);CHKERRQ(ierr);
  ierr = TSSetDuration(ts,PETSC_DEFAULT,1.0);CHKERRQ(ierr);
  ierr = TSSetFromOptions(ts);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Solve nonlinear system
     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = TSSolve(ts,U);CHKERRQ(ierr);

  /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     Free work space.  All PETSc objects should be destroyed when they
     are no longer needed.
   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
  ierr = VecDestroy(&U);CHKERRQ(ierr);
  ierr = TSDestroy(&ts);CHKERRQ(ierr);
  ierr = DMDestroy(&da);CHKERRQ(ierr);

  ierr = PetscFinalize();
  PetscFunctionReturn(0);
}