int main(int argc,char **argv)
{
PetscErrorCode ierr;
AppCtx ctx;
TS ts;
Vec tsrhs,U;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
ierr = TSSetType(ts,TSEULER);CHKERRQ(ierr);
ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
ierr = VecCreateMPI(PETSC_COMM_WORLD,PETSC_DECIDE,1,&tsrhs);CHKERRQ(ierr);
ierr = VecCreateMPI(PETSC_COMM_WORLD,PETSC_DECIDE,1,&U);CHKERRQ(ierr);
ierr = TSSetRHSFunction(ts,tsrhs,TSFunction,&ctx);CHKERRQ(ierr);
ctx.f = f;
ierr = SNESCreate(PETSC_COMM_WORLD,&ctx.snes);CHKERRQ(ierr);
ierr = SNESSetFromOptions(ctx.snes);CHKERRQ(ierr);
ierr = SNESSetFunction(ctx.snes,NULL,SNESFunction,&ctx);CHKERRQ(ierr);
ierr = SNESSetJacobian(ctx.snes,NULL,NULL,SNESComputeJacobianDefault,&ctx);CHKERRQ(ierr);
ctx.F = F;
ierr = VecCreateMPI(PETSC_COMM_WORLD,PETSC_DECIDE,1,&ctx.V);CHKERRQ(ierr);
ierr = VecSet(U,1.0);CHKERRQ(ierr);
ierr = TSSolve(ts,U);CHKERRQ(ierr);
ierr = VecDestroy(&ctx.V);CHKERRQ(ierr);
ierr = VecDestroy(&tsrhs);CHKERRQ(ierr);
ierr = VecDestroy(&U);CHKERRQ(ierr);
ierr = SNESDestroy(&ctx.snes);CHKERRQ(ierr);
ierr = TSDestroy(&ts);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
UserCtx user;
DM red,da;
SNES snes;
DM packer;
PetscBool use_monitor = PETSC_FALSE;
ierr = PetscInitialize(&argc,&argv,NULL,help);if (ierr) return ierr;
ierr = PetscOptionsSetFromOptions(NULL);CHKERRQ(ierr);
/* Hardwire several options; can be changed at command line */
ierr = PetscOptionsInsertString(NULL,common_options);CHKERRQ(ierr);
ierr = PetscOptionsInsertString(NULL,matrix_free_options);CHKERRQ(ierr);
ierr = PetscOptionsInsert(NULL,&argc,&argv,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,NULL,"-use_monitor",&use_monitor,PETSC_IGNORE);CHKERRQ(ierr);
/* Create a global vector that includes a single redundant array and two da arrays */
ierr = DMCompositeCreate(PETSC_COMM_WORLD,&packer);CHKERRQ(ierr);
ierr = DMRedundantCreate(PETSC_COMM_WORLD,0,1,&red);CHKERRQ(ierr);
ierr = DMSetOptionsPrefix(red,"red_");CHKERRQ(ierr);
ierr = DMCompositeAddDM(packer,red);CHKERRQ(ierr);
ierr = DMDACreate1d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,-5,2,1,NULL,&da);CHKERRQ(ierr);
ierr = DMSetOptionsPrefix(red,"da_");CHKERRQ(ierr);
ierr = DMCompositeAddDM(packer,(DM)da);CHKERRQ(ierr);
ierr = DMSetApplicationContext(packer,&user);CHKERRQ(ierr);
packer->ops->creatematrix = DMCreateMatrix_MF;
/* create nonlinear multi-level solver */
ierr = SNESCreate(PETSC_COMM_WORLD,&snes);CHKERRQ(ierr);
ierr = SNESSetDM(snes,packer);CHKERRQ(ierr);
ierr = SNESSetFunction(snes,NULL,ComputeFunction,NULL);CHKERRQ(ierr);
ierr = SNESSetJacobian(snes,NULL, NULL,ComputeJacobian_MF,NULL);CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
if (use_monitor) {
/* create graphics windows */
ierr = PetscViewerDrawOpen(PETSC_COMM_WORLD,0,"u_lambda - state variables and Lagrange multipliers",-1,-1,-1,-1,&user.u_lambda_viewer);CHKERRQ(ierr);
ierr = PetscViewerDrawOpen(PETSC_COMM_WORLD,0,"fu_lambda - derivate w.r.t. state variables and Lagrange multipliers",-1,-1,-1,-1,&user.fu_lambda_viewer);CHKERRQ(ierr);
ierr = SNESMonitorSet(snes,Monitor,0,0);CHKERRQ(ierr);
}
ierr = SNESSolve(snes,NULL,NULL);CHKERRQ(ierr);
ierr = SNESDestroy(&snes);CHKERRQ(ierr);
ierr = DMDestroy(&red);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = DMDestroy(&packer);CHKERRQ(ierr);
if (use_monitor) {
ierr = PetscViewerDestroy(&user.u_lambda_viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&user.fu_lambda_viewer);CHKERRQ(ierr);
}
ierr = PetscFinalize();
return ierr;
}
unsigned int PetscDiffSolver::solve()
{
this->init();
START_LOG("solve()", "PetscDiffSolver");
PetscVector<Number> &x =
*(libmesh_cast_ptr<PetscVector<Number>*>(_system.solution.get()));
PetscMatrix<Number> &jac =
*(libmesh_cast_ptr<PetscMatrix<Number>*>(_system.matrix));
PetscVector<Number> &r =
*(libmesh_cast_ptr<PetscVector<Number>*>(_system.rhs));
#ifdef LIBMESH_ENABLE_CONSTRAINTS
_system.get_dof_map().enforce_constraints_exactly(_system);
#endif
int ierr = 0;
ierr = SNESSetFunction (_snes, r.vec(),
__libmesh_petsc_diff_solver_residual, this);
LIBMESH_CHKERRABORT(ierr);
ierr = SNESSetJacobian (_snes, jac.mat(), jac.mat(),
__libmesh_petsc_diff_solver_jacobian, this);
LIBMESH_CHKERRABORT(ierr);
# if PETSC_VERSION_LESS_THAN(2,2,0)
ierr = SNESSolve (_snes, x.vec(), &_outer_iterations);
LIBMESH_CHKERRABORT(ierr);
// 2.2.x style
#elif PETSC_VERSION_LESS_THAN(2,3,0)
ierr = SNESSolve (_snes, x.vec());
LIBMESH_CHKERRABORT(ierr);
// 2.3.x & newer style
#else
ierr = SNESSolve (_snes, PETSC_NULL, x.vec());
LIBMESH_CHKERRABORT(ierr);
#endif
STOP_LOG("solve()", "PetscDiffSolver");
SNESConvergedReason reason;
SNESGetConvergedReason(_snes, &reason);
this->clear();
return convert_solve_result(reason);
}
unsigned int PetscDiffSolver::solve()
{
this->init();
START_LOG("solve()", "PetscDiffSolver");
PetscVector<Number> &x =
*(libmesh_cast_ptr<PetscVector<Number>*>(_system.solution.get()));
PetscMatrix<Number> &jac =
*(libmesh_cast_ptr<PetscMatrix<Number>*>(_system.matrix));
PetscVector<Number> &r =
*(libmesh_cast_ptr<PetscVector<Number>*>(_system.rhs));
#ifdef LIBMESH_ENABLE_CONSTRAINTS
_system.get_dof_map().enforce_constraints_exactly(_system);
#endif
int ierr = 0;
ierr = SNESSetFunction (_snes, r.vec(),
__libmesh_petsc_diff_solver_residual, this);
CHKERRABORT(libMesh::COMM_WORLD,ierr);
ierr = SNESSetJacobian (_snes, jac.mat(), jac.mat(),
__libmesh_petsc_diff_solver_jacobian, this);
CHKERRABORT(libMesh::COMM_WORLD,ierr);
# if PETSC_VERSION_LESS_THAN(2,2,0)
ierr = SNESSolve (_snes, x.vec(), &_outer_iterations);
CHKERRABORT(libMesh::COMM_WORLD,ierr);
// 2.2.x style
#elif PETSC_VERSION_LESS_THAN(2,3,0)
ierr = SNESSolve (_snes, x.vec());
CHKERRABORT(libMesh::COMM_WORLD,ierr);
// 2.3.x & newer style
#else
ierr = SNESSolve (_snes, PETSC_NULL, x.vec());
CHKERRABORT(libMesh::COMM_WORLD,ierr);
#endif
STOP_LOG("solve()", "PetscDiffSolver");
this->clear();
// FIXME - We'll worry about getting the solve result right later...
return DiffSolver::CONVERGED_RELATIVE_RESIDUAL;
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
AppCtx ctx;
TS ts;
Vec tsrhs,U;
IS is;
PetscInt I;
PetscMPIInt rank;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
ierr = TSSetType(ts,TSEULER);CHKERRQ(ierr);
ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
ierr = VecCreateMPI(PETSC_COMM_WORLD,1,PETSC_DETERMINE,&tsrhs);CHKERRQ(ierr);
ierr = VecCreateMPI(PETSC_COMM_WORLD,1,PETSC_DETERMINE,&U);CHKERRQ(ierr);
ierr = TSSetRHSFunction(ts,tsrhs,TSFunction,&ctx);CHKERRQ(ierr);
ctx.f = f;
ierr = SNESCreate(PETSC_COMM_WORLD,&ctx.snes);CHKERRQ(ierr);
ierr = SNESSetFromOptions(ctx.snes);CHKERRQ(ierr);
ierr = SNESSetFunction(ctx.snes,NULL,SNESFunction,&ctx);CHKERRQ(ierr);
ierr = SNESSetJacobian(ctx.snes,NULL,NULL,SNESComputeJacobianDefault,&ctx);CHKERRQ(ierr);
ctx.F = F;
ierr = VecCreateMPI(PETSC_COMM_WORLD,1,PETSC_DETERMINE,&ctx.V);CHKERRQ(ierr);
/* Create scatters to move between separate U and V representation and UV representation of solution */
ierr = VecCreateMPI(PETSC_COMM_WORLD,2,PETSC_DETERMINE,&ctx.UV);CHKERRQ(ierr);
I = 2*rank;
ierr = ISCreateGeneral(PETSC_COMM_WORLD,1,&I,PETSC_COPY_VALUES,&is);CHKERRQ(ierr);
ierr = VecScatterCreateWithData(U,NULL,ctx.UV,is,&ctx.scatterU);CHKERRQ(ierr);
ierr = ISDestroy(&is);CHKERRQ(ierr);
I = 2*rank + 1;
ierr = ISCreateGeneral(PETSC_COMM_WORLD,1,&I,PETSC_COPY_VALUES,&is);CHKERRQ(ierr);
ierr = VecScatterCreateWithData(ctx.V,NULL,ctx.UV,is,&ctx.scatterV);CHKERRQ(ierr);
ierr = ISDestroy(&is);CHKERRQ(ierr);
ierr = VecSet(U,1.0);CHKERRQ(ierr);
ierr = TSSolve(ts,U);CHKERRQ(ierr);
ierr = VecDestroy(&ctx.V);CHKERRQ(ierr);
ierr = VecDestroy(&ctx.UV);CHKERRQ(ierr);
ierr = VecScatterDestroy(&ctx.scatterU);CHKERRQ(ierr);
ierr = VecScatterDestroy(&ctx.scatterV);CHKERRQ(ierr);
ierr = VecDestroy(&tsrhs);CHKERRQ(ierr);
ierr = VecDestroy(&U);CHKERRQ(ierr);
ierr = SNESDestroy(&ctx.snes);CHKERRQ(ierr);
ierr = TSDestroy(&ts);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
int main(int argc, char **argv)
{
SNES snes; /* nonlinear solver */
Mat A,J; /* Jacobian,preconditioner matrix */
Vec u,r; /* solution, residual vectors */
AppCtx user; /* user-defined work context */
PetscReal error = 0.0; /* L_2 error in the solution */
PetscErrorCode ierr;
ierr = PetscInitialize(&argc, &argv, PETSC_NULL, help);CHKERRQ(ierr);
ierr = ProcessOptions(PETSC_COMM_WORLD, &user);CHKERRQ(ierr);
ierr = SNESCreate(PETSC_COMM_WORLD, &snes);CHKERRQ(ierr);
ierr = CreateMesh(PETSC_COMM_WORLD, &user, &user.dm);CHKERRQ(ierr);
ierr = SNESSetDM(snes, user.dm);CHKERRQ(ierr);
ierr = SetupSection(user.dm, &user);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(user.dm, &u);CHKERRQ(ierr);
ierr = VecDuplicate(u, &r);CHKERRQ(ierr);
ierr = DMCreateMatrix(user.dm, MATAIJ, &J);CHKERRQ(ierr);
A = J;
ierr = DMSetLocalFunction(user.dm, (DMLocalFunction1) FormFunctionLocal);CHKERRQ(ierr);
ierr = DMSetLocalJacobian(user.dm, (DMLocalJacobian1) FormJacobianLocal);CHKERRQ(ierr);
ierr = SNESSetFunction(snes, r, SNESDMComputeFunction, &user);CHKERRQ(ierr);
ierr = SNESSetJacobian(snes, A, J, SNESDMComputeJacobian, &user);CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
{
PetscReal res;
/* Check discretization error */
ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial guess\n");CHKERRQ(ierr);
ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
/* ierr = ComputeError(u, &error, &user);CHKERRQ(ierr); */
ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: %g\n", error);CHKERRQ(ierr);
/* Check residual */
ierr = SNESDMComputeFunction(snes, u, r, &user);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial Residual\n");CHKERRQ(ierr);
ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr);
ierr = VecView(r, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Residual: %g\n", res);CHKERRQ(ierr);
}
ierr = VecDestroy(&u);CHKERRQ(ierr);
ierr = VecDestroy(&r);CHKERRQ(ierr);
ierr = SNESDestroy(&snes);CHKERRQ(ierr);
ierr = DMDestroy(&user.dm);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
void Solve_Distance(UserCtx *user, int iter)
{
SNES snes_distance;
KSP ksp;
PC pc;
Vec r;
Mat J;
double norm;
int bi=0;
VecDuplicate(LevelSet, &r);
SNESCreate(PETSC_COMM_WORLD,&snes_distance);
SNESSetFunction(snes_distance,r,FormFunction_Distance,(void *)&user[bi]);
MatCreateSNESMF(snes_distance, &J);
SNESSetJacobian(snes_distance,J,J,MatMFFDComputeJacobian,(void *)&user[bi]);
SNESSetType(snes_distance, SNESTR); //SNESTR,SNESLS
double tol=1.e-2;
SNESSetMaxLinearSolveFailures(snes_distance,10000);
SNESSetMaxNonlinearStepFailures(snes_distance,10000);
SNESKSPSetUseEW(snes_distance, PETSC_TRUE);
SNESKSPSetParametersEW(snes_distance,3,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT);
SNESSetTolerances(snes_distance,PETSC_DEFAULT,tol,PETSC_DEFAULT,5,50000); // snes iter
SNESGetKSP(snes_distance, &ksp);
KSPSetType(ksp, KSPGMRES);
//KSPGMRESSetPreAllocateVectors(ksp);
KSPGetPC(ksp,&pc);
PCSetType(pc,PCNONE);
//int maxits=10;
int maxits=4; // ksp iter
double rtol=tol, atol=PETSC_DEFAULT, dtol=PETSC_DEFAULT;
KSPSetTolerances(ksp,rtol,atol,dtol,maxits);
extern PetscErrorCode MySNESMonitor(SNES snes,PetscInt n,PetscReal rnorm,void *dummy);
SNESMonitorSet(snes_distance,MySNESMonitor,PETSC_NULL,PETSC_NULL);
SNESSolve(snes_distance, PETSC_NULL, LevelSet);
SNESGetFunctionNorm(snes_distance, &norm);
//PetscPrintf(PETSC_COMM_WORLD, "\nDistance SNES residual norm=%.5e\n\n", norm);
VecDestroy(r);
MatDestroy(J);
SNESDestroy(snes_distance);
};
int main(int argc,char **argv) {
SNES snes; Vec x,f; Mat J; DA da;
PetscInitialize(&argc,&argv,(char *)0,help);
DACreate1d(PETSC_COMM_WORLD,DA_NONPERIODIC,8,1,1,PETSC_NULL,&da);
DACreateGlobalVector(da,&x); VecDuplicate(x,&f);
DAGetMatrix(da,MATAIJ,&J);
SNESCreate(PETSC_COMM_WORLD,&snes);
SNESSetFunction(snes,f,ComputeFunction,da);
SNESSetJacobian(snes,J,J,ComputeJacobian,da);
SNESSetFromOptions(snes);
SNESSolve(snes,PETSC_NULL,x);
MatDestroy(J); VecDestroy(x); VecDestroy(f); SNESDestroy(snes); DADestroy(da);
PetscFinalize();
return 0;}
// -------------------------------------------------------------
// PetscNonlinearSolverImplementation::p_build
// -------------------------------------------------------------
void
PetscNonlinearSolverImplementation::p_build(const std::string& option_prefix)
{
PetscErrorCode ierr(0);
try {
ierr = SNESCreate(this->communicator(), &p_snes); CHKERRXX(ierr);
p_petsc_F = PETScVector(*p_F);
if (!p_function.empty()) {
ierr = SNESSetFunction(p_snes, *p_petsc_F, FormFunction,
static_cast<void *>(this)); CHKERRXX(ierr);
}
p_petsc_J = PETScMatrix(*p_J);
if (!p_jacobian.empty()) {
ierr = SNESSetJacobian(p_snes, *p_petsc_J, *p_petsc_J, FormJacobian,
static_cast<void *>(this)); CHKERRXX(ierr);
}
// set the
ierr = SNESSetOptionsPrefix(p_snes, option_prefix.c_str()); CHKERRXX(ierr);
KSP ksp;
ierr = SNESGetKSP(p_snes, &ksp); CHKERRXX(ierr);
ierr = KSPSetOptionsPrefix(ksp, option_prefix.c_str()); CHKERRXX(ierr);
PC pc;
ierr = KSPGetPC(ksp, &pc); CHKERRXX(ierr);
ierr = PCSetOptionsPrefix(pc, option_prefix.c_str()); CHKERRXX(ierr);
ierr = SNESMonitorSet(p_snes, MonitorNorms, PETSC_NULL, PETSC_NULL); CHKERRXX(ierr);
ierr = SNESSetTolerances(p_snes,
p_functionTolerance,
PETSC_DEFAULT,
p_solutionTolerance,
p_maxIterations,
PETSC_DEFAULT);
ierr = SNESSetFromOptions(p_snes); CHKERRXX(ierr);
} catch (const PETSC_EXCEPTION_TYPE& e) {
throw PETScException(ierr, e);
}
}
int main(int argc, char** argv) {
PetscInitialize( &argc, &argv, (char *)0, 0 ) ;
int ncpus;
MPI_Comm_size(PETSC_COMM_WORLD,&ncpus);
if (ncpus > 1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,
"Example is only for sequential runs");
Vec x, r;
VecCreate(PETSC_COMM_WORLD, &x);
VecSetSizes(x, PETSC_DECIDE, 2);
VecSetFromOptions(x);
VecDuplicate(x, &r);
Mat J;
MatCreate(PETSC_COMM_WORLD, &J);
MatSetSizes(J, PETSC_DECIDE, PETSC_DECIDE, 2, 2);
MatSetFromOptions(J);
MatSetUp(J);
SNES snes;
SNESCreate(PETSC_COMM_WORLD, &snes);
SNESSetFunction(snes, r, CalculateFunc, NULL);
SNESSetJacobian(snes, J, J, CalculateJacobian, NULL);
SNESSetFromOptions(snes);
VecSet(x, 1.0);
SNESSolve(snes, NULL, x);
VecView(x,PETSC_VIEWER_STDOUT_WORLD);
SNESGetFunction(snes,&r,0,0);
VecView(r,PETSC_VIEWER_STDOUT_WORLD);
SNESDestroy(&snes);
MatDestroy(&J);
VecDestroy(&r);
VecDestroy(&x);
PetscFinalize();
return 0;
}
int main(int argc,char **argv)
{
SNES snes; /* nonlinear solver context */
Vec r; /* solution, residual vectors */
PetscErrorCode ierr;
AppCtx user; /* user-defined work context */
PetscViewer viewer;
PetscInitialize(&argc,&argv,(char*)0,help);
ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,"videfinition",FILE_MODE_READ,&viewer);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_SELF,&user.M);CHKERRQ(ierr); ierr = MatLoad(user.M,viewer);CHKERRQ(ierr);
ierr = MatDuplicate(user.M,MAT_COPY_VALUES,&user.Jac);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_SELF,&user.q);CHKERRQ(ierr); ierr = VecLoad(user.q,viewer);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_SELF,&user.lb);CHKERRQ(ierr); ierr = VecLoad(user.lb,viewer);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_SELF,&user.ub);CHKERRQ(ierr);ierr = VecLoad(user.ub,viewer);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_SELF,&user.zz);CHKERRQ(ierr);ierr = VecLoad(user.zz,viewer);CHKERRQ(ierr);
ierr = VecView(user.zz,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
/* ierr = VecSet(user.zz,0.01);CHKERRQ(ierr);*/
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = VecDuplicate(user.q,&r);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create nonlinear solver context
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = SNESCreate(PETSC_COMM_WORLD,&snes);CHKERRQ(ierr);
ierr = SNESSetFunction(snes,r,FormFunction1,&user);CHKERRQ(ierr);
ierr = SNESSetJacobian(snes,user.Jac,user.Jac,FormJacobian1,&user);CHKERRQ(ierr);
ierr = SNESVISetVariableBounds(snes,user.lb,user.ub);CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
ierr = SNESSolve(snes,NULL,user.zz);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)user.zz,"x*");CHKERRQ(ierr);
ierr = VecView(user.zz,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)r,"f(x*)");CHKERRQ(ierr);
ierr = FormFunction1(snes,user.zz,r,&user);CHKERRQ(ierr);
ierr = VecView(r,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
/*MC
SNESASPIN - Helper SNES type for Additive-Schwarz Preconditioned Inexact Newton
Options Database:
+ -npc_snes_ - options prefix of the nonlinear subdomain solver (must be of type NASM)
. -npc_sub_snes_ - options prefix of the subdomain nonlinear solves
. -npc_sub_ksp_ - options prefix of the subdomain Krylov solver
- -npc_sub_pc_ - options prefix of the subdomain preconditioner
Notes: This routine sets up an instance of NETWONLS with nonlinear left preconditioning. It differs from other
similar functionality in SNES as it creates a linear shell matrix that corresponds to the product:
\sum_{i=0}^{N_b}J_b({X^b_{converged}})^{-1}J(X + \sum_{i=0}^{N_b}(X^b_{converged} - X^b))
which is the ASPIN preconditioned matrix. Similar solvers may be constructed by having matrix-free differencing of
nonlinear solves per linear iteration, but this is far more efficient when subdomain sparse-direct preconditioner
factorizations are reused on each application of J_b^{-1}.
