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; }
/* * 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); }
virtual void setupInternal(NumericVector<Number> &X) { PetscVector<Number> *pX = cast_ptr<PetscVector<Number> *>(&X); PetscErrorCode ierr; ierr = TSSetIFunction(this->_ts,PETSC_NULL,this->_computeIFunction,this); CHKERRABORT(libMesh::COMM_WORLD,ierr); PetscMatrix<Number> *mat = cast_ptr<PetscMatrix<Number> *>(this->_fe_problem.getNonlinearSystem().sys().matrix); Mat pmat = mat->mat(); ierr = TSSetIJacobian(this->_ts,pmat,pmat,this->_computeIJacobian,this); CHKERRABORT(libMesh::COMM_WORLD,ierr); ierr = TSSetFromOptions(this->_ts); CHKERRABORT(libMesh::COMM_WORLD,ierr); ierr = TSSetSolution(_ts,pX->vec()); CHKERRABORT(libMesh::COMM_WORLD,ierr); }
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); }
PetscErrorCode PostEventFunction(TS ts,PetscInt nevents,PetscInt event_list[],PetscReal t,Vec U,void* ctx) { PetscErrorCode ierr; PetscScalar *u; PetscMPIInt rank; PetscFunctionBegin; ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr); if (nevents) { ierr = VecGetArray(U,&u);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_SELF,"Processor [%d]: Ball hit the ground at t = %f seconds\n",rank,t);CHKERRQ(ierr); /* Set new initial conditions with .9 attenuation */ u[0] = 1.0*rank; u[1] = -0.9*u[1]; ierr = VecRestoreArray(U,&u);CHKERRQ(ierr); } ierr = TSSetSolution(ts,U);CHKERRQ(ierr); 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); }
PetscErrorCode DMTSCheckFromOptions(TS ts, Vec u, PetscErrorCode (**exactFuncs)(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void *ctx), void **ctxs) { DM dm; SNES snes; Vec sol; PetscBool check; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscOptionsHasName(((PetscObject)ts)->options,((PetscObject)ts)->prefix, "-dmts_check", &check);CHKERRQ(ierr); if (!check) PetscFunctionReturn(0); ierr = VecDuplicate(u, &sol);CHKERRQ(ierr); ierr = TSSetSolution(ts, sol);CHKERRQ(ierr); ierr = TSGetDM(ts, &dm);CHKERRQ(ierr); ierr = TSSetUp(ts);CHKERRQ(ierr); ierr = TSGetSNES(ts, &snes);CHKERRQ(ierr); ierr = SNESSetSolution(snes, sol);CHKERRQ(ierr); ierr = DMSNESCheckFromOptions_Internal(snes, dm, u, sol, exactFuncs, ctxs);CHKERRQ(ierr); ierr = VecDestroy(&sol);CHKERRQ(ierr); PetscFunctionReturn(0); }
TimeIntegration_PETSc::TimeIntegration_PETSc(Setup *setup, Grid *grid, Parallel *parallel, Vlasov *vlasov, Fields *fields, Eigenvalue *eigenvalue) : TimeIntegration(setup, grid, parallel, vlasov, fields,eigenvalue) { PetscInitialize(&setup->argc, &setup->argv, (char *) 0, help); // create Matrix Operations int subDiv=0; // create Matrix, a shell for Matrix-free methods MatCreateShell(parallel->Comm[DIR_ALL], grid->getLocalSize(), grid->getLocalSize(), grid->getGlobalSize(), grid->getGlobalSize(), &subDiv, &A_F1); MatSetFromOptions(A_F1); MatShellSetOperation(A_F1, MATOP_MULT, (void(*)()) PETScMatrixVector::MatrixVectorProduct); // Initialize implicit solver TSCreate(parallel->Comm[DIR_ALL], &ts); TSSetProblemType(ts, TS_LINEAR); TSSetRHSFunction(ts, PETSC_NULL,TSComputeRHSFunctionLinear, PETSC_NULL); TSSetRHSJacobian(ts, A_F1, A_F1, TSComputeRHSJacobianConstant, PETSC_NULL); TSSetType(ts, TSBEULER); TSSetFromOptions(ts); // Setup inital vector Vec Vec_init; cmplxd *init_x = PETScMatrixVector::getCreateVector(grid, Vec_init); for(int x = NxLlD, n = 0; x <= NxLuD; x++) { for(int y_k = NkyLlD; y_k <= NkyLuD; y_k++) { for(int z = NzLlD; z <= NzLuD; z++) { for(int v = NvLlD ; v <= NvLuD; v++) { for(int m = NmLlD ; m <= NmLuD ; m++ ) { for(int s = NsLlD; s <= NsLuD; s++) { init_x[n++] = vlasov->f(x,y_k,z,v,m,s); }}} }}} VecRestoreArray(Vec_init, &init_x); TSSetSolution(ts, Vec_init); VecDestroy(&Vec_init); }
