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;
}
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;
}
/*
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);
}
/*
* 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, ¤t_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);
}
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);
}
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;
}
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;
}
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;
}
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;
}
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);
}
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;
}
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);
}
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;
}
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;
}
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;
}
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);
}
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);
}
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);
}
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));
}
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;
}
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);
}
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;
}
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);
}
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;
}
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;
}
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);
}
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);
}
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);
}
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);
}
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
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ierr = DMCreateGlobalVector(da,&U);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create timestepping solver context
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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
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ierr = InitialConditions(da,U);CHKERRQ(ierr);
ierr = TSSetSolution(ts,U);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Set solver options
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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
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ierr = TSSolve(ts,U);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Free work space. All PETSc objects should be destroyed when they
are no longer needed.
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ierr = VecDestroy(&U);CHKERRQ(ierr);
ierr = TSDestroy(&ts);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscFinalize();
PetscFunctionReturn(0);
}