Level: intermediate
.seealso: SNESCreate(), SNES, SNESSetType(), SNESNEWTONLS, SNESNASM, SNESGetNPC(), SNESGetNPCSide()
M*/
PETSC_EXTERN PetscErrorCode SNESCreate_ASPIN(SNES snes)
{
PetscErrorCode ierr;
SNES npc;
KSP ksp;
PC pc;
Mat aspinmat;
MPI_Comm comm;
Vec F;
PetscInt n;
SNESLineSearch linesearch;
PetscFunctionBegin;
/* set up the solver */
ierr = SNESSetType(snes,SNESNEWTONLS);CHKERRQ(ierr);
ierr = SNESSetNPCSide(snes,PC_LEFT);CHKERRQ(ierr);
ierr = SNESSetFunctionType(snes,SNES_FUNCTION_PRECONDITIONED);CHKERRQ(ierr);
ierr = SNESGetNPC(snes,&npc);CHKERRQ(ierr);
ierr = SNESSetType(npc,SNESNASM);CHKERRQ(ierr);
ierr = SNESNASMSetType(npc,PC_ASM_BASIC);CHKERRQ(ierr);
ierr = SNESNASMSetComputeFinalJacobian(npc,PETSC_TRUE);CHKERRQ(ierr);
ierr = SNESGetKSP(snes,&ksp);CHKERRQ(ierr);
ierr = KSPGetPC(ksp,&pc);CHKERRQ(ierr);
ierr = PCSetType(pc,PCNONE);CHKERRQ(ierr);
ierr = PetscObjectGetComm((PetscObject)snes,&comm);CHKERRQ(ierr);
ierr = SNESGetLineSearch(snes,&linesearch);CHKERRQ(ierr);
ierr = SNESLineSearchSetType(linesearch,SNESLINESEARCHBT);CHKERRQ(ierr);
/* set up the shell matrix */
ierr = SNESGetFunction(snes,&F,NULL,NULL);CHKERRQ(ierr);
ierr = VecGetLocalSize(F,&n);CHKERRQ(ierr);
ierr = MatCreateShell(comm,n,n,PETSC_DECIDE,PETSC_DECIDE,snes,&aspinmat);CHKERRQ(ierr);
ierr = MatSetType(aspinmat,MATSHELL);CHKERRQ(ierr);
ierr = MatShellSetOperation(aspinmat,MATOP_MULT,(void(*)(void))MatMultASPIN);CHKERRQ(ierr);
ierr = SNESSetJacobian(snes,aspinmat,NULL,NULL,NULL);CHKERRQ(ierr);
ierr = MatDestroy(&aspinmat);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
void
NonlinearSystem::setupStandardFiniteDifferencedPreconditioner()
{
#if LIBMESH_HAVE_PETSC
// Make sure that libMesh isn't going to override our preconditioner
_transient_sys.nonlinear_solver->jacobian = nullptr;
PetscNonlinearSolver<Number> * petsc_nonlinear_solver =
static_cast<PetscNonlinearSolver<Number> *>(_transient_sys.nonlinear_solver.get());
PetscMatrix<Number> * petsc_mat = static_cast<PetscMatrix<Number> *>(_transient_sys.matrix);
SNESSetJacobian(petsc_nonlinear_solver->snes(),
petsc_mat->mat(),
petsc_mat->mat(),
#if PETSC_VERSION_LESS_THAN(3, 4, 0)
SNESDefaultComputeJacobian,
#else
SNESComputeJacobianDefault,
#endif
nullptr);
#endif
}
int main(int argc,char **argv)
{
AppCtx user; /* user-defined work context */
PetscInt mx,my;
PetscErrorCode ierr;
MPI_Comm comm;
DM da;
Vec x;
Mat J = NULL,Jmf = NULL;
MatShellCtx matshellctx;
PetscInt mlocal,nlocal;
PC pc;
KSP ksp;
PetscBool errorinmatmult = PETSC_FALSE,errorinpcapply = PETSC_FALSE,errorinpcsetup = PETSC_FALSE;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return(1);
PetscFunctionBeginUser;
ierr = PetscOptionsGetBool(NULL,"-error_in_matmult",&errorinmatmult,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,"-error_in_pcapply",&errorinpcapply,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,"-error_in_pcsetup",&errorinpcsetup,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,"-error_in_domain",&user.errorindomain,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,"-error_in_domainmf",&user.errorindomainmf,NULL);CHKERRQ(ierr);
comm = PETSC_COMM_WORLD;
ierr = SNESCreate(comm,&user.snes);CHKERRQ(ierr);
/*
Create distributed array object to manage parallel grid and vectors
for principal unknowns (x) and governing residuals (f)
*/
ierr = DMDACreate2d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,-4,-4,PETSC_DECIDE,PETSC_DECIDE,4,1,0,0,&da);CHKERRQ(ierr);
ierr = SNESSetDM(user.snes,da);CHKERRQ(ierr);
ierr = DMDAGetInfo(da,0,&mx,&my,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,
PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE);CHKERRQ(ierr);
/*
Problem parameters (velocity of lid, prandtl, and grashof numbers)
*/
user.lidvelocity = 1.0/(mx*my);
user.prandtl = 1.0;
user.grashof = 1.0;
ierr = PetscOptionsGetReal(NULL,"-lidvelocity",&user.lidvelocity,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetReal(NULL,"-prandtl",&user.prandtl,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetReal(NULL,"-grashof",&user.grashof,NULL);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,"-contours",&user.draw_contours);CHKERRQ(ierr);
ierr = DMDASetFieldName(da,0,"x_velocity");CHKERRQ(ierr);
ierr = DMDASetFieldName(da,1,"y_velocity");CHKERRQ(ierr);
ierr = DMDASetFieldName(da,2,"Omega");CHKERRQ(ierr);
ierr = DMDASetFieldName(da,3,"temperature");CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create user context, set problem data, create vector data structures.
Also, compute the initial guess.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create nonlinear solver context
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = DMSetApplicationContext(da,&user);CHKERRQ(ierr);
ierr = DMDASNESSetFunctionLocal(da,INSERT_VALUES,(PetscErrorCode (*)(DMDALocalInfo*,void*,void*,void*))FormFunctionLocal,&user);CHKERRQ(ierr);
if (errorinmatmult) {
ierr = MatCreateSNESMF(user.snes,&Jmf);CHKERRQ(ierr);
ierr = MatSetFromOptions(Jmf);CHKERRQ(ierr);
ierr = MatGetLocalSize(Jmf,&mlocal,&nlocal);CHKERRQ(ierr);
matshellctx.Jmf = Jmf;
ierr = MatCreateShell(PetscObjectComm((PetscObject)Jmf),mlocal,nlocal,PETSC_DECIDE,PETSC_DECIDE,&matshellctx,&J);CHKERRQ(ierr);
ierr = MatShellSetOperation(J,MATOP_MULT,(void (*)(void))MatMult_MyShell);CHKERRQ(ierr);
ierr = MatShellSetOperation(J,MATOP_ASSEMBLY_END,(void (*)(void))MatAssemblyEnd_MyShell);CHKERRQ(ierr);
ierr = SNESSetJacobian(user.snes,J,J,MatMFFDComputeJacobian,NULL);CHKERRQ(ierr);
}
ierr = SNESSetFromOptions(user.snes);CHKERRQ(ierr);
ierr = PetscPrintf(comm,"lid velocity = %g, prandtl # = %g, grashof # = %g\n",(double)user.lidvelocity,(double)user.prandtl,(double)user.grashof);CHKERRQ(ierr);
if (errorinpcapply) {
ierr = SNESGetKSP(user.snes,&ksp);CHKERRQ(ierr);
ierr = KSPGetPC(ksp,&pc);CHKERRQ(ierr);
ierr = PCSetType(pc,PCSHELL);CHKERRQ(ierr);
ierr = PCShellSetApply(pc,PCApply_MyShell);CHKERRQ(ierr);
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Solve the nonlinear system
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = DMCreateGlobalVector(da,&x);CHKERRQ(ierr);
ierr = FormInitialGuess(&user,da,x);CHKERRQ(ierr);
if (errorinpcsetup) {
ierr = SNESSetUp(user.snes);CHKERRQ(ierr);
ierr = SNESSetJacobian(user.snes,NULL,NULL,SNESComputeJacobian_MyShell,NULL);CHKERRQ(ierr);
}
ierr = SNESSolve(user.snes,NULL,x);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Free work space. All PETSc objects should be destroyed when they
are no longer needed.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = MatDestroy(&J);CHKERRQ(ierr);
ierr = MatDestroy(&Jmf);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = SNESDestroy(&user.snes);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **args)
{
Mat Amat;
PetscErrorCode ierr;
SNES snes;
KSP ksp;
MPI_Comm comm;
PetscMPIInt npe,rank;
PetscLogStage stage[7];
PetscBool test_nonzero_cols=PETSC_FALSE,use_nearnullspace=PETSC_TRUE;
Vec xx,bb;
PetscInt iter,i,N,dim=3,cells[3]={1,1,1},max_conv_its,local_sizes[7],run_type=1;
DM dm,distdm,basedm;
PetscBool flg;
char convType[256];
PetscReal Lx,mdisp[10],err[10];
const char * const options[10] = {"-ex56_dm_refine 0",
"-ex56_dm_refine 1",
"-ex56_dm_refine 2",
"-ex56_dm_refine 3",
"-ex56_dm_refine 4",
"-ex56_dm_refine 5",
"-ex56_dm_refine 6",
"-ex56_dm_refine 7",
"-ex56_dm_refine 8",
"-ex56_dm_refine 9"};
PetscFunctionBeginUser;
ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
comm = PETSC_COMM_WORLD;
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm, &npe);CHKERRQ(ierr);
/* options */
ierr = PetscOptionsBegin(comm,NULL,"3D bilinear Q1 elasticity options","");CHKERRQ(ierr);
{
i = 3;
ierr = PetscOptionsIntArray("-cells", "Number of (flux tube) processor in each dimension", "ex56.c", cells, &i, NULL);CHKERRQ(ierr);
Lx = 1.; /* or ne for rod */
max_conv_its = 3;
ierr = PetscOptionsInt("-max_conv_its","Number of iterations in convergence study","",max_conv_its,&max_conv_its,NULL);CHKERRQ(ierr);
if (max_conv_its<=0 || max_conv_its>7) SETERRQ1(PETSC_COMM_WORLD, PETSC_ERR_USER, "Bad number of iterations for convergence test (%D)",max_conv_its);
ierr = PetscOptionsReal("-lx","Length of domain","",Lx,&Lx,NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-alpha","material coefficient inside circle","",s_soft_alpha,&s_soft_alpha,NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-test_nonzero_cols","nonzero test","",test_nonzero_cols,&test_nonzero_cols,NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-use_mat_nearnullspace","MatNearNullSpace API test","",use_nearnullspace,&use_nearnullspace,NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-run_type","0: twisting load on cantalever, 1: 3rd order accurate convergence test","",run_type,&run_type,NULL);CHKERRQ(ierr);
i = 3;
ierr = PetscOptionsInt("-mat_block_size","","",i,&i,&flg);CHKERRQ(ierr);
if (!flg || i!=3) SETERRQ2(PETSC_COMM_WORLD, PETSC_ERR_USER, "'-mat_block_size 3' must be set (%D) and = 3 (%D)",flg,flg? i : 3);
}
ierr = PetscOptionsEnd();CHKERRQ(ierr);
ierr = PetscLogStageRegister("Mesh Setup", &stage[6]);CHKERRQ(ierr);
ierr = PetscLogStageRegister("1st Setup", &stage[0]);CHKERRQ(ierr);
ierr = PetscLogStageRegister("1st Solve", &stage[1]);CHKERRQ(ierr);
/* create DM, Plex calls DMSetup */
ierr = PetscLogStagePush(stage[6]);CHKERRQ(ierr);
ierr = DMPlexCreateHexBoxMesh(comm, dim, cells, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, &dm);CHKERRQ(ierr);
{
DMLabel label;
IS is;
ierr = DMCreateLabel(dm, "boundary");CHKERRQ(ierr);
ierr = DMGetLabel(dm, "boundary", &label);CHKERRQ(ierr);
ierr = DMPlexMarkBoundaryFaces(dm, label);CHKERRQ(ierr);
if (run_type==0) {
ierr = DMGetStratumIS(dm, "boundary", 1, &is);CHKERRQ(ierr);
ierr = DMCreateLabel(dm,"Faces");CHKERRQ(ierr);
if (is) {
PetscInt d, f, Nf;
const PetscInt *faces;
PetscInt csize;
PetscSection cs;
Vec coordinates ;
DM cdm;
ierr = ISGetLocalSize(is, &Nf);CHKERRQ(ierr);
ierr = ISGetIndices(is, &faces);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr);
ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr);
ierr = DMGetDefaultSection(cdm, &cs);CHKERRQ(ierr);
/* Check for each boundary face if any component of its centroid is either 0.0 or 1.0 */
for (f = 0; f < Nf; ++f) {
PetscReal faceCoord;
PetscInt b,v;
PetscScalar *coords = NULL;
PetscInt Nv;
ierr = DMPlexVecGetClosure(cdm, cs, coordinates, faces[f], &csize, &coords);CHKERRQ(ierr);
Nv = csize/dim; /* Calculate mean coordinate vector */
for (d = 0; d < dim; ++d) {
faceCoord = 0.0;
for (v = 0; v < Nv; ++v) faceCoord += PetscRealPart(coords[v*dim+d]);
faceCoord /= Nv;
for (b = 0; b < 2; ++b) {
if (PetscAbs(faceCoord - b) < PETSC_SMALL) { /* domain have not been set yet, still [0,1]^3 */
ierr = DMSetLabelValue(dm, "Faces", faces[f], d*2+b+1);CHKERRQ(ierr);
}
}
}
ierr = DMPlexVecRestoreClosure(cdm, cs, coordinates, faces[f], &csize, &coords);CHKERRQ(ierr);
}
ierr = ISRestoreIndices(is, &faces);CHKERRQ(ierr);
}
ierr = ISDestroy(&is);CHKERRQ(ierr);
ierr = DMGetLabel(dm, "Faces", &label);CHKERRQ(ierr);
ierr = DMPlexLabelComplete(dm, label);CHKERRQ(ierr);
}
}
{
PetscInt dimEmbed, i;
PetscInt nCoords;
PetscScalar *coords,bounds[] = {0,Lx,-.5,.5,-.5,.5,}; /* x_min,x_max,y_min,y_max */
Vec coordinates;
if (run_type==1) {
for (i = 0; i < 2*dim; i++) bounds[i] = (i%2) ? 1 : 0;
}
ierr = DMGetCoordinatesLocal(dm,&coordinates);CHKERRQ(ierr);
ierr = DMGetCoordinateDim(dm,&dimEmbed);CHKERRQ(ierr);
if (dimEmbed != dim) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"dimEmbed != dim %D",dimEmbed);CHKERRQ(ierr);
ierr = VecGetLocalSize(coordinates,&nCoords);CHKERRQ(ierr);
if (nCoords % dimEmbed) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Coordinate vector the wrong size");CHKERRQ(ierr);
ierr = VecGetArray(coordinates,&coords);CHKERRQ(ierr);
for (i = 0; i < nCoords; i += dimEmbed) {
PetscInt j;
PetscScalar *coord = &coords[i];
for (j = 0; j < dimEmbed; j++) {
coord[j] = bounds[2 * j] + coord[j] * (bounds[2 * j + 1] - bounds[2 * j]);
}
}
ierr = VecRestoreArray(coordinates,&coords);CHKERRQ(ierr);
ierr = DMSetCoordinatesLocal(dm,coordinates);CHKERRQ(ierr);
}
/* convert to p4est, and distribute */
ierr = PetscOptionsBegin(comm, "", "Mesh conversion options", "DMPLEX");CHKERRQ(ierr);
ierr = PetscOptionsFList("-dm_type","Convert DMPlex to another format (should not be Plex!)","ex56.c",DMList,DMPLEX,convType,256,&flg);CHKERRQ(ierr);
ierr = PetscOptionsEnd();
if (flg) {
DM newdm;
ierr = DMConvert(dm,convType,&newdm);CHKERRQ(ierr);
if (newdm) {
const char *prefix;
PetscBool isForest;
ierr = PetscObjectGetOptionsPrefix((PetscObject)dm,&prefix);CHKERRQ(ierr);
ierr = PetscObjectSetOptionsPrefix((PetscObject)newdm,prefix);CHKERRQ(ierr);
ierr = DMIsForest(newdm,&isForest);CHKERRQ(ierr);
if (isForest) {
} else SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_USER, "Converted to non Forest?");
ierr = DMDestroy(&dm);CHKERRQ(ierr);
dm = newdm;
} else SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_USER, "Convert failed?");
} else {
/* Plex Distribute mesh over processes */
ierr = DMPlexDistribute(dm, 0, NULL, &distdm);CHKERRQ(ierr);
if (distdm) {
const char *prefix;
ierr = PetscObjectGetOptionsPrefix((PetscObject)dm,&prefix);CHKERRQ(ierr);
ierr = PetscObjectSetOptionsPrefix((PetscObject)distdm,prefix);CHKERRQ(ierr);
ierr = DMDestroy(&dm);CHKERRQ(ierr);
dm = distdm;
}
}
ierr = PetscLogStagePop();CHKERRQ(ierr);
basedm = dm; dm = NULL;
for (iter=0 ; iter<max_conv_its ; iter++) {
ierr = PetscLogStagePush(stage[6]);CHKERRQ(ierr);
/* make new DM */
ierr = DMClone(basedm, &dm);CHKERRQ(ierr);
ierr = PetscObjectSetOptionsPrefix((PetscObject) dm, "ex56_");CHKERRQ(ierr);
ierr = PetscObjectSetName( (PetscObject)dm,"Mesh");CHKERRQ(ierr);
ierr = PetscOptionsClearValue(NULL,"-ex56_dm_refine");CHKERRQ(ierr);
ierr = PetscOptionsInsertString(NULL,options[iter]);CHKERRQ(ierr);
ierr = DMSetFromOptions(dm);CHKERRQ(ierr); /* refinement done here in Plex, p4est */
/* snes */
ierr = SNESCreate(comm, &snes);CHKERRQ(ierr);
ierr = SNESSetDM(snes, dm);CHKERRQ(ierr);
/* fem */
{
const PetscInt Ncomp = dim;
const PetscInt components[] = {0,1,2};
const PetscInt Nfid = 1, Npid = 1;
const PetscInt fid[] = {1}; /* The fixed faces (x=0) */
const PetscInt pid[] = {2}; /* The faces with loading (x=L_x) */
PetscFE fe;
PetscDS prob;
DM cdm = dm;
ierr = PetscFECreateDefault(dm, dim, dim, PETSC_FALSE, NULL, PETSC_DECIDE, &fe);CHKERRQ(ierr); /* elasticity */
ierr = PetscObjectSetName((PetscObject) fe, "deformation");CHKERRQ(ierr);
/* FEM prob */
ierr = DMGetDS(dm, &prob);CHKERRQ(ierr);
ierr = PetscDSSetDiscretization(prob, 0, (PetscObject) fe);CHKERRQ(ierr);
/* setup problem */
if (run_type==1) {
ierr = PetscDSSetJacobian(prob, 0, 0, NULL, NULL, NULL, g3_uu_3d);CHKERRQ(ierr);
ierr = PetscDSSetResidual(prob, 0, f0_u_x4, f1_u_3d);CHKERRQ(ierr);
} else {
ierr = PetscDSSetJacobian(prob, 0, 0, NULL, NULL, NULL, g3_uu_3d_alpha);CHKERRQ(ierr);
ierr = PetscDSSetResidual(prob, 0, f0_u, f1_u_3d_alpha);CHKERRQ(ierr);
ierr = PetscDSSetBdResidual(prob, 0, f0_bd_u_3d, f1_bd_u);CHKERRQ(ierr);
}
/* bcs */
if (run_type==1) {
PetscInt id = 1;