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) { 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) { 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) { PetscErrorCode ierr; int time; /* amount of loops */ struct in put; PetscScalar rh; /* relative humidity */ PetscScalar x; /* memory varialbe for relative humidity calculation */ PetscScalar deep_grnd_temp; /* temperature of ground under top soil surface layer */ PetscScalar emma; /* absorption-emission constant for air */ PetscScalar pressure1 = 101300; /* surface pressure */ PetscScalar mixratio; /* mixing ratio */ PetscScalar airtemp; /* temperature of air near boundary layer inversion */ PetscScalar dewtemp; /* dew point temperature */ PetscScalar sfctemp; /* temperature at surface */ PetscScalar pwat; /* total column precipitable water */ PetscScalar cloudTemp; /* temperature at base of cloud */ AppCtx user; /* user-defined work context */ MonitorCtx usermonitor; /* user-defined monitor context */ PetscMPIInt rank,size; TS ts; SNES snes; DM da; Vec T,rhs; /* solution vector */ Mat J; /* Jacobian matrix */ PetscReal ftime,dt; PetscInt steps,dof = 5; PetscBool use_coloring = PETSC_TRUE; MatFDColoring matfdcoloring = 0; PetscBool monitor_off = PETSC_FALSE; PetscInitialize(&argc,&argv,(char*)0,help); ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr); ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr); /* Inputs */ readinput(&put); sfctemp = put.Ts; dewtemp = put.Td; cloudTemp = put.Tc; airtemp = put.Ta; pwat = put.pwt; if (!rank) PetscPrintf(PETSC_COMM_SELF,"Initial Temperature = %g\n",sfctemp); /* input surface temperature */ deep_grnd_temp = sfctemp - 10; /* set underlying ground layer temperature */ emma = emission(pwat); /* accounts for radiative effects of water vapor */ /* Converts from Fahrenheit to Celsuis */ sfctemp = fahr_to_cel(sfctemp); airtemp = fahr_to_cel(airtemp); dewtemp = fahr_to_cel(dewtemp); cloudTemp = fahr_to_cel(cloudTemp); deep_grnd_temp = fahr_to_cel(deep_grnd_temp); /* Converts from Celsius to Kelvin */ sfctemp += 273; airtemp += 273; dewtemp += 273; cloudTemp += 273; deep_grnd_temp += 273; /* Calculates initial relative humidity */ x = calcmixingr(dewtemp,pressure1); mixratio = calcmixingr(sfctemp,pressure1); rh = (x/mixratio)*100; if (!rank) printf("Initial RH = %.1f percent\n\n",rh); /* prints initial relative humidity */ time = 3600*put.time; /* sets amount of timesteps to run model */ /* Configure PETSc TS solver */ /*------------------------------------------*/ /* Create grid */ ierr = DMDACreate2d(PETSC_COMM_WORLD,DMDA_BOUNDARY_PERIODIC,DMDA_BOUNDARY_PERIODIC,DMDA_STENCIL_STAR,-20,-20, PETSC_DECIDE,PETSC_DECIDE,dof,1,NULL,NULL,&da);CHKERRQ(ierr); ierr = DMDASetUniformCoordinates(da, 0.0, 1.0, 0.0, 1.0, 0.0, 1.0);CHKERRQ(ierr); /* Define output window for each variable of interest */ ierr = DMDASetFieldName(da,0,"Ts");CHKERRQ(ierr); ierr = DMDASetFieldName(da,1,"Ta");CHKERRQ(ierr); ierr = DMDASetFieldName(da,2,"u");CHKERRQ(ierr); ierr = DMDASetFieldName(da,3,"v");CHKERRQ(ierr); ierr = DMDASetFieldName(da,4,"p");CHKERRQ(ierr); /* set values for appctx */ user.da = da; user.Ts = sfctemp; user.fract = put.fr; /* fraction of sky covered by clouds */ user.dewtemp = dewtemp; /* dew point temperature (mositure in air) */ user.csoil = 2000000; /* heat constant for layer */ user.dzlay = 0.08; /* thickness of top soil layer */ user.emma = emma; /* emission parameter */ user.wind = put.wnd; /* wind spped */ user.pressure1 = pressure1; /* sea level pressure */ user.airtemp = airtemp; /* temperature of air near boundar layer inversion */ user.Tc = cloudTemp; /* temperature at base of lowest cloud layer */ user.init = put.init; /* user chosen initiation scenario */ user.lat = 70*0.0174532; /* converts latitude degrees to latitude in radians */ user.deep_grnd_temp = deep_grnd_temp; /* temp in lowest ground layer */ /* set values for MonitorCtx */ usermonitor.drawcontours = PETSC_FALSE; ierr = PetscOptionsHasName(NULL,"-drawcontours",&usermonitor.drawcontours);CHKERRQ(ierr); if (usermonitor.drawcontours) { PetscReal bounds[] = {1000.0,-1000., -1000.,-1000., 1000.,-1000., 1000.,-1000., 1000,-1000, 100700,100800}; ierr = PetscViewerDrawOpen(PETSC_COMM_WORLD,0,0,0,0,300,300,&usermonitor.drawviewer);CHKERRQ(ierr); ierr = PetscViewerDrawSetBounds(usermonitor.drawviewer,dof,bounds);CHKERRQ(ierr); } usermonitor.interval = 1; ierr = PetscOptionsGetInt(NULL,"-monitor_interval",&usermonitor.interval,NULL);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Extract global vectors from DA; - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMCreateGlobalVector(da,&T);CHKERRQ(ierr); ierr = VecDuplicate(T,&rhs);CHKERRQ(ierr); /* r: vector to put the computed right hand side */ ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr); ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr); ierr = TSSetType(ts,TSBEULER);CHKERRQ(ierr); ierr = TSSetRHSFunction(ts,rhs,RhsFunc,&user);CHKERRQ(ierr); /* Set Jacobian evaluation routine - use coloring to compute finite difference Jacobian efficiently */ ierr = DMSetMatType(da,MATAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(da,&J);CHKERRQ(ierr); ierr = TSGetSNES(ts,&snes);CHKERRQ(ierr); if (use_coloring) { ISColoring iscoloring; ierr = DMCreateColoring(da,IS_COLORING_GLOBAL,&iscoloring);CHKERRQ(ierr); ierr = MatFDColoringCreate(J,iscoloring,&matfdcoloring);CHKERRQ(ierr); ierr = MatFDColoringSetFromOptions(matfdcoloring);CHKERRQ(ierr); ierr = MatFDColoringSetUp(J,iscoloring,matfdcoloring);CHKERRQ(ierr); ierr = ISColoringDestroy(&iscoloring);CHKERRQ(ierr); ierr = MatFDColoringSetFunction(matfdcoloring,(PetscErrorCode (*)(void))SNESTSFormFunction,ts);CHKERRQ(ierr); ierr = SNESSetJacobian(snes,J,J,SNESComputeJacobianDefaultColor,matfdcoloring);CHKERRQ(ierr); } else { ierr = SNESSetJacobian(snes,J,J,SNESComputeJacobianDefault,NULL);CHKERRQ(ierr); } /* Define what to print for ts_monitor option */ ierr = PetscOptionsHasName(NULL,"-monitor_off",&monitor_off);CHKERRQ(ierr); if (!monitor_off) { ierr = TSMonitorSet(ts,Monitor,&usermonitor,NULL);CHKERRQ(ierr); } ierr = FormInitialSolution(da,T,&user);CHKERRQ(ierr); dt = TIMESTEP; /* initial time step */ ftime = TIMESTEP*time; if (!rank) printf("time %d, ftime %g hour, TIMESTEP %g\n",time,ftime/3600,dt); ierr = TSSetInitialTimeStep(ts,0.0,dt);CHKERRQ(ierr); ierr = TSSetDuration(ts,time,ftime);CHKERRQ(ierr); ierr = TSSetSolution(ts,T);CHKERRQ(ierr); ierr = TSSetDM(ts,da);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set runtime options - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSetFromOptions(ts);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Solve nonlinear system - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSolve(ts,T);CHKERRQ(ierr); ierr = TSGetSolveTime(ts,&ftime);CHKERRQ(ierr); ierr = TSGetTimeStepNumber(ts,&steps);CHKERRQ(ierr); if (!rank) PetscPrintf(PETSC_COMM_WORLD,"Solution T after %g hours %d steps\n",ftime/3600,steps); if (matfdcoloring) {ierr = MatFDColoringDestroy(&matfdcoloring);CHKERRQ(ierr);} if (usermonitor.drawcontours) { ierr = PetscViewerDestroy(&usermonitor.drawviewer);CHKERRQ(ierr); } ierr = MatDestroy(&J);CHKERRQ(ierr); ierr = VecDestroy(&T);CHKERRQ(ierr); ierr = VecDestroy(&rhs);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); PetscFinalize(); return 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; /* 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; /* solution, residual vectors */ Mat J; /* Jacobian matrix */ PetscInt maxsteps = 1000; PetscErrorCode ierr; DM da; AppCtx user; PetscInt i; char Name[16]; /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Initialize program - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ PetscInitialize(&argc,&argv,(char*)0,help); user.N = 1; ierr = PetscOptionsGetInt(NULL,"-N",&user.N,NULL);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create distributed array (DMDA) to manage parallel grid and vectors - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMDACreate1d(PETSC_COMM_WORLD, DMDA_BOUNDARY_MIRROR,-8,user.N,1,NULL,&da);CHKERRQ(ierr); for (i=0; i<user.N; i++) { ierr = PetscSNPrintf(Name,16,"Void size %d",(int)(i+1)); ierr = DMDASetFieldName(da,i,Name);CHKERRQ(ierr); } /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Extract global vectors from DMDA; then duplicate for remaining vectors that are the same types - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMCreateGlobalVector(da,&U);CHKERRQ(ierr); ierr = DMCreateMatrix(da,MATAIJ,&J);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create timestepping solver context - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr); ierr = TSSetType(ts,TSARKIMEX);CHKERRQ(ierr); ierr = TSSetDM(ts,da);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); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set initial conditions - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = InitialConditions(da,U);CHKERRQ(ierr); ierr = TSSetSolution(ts,U);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set solver options - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSetInitialTimeStep(ts,0.0,.001);CHKERRQ(ierr); ierr = TSSetDuration(ts,maxsteps,1.0);CHKERRQ(ierr); ierr = TSSetFromOptions(ts);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Solve nonlinear system - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSolve(ts,U);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Free work space. All PETSc objects should be destroyed when they are no longer needed. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = VecDestroy(&U);CHKERRQ(ierr); ierr = MatDestroy(&J);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); ierr = PetscFinalize(); PetscFunctionReturn(0); }