ierr = DMAddBoundary(dm, DM_BC_ESSENTIAL, "wall", "boundary", 0, 0, NULL, (void (*)()) zero, 1, &id, NULL);CHKERRQ(ierr);
} else {
ierr = PetscDSAddBoundary(prob, DM_BC_ESSENTIAL, "fixed", "Faces", 0, Ncomp, components, (void (*)()) zero, Nfid, fid, NULL);CHKERRQ(ierr);
ierr = PetscDSAddBoundary(prob, DM_BC_NATURAL, "traction", "Faces", 0, Ncomp, components, NULL, Npid, pid, NULL);CHKERRQ(ierr);
}
while (cdm) {
ierr = DMSetDS(cdm,prob);CHKERRQ(ierr);
ierr = DMGetCoarseDM(cdm, &cdm);CHKERRQ(ierr);
}
ierr = PetscFEDestroy(&fe);CHKERRQ(ierr);
}
/* vecs & mat */
ierr = DMCreateGlobalVector(dm,&xx);CHKERRQ(ierr);
ierr = VecDuplicate(xx, &bb);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) bb, "b");CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) xx, "u");CHKERRQ(ierr);
ierr = DMCreateMatrix(dm, &Amat);CHKERRQ(ierr);
ierr = VecGetSize(bb,&N);CHKERRQ(ierr);
local_sizes[iter] = N;
ierr = PetscPrintf(PETSC_COMM_WORLD,"[%d]%s %d global equations, %d vertices\n",rank,PETSC_FUNCTION_NAME,N,N/dim);CHKERRQ(ierr);
if (use_nearnullspace && N/dim > 1) {
/* Set up the near null space (a.k.a. rigid body modes) that will be used by the multigrid preconditioner */
DM subdm;
MatNullSpace nearNullSpace;
PetscInt fields = 0;
PetscObject deformation;
ierr = DMCreateSubDM(dm, 1, &fields, NULL, &subdm);CHKERRQ(ierr);
ierr = DMPlexCreateRigidBody(subdm, &nearNullSpace);CHKERRQ(ierr);
ierr = DMGetField(dm, 0, &deformation);CHKERRQ(ierr);
ierr = PetscObjectCompose(deformation, "nearnullspace", (PetscObject) nearNullSpace);CHKERRQ(ierr);
ierr = DMDestroy(&subdm);CHKERRQ(ierr);
ierr = MatNullSpaceDestroy(&nearNullSpace);CHKERRQ(ierr); /* created by DM and destroyed by Mat */
}
ierr = DMPlexSetSNESLocalFEM(dm,NULL,NULL,NULL);CHKERRQ(ierr);
ierr = SNESSetJacobian(snes, Amat, Amat, NULL, NULL);CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
ierr = DMSetUp(dm);CHKERRQ(ierr);
ierr = PetscLogStagePop();CHKERRQ(ierr);
ierr = PetscLogStagePush(stage[0]);CHKERRQ(ierr);
/* ksp */
ierr = SNESGetKSP(snes, &ksp);CHKERRQ(ierr);
ierr = KSPSetComputeSingularValues(ksp,PETSC_TRUE);CHKERRQ(ierr);
/* test BCs */
ierr = VecZeroEntries(xx);CHKERRQ(ierr);
if (test_nonzero_cols) {
if (rank==0) ierr = VecSetValue(xx,0,1.0,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecAssemblyBegin(xx);CHKERRQ(ierr);
ierr = VecAssemblyEnd(xx);CHKERRQ(ierr);
}
ierr = VecZeroEntries(bb);CHKERRQ(ierr);
ierr = VecGetSize(bb,&i);CHKERRQ(ierr);
local_sizes[iter] = i;
ierr = PetscPrintf(PETSC_COMM_WORLD,"[%d]%s %d equations in vector, %d vertices\n",rank,PETSC_FUNCTION_NAME,i,i/dim);CHKERRQ(ierr);
/* setup solver, dummy solve to really setup */
if (0) {
ierr = KSPSetTolerances(ksp,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT,1);CHKERRQ(ierr);
ierr = SNESSolve(snes, bb, xx);CHKERRQ(ierr);
ierr = KSPSetTolerances(ksp,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT,50);CHKERRQ(ierr);
ierr = VecZeroEntries(xx);CHKERRQ(ierr);
}
ierr = PetscLogStagePop();CHKERRQ(ierr);
/* solve */
ierr = PetscLogStagePush(stage[1]);CHKERRQ(ierr);
ierr = SNESSolve(snes, bb, xx);CHKERRQ(ierr);
ierr = PetscLogStagePop();CHKERRQ(ierr);
ierr = VecNorm(xx,NORM_INFINITY,&mdisp[iter]);CHKERRQ(ierr);
ierr = DMViewFromOptions(dm, NULL, "-dm_view");CHKERRQ(ierr);
{
PetscViewer viewer = NULL;
PetscViewerFormat fmt;
ierr = PetscOptionsGetViewer(comm,"ex56_","-vec_view",&viewer,&fmt,&flg);CHKERRQ(ierr);
if (flg) {
ierr = PetscViewerPushFormat(viewer,fmt);CHKERRQ(ierr);
ierr = VecView(xx,viewer);CHKERRQ(ierr);
ierr = VecView(bb,viewer);CHKERRQ(ierr);
ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);
}
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
/* Free work space */
ierr = DMDestroy(&dm);CHKERRQ(ierr);
ierr = SNESDestroy(&snes);CHKERRQ(ierr);
ierr = VecDestroy(&xx);CHKERRQ(ierr);
ierr = VecDestroy(&bb);CHKERRQ(ierr);
ierr = MatDestroy(&Amat);CHKERRQ(ierr);
}
ierr = DMDestroy(&basedm);CHKERRQ(ierr);
if (run_type==1) {
err[0] = 59.975208 - mdisp[0]; /* error with what I think is the exact solution */
} else {
err[0] = 171.038 - mdisp[0];
}
for (iter=1 ; iter<max_conv_its ; iter++) {
if (run_type==1) {
err[iter] = 59.975208 - mdisp[iter];
} else {
err[iter] = 171.038 - mdisp[iter];
}
PetscPrintf(PETSC_COMM_WORLD,"[%d]%s %D) N=%12D, max displ=%9.7e, disp diff=%9.2e, error=%4.3e, rate=%3.2g\n",
rank,PETSC_FUNCTION_NAME,iter,local_sizes[iter],mdisp[iter],
mdisp[iter]-mdisp[iter-1],err[iter],log(err[iter-1]/err[iter])/log(2.));
}
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)
{
SNES snes; /* nonlinear solver */
DM dm; /* problem definition */
Vec u,r; /* solution, residual vectors */
Mat A,J; /* Jacobian matrix */
MatNullSpace nullSpace; /* May be necessary for pressure */
AppCtx user; /* user-defined work context */
JacActionCtx userJ; /* context for Jacobian MF action */
PetscInt its; /* iterations for convergence */
PetscReal error = 0.0; /* L_2 error in the solution */
PetscInt numComponents = 0, f;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc, &argv, NULL, help);CHKERRQ(ierr);
ierr = ProcessOptions(PETSC_COMM_WORLD, &user);CHKERRQ(ierr);
ierr = SNESCreate(PETSC_COMM_WORLD, &snes);CHKERRQ(ierr);
ierr = CreateMesh(PETSC_COMM_WORLD, &user, &dm);CHKERRQ(ierr);
ierr = SNESSetDM(snes, dm);CHKERRQ(ierr);
ierr = SetupElement(dm, &user);CHKERRQ(ierr);
for (f = 0; f < NUM_FIELDS; ++f) {
PetscInt numComp;
ierr = PetscFEGetNumComponents(user.fe[f], &numComp);CHKERRQ(ierr);
numComponents += numComp;
}
ierr = PetscMalloc(NUM_FIELDS * sizeof(void (*)(const PetscReal[], PetscScalar *)), &user.exactFuncs);CHKERRQ(ierr);
user.fem.bcFuncs = (void (**)(const PetscReal[], PetscScalar *)) user.exactFuncs;
ierr = SetupExactSolution(dm, &user);CHKERRQ(ierr);
ierr = SetupSection(dm, &user);CHKERRQ(ierr);
ierr = DMPlexCreateClosureIndex(dm, NULL);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(dm, &u);CHKERRQ(ierr);
ierr = VecDuplicate(u, &r);CHKERRQ(ierr);
ierr = DMSetMatType(dm,MATAIJ);CHKERRQ(ierr);
ierr = DMCreateMatrix(dm, &J);CHKERRQ(ierr);
if (user.jacobianMF) {
PetscInt M, m, N, n;
ierr = MatGetSize(J, &M, &N);CHKERRQ(ierr);
ierr = MatGetLocalSize(J, &m, &n);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD, &A);CHKERRQ(ierr);
ierr = MatSetSizes(A, m, n, M, N);CHKERRQ(ierr);
ierr = MatSetType(A, MATSHELL);CHKERRQ(ierr);
ierr = MatSetUp(A);CHKERRQ(ierr);
ierr = MatShellSetOperation(A, MATOP_MULT, (void (*)(void))FormJacobianAction);CHKERRQ(ierr);
userJ.dm = dm;
userJ.J = J;
userJ.user = &user;
ierr = DMCreateLocalVector(dm, &userJ.u);CHKERRQ(ierr);
ierr = DMPlexProjectFunctionLocal(dm, user.fe, user.exactFuncs, INSERT_BC_VALUES, userJ.u);CHKERRQ(ierr);
ierr = MatShellSetContext(A, &userJ);CHKERRQ(ierr);
} else {
A = J;
}
ierr = CreatePressureNullSpace(dm, &user, &nullSpace);CHKERRQ(ierr);
ierr = MatSetNullSpace(J, nullSpace);CHKERRQ(ierr);
if (A != J) {
ierr = MatSetNullSpace(A, nullSpace);CHKERRQ(ierr);
}
ierr = DMSNESSetFunctionLocal(dm, (PetscErrorCode (*)(DM,Vec,Vec,void*))DMPlexComputeResidualFEM,&user);CHKERRQ(ierr);
ierr = DMSNESSetJacobianLocal(dm, (PetscErrorCode (*)(DM,Vec,Mat,Mat,MatStructure*,void*))DMPlexComputeJacobianFEM,&user);CHKERRQ(ierr);
ierr = SNESSetJacobian(snes, A, J, NULL, NULL);CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
ierr = DMPlexProjectFunction(dm, user.fe, user.exactFuncs, INSERT_ALL_VALUES, u);CHKERRQ(ierr);
if (user.showInitial) {ierr = DMVecViewLocal(dm, u, PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);}
if (user.runType == RUN_FULL) {
ierr = DMPlexProjectFunction(dm, user.fe, user.initialGuess, INSERT_VALUES, u);CHKERRQ(ierr);
if (user.showInitial) {ierr = DMVecViewLocal(dm, u, PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);}
if (user.debug) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial guess\n");CHKERRQ(ierr);
ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = SNESSolve(snes, NULL, u);CHKERRQ(ierr);
ierr = SNESGetIterationNumber(snes, &its);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Number of SNES iterations = %D\n", its);CHKERRQ(ierr);
ierr = DMPlexComputeL2Diff(dm, user.fe, user.exactFuncs, u, &error);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: %.3g\n", error);CHKERRQ(ierr);
if (user.showSolution) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "Solution\n");CHKERRQ(ierr);
ierr = VecChop(u, 3.0e-9);CHKERRQ(ierr);
ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
} else {
PetscReal res = 0.0;
/* Check discretization error */
ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial guess\n");CHKERRQ(ierr);
ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = DMPlexComputeL2Diff(dm, user.fe, user.exactFuncs, u, &error);CHKERRQ(ierr);
if (error >= 1.0e-11) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: %g\n", error);CHKERRQ(ierr);
} else {
ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: < 1.0e-11\n", error);CHKERRQ(ierr);
}
/* Check residual */
ierr = SNESComputeFunction(snes, u, r);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial Residual\n");CHKERRQ(ierr);
ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr);
ierr = VecView(r, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Residual: %g\n", res);CHKERRQ(ierr);
/* Check Jacobian */
{
Vec b;
MatStructure flag;
PetscBool isNull;
ierr = SNESComputeJacobian(snes, u, &A, &A, &flag);CHKERRQ(ierr);
ierr = MatNullSpaceTest(nullSpace, J, &isNull);CHKERRQ(ierr);
if (!isNull) SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_PLIB, "The null space calculated for the system operator is invalid.");
ierr = VecDuplicate(u, &b);CHKERRQ(ierr);
ierr = VecSet(r, 0.0);CHKERRQ(ierr);
ierr = SNESComputeFunction(snes, r, b);CHKERRQ(ierr);
ierr = MatMult(A, u, r);CHKERRQ(ierr);
ierr = VecAXPY(r, 1.0, b);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Au - b = Au + F(0)\n");CHKERRQ(ierr);
ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr);
ierr = VecView(r, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Linear L_2 Residual: %g\n", res);CHKERRQ(ierr);
}
}
if (user.runType == RUN_FULL) {
PetscViewer viewer;
Vec uLocal;
const char *name;
ierr = PetscViewerCreate(PETSC_COMM_WORLD, &viewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer, PETSCVIEWERVTK);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(viewer, PETSC_VIEWER_ASCII_VTK);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(viewer, "ex62_sol.vtk");CHKERRQ(ierr);
ierr = DMGetLocalVector(dm, &uLocal);CHKERRQ(ierr);
ierr = PetscObjectGetName((PetscObject) u, &name);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) uLocal, name);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dm, u, INSERT_VALUES, uLocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dm, u, INSERT_VALUES, uLocal);CHKERRQ(ierr);
ierr = VecView(uLocal, viewer);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm, &uLocal);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
ierr = PetscFree(user.exactFuncs);CHKERRQ(ierr);
ierr = DestroyElement(&user);CHKERRQ(ierr);
ierr = MatNullSpaceDestroy(&nullSpace);CHKERRQ(ierr);
if (user.jacobianMF) {
ierr = VecDestroy(&userJ.u);CHKERRQ(ierr);
}
if (A != J) {
ierr = MatDestroy(&A);CHKERRQ(ierr);
}
ierr = MatDestroy(&J);CHKERRQ(ierr);
ierr = VecDestroy(&u);CHKERRQ(ierr);
ierr = VecDestroy(&r);CHKERRQ(ierr);
ierr = SNESDestroy(&snes);CHKERRQ(ierr);
ierr = DMDestroy(&dm);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char ** argv)
{
PetscErrorCode ierr;
char pfdata_file[PETSC_MAX_PATH_LEN]="datafiles/case9.m";
PFDATA *pfdata;
PetscInt numEdges=0,numVertices=0;
int *edges = NULL;
PetscInt i;
DM networkdm;
PetscInt componentkey[4];
UserCtx User;
PetscLogStage stage1,stage2;
PetscMPIInt size,rank;
PetscInt eStart, eEnd, vStart, vEnd,j;
PetscInt genj,loadj;
Vec X,F;
Mat J;
SNES snes;
ierr = PetscInitialize(&argc,&argv,"pfoptions",help);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
{
/* introduce the const crank so the clang static analyzer realizes that if it enters any of the if (crank) then it must have entered the first */
/* this is an experiment to see how the analyzer reacts */
const PetscMPIInt crank = rank;
/* Create an empty network object */
ierr = DMNetworkCreate(PETSC_COMM_WORLD,&networkdm);CHKERRQ(ierr);
/* Register the components in the network */
ierr = DMNetworkRegisterComponent(networkdm,"branchstruct",sizeof(struct _p_EDGEDATA),&componentkey[0]);CHKERRQ(ierr);
ierr = DMNetworkRegisterComponent(networkdm,"busstruct",sizeof(struct _p_VERTEXDATA),&componentkey[1]);CHKERRQ(ierr);
ierr = DMNetworkRegisterComponent(networkdm,"genstruct",sizeof(struct _p_GEN),&componentkey[2]);CHKERRQ(ierr);
ierr = DMNetworkRegisterComponent(networkdm,"loadstruct",sizeof(struct _p_LOAD),&componentkey[3]);CHKERRQ(ierr);
ierr = PetscLogStageRegister("Read Data",&stage1);CHKERRQ(ierr);
PetscLogStagePush(stage1);
/* READ THE DATA */
if (!crank) {
/* READ DATA */
/* Only rank 0 reads the data */
ierr = PetscOptionsGetString(NULL,NULL,"-pfdata",pfdata_file,PETSC_MAX_PATH_LEN-1,NULL);CHKERRQ(ierr);
ierr = PetscNew(&pfdata);CHKERRQ(ierr);
ierr = PFReadMatPowerData(pfdata,pfdata_file);CHKERRQ(ierr);
User.Sbase = pfdata->sbase;
numEdges = pfdata->nbranch;
numVertices = pfdata->nbus;
ierr = PetscMalloc(2*numEdges*sizeof(int),&edges);CHKERRQ(ierr);
ierr = GetListofEdges(pfdata->nbranch,pfdata->branch,edges);CHKERRQ(ierr);
}
PetscLogStagePop();
ierr = MPI_Barrier(PETSC_COMM_WORLD);CHKERRQ(ierr);
ierr = PetscLogStageRegister("Create network",&stage2);CHKERRQ(ierr);
PetscLogStagePush(stage2);
/* Set number of nodes/edges */
ierr = DMNetworkSetSizes(networkdm,numVertices,numEdges,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr);
/* Add edge connectivity */
ierr = DMNetworkSetEdgeList(networkdm,edges);CHKERRQ(ierr);
/* Set up the network layout */
ierr = DMNetworkLayoutSetUp(networkdm);CHKERRQ(ierr);
if (!crank) {
ierr = PetscFree(edges);CHKERRQ(ierr);
}
/* Add network components only process 0 has any data to add*/
if (!crank) {
genj=0; loadj=0;
ierr = DMNetworkGetEdgeRange(networkdm,&eStart,&eEnd);CHKERRQ(ierr);
for (i = eStart; i < eEnd; i++) {
ierr = DMNetworkAddComponent(networkdm,i,componentkey[0],&pfdata->branch[i-eStart]);CHKERRQ(ierr);
}
ierr = DMNetworkGetVertexRange(networkdm,&vStart,&vEnd);CHKERRQ(ierr);
for (i = vStart; i < vEnd; i++) {
ierr = DMNetworkAddComponent(networkdm,i,componentkey[1],&pfdata->bus[i-vStart]);CHKERRQ(ierr);
if (pfdata->bus[i-vStart].ngen) {
for (j = 0; j < pfdata->bus[i-vStart].ngen; j++) {
ierr = DMNetworkAddComponent(networkdm,i,componentkey[2],&pfdata->gen[genj++]);CHKERRQ(ierr);
}
}
if (pfdata->bus[i-vStart].nload) {
for (j=0; j < pfdata->bus[i-vStart].nload; j++) {
ierr = DMNetworkAddComponent(networkdm,i,componentkey[3],&pfdata->load[loadj++]);CHKERRQ(ierr);
}
}
/* Add number of variables */
ierr = DMNetworkAddNumVariables(networkdm,i,2);CHKERRQ(ierr);
}
}
/* Set up DM for use */
ierr = DMSetUp(networkdm);CHKERRQ(ierr);
if (!crank) {
ierr = PetscFree(pfdata->bus);CHKERRQ(ierr);
ierr = PetscFree(pfdata->gen);CHKERRQ(ierr);
ierr = PetscFree(pfdata->branch);CHKERRQ(ierr);
ierr = PetscFree(pfdata->load);CHKERRQ(ierr);
ierr = PetscFree(pfdata);CHKERRQ(ierr);
}