int main(int argc,char **argv) { TS ts; /* nonlinear solver */ Vec X; /* solution, residual vectors */ Mat J; /* Jacobian matrix */ PetscInt steps,maxsteps,mx; PetscErrorCode ierr; DM da; PetscReal ftime,hx,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 = 1; user.B = 3; user.alpha = 0.02; user.uleft = 1; user.uright = 1; user.vleft = 3; user.vright = 3; ierr = PetscOptionsReal("-A","Reaction rate","",user.A,&user.A,NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-B","Reaction rate","",user.B,&user.B,NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-alpha","Diffusion coefficient","",user.alpha,&user.alpha,NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-uleft","Dirichlet boundary condition","",user.uleft,&user.uleft,NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-uright","Dirichlet boundary condition","",user.uright,&user.uright,NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-vleft","Dirichlet boundary condition","",user.vleft,&user.vleft,NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-vright","Dirichlet boundary condition","",user.vright,&user.vright,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); ftime = 10.0; 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); hx = 1.0/(PetscReal)(mx/2-1); dt = 0.4 * PetscSqr(hx) / user.alpha; /* Diffusive stability limit */ 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; }
/* FormFunction - 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 */ PetscErrorCode FormFunction(Tao tao,Vec P,PetscReal *f,void *ctx0) { AppCtx *ctx = (AppCtx*)ctx0; TS ts; Vec U; /* solution will be stored here */ Mat A; /* Jacobian matrix */ Mat Jacp; /* Jacobian matrix */ PetscErrorCode ierr; PetscInt n = 2; PetscReal ftime; PetscInt steps; PetscScalar *u; PetscScalar *x_ptr,*y_ptr; Vec lambda[1],q,mu[1]; ierr = VecGetArray(P,&x_ptr);CHKERRQ(ierr); ctx->Pm = x_ptr[0]; /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 = TSSetIFunction(ts,NULL,(TSIFunction) IFunction,ctx);CHKERRQ(ierr); ierr = TSSetIJacobian(ts,A,A,(TSIJacobian)IJacobian,ctx);CHKERRQ(ierr); ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_MATCHSTEP);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set initial conditions - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = VecGetArray(U,&u);CHKERRQ(ierr); u[0] = PetscAsinScalar(ctx->Pm/ctx->Pmax); u[1] = 1.0; ierr = VecRestoreArray(U,&u);CHKERRQ(ierr); 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 = TSSetDuration(ts,PETSC_DEFAULT,10.0);CHKERRQ(ierr); ierr = TSSetInitialTimeStep(ts,0.0,.01);CHKERRQ(ierr); 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); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Adjoint model starts here - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ 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 = TSAdjointSetCostGradients(ts,1,lambda,mu);CHKERRQ(ierr); ierr = TSAdjointSetRHSJacobian(ts,Jacp,RHSJacobianP,ctx);CHKERRQ(ierr); ierr = TSAdjointSetCostIntegrand(ts,1,(PetscErrorCode (*)(TS,PetscReal,Vec,Vec,void*))CostIntegrand, (PetscErrorCode (*)(TS,PetscReal,Vec,Vec*,void*))DRDYFunction, (PetscErrorCode (*)(TS,PetscReal,Vec,Vec*,void*))DRDPFunction,ctx);CHKERRQ(ierr); ierr = TSAdjointSolve(ts);CHKERRQ(ierr); ierr = TSAdjointGetCostIntegral(ts,&q);CHKERRQ(ierr); ierr = ComputeSensiP(lambda[0],mu[0],ctx);CHKERRQ(ierr); ierr = VecGetArray(q,&x_ptr);CHKERRQ(ierr); *f = -ctx->Pm + x_ptr[0]; /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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); return 0; }
int main(int argc,char **argv) { TS ts; /* ODE integrator */ Vec x; /* solution */ PetscErrorCode ierr; DM da; AppCtx appctx; Vec lambda[1]; PetscScalar *x_ptr; /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Initialize program - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr; PetscFunctionBeginUser; appctx.D1 = 8.0e-5; appctx.D2 = 4.0e-5; appctx.gamma = .024; appctx.kappa = .06; /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create distributed array (DMDA) to manage parallel grid and vectors - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMDACreate2d(PETSC_COMM_WORLD,DM_BOUNDARY_PERIODIC,DM_BOUNDARY_PERIODIC,DMDA_STENCIL_STAR,65,65,PETSC_DECIDE,PETSC_DECIDE,2,1,NULL,NULL,&da);CHKERRQ(ierr); ierr = DMSetFromOptions(da);CHKERRQ(ierr); ierr = DMSetUp(da);CHKERRQ(ierr); ierr = DMDASetFieldName(da,0,"u");CHKERRQ(ierr); ierr = DMDASetFieldName(da,1,"v");CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Extract global vectors from DMDA; then duplicate for remaining vectors that are the same types - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMCreateGlobalVector(da,&x);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create timestepping solver context - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr); ierr = TSSetType(ts,TSCN);CHKERRQ(ierr); ierr = TSSetDM(ts,da);CHKERRQ(ierr); ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr); ierr = TSSetRHSFunction(ts,NULL,RHSFunction,&appctx);CHKERRQ(ierr); ierr = TSSetRHSJacobian(ts,NULL,NULL,RHSJacobian,&appctx);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set initial conditions - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = InitialConditions(da,x);CHKERRQ(ierr); ierr = TSSetSolution(ts,x);CHKERRQ(ierr); /* Have the TS save its trajectory so that TSAdjointSolve() may be used */ ierr = TSSetSaveTrajectory(ts);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set solver options - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSetDuration(ts,PETSC_DEFAULT,2000.0);CHKERRQ(ierr); ierr = TSSetInitialTimeStep(ts,0.0,.0001);CHKERRQ(ierr); ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_STEPOVER);CHKERRQ(ierr); ierr = TSSetFromOptions(ts);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Solve ODE system - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSolve(ts,x);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Start the Adjoint model - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = VecDuplicate(x,&lambda[0]);CHKERRQ(ierr); /* Reset initial conditions for the adjoint integration */ ierr = VecGetArray(lambda[0],&x_ptr);CHKERRQ(ierr); ierr = InitializeLambda(da,lambda[0],0.5,0.5);CHKERRQ(ierr); ierr = TSSetCostGradients(ts,1,lambda,NULL);CHKERRQ(ierr); ierr = TSAdjointSolve(ts);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Free work space. All PETSc objects should be destroyed when they are no longer needed. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = VecDestroy(&lambda[0]);CHKERRQ(ierr); ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); ierr = DMDestroy(&da);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 */ PetscErrorCode ierr; PetscMPIInt size; PetscInt n = 2; AppCtx ctx; PetscScalar *u; /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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"); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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,&U,NULL);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set runtime options - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"Reaction options","");CHKERRQ(ierr); { ctx.omega_s = 1.0; ierr = PetscOptionsScalar("-omega_s","","",ctx.omega_s,&ctx.omega_s,NULL);CHKERRQ(ierr); ctx.H = 1.0; ierr = PetscOptionsScalar("-H","","",ctx.H,&ctx.H,NULL);CHKERRQ(ierr); ctx.E = 1.0; ierr = PetscOptionsScalar("-E","","",ctx.E,&ctx.E,NULL);CHKERRQ(ierr); ctx.V = 1.0; ierr = PetscOptionsScalar("-V","","",ctx.V,&ctx.V,NULL);CHKERRQ(ierr); ctx.X = 1.0; ierr = PetscOptionsScalar("-X","","",ctx.X,&ctx.X,NULL);CHKERRQ(ierr); ierr = VecGetArray(U,&u);CHKERRQ(ierr); u[0] = 1; u[1] = .7; ierr = VecRestoreArray(U,&u);CHKERRQ(ierr); ierr = PetscOptionsGetVec(NULL,NULL,"-initial",U,NULL);CHKERRQ(ierr); } ierr = PetscOptionsEnd();CHKERRQ(ierr); ierr = PetscRandomCreate(PETSC_COMM_WORLD,&ctx.rand);CHKERRQ(ierr); ierr = PetscRandomSetFromOptions(ctx.rand);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,100000,2000.0);CHKERRQ(ierr); ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_STEPOVER);CHKERRQ(ierr); ierr = TSSetInitialTimeStep(ts,0.0,.001);CHKERRQ(ierr); ierr = TSSetFromOptions(ts);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Solve nonlinear system - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSolve(ts,U);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Free work space. All PETSc objects should be destroyed when they are no longer needed. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = VecDestroy(&U);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); ierr = PetscRandomDestroy(&ctx.rand);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