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size > 1) {
DM distnetworkdm;
/* Network partitioning and distribution of data */
ierr = DMNetworkDistribute(networkdm,0,&distnetworkdm);CHKERRQ(ierr);
ierr = DMDestroy(&networkdm);CHKERRQ(ierr);
networkdm = distnetworkdm;
}
PetscLogStagePop();
ierr = DMNetworkGetEdgeRange(networkdm,&eStart,&eEnd);CHKERRQ(ierr);
ierr = DMNetworkGetVertexRange(networkdm,&vStart,&vEnd);CHKERRQ(ierr);
#if 0
PetscInt numComponents;
EDGEDATA edge;
PetscInt offset,key,kk;
DMNetworkComponentGenericDataType *arr;
VERTEXDATA bus;
GEN gen;
LOAD load;
for (i = eStart; i < eEnd; i++) {
ierr = DMNetworkGetComponentDataArray(networkdm,&arr);CHKERRQ(ierr);
ierr = DMNetworkGetComponentTypeOffset(networkdm,i,0,&key,&offset);CHKERRQ(ierr);
edge = (EDGEDATA)(arr+offset);
ierr = DMNetworkGetNumComponents(networkdm,i,&numComponents);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF,"Rank %d ncomps = %d Line %d ---- %d\n",crank,numComponents,edge->internal_i,edge->internal_j);CHKERRQ(ierr);
}
for (i = vStart; i < vEnd; i++) {
ierr = DMNetworkGetComponentDataArray(networkdm,&arr);CHKERRQ(ierr);
ierr = DMNetworkGetNumComponents(networkdm,i,&numComponents);CHKERRQ(ierr);
for (kk=0; kk < numComponents; kk++) {
ierr = DMNetworkGetComponentTypeOffset(networkdm,i,kk,&key,&offset);CHKERRQ(ierr);
if (key == 1) {
bus = (VERTEXDATA)(arr+offset);
ierr = PetscPrintf(PETSC_COMM_SELF,"Rank %d ncomps = %d Bus %d\n",crank,numComponents,bus->internal_i);CHKERRQ(ierr);
} else if (key == 2) {
gen = (GEN)(arr+offset);
ierr = PetscPrintf(PETSC_COMM_SELF,"Rank %d Gen pg = %f qg = %f\n",crank,gen->pg,gen->qg);CHKERRQ(ierr);
} else if (key == 3) {
load = (LOAD)(arr+offset);
ierr = PetscPrintf(PETSC_COMM_SELF,"Rank %d Load pl = %f ql = %f\n",crank,load->pl,load->ql);CHKERRQ(ierr);
}
}
}
#endif
/* Broadcast Sbase to all processors */
ierr = MPI_Bcast(&User.Sbase,1,MPIU_SCALAR,0,PETSC_COMM_WORLD);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(networkdm,&X);CHKERRQ(ierr);
ierr = VecDuplicate(X,&F);CHKERRQ(ierr);
ierr = DMCreateMatrix(networkdm,&J);CHKERRQ(ierr);
ierr = MatSetOption(J,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr);
ierr = SetInitialValues(networkdm,X,&User);CHKERRQ(ierr);
/* HOOK UP SOLVER */
ierr = SNESCreate(PETSC_COMM_WORLD,&snes);CHKERRQ(ierr);
ierr = SNESSetDM(snes,networkdm);CHKERRQ(ierr);
ierr = SNESSetFunction(snes,F,FormFunction,&User);CHKERRQ(ierr);
ierr = SNESSetJacobian(snes,J,J,FormJacobian,&User);CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
ierr = SNESSolve(snes,NULL,X);CHKERRQ(ierr);
ierr = VecDestroy(&X);CHKERRQ(ierr);
ierr = VecDestroy(&F);CHKERRQ(ierr);
ierr = MatDestroy(&J);CHKERRQ(ierr);
ierr = SNESDestroy(&snes);CHKERRQ(ierr);
ierr = DMDestroy(&networkdm);CHKERRQ(ierr);
}
ierr = PetscFinalize();
return ierr;
}
int main(int argc,char **argv)
{
SNES snes; /* nonlinear solver context */
KSP ksp; /* linear solver context */
PC pc; /* preconditioner context */
Vec x,r; /* solution, residual vectors */
Mat J; /* Jacobian matrix */
PetscErrorCode ierr;
PetscInt its;
PetscMPIInt size,rank;
PetscScalar pfive = .5,*xx;
PetscBool flg;
AppCtx user; /* user-defined work context */
IS isglobal,islocal;
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);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create nonlinear solver context
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = SNESCreate(PETSC_COMM_WORLD,&snes);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create matrix and vector data structures; set corresponding routines
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Create vectors for solution and nonlinear function
*/
ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
ierr = VecSetSizes(x,PETSC_DECIDE,2);CHKERRQ(ierr);
ierr = VecSetFromOptions(x);CHKERRQ(ierr);
ierr = VecDuplicate(x,&r);CHKERRQ(ierr);
if (size > 1){
ierr = VecCreateSeq(PETSC_COMM_SELF,2,&user.xloc);CHKERRQ(ierr);
ierr = VecDuplicate(user.xloc,&user.rloc);CHKERRQ(ierr);
/* Create the scatter between the global x and local xloc */
ierr = ISCreateStride(MPI_COMM_SELF,2,0,1,&islocal);CHKERRQ(ierr);
ierr = ISCreateStride(MPI_COMM_SELF,2,0,1,&isglobal);CHKERRQ(ierr);
ierr = VecScatterCreate(x,isglobal,user.xloc,islocal,&user.scatter);CHKERRQ(ierr);
ierr = ISDestroy(&isglobal);CHKERRQ(ierr);
ierr = ISDestroy(&islocal);CHKERRQ(ierr);
}
/*
Create Jacobian matrix data structure
*/
ierr = MatCreate(PETSC_COMM_WORLD,&J);CHKERRQ(ierr);
ierr = MatSetSizes(J,PETSC_DECIDE,PETSC_DECIDE,2,2);CHKERRQ(ierr);
ierr = MatSetFromOptions(J);CHKERRQ(ierr);
ierr = MatSetUp(J);CHKERRQ(ierr);
ierr = PetscOptionsHasName(PETSC_NULL,"-hard",&flg);CHKERRQ(ierr);
if (!flg) {
/*
Set function evaluation routine and vector.
*/
ierr = SNESSetFunction(snes,r,FormFunction1,&user);CHKERRQ(ierr);
/*
Set Jacobian matrix data structure and Jacobian evaluation routine
*/
ierr = SNESSetJacobian(snes,J,J,FormJacobian1,PETSC_NULL);CHKERRQ(ierr);
} else {
if (size != 1) SETERRQ(PETSC_COMM_SELF,1,"This case is a uniprocessor example only!");
ierr = SNESSetFunction(snes,r,FormFunction2,PETSC_NULL);CHKERRQ(ierr);
ierr = SNESSetJacobian(snes,J,J,FormJacobian2,PETSC_NULL);CHKERRQ(ierr);
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Customize nonlinear solver; set runtime options
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Set linear solver defaults for this problem. By extracting the
KSP, KSP, and PC contexts from the SNES context, we can then
directly call any KSP, KSP, and PC routines to set various options.
*/
ierr = SNESGetKSP(snes,&ksp);CHKERRQ(ierr);
ierr = KSPGetPC(ksp,&pc);CHKERRQ(ierr);
ierr = PCSetType(pc,PCNONE);CHKERRQ(ierr);
ierr = KSPSetTolerances(ksp,1.e-4,PETSC_DEFAULT,PETSC_DEFAULT,20);CHKERRQ(ierr);
/*
Set SNES/KSP/KSP/PC runtime options, e.g.,
-snes_view -snes_monitor -ksp_type <ksp> -pc_type <pc>
These options will override those specified above as long as
SNESSetFromOptions() is called _after_ any other customization
routines.
*/
ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Evaluate initial guess; then solve nonlinear system
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
if (!flg) {
ierr = VecSet(x,pfive);CHKERRQ(ierr);
} else {
ierr = VecGetArray(x,&xx);CHKERRQ(ierr);
xx[0] = 2.0; xx[1] = 3.0;
ierr = VecRestoreArray(x,&xx);CHKERRQ(ierr);
}
/*
Note: The user should initialize the vector, x, with the initial guess
for the nonlinear solver prior to calling SNESSolve(). In particular,
to employ an initial guess of zero, the user should explicitly set
this vector to zero by calling VecSet().
*/
ierr = SNESSolve(snes,PETSC_NULL,x);CHKERRQ(ierr);
ierr = SNESGetIterationNumber(snes,&its);CHKERRQ(ierr);
if (flg) {
Vec f;
ierr = VecView(x,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = SNESGetFunction(snes,&f,0,0);CHKERRQ(ierr);
ierr = VecView(r,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = PetscPrintf(PETSC_COMM_WORLD,"number of SNES iterations = %D\n",its);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Free work space. All PETSc objects should be destroyed when they
are no longer needed.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = VecDestroy(&r);CHKERRQ(ierr);
ierr = MatDestroy(&J);CHKERRQ(ierr); ierr = SNESDestroy(&snes);CHKERRQ(ierr);
if (size > 1){
ierr = VecDestroy(&user.xloc);CHKERRQ(ierr);
ierr = VecDestroy(&user.rloc);CHKERRQ(ierr);
ierr = VecScatterDestroy(&user.scatter);CHKERRQ(ierr);
}
ierr = PetscFinalize();
return 0;
}
int main(int argc, char **argv)
{
SNES snes; /* nonlinear solver */
Vec u,r; /* solution, residual vectors */
Mat A,J; /* Jacobian matrix */
MatNullSpace nullSpace; /* May be necessary for pressure */
AppCtx user; /* user-defined work context */
JacActionCtx userJ; /* context for Jacobian MF action */
PetscInt its; /* iterations for convergence */
PetscReal error = 0.0; /* L_2 error in the solution */
const PetscInt numComponents = NUM_BASIS_COMPONENTS_TOTAL;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc, &argv, NULL, help);CHKERRQ(ierr);
ierr = ProcessOptions(PETSC_COMM_WORLD, &user);CHKERRQ(ierr);
ierr = SNESCreate(PETSC_COMM_WORLD, &snes);CHKERRQ(ierr);
ierr = CreateMesh(PETSC_COMM_WORLD, &user, &user.dm);CHKERRQ(ierr);
ierr = SNESSetDM(snes, user.dm);CHKERRQ(ierr);
ierr = SetupExactSolution(user.dm, &user);CHKERRQ(ierr);
ierr = SetupQuadrature(&user);CHKERRQ(ierr);
ierr = SetupSection(user.dm, &user);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(user.dm, &u);CHKERRQ(ierr);
ierr = VecDuplicate(u, &r);CHKERRQ(ierr);
ierr = DMCreateMatrix(user.dm, MATAIJ, &J);CHKERRQ(ierr);
if (user.jacobianMF) {
PetscInt M, m, N, n;
ierr = MatGetSize(J, &M, &N);CHKERRQ(ierr);
ierr = MatGetLocalSize(J, &m, &n);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD, &A);CHKERRQ(ierr);
ierr = MatSetSizes(A, m, n, M, N);CHKERRQ(ierr);
ierr = MatSetType(A, MATSHELL);CHKERRQ(ierr);
ierr = MatSetUp(A);CHKERRQ(ierr);
ierr = MatShellSetOperation(A, MATOP_MULT, (void (*)(void))FormJacobianAction);CHKERRQ(ierr);
userJ.dm = user.dm;
userJ.J = J;
userJ.user = &user;
ierr = DMCreateLocalVector(user.dm, &userJ.u);CHKERRQ(ierr);
ierr = DMPlexProjectFunctionLocal(user.dm, numComponents, user.exactFuncs, INSERT_BC_VALUES, userJ.u);CHKERRQ(ierr);
ierr = MatShellSetContext(A, &userJ);CHKERRQ(ierr);
} else {
A = J;
}
ierr = CreatePressureNullSpace(user.dm, &user, &nullSpace);CHKERRQ(ierr);
ierr = MatSetNullSpace(J, nullSpace);CHKERRQ(ierr);
if (A != J) {
ierr = MatSetNullSpace(A, nullSpace);CHKERRQ(ierr);
}
ierr = DMSNESSetFunctionLocal(user.dm, (PetscErrorCode (*)(DM,Vec,Vec,void*))DMPlexComputeResidualFEM,&user);CHKERRQ(ierr);
ierr = DMSNESSetJacobianLocal(user.dm, (PetscErrorCode (*)(DM,Vec,Mat,Mat,MatStructure*,void*))DMPlexComputeJacobianFEM,&user);CHKERRQ(ierr);
ierr = SNESSetJacobian(snes, A, J, NULL, NULL);CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
ierr = DMPlexProjectFunction(user.dm, numComponents, user.exactFuncs, INSERT_ALL_VALUES, u);CHKERRQ(ierr);
if (user.showInitial) {ierr = DMVecViewLocal(user.dm, u, PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);}
if (user.runType == RUN_FULL) {
PetscScalar (*initialGuess[numComponents])(const PetscReal x[]);
PetscInt c;
for (c = 0; c < numComponents; ++c) initialGuess[c] = zero;
ierr = DMPlexProjectFunction(user.dm, numComponents, initialGuess, INSERT_VALUES, u);CHKERRQ(ierr);
if (user.showInitial) {ierr = DMVecViewLocal(user.dm, u, PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);}
if (user.debug) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial guess\n");CHKERRQ(ierr);
ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = SNESSolve(snes, NULL, u);CHKERRQ(ierr);
ierr = SNESGetIterationNumber(snes, &its);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Number of SNES iterations = %D\n", its);CHKERRQ(ierr);
ierr = DMPlexComputeL2Diff(user.dm, user.fem.quad, user.exactFuncs, u, &error);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: %.3g\n", error);CHKERRQ(ierr);
if (user.showSolution) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "Solution\n");CHKERRQ(ierr);
ierr = VecChop(u, 3.0e-9);CHKERRQ(ierr);
ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
} else {
PetscReal res = 0.0;
/* Check discretization error */
ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial guess\n");CHKERRQ(ierr);
ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = DMPlexComputeL2Diff(user.dm, user.fem.quad, user.exactFuncs, u, &error);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: %g\n", error);CHKERRQ(ierr);
/* Check residual */
ierr = SNESComputeFunction(snes, u, r);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial Residual\n");CHKERRQ(ierr);
ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr);
ierr = VecView(r, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Residual: %g\n", res);CHKERRQ(ierr);
/* Check Jacobian */
{
Vec b;
MatStructure flag;
PetscBool isNull;
ierr = SNESComputeJacobian(snes, u, &A, &A, &flag);CHKERRQ(ierr);
ierr = MatNullSpaceTest(nullSpace, J, &isNull);CHKERRQ(ierr);
if (!isNull) SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_PLIB, "The null space calculated for the system operator is invalid.");
ierr = VecDuplicate(u, &b);CHKERRQ(ierr);
ierr = VecSet(r, 0.0);CHKERRQ(ierr);
ierr = SNESComputeFunction(snes, r, b);CHKERRQ(ierr);
ierr = MatMult(A, u, r);CHKERRQ(ierr);
ierr = VecAXPY(r, 1.0, b);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Au - b = Au + F(0)\n");CHKERRQ(ierr);
ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr);
ierr = VecView(r, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Linear L_2 Residual: %g\n", res);CHKERRQ(ierr);
}
}
if (user.runType == RUN_FULL) {
PetscViewer viewer;
Vec uLocal;
ierr = PetscViewerCreate(PETSC_COMM_WORLD, &viewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer, PETSCVIEWERVTK);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(viewer, PETSC_VIEWER_ASCII_VTK);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(viewer, "ex62_sol.vtk");CHKERRQ(ierr);
ierr = DMGetLocalVector(user.dm, &uLocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(user.dm, u, INSERT_VALUES, uLocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(user.dm, u, INSERT_VALUES, uLocal);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject) user.dm);CHKERRQ(ierr); /* Needed because viewer destroys the DM */
ierr = PetscObjectReference((PetscObject) uLocal);CHKERRQ(ierr); /* Needed because viewer destroys the Vec */
ierr = PetscViewerVTKAddField(viewer, (PetscObject) user.dm, DMPlexVTKWriteAll, PETSC_VTK_POINT_FIELD, (PetscObject) uLocal);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(user.dm, &uLocal);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
ierr = DestroyQuadrature(&user);CHKERRQ(ierr);
ierr = MatNullSpaceDestroy(&nullSpace);CHKERRQ(ierr);
if (user.jacobianMF) {
ierr = VecDestroy(&userJ.u);CHKERRQ(ierr);
}
if (A != J) {
ierr = MatDestroy(&A);CHKERRQ(ierr);
}
ierr = MatDestroy(&J);CHKERRQ(ierr);
ierr = VecDestroy(&u);CHKERRQ(ierr);
ierr = VecDestroy(&r);CHKERRQ(ierr);
ierr = SNESDestroy(&snes);CHKERRQ(ierr);
ierr = DMDestroy(&user.dm);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
std::pair<unsigned int, Real>
PetscNonlinearSolver<T>::solve (SparseMatrix<T>& jac_in, // System Jacobian Matrix
NumericVector<T>& x_in, // Solution vector
NumericVector<T>& r_in, // Residual vector
const double, // Stopping tolerance
const unsigned int)
{
START_LOG("solve()", "PetscNonlinearSolver");
this->init ();
// Make sure the data passed in are really of Petsc types
PetscMatrix<T>* jac = libmesh_cast_ptr<PetscMatrix<T>*>(&jac_in);
PetscVector<T>* x = libmesh_cast_ptr<PetscVector<T>*>(&x_in);
PetscVector<T>* r = libmesh_cast_ptr<PetscVector<T>*>(&r_in);
PetscErrorCode ierr=0;
PetscInt n_iterations =0;
// Should actually be a PetscReal, but I don't know which version of PETSc first introduced PetscReal
Real final_residual_norm=0.;
ierr = SNESSetFunction (_snes, r->vec(), __libmesh_petsc_snes_residual, this);
LIBMESH_CHKERRABORT(ierr);
// Only set the jacobian function if we've been provided with something to call.
// This allows a user to set their own jacobian function if they want to
if (this->jacobian || this->jacobian_object || this->residual_and_jacobian_object)
{
ierr = SNESSetJacobian (_snes, jac->mat(), jac->mat(), __libmesh_petsc_snes_jacobian, this);
LIBMESH_CHKERRABORT(ierr);
}
#if !PETSC_VERSION_LESS_THAN(3,3,0)
// Only set the nullspace if we have a way of computing it and the result is non-empty.
if (this->nullspace || this->nullspace_object)
{
MatNullSpace msp;
this->build_mat_null_space(this->nullspace_object, this->nullspace, &msp);
if (msp)
{
ierr = MatSetNullSpace(jac->mat(), msp);
LIBMESH_CHKERRABORT(ierr);
ierr = MatNullSpaceDestroy(&msp);
LIBMESH_CHKERRABORT(ierr);
}
}
// Only set the nearnullspace if we have a way of computing it and the result is non-empty.
if (this->nearnullspace || this->nearnullspace_object)
{
MatNullSpace msp = PETSC_NULL;
this->build_mat_null_space(this->nearnullspace_object, this->nearnullspace, &msp);
if(msp) {
ierr = MatSetNearNullSpace(jac->mat(), msp);
LIBMESH_CHKERRABORT(ierr);
ierr = MatNullSpaceDestroy(&msp);
LIBMESH_CHKERRABORT(ierr);
}
}
#endif
// Have the Krylov subspace method use our good initial guess rather than 0
KSP ksp;
ierr = SNESGetKSP (_snes, &ksp);
LIBMESH_CHKERRABORT(ierr);
// Set the tolerances for the iterative solver. Use the user-supplied
// tolerance for the relative residual & leave the others at default values
ierr = KSPSetTolerances (ksp, this->initial_linear_tolerance, PETSC_DEFAULT,
PETSC_DEFAULT, this->max_linear_iterations);
LIBMESH_CHKERRABORT(ierr);
// Set the tolerances for the non-linear solver.
ierr = SNESSetTolerances(_snes, this->absolute_residual_tolerance, this->relative_residual_tolerance,
this->relative_step_tolerance, this->max_nonlinear_iterations, this->max_function_evaluations);
LIBMESH_CHKERRABORT(ierr);
//Pull in command-line options
KSPSetFromOptions(ksp);
SNESSetFromOptions(_snes);
if (this->user_presolve)
this->user_presolve(this->system());
//Set the preconditioning matrix
if(this->_preconditioner)
{
this->_preconditioner->set_matrix(jac_in);
this->_preconditioner->init();
}
// ierr = KSPSetInitialGuessNonzero (ksp, PETSC_TRUE);
// LIBMESH_CHKERRABORT(ierr);
// Older versions (at least up to 2.1.5) of SNESSolve took 3 arguments,
// the last one being a pointer to an int to hold the number of iterations required.
# if PETSC_VERSION_LESS_THAN(2,2,0)
ierr = SNESSolve (_snes, x->vec(), &n_iterations);
LIBMESH_CHKERRABORT(ierr);
// 2.2.x style
#elif PETSC_VERSION_LESS_THAN(2,3,0)
ierr = SNESSolve (_snes, x->vec());
LIBMESH_CHKERRABORT(ierr);
// 2.3.x & newer style
#else
ierr = SNESSolve (_snes, PETSC_NULL, x->vec());
LIBMESH_CHKERRABORT(ierr);
ierr = SNESGetIterationNumber(_snes,&n_iterations);
LIBMESH_CHKERRABORT(ierr);
ierr = SNESGetLinearSolveIterations(_snes, &_n_linear_iterations);
LIBMESH_CHKERRABORT(ierr);
ierr = SNESGetFunctionNorm(_snes,&final_residual_norm);
LIBMESH_CHKERRABORT(ierr);
#endif
// Get and store the reason for convergence
SNESGetConvergedReason(_snes, &_reason);
//Based on Petsc 2.3.3 documentation all diverged reasons are negative
this->converged = (_reason >= 0);
this->clear();
STOP_LOG("solve()", "PetscNonlinearSolver");
// return the # of its. and the final residual norm.
return std::make_pair(n_iterations, final_residual_norm);
}
/*
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)
{
TS ts;
SNES snes_alg;
PetscErrorCode ierr;
Userctx *ctx = (Userctx*)ctx0;
Vec X;
Mat J;
/* sensitivity context */
PetscScalar *x_ptr;
PetscViewer Xview,Ybusview;
Vec F_alg;
Vec Xdot;
PetscInt row_loc,col_loc;
PetscScalar val;
ierr = VecGetArray(P,&x_ptr);CHKERRQ(ierr);
PG[0] = x_ptr[0];
PG[1] = x_ptr[1];
PG[2] = x_ptr[2];
ierr = VecRestoreArray(P,&x_ptr);CHKERRQ(ierr);
ctx->stepnum = 0;
ierr = VecZeroEntries(ctx->vec_q);CHKERRQ(ierr);
/* Read initial voltage vector and Ybus */
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"X.bin",FILE_MODE_READ,&Xview);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"Ybus.bin",FILE_MODE_READ,&Ybusview);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,&ctx->V0);CHKERRQ(ierr);
ierr = VecSetSizes(ctx->V0,PETSC_DECIDE,ctx->neqs_net);CHKERRQ(ierr);
ierr = VecLoad(ctx->V0,Xview);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&ctx->Ybus);CHKERRQ(ierr);
ierr = MatSetSizes(ctx->Ybus,PETSC_DECIDE,PETSC_DECIDE,ctx->neqs_net,ctx->neqs_net);CHKERRQ(ierr);
ierr = MatSetType(ctx->Ybus,MATBAIJ);CHKERRQ(ierr);
/* ierr = MatSetBlockSize(ctx->Ybus,2);CHKERRQ(ierr); */
ierr = MatLoad(ctx->Ybus,Ybusview);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&Xview);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&Ybusview);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(ctx->dmpgrid,&X);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&J);CHKERRQ(ierr);
ierr = MatSetSizes(J,PETSC_DECIDE,PETSC_DECIDE,ctx->neqs_pgrid,ctx->neqs_pgrid);CHKERRQ(ierr);
ierr = MatSetFromOptions(J);CHKERRQ(ierr);
ierr = PreallocateJacobian(J,ctx);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,ctx);CHKERRQ(ierr);
ierr = TSSetIJacobian(ts,J,J,(TSIJacobian)IJacobian,ctx);CHKERRQ(ierr);
ierr = TSSetApplicationContext(ts,ctx);CHKERRQ(ierr);
ierr = TSMonitorSet(ts,MonitorUpdateQ,ctx,NULL);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Set initial conditions
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = SetInitialGuess(X,ctx);CHKERRQ(ierr);
ierr = VecDuplicate(X,&F_alg);CHKERRQ(ierr);
ierr = SNESCreate(PETSC_COMM_WORLD,&snes_alg);CHKERRQ(ierr);
ierr = SNESSetFunction(snes_alg,F_alg,AlgFunction,ctx);CHKERRQ(ierr);
ierr = MatZeroEntries(J);CHKERRQ(ierr);
ierr = SNESSetJacobian(snes_alg,J,J,AlgJacobian,ctx);CHKERRQ(ierr);
ierr = SNESSetOptionsPrefix(snes_alg,"alg_");CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes_alg);CHKERRQ(ierr);
ctx->alg_flg = PETSC_TRUE;
/* Solve the algebraic equations */
ierr = SNESSolve(snes_alg,NULL,X);CHKERRQ(ierr);
/* Just to set up the Jacobian structure */
ierr = VecDuplicate(X,&Xdot);CHKERRQ(ierr);
ierr = IJacobian(ts,0.0,X,Xdot,0.0,J,J,ctx);CHKERRQ(ierr);
ierr = VecDestroy(&Xdot);CHKERRQ(ierr);
ctx->stepnum++;
ierr = TSSetDuration(ts,1000,ctx->tfaulton);CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts,0.0,0.01);CHKERRQ(ierr);
ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
/* ierr = TSSetPostStep(ts,SaveSolution);CHKERRQ(ierr); */
ctx->alg_flg = PETSC_FALSE;
/* Prefault period */
ierr = TSSolve(ts,X);CHKERRQ(ierr);
/* Create the nonlinear solver for solving the algebraic system */
/* Note that although the algebraic system needs to be solved only for
Idq and V, we reuse the entire system including xgen. The xgen
variables are held constant by setting their residuals to 0 and
putting a 1 on the Jacobian diagonal for xgen rows
*/
ierr = MatZeroEntries(J);CHKERRQ(ierr);
/* Apply disturbance - resistive fault at ctx->faultbus */
/* This is done by adding shunt conductance to the diagonal location
in the Ybus matrix */
row_loc = 2*ctx->faultbus; col_loc = 2*ctx->faultbus+1; /* Location for G */
val = 1/ctx->Rfault;
ierr = MatSetValues(ctx->Ybus,1,&row_loc,1,&col_loc,&val,ADD_VALUES);CHKERRQ(ierr);
row_loc = 2*ctx->faultbus+1; col_loc = 2*ctx->faultbus; /* Location for G */
val = 1/ctx->Rfault;
ierr = MatSetValues(ctx->Ybus,1,&row_loc,1,&col_loc,&val,ADD_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(ctx->Ybus,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(ctx->Ybus,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ctx->alg_flg = PETSC_TRUE;
/* Solve the algebraic equations */
ierr = SNESSolve(snes_alg,NULL,X);CHKERRQ(ierr);
ctx->stepnum++;
/* Disturbance period */
ierr = TSSetDuration(ts,1000,ctx->tfaultoff);CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts,ctx->tfaulton,.01);CHKERRQ(ierr);
ctx->alg_flg = PETSC_FALSE;
ierr = TSSolve(ts,X);CHKERRQ(ierr);
/* Remove the fault */
row_loc = 2*ctx->faultbus; col_loc = 2*ctx->faultbus+1;
val = -1/ctx->Rfault;
ierr = MatSetValues(ctx->Ybus,1,&row_loc,1,&col_loc,&val,ADD_VALUES);CHKERRQ(ierr);
row_loc = 2*ctx->faultbus+1; col_loc = 2*ctx->faultbus;
val = -1/ctx->Rfault;
ierr = MatSetValues(ctx->Ybus,1,&row_loc,1,&col_loc,&val,ADD_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(ctx->Ybus,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(ctx->Ybus,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatZeroEntries(J);CHKERRQ(ierr);
ctx->alg_flg = PETSC_TRUE;
/* Solve the algebraic equations */
ierr = SNESSolve(snes_alg,NULL,X);CHKERRQ(ierr);
ctx->stepnum++;
/* Post-disturbance period */
ierr = TSSetDuration(ts,1000,ctx->tmax);CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts,ctx->tfaultoff,.01);CHKERRQ(ierr);
ctx->alg_flg = PETSC_TRUE;
ierr = TSSolve(ts,X);CHKERRQ(ierr);
ierr = VecGetArray(ctx->vec_q,&x_ptr);CHKERRQ(ierr);
*f = x_ptr[0];
ierr = VecRestoreArray(ctx->vec_q,&x_ptr);CHKERRQ(ierr);
ierr = MatDestroy(&ctx->Ybus);CHKERRQ(ierr);
ierr = VecDestroy(&ctx->V0);CHKERRQ(ierr);
ierr = SNESDestroy(&snes_alg);CHKERRQ(ierr);
ierr = VecDestroy(&F_alg);CHKERRQ(ierr);
ierr = MatDestroy(&J);CHKERRQ(ierr);
ierr = VecDestroy(&X);CHKERRQ(ierr);
ierr = TSDestroy(&ts);CHKERRQ(ierr);
return 0;
}
int main(int argc, char **argv)
{
MPI_Comm comm;
PetscMPIInt rank;
PetscErrorCode ierr;
User user;
PetscLogDouble v1, v2;
PetscInt nplot = 0;
char filename1[2048], fileName[2048];
PetscBool set = PETSC_FALSE;
PetscInt steps_output;
ierr = PetscInitialize(&argc, &argv, (char*) 0, help);CHKERRQ(ierr);
comm = PETSC_COMM_WORLD;
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = PetscNew(&user);CHKERRQ(ierr);
ierr = PetscNew(&user->algebra);CHKERRQ(ierr);
ierr = PetscNew(&user->model);CHKERRQ(ierr);
ierr = PetscNew(&user->model->physics);CHKERRQ(ierr);
Algebra algebra = user->algebra;
ierr = LoadOptions(comm, user);CHKERRQ(ierr);
ierr = PetscTime(&v1);CHKERRQ(ierr);
ierr = CreateMesh(comm, user);CHKERRQ(ierr);
ierr = PetscTime(&v2);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,
"Read and Distribute mesh takes %f sec \n", v2 - v1);CHKERRQ(ierr);
ierr = SetUpLocalSpace(user);CHKERRQ(ierr); //Set up the dofs of each element
ierr = ConstructGeometryFVM(&user->facegeom, &user->cellgeom, user);CHKERRQ(ierr);
ierr = LimiterSetup(user);CHKERRQ(ierr);
if(user->output_solution){
// the output file options
ierr = PetscOptionsBegin(PETSC_COMM_WORLD,0,"Options for output solution",0);CHKERRQ(ierr);
ierr = PetscOptionsString("-solutionfile", "solution file", "AeroSim.c", filename1,filename1, 2048, &set);CHKERRQ(ierr);
if(!set){SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_NULL,"please use option -solutionfile to specify solution file name \n");}
ierr = PetscOptionsInt("-steps_output", "the number of time steps between two outputs", "", steps_output, &steps_output, &set);CHKERRQ(ierr);
if(!set){ steps_output = 1;}
ierr = PetscOptionsEnd();CHKERRQ(ierr);
}
if (user->TimeIntegralMethod == EXPLICITMETHOD) {
if(user->myownexplicitmethod){
ierr = PetscPrintf(PETSC_COMM_WORLD,"Using the fully explicit method based on my own routing\n");CHKERRQ(ierr);
user->current_time = user->initial_time;
user->current_step = 1;
ierr = DMCreateGlobalVector(user->dm, &algebra->solution);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) algebra->solution, "solution");CHKERRQ(ierr);
ierr = SetInitialCondition(user->dm, algebra->solution, user);CHKERRQ(ierr);
ierr = VecDuplicate(algebra->solution, &algebra->fn);CHKERRQ(ierr);
ierr = VecDuplicate(algebra->solution, &algebra->oldsolution);CHKERRQ(ierr);
if(user->Explicit_RK2){
ierr = PetscPrintf(PETSC_COMM_WORLD,"Use the second order Runge Kutta method \n");CHKERRQ(ierr);
}else{
ierr = PetscPrintf(PETSC_COMM_WORLD,"Use the first order forward Euler method \n");CHKERRQ(ierr);
}
nplot = 0; //the plot step
while(user->current_time < (user->final_time - 0.05 * user->dt)){
user->current_time = user->current_time + user->dt;
ierr = FormTimeStepFunction(user, algebra, algebra->solution, algebra->fn);CHKERRQ(ierr);
PetscReal fnnorm;
ierr = VecNorm(algebra->fn,NORM_INFINITY,&fnnorm);CHKERRQ(ierr);
if(0){
PetscViewer viewer;
ierr = OutputVTK(user->dm, "function.vtk", &viewer);CHKERRQ(ierr);
ierr = VecView(algebra->fn, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Step %D at time %g with founction norm = %g \n",
user->current_step, user->current_time, fnnorm);CHKERRQ(ierr);
//break;
}
if(user->Explicit_RK2){
ierr = VecCopy(algebra->solution, algebra->oldsolution);CHKERRQ(ierr);//U^n
ierr = VecAXPY(algebra->solution, user->dt, algebra->fn);CHKERRQ(ierr);//U^{(1)}
ierr = FormTimeStepFunction(user, algebra, algebra->solution, algebra->fn);CHKERRQ(ierr);//f(U^{(1)})
ierr = VecAXPY(algebra->solution, 1.0, algebra->oldsolution);CHKERRQ(ierr);//U^n + U^{(1)}
ierr = VecAXPY(algebra->solution, user->dt, algebra->fn);CHKERRQ(ierr);// + dt*f(U^{(1)})
ierr = VecScale(algebra->solution, 0.5);CHKERRQ(ierr);
}else{
ierr = VecCopy(algebra->solution, algebra->oldsolution);CHKERRQ(ierr);
ierr = VecAXPY(algebra->solution, user->dt, algebra->fn);CHKERRQ(ierr);
}
{// Monitor the solution and function norms
PetscReal norm;
PetscLogDouble space =0;
PetscInt size;
ierr = VecNorm(algebra->solution,NORM_INFINITY,&norm);CHKERRQ(ierr);
ierr = VecGetSize(algebra->solution, &size);CHKERRQ(ierr);
norm = norm/size;
if (norm>1.e5) {
SETERRQ2(PETSC_COMM_WORLD, PETSC_ERR_LIB,
"The norm of the solution is: %f (current time: %f). The explicit method is going to DIVERGE!!!", norm, user->current_time);
}
if (user->current_step%10==0) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Step %D at time %g with solution norm = %g and founction norm = %g \n",
user->current_step, user->current_time, norm, fnnorm);CHKERRQ(ierr);
}
ierr = PetscMallocGetCurrentUsage(&space);CHKERRQ(ierr);
// if (user->current_step%10==0) {
// ierr = PetscPrintf(PETSC_COMM_WORLD,"Current space PetscMalloc()ed %g M\n",
// space/(1024*1024));CHKERRQ(ierr);
// }
}
{ // Monitor the difference of two steps' solution
PetscReal norm;
ierr = VecAXPY(algebra->oldsolution, -1, algebra->solution);CHKERRQ(ierr);
ierr = VecNorm(algebra->oldsolution,NORM_INFINITY,&norm);CHKERRQ(ierr);
if (user->current_step%10==0) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Step %D at time %g with ||u_k-u_{k-1}|| = %g \n",
user->current_step, user->current_time, norm);CHKERRQ(ierr);
}
if((norm<1.e-6)||(user->current_step > user->max_time_its)) break;
}
// output the solution
if (user->output_solution && (user->current_step%steps_output==0)){
PetscViewer viewer;