int main(int argc,char **argv) { PetscFunctionList plist = NULL; char pname[256]; TS ts; /* nonlinear solver */ Vec x,r; /* solution, residual vectors */ Mat A; /* Jacobian matrix */ Problem problem; PetscBool use_monitor; PetscInt steps,maxsteps = 1000,nonlinits,linits,snesfails,rejects; PetscReal ftime; MonitorCtx mon; PetscErrorCode ierr; PetscMPIInt size; /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Initialize program - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ PetscInitialize(&argc,&argv,(char*)0,help); ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr); if (size > 1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"Only for sequential runs"); /* Register the available problems */ ierr = PetscFunctionListAdd(&plist,"rober",&RoberCreate);CHKERRQ(ierr); ierr = PetscFunctionListAdd(&plist,"ce",&CECreate);CHKERRQ(ierr); ierr = PetscFunctionListAdd(&plist,"orego",&OregoCreate);CHKERRQ(ierr); ierr = PetscStrcpy(pname,"ce");CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set runtime options - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"Timestepping benchmark options","");CHKERRQ(ierr); { ierr = PetscOptionsFList("-problem_type","Name of problem to run","",plist,pname,pname,sizeof(pname),NULL);CHKERRQ(ierr); use_monitor = PETSC_FALSE; ierr = PetscOptionsBool("-monitor_error","Display errors relative to exact solutions","",use_monitor,&use_monitor,NULL);CHKERRQ(ierr); } ierr = PetscOptionsEnd();CHKERRQ(ierr); /* Create the new problem */ ierr = PetscNew(&problem);CHKERRQ(ierr); problem->comm = MPI_COMM_WORLD; { PetscErrorCode (*pcreate)(Problem); ierr = PetscFunctionListFind(plist,pname,&pcreate);CHKERRQ(ierr); if (!pcreate) SETERRQ1(PETSC_COMM_SELF,1,"No problem '%s'",pname); ierr = (*pcreate)(problem);CHKERRQ(ierr); } /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create necessary matrix and vectors - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr); ierr = MatSetSizes(A,problem->n,problem->n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); ierr = MatSetFromOptions(A);CHKERRQ(ierr); ierr = MatSetUp(A);CHKERRQ(ierr); ierr = MatGetVecs(A,&x,NULL);CHKERRQ(ierr); ierr = VecDuplicate(x,&r);CHKERRQ(ierr); mon.comm = PETSC_COMM_WORLD; mon.problem = problem; ierr = VecDuplicate(x,&mon.x);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); /* Rosenbrock-W */ ierr = TSSetIFunction(ts,NULL,problem->function,problem->data);CHKERRQ(ierr); ierr = TSSetIJacobian(ts,A,A,problem->jacobian,problem->data);CHKERRQ(ierr); ierr = TSSetDuration(ts,maxsteps,problem->final_time);CHKERRQ(ierr); ierr = TSSetMaxStepRejections(ts,10);CHKERRQ(ierr); ierr = TSSetMaxSNESFailures(ts,-1);CHKERRQ(ierr); /* unlimited */ if (use_monitor) { ierr = TSMonitorSet(ts,&MonitorError,&mon,NULL);CHKERRQ(ierr); } /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set initial conditions - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = (*problem->solution)(0,x,problem->data);CHKERRQ(ierr); ierr = TSSetInitialTimeStep(ts,0.0,.001);CHKERRQ(ierr); ierr = TSSetSolution(ts,x);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 = TSGetSNESFailures(ts,&snesfails);CHKERRQ(ierr); ierr = TSGetStepRejections(ts,&rejects);CHKERRQ(ierr); ierr = TSGetSNESIterations(ts,&nonlinits);CHKERRQ(ierr); ierr = TSGetKSPIterations(ts,&linits);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"steps %D (%D rejected, %D SNES fails), ftime %G, nonlinits %D, linits %D\n",steps,rejects,snesfails,ftime,nonlinits,linits);CHKERRQ(ierr); if (problem->hasexact) { ierr = MonitorError(ts,steps,ftime,x,&mon);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 = VecDestroy(&r);CHKERRQ(ierr); ierr = VecDestroy(&mon.x);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); if (problem->destroy) { ierr = (*problem->destroy)(problem);CHKERRQ(ierr); } ierr = PetscFree(problem);CHKERRQ(ierr); ierr = PetscFunctionListDestroy(&plist);CHKERRQ(ierr); ierr = PetscFinalize(); PetscFunctionReturn(0); }