// update file name for the current time step
ierr = PetscSNPrintf(fileName, sizeof(fileName),"%s_%d.vtk",filename1, nplot);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Outputing solution %s (current time %f)\n", fileName, user->current_time);CHKERRQ(ierr);
ierr = OutputVTK(user->dm, fileName, &viewer);CHKERRQ(ierr);
ierr = VecView(algebra->solution, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
nplot++;
}
user->current_step++;
}
ierr = VecDestroy(&algebra->fn);CHKERRQ(ierr);
}else{
PetscReal ftime;
TS ts;
TSConvergedReason reason;
PetscInt nsteps;
ierr = PetscPrintf(PETSC_COMM_WORLD,"Using the fully explicit method based on the PETSC TS routing\n");CHKERRQ(ierr);
ierr = DMCreateGlobalVector(user->dm, &algebra->solution);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) algebra->solution, "solution");CHKERRQ(ierr);
ierr = SetInitialCondition(user->dm, algebra->solution, user);CHKERRQ(ierr);
ierr = TSCreate(comm, &ts);CHKERRQ(ierr);
ierr = TSSetType(ts, TSEULER);CHKERRQ(ierr);
ierr = TSSetDM(ts, user->dm);CHKERRQ(ierr);
ierr = TSMonitorSet(ts,TSMonitorFunctionError,&user,NULL);CHKERRQ(ierr);
ierr = TSSetRHSFunction(ts, NULL, MyRHSFunction, user);CHKERRQ(ierr);
ierr = TSSetDuration(ts, 1000, user->final_time);CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts, user->initial_time, user->dt);CHKERRQ(ierr);
ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
ierr = TSSolve(ts, algebra->solution);CHKERRQ(ierr);
ierr = TSGetSolveTime(ts, &ftime);CHKERRQ(ierr);
ierr = TSGetTimeStepNumber(ts, &nsteps);CHKERRQ(ierr);
ierr = TSGetConvergedReason(ts, &reason);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"%s at time %g after %D steps\n",TSConvergedReasons[reason],ftime,nsteps);CHKERRQ(ierr);
ierr = TSDestroy(&ts);CHKERRQ(ierr);
}
if(user->benchmark_couette) {
ierr = DMCreateGlobalVector(user->dm, &algebra->exactsolution);CHKERRQ(ierr);
ierr = ComputeExactSolution(user->dm, user->final_time, algebra->exactsolution, user);CHKERRQ(ierr);
}
if (user->output_solution){
PetscViewer viewer;
ierr = OutputVTK(user->dm, "solution.vtk", &viewer);CHKERRQ(ierr);
ierr = VecView(algebra->solution, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
if(user->benchmark_couette) {
PetscViewer viewer;
PetscReal norm;
ierr = OutputVTK(user->dm, "exact_solution.vtk", &viewer);CHKERRQ(ierr);
ierr = VecView(algebra->exactsolution, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = VecAXPY(algebra->exactsolution, -1, algebra->solution);CHKERRQ(ierr);
ierr = VecNorm(algebra->exactsolution,NORM_INFINITY,&norm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Final time at %f, Error: ||u_k-u|| = %g \n", user->final_time, norm);CHKERRQ(ierr);
ierr = OutputVTK(user->dm, "Error.vtk", &viewer);CHKERRQ(ierr);
ierr = VecView(algebra->exactsolution, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
ierr = VecDestroy(&algebra->solution);CHKERRQ(ierr);
ierr = VecDestroy(&algebra->oldsolution);CHKERRQ(ierr);
ierr = DMDestroy(&user->dm);CHKERRQ(ierr);
} else if (user->TimeIntegralMethod == IMPLICITMETHOD) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Using the fully implicit method\n");CHKERRQ(ierr);
ierr = SNESCreate(comm,&user->snes);CHKERRQ(ierr);
ierr = SNESSetDM(user->snes,user->dm);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(user->dm, &algebra->solution);CHKERRQ(ierr);
ierr = VecDuplicate(algebra->solution, &algebra->oldsolution);CHKERRQ(ierr);
ierr = VecDuplicate(algebra->solution, &algebra->f);CHKERRQ(ierr);
ierr = VecDuplicate(algebra->solution, &algebra->fn);CHKERRQ(ierr);
ierr = VecDuplicate(algebra->solution, &algebra->oldfn);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) algebra->solution, "solution");CHKERRQ(ierr);
ierr = SetInitialCondition(user->dm, algebra->solution, user);CHKERRQ(ierr);
ierr = DMSetMatType(user->dm, MATAIJ);CHKERRQ(ierr);
// ierr = DMCreateMatrix(user->dm, &algebra->A);CHKERRQ(ierr);
ierr = DMCreateMatrix(user->dm, &algebra->J);CHKERRQ(ierr);
if (user->JdiffP) {
/*Set up the preconditioner matrix*/
ierr = DMCreateMatrix(user->dm, &algebra->P);CHKERRQ(ierr);
}else{
algebra->P = algebra->J;
}
ierr = MatSetOption(algebra->J, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);CHKERRQ(ierr);
/*set nonlinear function */
ierr = SNESSetFunction(user->snes, algebra->f, FormFunction, (void*)user);CHKERRQ(ierr);
/* compute Jacobian */
ierr = SNESSetJacobian(user->snes, algebra->J, algebra->P, FormJacobian, (void*)user);CHKERRQ(ierr);
ierr = SNESSetFromOptions(user->snes);CHKERRQ(ierr);
/* do the solve */
if (user->timestep == TIMESTEP_STEADY_STATE) {
ierr = SolveSteadyState(user);CHKERRQ(ierr);
} else {
ierr = SolveTimeDependent(user);CHKERRQ(ierr);
}
if (user->output_solution){
PetscViewer viewer;
ierr = OutputVTK(user->dm, "solution.vtk", &viewer);CHKERRQ(ierr);
ierr = VecView(algebra->solution, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
if(user->benchmark_couette) {
PetscViewer viewer;
PetscReal norm;
ierr = OutputVTK(user->dm, "exact_solution.vtk", &viewer);CHKERRQ(ierr);
ierr = VecView(algebra->exactsolution, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = VecAXPY(algebra->exactsolution, -1, algebra->solution);CHKERRQ(ierr);
ierr = VecNorm(algebra->exactsolution,NORM_INFINITY,&norm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Error: ||u_k-u|| = %g \n", norm);CHKERRQ(ierr);
ierr = OutputVTK(user->dm, "Error.vtk", &viewer);CHKERRQ(ierr);
ierr = VecView(algebra->exactsolution, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
ierr = VecDestroy(&algebra->solution);CHKERRQ(ierr);
ierr = VecDestroy(&algebra->f);CHKERRQ(ierr);
ierr = VecDestroy(&algebra->oldsolution);CHKERRQ(ierr);
ierr = VecDestroy(&algebra->fn);CHKERRQ(ierr);
ierr = VecDestroy(&algebra->oldfn);CHKERRQ(ierr);
ierr = SNESDestroy(&user->snes);CHKERRQ(ierr);
ierr = DMDestroy(&user->dm);CHKERRQ(ierr);
} else {
SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"WRONG option for the time integral method. Using the option '-time_integral_method 0 or 1'");
}
ierr = VecDestroy(&user->cellgeom);CHKERRQ(ierr);
ierr = VecDestroy(&user->facegeom);CHKERRQ(ierr);
ierr = DMDestroy(&user->dmGrad);CHKERRQ(ierr);
ierr = PetscFunctionListDestroy(&LimitList);CHKERRQ(ierr);
ierr = PetscFree(user->model->physics);CHKERRQ(ierr);
ierr = PetscFree(user->algebra);CHKERRQ(ierr);
ierr = PetscFree(user->model);CHKERRQ(ierr);
ierr = PetscFree(user);CHKERRQ(ierr);
{
PetscLogDouble space =0;
ierr = PetscMallocGetCurrentUsage(&space);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Unfreed space at the End %g M\n", space/(1024*1024));CHKERRQ(ierr);
}
ierr = PetscFinalize();
return(0);
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
SNES snes; /* nonlinear solver */
Vec Hu,r; /* solution, residual vectors */
Mat J; /* Jacobian matrix */
AppCtx user; /* user-defined work context */
PetscInt its, i, tmpxs, tmpxm; /* iteration count, index, etc. */
PetscReal tmp1, tmp2, tmp3, tmp4, tmp5,
errnorms[2], descaleNode[2];
PetscTruth eps_set = PETSC_FALSE, dump = PETSC_FALSE, exactinitial = PETSC_FALSE,
snes_mf_set, snes_fd_set;
MatFDColoring matfdcoloring = 0;
ISColoring iscoloring;
SNESConvergedReason reason; /* Check convergence */
PetscInitialize(&argc,&argv,(char *)0,help);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD, &user.rank); CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,
"BODVARDSSON solves for thickness and velocity in 1D, steady ice stream\n"
" [run with -help for info and options]\n");CHKERRQ(ierr);
user.n = 3.0; /* Glen flow law exponent */
user.secpera = 31556926.0;
user.rho = 910.0; /* kg m^-3 */
user.rhow = 1028.0; /* kg m^-3 */
user.g = 9.81; /* m s^-2 */
/* ask Test N for its parameters, but only those we need to solve */
ierr = params_exactN(&(user.H0), &tmp1, &(user.xc), &tmp2, &tmp3, &tmp4, &tmp5,
&(user.Txc)); CHKERRQ(ierr);
/* regularize using strain rate of 1/xc per year */
user.epsilon = (1.0 / user.secpera) / user.xc;
/* tools for non-dimensionalizing to improve equation scaling */
user.scaleNode[0] = 1000.0; user.scaleNode[1] = 100.0 / user.secpera;
ierr = PetscOptionsTruth("-snes_mf","","",PETSC_FALSE,&snes_mf_set,NULL);CHKERRQ(ierr);
ierr = PetscOptionsTruth("-snes_fd","","",PETSC_FALSE,&snes_fd_set,NULL);CHKERRQ(ierr);
if (!snes_mf_set && !snes_fd_set) {
PetscPrintf(PETSC_COMM_WORLD,
"\n***ERROR: bodvardsson needs one or zero of '-snes_mf', '-snes_fd'***\n\n"
"USAGE FOLLOWS ...\n\n%s",help);
PetscEnd();
}
if (snes_fd_set) {
ierr = PetscPrintf(PETSC_COMM_WORLD,
" using approximate Jacobian; finite-differencing using coloring\n");
CHKERRQ(ierr);
} else if (snes_mf_set) {
ierr = PetscPrintf(PETSC_COMM_WORLD,
" matrix free; no preconditioner\n"); CHKERRQ(ierr);
} else {
ierr = PetscPrintf(PETSC_COMM_WORLD,
" true Jacobian\n"); CHKERRQ(ierr);
}
ierr = PetscOptionsBegin(PETSC_COMM_WORLD,NULL,
"bodvardsson program options",__FILE__);CHKERRQ(ierr);
{
ierr = PetscOptionsTruth("-bod_up_one","","",PETSC_FALSE,&user.upwind1,NULL);CHKERRQ(ierr);
ierr = PetscOptionsTruth("-bod_exact_init","","",PETSC_FALSE,&exactinitial,NULL);CHKERRQ(ierr);
ierr = PetscOptionsTruth("-bod_dump",
"dump out exact and approximate solution and residual, as asci","",
dump,&dump,NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-bod_epsilon","regularization (a strain rate in units of 1/a)","",
user.epsilon * user.secpera,&user.epsilon,&eps_set);CHKERRQ(ierr);
if (eps_set) user.epsilon *= 1.0 / user.secpera;
}
ierr = PetscOptionsEnd();CHKERRQ(ierr);
/* Create machinery for parallel grid management (DA), nonlinear solver (SNES),
and Vecs for fields (solution, RHS). Note default Mx=46 grid points means
dx=10 km. Also degrees of freedom = 2 (thickness and velocity
at each point) and stencil radius = ghost width = 2 for 2nd-order upwinding. */
user.solnghostwidth = 2;
ierr = DACreate1d(PETSC_COMM_WORLD,DA_NONPERIODIC,-46,2,user.solnghostwidth,PETSC_NULL,&user.da);
CHKERRQ(ierr);
ierr = DASetUniformCoordinates(user.da,0.0,user.xc,
PETSC_NULL,PETSC_NULL,PETSC_NULL,PETSC_NULL);CHKERRQ(ierr);
ierr = DASetFieldName(user.da,0,"ice thickness [non-dimensional]"); CHKERRQ(ierr);
ierr = DASetFieldName(user.da,1,"ice velocity [non-dimensional]"); CHKERRQ(ierr);
ierr = DAGetInfo(user.da,PETSC_IGNORE,&user.Mx,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,
PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE);
ierr = DAGetCorners(user.da,&user.xs,PETSC_NULL,PETSC_NULL,&user.xm,PETSC_NULL,PETSC_NULL);
CHKERRQ(ierr);
user.dx = user.xc / (PetscReal)(user.Mx-1);
/* another DA for scalar parameters, with same length */
ierr = DACreate1d(PETSC_COMM_WORLD,DA_NONPERIODIC,user.Mx,1,1,PETSC_NULL,&user.scalarda);CHKERRQ(ierr);
ierr = DASetUniformCoordinates(user.scalarda,0.0,user.xc,
PETSC_NULL,PETSC_NULL,PETSC_NULL,PETSC_NULL);CHKERRQ(ierr);
/* check that parallel layout of scalar DA is same as dof=2 DA */
ierr = DAGetCorners(user.scalarda,&tmpxs,PETSC_NULL,PETSC_NULL,&tmpxm,PETSC_NULL,PETSC_NULL);
CHKERRQ(ierr);
if ((tmpxs != user.xs) || (tmpxm != user.xm)) {
PetscPrintf(PETSC_COMM_SELF,
"\n***ERROR: rank %d gets different ownership range for the two DAs! ENDING ...***\n\n",
user.rank);
PetscEnd();
}
ierr = PetscPrintf(PETSC_COMM_WORLD,
" Mx = %D points, dx = %.3f m\n H0 = %.2f m, xc = %.2f km, Txc = %.5e Pa m\n",
user.Mx, user.dx, user.H0, user.xc/1000.0, user.Txc);CHKERRQ(ierr);
/* Extract/allocate global vectors from DAs and duplicate for remaining same types */
ierr = DACreateGlobalVector(user.da,&Hu);CHKERRQ(ierr);
ierr = VecSetBlockSize(Hu,2);CHKERRQ(ierr);
ierr = VecDuplicate(Hu,&r);CHKERRQ(ierr); /* inherits block size */
ierr = VecDuplicate(Hu,&user.Huexact);CHKERRQ(ierr); /* ditto */
ierr = DACreateGlobalVector(user.scalarda,&user.M);CHKERRQ(ierr);
ierr = VecDuplicate(user.M,&user.Bstag);CHKERRQ(ierr);
ierr = VecDuplicate(user.M,&user.beta);CHKERRQ(ierr);
ierr = DASetLocalFunction(user.da,(DALocalFunction1)scshell);CHKERRQ(ierr);
ierr = DASetLocalJacobian(user.da,(DALocalFunction1)BodJacobianMatrixLocal);CHKERRQ(ierr);
ierr = SNESCreate(PETSC_COMM_WORLD,&snes);CHKERRQ(ierr);
ierr = SNESSetFunction(snes,r,SNESDAFormFunction,&user);CHKERRQ(ierr);
/* setting up a matrix is only actually needed for -snes_fd case */
ierr = DAGetMatrix(user.da,MATAIJ,&J);CHKERRQ(ierr);
if (snes_fd_set) {
/* tools needed so DA can use sparse matrix for its F.D. Jacobian approx */
ierr = DAGetColoring(user.da,IS_COLORING_GLOBAL,MATAIJ,&iscoloring);CHKERRQ(ierr);
ierr = MatFDColoringCreate(J,iscoloring,&matfdcoloring);CHKERRQ(ierr);
ierr = ISColoringDestroy(iscoloring);CHKERRQ(ierr);
ierr = MatFDColoringSetFunction(matfdcoloring,
(PetscErrorCode (*)(void))SNESDAFormFunction,&user);CHKERRQ(ierr);
ierr = MatFDColoringSetFromOptions(matfdcoloring);CHKERRQ(ierr);
ierr = SNESSetJacobian(snes,J,J,SNESDefaultComputeJacobianColor,matfdcoloring);CHKERRQ(ierr);
} else {
ierr = SNESSetJacobian(snes,J,J,SNESDAComputeJacobian,&user);CHKERRQ(ierr);
}
ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
/* the the Bodvardsson (1955) exact solution allows setting M(x), B(x), beta(x), T(xc) */
ierr = FillDistributedParams(&user);CHKERRQ(ierr);
/* the exact thickness and exact ice velocity (user.uHexact) are known from Bodvardsson (1955) */
ierr = FillExactSoln(&user); CHKERRQ(ierr);
if (exactinitial) {
ierr = PetscPrintf(PETSC_COMM_WORLD," using exact solution as initial guess\n");
CHKERRQ(ierr);
/* the initial guess is the exact continuum solution */
ierr = VecCopy(user.Huexact,Hu); CHKERRQ(ierr);
} else {
ierr = FillInitial(&user, &Hu); CHKERRQ(ierr);
}
/************ SOLVE NONLINEAR SYSTEM ************/
/* recall that RHS r is used internally by KSP, and is set by the SNES */
for (i = 0; i < 2; i++) descaleNode[i] = 1.0 / user.scaleNode[i];
ierr = VecStrideScaleAll(Hu,descaleNode); CHKERRQ(ierr); /* de-dimensionalize initial guess */
ierr = SNESSolve(snes,PETSC_NULL,Hu);CHKERRQ(ierr);
ierr = VecStrideScaleAll(Hu,user.scaleNode); CHKERRQ(ierr); /* put back in "real" scale */
ierr = SNESGetIterationNumber(snes,&its);CHKERRQ(ierr);
ierr = SNESGetConvergedReason(snes,&reason);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,
" %s Number of Newton iterations = %D\n",
SNESConvergedReasons[reason],its);CHKERRQ(ierr);
if (dump) {
ierr = PetscPrintf(PETSC_COMM_WORLD,
" viewing combined result Hu\n");CHKERRQ(ierr);
ierr = VecView(Hu,PETSC_VIEWER_STDOUT_WORLD); CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,
" viewing combined exact result Huexact\n");CHKERRQ(ierr);