int main(int argc,char **argv) { TS ts; /* ODE integrator */ Vec U; /* solution will be stored here */ Vec Utrue; PetscErrorCode ierr; PetscMPIInt size; AppCtx ctx; PetscScalar *u; IS iss; IS isf; PetscInt *indicess; PetscInt *indicesf; PetscInt n=2; PetscReal error,tt; /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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"); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create index for slow part and fast part - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = PetscMalloc1(1,&indicess);CHKERRQ(ierr); indicess[0]=0; ierr = PetscMalloc1(1,&indicesf);CHKERRQ(ierr); indicesf[0]=1; ierr = ISCreateGeneral(PETSC_COMM_SELF,1,indicess,PETSC_COPY_VALUES,&iss);CHKERRQ(ierr); ierr = ISCreateGeneral(PETSC_COMM_SELF,1,indicesf,PETSC_COPY_VALUES,&isf);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create necesary vector - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = VecCreate(PETSC_COMM_WORLD,&U);CHKERRQ(ierr); ierr = VecSetSizes(U,n,PETSC_DETERMINE);CHKERRQ(ierr); ierr = VecSetFromOptions(U);CHKERRQ(ierr); ierr = VecDuplicate(U,&Utrue); ierr = VecCopy(U,Utrue); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set initial condition - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = VecGetArray(U,&u);CHKERRQ(ierr); u[0] = PetscSqrtScalar(2.0); u[1] = PetscSqrtScalar(3.0); ierr = VecRestoreArray(U,&u);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create timestepping solver context - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr); ierr = TSSetType(ts,TSMPRK);CHKERRQ(ierr); ierr = TSSetRHSFunction(ts,NULL,(TSRHSFunction)RHSFunction,&ctx);CHKERRQ(ierr); ierr = TSRHSSplitSetIS(ts,"slow",iss);CHKERRQ(ierr); ierr = TSRHSSplitSetIS(ts,"fast",isf);CHKERRQ(ierr); ierr = TSRHSSplitSetRHSFunction(ts,"slow",NULL,(TSRHSFunctionslow)RHSFunctionslow,&ctx);CHKERRQ(ierr); ierr = TSRHSSplitSetRHSFunction(ts,"fast",NULL,(TSRHSFunctionfast)RHSFunctionfast,&ctx);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set initial conditions - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSetSolution(ts,U);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set solver options - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"ODE options","");CHKERRQ(ierr); { ctx.Tf = 0.3; ctx.dt = 0.01; ierr = PetscOptionsScalar("-Tf","","",ctx.Tf,&ctx.Tf,NULL);CHKERRQ(ierr); ierr = PetscOptionsScalar("-dt","","",ctx.dt,&ctx.dt,NULL);CHKERRQ(ierr); } ierr = PetscOptionsEnd();CHKERRQ(ierr); ierr = TSSetMaxTime(ts,ctx.Tf);CHKERRQ(ierr); ierr = TSSetTimeStep(ts,ctx.dt);CHKERRQ(ierr); ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_MATCHSTEP);CHKERRQ(ierr); ierr = TSSetFromOptions(ts);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Solve linear system - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSolve(ts,U);CHKERRQ(ierr); ierr = VecView(U,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Check the error of the Petsc solution - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSGetTime(ts,&tt);CHKERRQ(ierr); ierr = sol_true(tt,Utrue);CHKERRQ(ierr); ierr = VecAXPY(Utrue,-1.0,U);CHKERRQ(ierr); ierr = VecNorm(Utrue,NORM_2,&error); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Print norm2 error - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = PetscPrintf(PETSC_COMM_WORLD,"l2 error norm: %g\n", error);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Free work space. All PETSc objects should be destroyed when they are no longer needed. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = VecDestroy(&U);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); ierr = VecDestroy(&Utrue);CHKERRQ(ierr); ierr = ISDestroy(&iss);CHKERRQ(ierr); ierr = ISDestroy(&isf);CHKERRQ(ierr); ierr = PetscFree(indicess);CHKERRQ(ierr); ierr = PetscFree(indicesf);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
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 */ 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; /* nonlinear solver */ Vec U; /* solution, residual vectors */ PetscErrorCode ierr; DM da; AppCtx appctx; /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Initialize program - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ PetscInitialize(&argc,&argv,(char*)0,help); appctx.epsilon = 1.0e-3; appctx.delta = 1.0; appctx.alpha = 10.0; appctx.beta = 4.0; appctx.gamma = 1.0; appctx.kappa = .75; appctx.lambda = 1.0; appctx.mu = 100.; appctx.cstar = .2; appctx.upwind = PETSC_TRUE; ierr = PetscOptionsGetScalar(NULL,"-delta",&appctx.delta,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetBool(NULL,"-upwind",&appctx.upwind,NULL);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create distributed array (DMDA) to manage parallel grid and vectors - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMDACreate1d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE,-8,2,1,NULL,&da);CHKERRQ(ierr); ierr = DMDASetFieldName(da,0,"rho");CHKERRQ(ierr); ierr = DMDASetFieldName(da,1,"c");CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Extract global vectors from DMDA; then duplicate for remaining vectors that are the same types - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMCreateGlobalVector(da,&U);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create timestepping solver context - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr); ierr = TSSetType(ts,TSROSW);CHKERRQ(ierr); ierr = TSSetDM(ts,da);CHKERRQ(ierr); ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr); ierr = TSSetIFunction(ts,NULL,IFunction,&appctx);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set initial conditions - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = InitialConditions(da,U);CHKERRQ(ierr); ierr = TSSetSolution(ts,U);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set solver options - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSetInitialTimeStep(ts,0.0,.0001);CHKERRQ(ierr); ierr = TSSetDuration(ts,PETSC_DEFAULT,1.0);CHKERRQ(ierr); ierr = TSSetFromOptions(ts);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Solve nonlinear system - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSolve(ts,U);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Free work space. All PETSc objects should be destroyed when they are no longer needed. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = VecDestroy(&U);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); ierr = PetscFinalize(); PetscFunctionReturn(0); }
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; /* 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 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; /* ODE integrator */ Vec U; /* solution */ Mat A; /* Jacobian matrix */ PetscErrorCode ierr; PetscMPIInt size; PetscInt n = 4; AppCtx ctx; PetscScalar *u; /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Initialize program - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ PetscInitialize(&argc,&argv,(char*)0,help); 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,&U,NULL);CHKERRQ(ierr); ctx.k1 = 1.0e-5; ctx.k2 = 1.0e5; ctx.k3 = 1.0e-16; ctx.sigma2 = 1.0e6; ierr = VecDuplicate(U,&ctx.initialsolution);CHKERRQ(ierr); ierr = VecGetArray(ctx.initialsolution,&u);CHKERRQ(ierr); u[0] = 0.0; u[1] = 1.3e8; u[2] = 5.0e11; u[3] = 8.0e11; ierr = VecRestoreArray(ctx.initialsolution,&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,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 = Solution(ts,0,U,&ctx);CHKERRQ(ierr); ierr = TSSetInitialTimeStep(ts,4.0*3600,1.0);CHKERRQ(ierr); ierr = TSSetSolution(ts,U);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set solver options - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSetDuration(ts,1000000,518400.0);CHKERRQ(ierr); ierr = TSSetMaxStepRejections(ts,100);CHKERRQ(ierr); ierr = TSSetMaxSNESFailures(ts,-1);CHKERRQ(ierr); /* unlimited */ ierr = TSSetFromOptions(ts);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Solve nonlinear system - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSolve(ts,U);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Free work space. All PETSc objects should be destroyed when they are no longer needed. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = VecDestroy(&ctx.initialsolution);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = VecDestroy(&U);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); ierr = PetscFinalize(); PetscFunctionReturn(0); }