ierr = VecView(user.Huexact,PETSC_VIEWER_STDOUT_WORLD); CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,
" viewing final combined residual at Hu\n");CHKERRQ(ierr);
ierr = VecView(r,PETSC_VIEWER_STDOUT_WORLD); CHKERRQ(ierr);
}
/* evaluate error relative to exact solution */
ierr = VecAXPY(Hu,-1.0,user.Huexact); CHKERRQ(ierr); /* Hu = - Huexact + Hu */
ierr = VecStrideNormAll(Hu,NORM_INFINITY,errnorms); CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,
"(dx,errHinf,erruinf) %.3f %.4e %.4e\n",
user.dx,errnorms[0],errnorms[1]*user.secpera);CHKERRQ(ierr);
ierr = VecDestroy(Hu);CHKERRQ(ierr);
ierr = VecDestroy(r);CHKERRQ(ierr);
ierr = VecDestroy(user.Huexact);CHKERRQ(ierr);
ierr = VecDestroy(user.M);CHKERRQ(ierr);
ierr = VecDestroy(user.Bstag);CHKERRQ(ierr);
ierr = VecDestroy(user.beta);CHKERRQ(ierr);
ierr = MatDestroy(J); CHKERRQ(ierr);
ierr = SNESDestroy(snes);CHKERRQ(ierr);
ierr = DADestroy(user.da);CHKERRQ(ierr);
ierr = DADestroy(user.scalarda);CHKERRQ(ierr);
ierr = PetscFinalize();CHKERRQ(ierr);
return 0;
}
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)
{
SNES snes; /* SNES context */
Vec x,r,F,U; /* vectors */
Mat J; /* Jacobian matrix */
MonitorCtx monP; /* monitoring context */
PetscErrorCode ierr;
PetscInt its,n = 5,i,maxit,maxf;
PetscMPIInt size;
PetscScalar h,xp,v,none = -1.0;
PetscReal abstol,rtol,stol,norm;
PetscInitialize(&argc,&argv,(char*)0,help);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"This is a uniprocessor example only!");
ierr = PetscOptionsGetInt(NULL,"-n",&n,NULL);CHKERRQ(ierr);
h = 1.0/(n-1);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create nonlinear solver context
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = SNESCreate(PETSC_COMM_WORLD,&snes);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create vector data structures; set function evaluation routine
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Note that we form 1 vector from scratch and then duplicate as needed.
*/
ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
ierr = VecSetSizes(x,PETSC_DECIDE,n);CHKERRQ(ierr);
ierr = VecSetFromOptions(x);CHKERRQ(ierr);
ierr = VecDuplicate(x,&r);CHKERRQ(ierr);
ierr = VecDuplicate(x,&F);CHKERRQ(ierr);
ierr = VecDuplicate(x,&U);CHKERRQ(ierr);
/*
Set function evaluation routine and vector
*/
ierr = SNESSetFunction(snes,r,FormFunction,(void*)F);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create matrix data structure; set Jacobian evaluation routine
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = MatCreate(PETSC_COMM_WORLD,&J);CHKERRQ(ierr);
ierr = MatSetSizes(J,PETSC_DECIDE,PETSC_DECIDE,n,n);CHKERRQ(ierr);
ierr = MatSetFromOptions(J);CHKERRQ(ierr);
ierr = MatSeqAIJSetPreallocation(J,3,NULL);CHKERRQ(ierr);
/*
Set Jacobian matrix data structure and default Jacobian evaluation
routine. User can override with:
-snes_fd : default finite differencing approximation of Jacobian
-snes_mf : matrix-free Newton-Krylov method with no preconditioning
(unless user explicitly sets preconditioner)
-snes_mf_operator : form preconditioning matrix as set by the user,
but use matrix-free approx for Jacobian-vector
products within Newton-Krylov method
*/
ierr = SNESSetJacobian(snes,J,J,FormJacobian,NULL);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Customize nonlinear solver; set runtime options
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Set an optional user-defined monitoring routine
*/
ierr = PetscViewerDrawOpen(PETSC_COMM_WORLD,0,0,0,0,400,400,&monP.viewer);CHKERRQ(ierr);
ierr = SNESMonitorSet(snes,Monitor,&monP,0);CHKERRQ(ierr);
/*
Set names for some vectors to facilitate monitoring (optional)
*/
ierr = PetscObjectSetName((PetscObject)x,"Approximate Solution");CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)U,"Exact Solution");CHKERRQ(ierr);
/*
Set SNES/KSP/KSP/PC runtime options, e.g.,
-snes_view -snes_monitor -ksp_type <ksp> -pc_type <pc>
*/
ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
/*
Print parameters used for convergence testing (optional) ... just
to demonstrate this routine; this information is also printed with
the option -snes_view
*/
ierr = SNESGetTolerances(snes,&abstol,&rtol,&stol,&maxit,&maxf);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"atol=%G, rtol=%G, stol=%G, maxit=%D, maxf=%D\n",abstol,rtol,stol,maxit,maxf);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Initialize application:
Store right-hand-side of PDE and exact solution
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
xp = 0.0;
for (i=0; i<n; i++) {
v = 6.0*xp + PetscPowScalar(xp+1.e-12,6.0); /* +1.e-12 is to prevent 0^6 */
ierr = VecSetValues(F,1,&i,&v,INSERT_VALUES);CHKERRQ(ierr);
v = xp*xp*xp;
ierr = VecSetValues(U,1,&i,&v,INSERT_VALUES);CHKERRQ(ierr);
xp += h;
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Evaluate initial guess; then solve nonlinear system
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Note: The user should initialize the vector, x, with the initial guess
for the nonlinear solver prior to calling SNESSolve(). In particular,
to employ an initial guess of zero, the user should explicitly set
this vector to zero by calling VecSet().
*/
ierr = FormInitialGuess(x);CHKERRQ(ierr);
ierr = SNESSolve(snes,NULL,x);CHKERRQ(ierr);
ierr = SNESGetIterationNumber(snes,&its);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"number of SNES iterations = %D\n\n",its);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Check solution and clean up
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Check the error
*/
ierr = VecAXPY(x,none,U);CHKERRQ(ierr);
ierr = VecNorm(x,NORM_2,&norm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Norm of error %G, Iterations %D\n",norm,its);CHKERRQ(ierr);
/*
Free work space. All PETSc objects should be destroyed when they
are no longer needed.
*/
ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = VecDestroy(&r);CHKERRQ(ierr);
ierr = VecDestroy(&U);CHKERRQ(ierr); ierr = VecDestroy(&F);CHKERRQ(ierr);
ierr = MatDestroy(&J);CHKERRQ(ierr); ierr = SNESDestroy(&snes);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&monP.viewer);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **argv)
{
SNES snes; /* SNES context */
Mat J; /* Jacobian matrix */
DM da;
Vec x,r; /* vectors */
PetscErrorCode ierr;
PetscInt N = 5;
MatNullSpace constants;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
ierr = PetscOptionsGetInt(NULL,NULL,"-n",&N,NULL);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create nonlinear solver context
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = SNESCreate(PETSC_COMM_WORLD,&snes);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create vector data structures; set function evaluation routine
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Create distributed array (DMDA) to manage parallel grid and vectors
*/
ierr = DMDACreate1d(PETSC_COMM_WORLD,DM_BOUNDARY_PERIODIC,N,1,1,NULL,&da);CHKERRQ(ierr);
ierr = DMSetFromOptions(da);CHKERRQ(ierr);
ierr = DMSetUp(da);CHKERRQ(ierr);
/*
Extract global and local vectors from DMDA; then duplicate for remaining
vectors that are the same types
*/
ierr = DMCreateGlobalVector(da,&x);CHKERRQ(ierr);
ierr = VecDuplicate(x,&r);CHKERRQ(ierr);
/*
Set function evaluation routine and vector. Whenever the nonlinear
solver needs to compute the nonlinear function, it will call this
routine.
- Note that the final routine argument is the user-defined
context that provides application-specific data for the
function evaluation routine.
*/
ierr = SNESSetFunction(snes,r,FormFunction,da);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create matrix data structure; set Jacobian evaluation routine
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = DMCreateMatrix(da,&J);CHKERRQ(ierr);
ierr = MatNullSpaceCreate(PETSC_COMM_WORLD,PETSC_TRUE,0,NULL,&constants);CHKERRQ(ierr);
ierr = MatSetNullSpace(J,constants);CHKERRQ(ierr);
ierr = SNESSetJacobian(snes,J,J,FormJacobian,da);CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
ierr = SNESSolve(snes,NULL,x);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&r);CHKERRQ(ierr);
ierr = MatDestroy(&J);CHKERRQ(ierr);
ierr = MatNullSpaceDestroy(&constants);CHKERRQ(ierr);
ierr = SNESDestroy(&snes);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
int main(int argc, char **argv)
{
MPI_Comm comm;
PetscMPIInt rank;
PetscErrorCode ierr;
User user;
PetscLogDouble v1, v2;
PetscInt nplot = 0;
char fileName[2048];
ierr = PetscInitialize(&argc, &argv, (char*) 0, help);CHKERRQ(ierr);
comm = PETSC_COMM_WORLD;
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = PetscNew(&user);CHKERRQ(ierr);
ierr = PetscNew(&user->algebra);CHKERRQ(ierr);
ierr = PetscNew(&user->model);CHKERRQ(ierr);
ierr = PetscNew(&user->model->physics);CHKERRQ(ierr);
Algebra algebra = user->algebra;
ierr = LoadOptions(comm, user);CHKERRQ(ierr);
ierr = PetscTime(&v1);CHKERRQ(ierr);
ierr = CreateMesh(comm, user);CHKERRQ(ierr);
ierr = PetscTime(&v2);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,
"Read and Distribute mesh takes %f sec \n", v2 - v1);CHKERRQ(ierr);
ierr = SetUpLocalSpace(user);CHKERRQ(ierr); //Set up the dofs of each element
ierr = ConstructGeometryFVM(&user->facegeom, &user->cellgeom, user);CHKERRQ(ierr);
ierr = LimiterSetup(user);CHKERRQ(ierr);
if (user->TimeIntegralMethod == EXPLICITMETHOD) { // explicit method
if(user->myownexplicitmethod){// Using the fully explicit method based on my own routing
ierr = PetscPrintf(PETSC_COMM_WORLD,"Using the fully explicit method based on my own routing\n");CHKERRQ(ierr);
user->current_time = user->initial_time;
user->current_step = 1;
ierr = DMCreateGlobalVector(user->dm, &algebra->solution);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) algebra->solution, "solution");CHKERRQ(ierr);
ierr = VecSet(algebra->solution, 0);CHKERRQ(ierr);
ierr = SetInitialCondition(user->dm, algebra->solution, user);CHKERRQ(ierr);
if(1){
PetscViewer viewer;
ierr = OutputVTK(user->dm, "intialcondition.vtk", &viewer);CHKERRQ(ierr);
ierr = VecView(algebra->solution, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Outputing the initial condition intialcondition.vtk!!! \n");CHKERRQ(ierr);
}
ierr = VecDuplicate(algebra->solution, &algebra->fn);CHKERRQ(ierr);
ierr = VecDuplicate(algebra->solution, &algebra->oldsolution);CHKERRQ(ierr);
if(user->Explicit_RK2||user->Explicit_RK4){
ierr = PetscPrintf(PETSC_COMM_WORLD,"Use the second order Runge Kutta method \n");CHKERRQ(ierr);
}else{
ierr = PetscPrintf(PETSC_COMM_WORLD,"Use the first order forward Euler method \n");CHKERRQ(ierr);
}
nplot = 0; //the plot step
while(user->current_time < (user->final_time - 0.05 * user->dt)){
user->current_time = user->current_time + user->dt;
ierr = FormTimeStepFunction(user, algebra, algebra->solution, algebra->fn);CHKERRQ(ierr);
if(0){
PetscViewer viewer;
ierr = OutputVTK(user->dm, "function.vtk", &viewer);CHKERRQ(ierr);
ierr = VecView(algebra->fn, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
if(user->Explicit_RK2){
/*
U^n_1 = U^n + 0.5*dt*f(U^n)
U^{n+1} = U^n + dt*f(U^n_1)
*/
ierr = VecCopy(algebra->solution, algebra->oldsolution);CHKERRQ(ierr);
//note that algebra->oldsolution and algebra->solution are both U^n
ierr = VecAXPY(algebra->solution, 0.5*user->dt, algebra->fn);CHKERRQ(ierr);
//U^n_1 = U^n + 0.5*dt*f(U^n), now algebra->solution is U^n_1, and algebra->fn is f(U^n)
ierr = FormTimeStepFunction(user, algebra, algebra->solution, algebra->fn);CHKERRQ(ierr);
//algebra->fn is f(U^n_1)
// reset the algebra->solution to U^n
ierr = VecCopy(algebra->oldsolution, algebra->solution);CHKERRQ(ierr);
ierr = VecAXPY(algebra->solution, user->dt, algebra->fn);CHKERRQ(ierr);
// now algebra->solution is U^{n+1} = U^n + dt*f(U^n_1)
}else if(user->Explicit_RK4){
/* refer to https://en.wikipedia.org/wiki/Runge%E2%80%93Kutta_methods
k_1 = f(U^n)
U^n_1 = U^n + 0.5*dt*k_1
k_2 = f(U^n_1)
U^n_2 = U^n + 0.5*dt*k_2
k_3 = f(U^n_2)
U^n_3 = U^n + 0.5*dt*k_3
k_4 = f(U^n_3)
U^{n+1} = U^n + dt/6*(k_1 + 2*k_2 + 2*k_3 + k_4)
*/
Vec VecTemp; // store the U^n_1
Vec k1, k2, k3, k4;
ierr = VecDuplicate(algebra->solution, &k1);CHKERRQ(ierr);
ierr = VecDuplicate(algebra->solution, &k2);CHKERRQ(ierr);
ierr = VecDuplicate(algebra->solution, &k3);CHKERRQ(ierr);
ierr = VecDuplicate(algebra->solution, &k4);CHKERRQ(ierr);
ierr = VecCopy(algebra->solution, algebra->oldsolution);CHKERRQ(ierr);
ierr = VecCopy(algebra->fn, k1);CHKERRQ(ierr);
//note that algebra->oldsolution and algebra->solution are both U^n
ierr = VecAXPY(algebra->solution, 0.5*user->dt, k1);CHKERRQ(ierr);
//U^n_1 = U^n + 0.5*dt*k1, now algebra->solution is U^n_1, and algebra->fn is f(U^n)
ierr = FormTimeStepFunction(user, algebra, algebra->solution, algebra->fn);CHKERRQ(ierr);
//algebra->fn is f(U^n_1)
ierr = VecCopy(algebra->fn, k2);CHKERRQ(ierr);
// reset the algebra->solution to U^n
ierr = VecCopy(algebra->oldsolution, algebra->solution);CHKERRQ(ierr);
ierr = VecAXPY(algebra->solution, 0.5*user->dt, k2);CHKERRQ(ierr);
//U^n_2 = U^n + 0.5*dt*k2, now algebra->solution is U^n_2, and algebra->fn is f(U^n_1)
ierr = FormTimeStepFunction(user, algebra, algebra->solution, algebra->fn);CHKERRQ(ierr);
//algebra->fn is f(U^n_2)
ierr = VecCopy(algebra->fn, k3);CHKERRQ(ierr);
// reset the algebra->solution to U^n
ierr = VecCopy(algebra->oldsolution, algebra->solution);CHKERRQ(ierr);
ierr = VecAXPY(algebra->solution, 0.5*user->dt, k3);CHKERRQ(ierr);
//U^n_3 = U^n + 0.5*dt*k3, now algebra->solution is U^n_3, and algebra->fn is f(U^n_2)
ierr = FormTimeStepFunction(user, algebra, algebra->solution, algebra->fn);CHKERRQ(ierr);
//algebra->fn is f(U^n_3)
ierr = VecCopy(algebra->fn, k4);CHKERRQ(ierr);
//U^{n+1} = U^n + dt/6*(k_1 + 2*k_2 + 2*k_3 + k_4)
PetscReal temp;
temp = user->dt/6;
// reset the algebra->solution to U^n
ierr = VecCopy(algebra->oldsolution, algebra->solution);CHKERRQ(ierr);
ierr = VecAXPY(algebra->solution, temp, k1);CHKERRQ(ierr);
// now algebra->solution is U^n + dt/6*k_1
ierr = VecAXPY(algebra->solution, 2*temp, k2);CHKERRQ(ierr);
// now algebra->solution is U^n + dt/6*k_1 + 2*dt/6*k_2
ierr = VecAXPY(algebra->solution, 2*temp, k3);CHKERRQ(ierr);
// now algebra->solution is U^n + dt/6*k_1 + 2*dt/6*k_2 + 2*dt/6*k_3
ierr = VecAXPY(algebra->solution, temp, k4);CHKERRQ(ierr);
// now algebra->solution is U^n + dt/6*k_1 + 2*dt/6*k_2 + 2*dt/6*k_3 + dt/6*k_4
ierr = VecDestroy(&k1);CHKERRQ(ierr);
ierr = VecDestroy(&k2);CHKERRQ(ierr);
ierr = VecDestroy(&k3);CHKERRQ(ierr);
ierr = VecDestroy(&k4);CHKERRQ(ierr);
}else{
ierr = VecCopy(algebra->solution, algebra->oldsolution);CHKERRQ(ierr);
ierr = VecAXPY(algebra->solution, user->dt, algebra->fn);CHKERRQ(ierr);
}
{// Monitor the solution and function norms
PetscReal norm;
PetscLogDouble space =0;
PetscInt size;
PetscReal fnnorm;
ierr = VecNorm(algebra->fn,NORM_2,&fnnorm);CHKERRQ(ierr);
//ierr = VecView(algebra->fn, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecNorm(algebra->solution,NORM_2,&norm);CHKERRQ(ierr);
ierr = VecGetSize(algebra->solution, &size);CHKERRQ(ierr);
norm = norm/size;
fnnorm = fnnorm/size;
if (norm>1.e5) {
SETERRQ2(PETSC_COMM_WORLD, PETSC_ERR_LIB,
"The norm of the solution is: %f (current time: %f). The explicit method is going to DIVERGE!!!", norm, user->current_time);
}
if (user->current_step%10==0) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Step %D at time %g with solution norm = %g and founction norm = %g \n",
user->current_step, user->current_time, norm, fnnorm);CHKERRQ(ierr);
}
// ierr = PetscMallocGetCurrentUsage(&space);CHKERRQ(ierr);
// if (user->current_step%10==0) {
// ierr = PetscPrintf(PETSC_COMM_WORLD,"Current space PetscMalloc()ed %g M\n",
// space/(1024*1024));CHKERRQ(ierr);
// }
}
{ // Monitor the difference of two steps' solution
PetscReal norm;
ierr = VecAXPY(algebra->oldsolution, -1, algebra->solution);CHKERRQ(ierr);
ierr = VecNorm(algebra->oldsolution,NORM_2,&norm);CHKERRQ(ierr);
if (user->current_step%10==0) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Step %D at time %g with ||u_k-u_{k-1}|| = %g \n",
user->current_step, user->current_time, norm);CHKERRQ(ierr);
}
if((norm<1.e-6)||(user->current_step > user->max_time_its)){
if(norm<1.e-6) ierr = PetscPrintf(PETSC_COMM_WORLD,"\n Convergence with ||u_k-u_{k-1}|| = %g < 1.e-6\n\n", norm);CHKERRQ(ierr);
if(user->current_step > user->max_time_its) ierr = PetscPrintf(PETSC_COMM_WORLD,"\n Convergence with reaching the max time its\n\n");CHKERRQ(ierr);
break;
}
}
// output the solution
if (user->output_solution && (user->current_step%user->steps_output==0)){
PetscViewer viewer;
Vec solution_unscaled; // Note the the algebra->solution is scaled by the density, so this is for the unscaled solution
nplot = user->current_step/user->steps_output;
// update file name for the current time step
ierr = VecDuplicate(algebra->solution, &solution_unscaled);CHKERRQ(ierr);
ierr = ReformatSolution(algebra->solution, solution_unscaled, user);CHKERRQ(ierr);
ierr = PetscSNPrintf(fileName, sizeof(fileName),"%s_%d.vtk",user->solutionfile, nplot);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Outputing solution %s (current time %f)\n", fileName, user->current_time);CHKERRQ(ierr);
ierr = OutputVTK(user->dm, fileName, &viewer);CHKERRQ(ierr);
ierr = VecView(solution_unscaled, viewer);CHKERRQ(ierr);
ierr = VecDestroy(&solution_unscaled);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
user->current_step++;
}
ierr = VecDestroy(&algebra->fn);CHKERRQ(ierr);
}else{ // Using the fully explicit method based on the PETSC TS routing
PetscReal ftime;
TS ts;
TSConvergedReason reason;
PetscInt nsteps;
//PetscReal minRadius;
//ierr = DMPlexTSGetGeometry(user->dm, NULL, NULL, &minRadius);CHKERRQ(ierr);
//user->dt = 0.9*4 * minRadius / 1.0;
ierr = PetscPrintf(PETSC_COMM_WORLD,"Using the fully explicit method based on the PETSC TS routing\n");CHKERRQ(ierr);
ierr = DMCreateGlobalVector(user->dm, &algebra->solution);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) algebra->solution, "solution");CHKERRQ(ierr);
ierr = VecSet(algebra->solution, 0.0);CHKERRQ(ierr);
ierr = SetInitialCondition(user->dm, algebra->solution, user);CHKERRQ(ierr);
ierr = TSCreate(comm, &ts);CHKERRQ(ierr);
ierr = TSSetType(ts, TSEULER);CHKERRQ(ierr);
ierr = TSSetDM(ts, user->dm);CHKERRQ(ierr);
ierr = TSMonitorSet(ts,TSMonitorFunctionError,(void*)user,NULL);CHKERRQ(ierr);
ierr = TSSetRHSFunction(ts, NULL, MyRHSFunction, user);CHKERRQ(ierr);
ierr = TSSetDuration(ts, 1000, user->final_time);CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts, user->initial_time, user->dt);CHKERRQ(ierr);
ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
ierr = TSSolve(ts, algebra->solution);CHKERRQ(ierr);
ierr = TSGetSolveTime(ts, &ftime);CHKERRQ(ierr);
ierr = TSGetTimeStepNumber(ts, &nsteps);CHKERRQ(ierr);
ierr = TSGetConvergedReason(ts, &reason);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"%s at time %g after %D steps\n",TSConvergedReasons[reason],ftime,nsteps);CHKERRQ(ierr);
ierr = TSDestroy(&ts);CHKERRQ(ierr);
}
if(user->benchmark_couette) {
ierr = DMCreateGlobalVector(user->dm, &algebra->exactsolution);CHKERRQ(ierr);
ierr = ComputeExactSolution(user->dm, user->current_time, algebra->exactsolution, user);CHKERRQ(ierr);
}
if(user->benchmark_couette) {
PetscViewer viewer;
PetscReal norm;
ierr = OutputVTK(user->dm, "exact_solution.vtk", &viewer);CHKERRQ(ierr);
ierr = VecView(algebra->exactsolution, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = VecAXPY(algebra->exactsolution, -1, algebra->solution);CHKERRQ(ierr);
ierr = VecNorm(algebra->exactsolution,NORM_INFINITY,&norm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Final time at %f, Error: ||u_k-u|| = %g \n", user->current_time, norm);CHKERRQ(ierr);
ierr = OutputVTK(user->dm, "Error.vtk", &viewer);CHKERRQ(ierr);
ierr = VecView(algebra->exactsolution, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
ierr = VecDestroy(&algebra->solution);CHKERRQ(ierr);
if(user->myownexplicitmethod){ierr = VecDestroy(&algebra->oldsolution);CHKERRQ(ierr);}
ierr = VecDestroy(&algebra->exactsolution);CHKERRQ(ierr);
ierr = DMDestroy(&user->dm);CHKERRQ(ierr);
} else if (user->TimeIntegralMethod == IMPLICITMETHOD) { // Using the fully implicit method
ierr = PetscPrintf(PETSC_COMM_WORLD,"Using the fully implicit method\n");CHKERRQ(ierr);
ierr = SNESCreate(comm,&user->snes);CHKERRQ(ierr);
ierr = SNESSetDM(user->snes,user->dm);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(user->dm, &algebra->solution);CHKERRQ(ierr);
ierr = VecDuplicate(algebra->solution, &algebra->oldsolution);CHKERRQ(ierr);
ierr = VecDuplicate(algebra->solution, &algebra->f);CHKERRQ(ierr);
ierr = VecDuplicate(algebra->solution, &algebra->fn);CHKERRQ(ierr);
ierr = VecDuplicate(algebra->solution, &algebra->oldfn);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) algebra->solution, "solution");CHKERRQ(ierr);
ierr = SetInitialCondition(user->dm, algebra->solution, user);CHKERRQ(ierr);
ierr = DMSetMatType(user->dm, MATAIJ);CHKERRQ(ierr);
// ierr = DMCreateMatrix(user->dm, &algebra->A);CHKERRQ(ierr);
ierr = DMCreateMatrix(user->dm, &algebra->J);CHKERRQ(ierr);
if (user->JdiffP) {
/*Set up the preconditioner matrix*/
ierr = DMCreateMatrix(user->dm, &algebra->P);CHKERRQ(ierr);
}else{
algebra->P = algebra->J;
}
ierr = MatSetOption(algebra->J, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);CHKERRQ(ierr);
/*set nonlinear function */
ierr = SNESSetFunction(user->snes, algebra->f, FormFunction, (void*)user);CHKERRQ(ierr);
/* compute Jacobian */
ierr = SNESSetJacobian(user->snes, algebra->J, algebra->P, FormJacobian, (void*)user);CHKERRQ(ierr);
ierr = SNESSetFromOptions(user->snes);CHKERRQ(ierr);
/* do the solve */
if (user->timestep == TIMESTEP_STEADY_STATE) {
ierr = SolveSteadyState(user);CHKERRQ(ierr);
} else {
ierr = SolveTimeDependent(user);CHKERRQ(ierr);
}
if (user->output_solution){
PetscViewer viewer;
Vec solution_unscaled; // Note the the algebra->solution is scaled by the density, so this is for the unscaled solution
ierr = VecDuplicate(algebra->solution, &solution_unscaled);CHKERRQ(ierr);
ierr = ReformatSolution(algebra->solution, solution_unscaled, user);CHKERRQ(ierr);
ierr = OutputVTK(user->dm, "solution.vtk", &viewer);CHKERRQ(ierr);
ierr = VecView(solution_unscaled, viewer);CHKERRQ(ierr);
ierr = VecDestroy(&solution_unscaled);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
if(user->benchmark_couette) {
PetscViewer viewer;
PetscReal norm;
ierr = OutputVTK(user->dm, "exact_solution.vtk", &viewer);CHKERRQ(ierr);
ierr = VecView(algebra->exactsolution, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = VecAXPY(algebra->exactsolution, -1, algebra->solution);CHKERRQ(ierr);
ierr = VecNorm(algebra->exactsolution,NORM_INFINITY,&norm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Error: ||u_k-u|| = %g \n", norm);CHKERRQ(ierr);
ierr = OutputVTK(user->dm, "Error.vtk", &viewer);CHKERRQ(ierr);
ierr = VecView(algebra->exactsolution, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
ierr = VecDestroy(&algebra->solution);CHKERRQ(ierr);
ierr = VecDestroy(&algebra->f);CHKERRQ(ierr);
ierr = VecDestroy(&algebra->oldsolution);CHKERRQ(ierr);
ierr = VecDestroy(&algebra->fn);CHKERRQ(ierr);
ierr = VecDestroy(&algebra->oldfn);CHKERRQ(ierr);
ierr = SNESDestroy(&user->snes);CHKERRQ(ierr);
ierr = DMDestroy(&user->dm);CHKERRQ(ierr);
} else {
SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"WRONG option for the time integral method. Using the option '-time_integral_method 0 or 1'");
}
ierr = VecDestroy(&user->cellgeom);CHKERRQ(ierr);
ierr = VecDestroy(&user->facegeom);CHKERRQ(ierr);
ierr = DMDestroy(&user->dmGrad);CHKERRQ(ierr);
ierr = PetscFunctionListDestroy(&LimitList);CHKERRQ(ierr);
ierr = PetscFree(user->model->physics);CHKERRQ(ierr);
ierr = PetscFree(user->algebra);CHKERRQ(ierr);
ierr = PetscFree(user->model);CHKERRQ(ierr);
ierr = PetscFree(user);CHKERRQ(ierr);
{
PetscLogDouble space =0;
ierr = PetscMallocGetCurrentUsage(&space);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Unfreed space at the End %g M\n", space/(1024*1024));CHKERRQ(ierr);
}
ierr = PetscFinalize();
return(0);
}
int main(int argc,char **argv)
{
SNES snes; /* nonlinear solver context */
Vec x,r; /* solution, residual vectors */
Mat J; /* Jacobian matrix */
PetscErrorCode ierr;
PetscInt its;
PetscScalar *xx;
SNESConvergedReason reason;
PetscInitialize(&argc,&argv,(char *)0,help);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create nonlinear solver context
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = SNESCreate(PETSC_COMM_WORLD,&snes);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create matrix and vector data structures; set corresponding routines
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Create vectors for solution and nonlinear function
*/
ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
ierr = VecSetSizes(x,PETSC_DECIDE,2);CHKERRQ(ierr);
ierr = VecSetFromOptions(x);CHKERRQ(ierr);
ierr = VecDuplicate(x,&r);CHKERRQ(ierr);
/*
Create Jacobian matrix data structure
*/
ierr = MatCreate(PETSC_COMM_WORLD,&J);CHKERRQ(ierr);
ierr = MatSetSizes(J,PETSC_DECIDE,PETSC_DECIDE,2,2);CHKERRQ(ierr);
ierr = MatSetFromOptions(J);CHKERRQ(ierr);
ierr = MatSetUp(J);CHKERRQ(ierr);
/*
Set function evaluation routine and vector.
*/
ierr = SNESSetFunction(snes,r,FormFunction1,PETSC_NULL);CHKERRQ(ierr);
/*
Set Jacobian matrix data structure and Jacobian evaluation routine
*/
ierr = SNESSetJacobian(snes,J,J,FormJacobian1,PETSC_NULL);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Customize nonlinear solver; set runtime options
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Evaluate initial guess; then solve nonlinear system
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = VecGetArray(x,&xx);CHKERRQ(ierr);
xx[0] = -1.2; xx[1] = 1.0;
ierr = VecRestoreArray(x,&xx);CHKERRQ(ierr);
/*
Note: The user should initialize the vector, x, with the initial guess
for the nonlinear solver prior to calling SNESSolve(). In particular,
to employ an initial guess of zero, the user should explicitly set
this vector to zero by calling VecSet().
*/
ierr = SNESSolve(snes,PETSC_NULL,x);CHKERRQ(ierr);
ierr = VecView(x,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = SNESGetIterationNumber(snes,&its);CHKERRQ(ierr);
ierr = SNESGetConvergedReason(snes,&reason);CHKERRQ(ierr);
/*
Some systems computes a residual that is identically zero, thus converging
due to FNORM_ABS, others converge due to FNORM_RELATIVE. Here, we only
report the reason if the iteration did not converge so that the tests are
reproducible.
*/
ierr = PetscPrintf(PETSC_COMM_WORLD,"%s number of SNES iterations = %D\n\n",reason>0?"CONVERGED":SNESConvergedReasons[reason],its);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Free work space. All PETSc objects should be destroyed when they
are no longer needed.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = VecDestroy(&r);CHKERRQ(ierr);
ierr = MatDestroy(&J);CHKERRQ(ierr); ierr = SNESDestroy(&snes);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc, char **argv)
{
MPI_Comm comm;
SNES snes; /* nonlinear solver */
Vec u,r,b; /* solution, residual, and rhs vectors */
Mat A,J; /* Jacobian matrix */
PetscInt problem = 1, N = 10;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc, &argv, NULL,help);
if (ierr) return ierr;
comm = PETSC_COMM_WORLD;
ierr = PetscOptionsGetInt(NULL,NULL, "-problem", &problem, NULL);
CHKERRQ(ierr);
ierr = VecCreate(comm, &u);
CHKERRQ(ierr);
ierr = VecSetSizes(u, PETSC_DETERMINE, N);
CHKERRQ(ierr);
ierr = VecSetFromOptions(u);
CHKERRQ(ierr);
ierr = VecDuplicate(u, &r);
CHKERRQ(ierr);
ierr = VecDuplicate(u, &b);
CHKERRQ(ierr);
ierr = MatCreate(comm, &A);
CHKERRQ(ierr);
ierr = MatSetSizes(A, PETSC_DETERMINE, PETSC_DETERMINE, N, N);
CHKERRQ(ierr);
ierr = MatSetFromOptions(A);
CHKERRQ(ierr);
ierr = MatSeqAIJSetPreallocation(A, 5, NULL);
CHKERRQ(ierr);
J = A;
switch (problem) {
case 1:
ierr = ConstructProblem1(A, b);
CHKERRQ(ierr);
break;
case 2:
ierr = ConstructProblem2(A, b);
CHKERRQ(ierr);
break;
default:
SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid problem number %d", problem);
}
ierr = SNESCreate(PETSC_COMM_WORLD, &snes);
CHKERRQ(ierr);
ierr = SNESSetJacobian(snes, A, J, ComputeJacobianLinear, NULL);
CHKERRQ(ierr);
ierr = SNESSetFunction(snes, r, ComputeFunctionLinear, A);
CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes);
CHKERRQ(ierr);
ierr = SNESSolve(snes, b, u);
CHKERRQ(ierr);
ierr = VecView(u, NULL);
CHKERRQ(ierr);
switch (problem) {
case 1:
ierr = CheckProblem1(A, b, u);
CHKERRQ(ierr);
break;
case 2:
ierr = CheckProblem2(A, b, u);
CHKERRQ(ierr);
break;
default:
SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid problem number %d", problem);
}
if (A != J) {
ierr = MatDestroy(&A);
CHKERRQ(ierr);
}
ierr = MatDestroy(&J);
CHKERRQ(ierr);
ierr = VecDestroy(&u);
CHKERRQ(ierr);
ierr = VecDestroy(&r);
CHKERRQ(ierr);
ierr = VecDestroy(&b);
CHKERRQ(ierr);
ierr = SNESDestroy(&snes);
CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}