int main(int argc,char **argv)
{
Mat A; /* operator matrix */
EPS eps; /* eigenproblem solver context */
EPSType type;
PetscMPIInt nproc, myproc;
PetscInt nev;
PetscErrorCode ierr;
SlepcInitialize(&argc, &argv, (char*)0, 0);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&nproc); CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&myproc); CHKERRQ(ierr);
int L = 8;
ierr = PetscOptionsGetInt(NULL,"-L", &L, NULL); CHKERRQ(ierr);
PetscInt N_global = 1 << L;
PetscInt N_local = N_global / nproc;
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Compute the operator matrix that defines the eigensystem, Ax=kx
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
model m;
m.comm = PETSC_COMM_WORLD;
m.L = L;
m.buffer = new double[N_local];
if (m.buffer == 0) {
MPI_Abort(MPI_COMM_WORLD, 4);
}
for (int i=0; i<L; ++i) {
m.lattice.push_back(std::make_pair(i, (i+1)%L));
}
ierr = MatCreateShell(PETSC_COMM_WORLD, N_local, N_local, N_global, N_global, &m, &A); CHKERRQ(ierr);
ierr = MatSetFromOptions(A); CHKERRQ(ierr);
ierr = MatShellSetOperation(A,MATOP_MULT,(void(*)())MatMult_myMat); CHKERRQ(ierr);
ierr = MatShellSetOperation(A,MATOP_MULT_TRANSPOSE,(void(*)())MatMult_myMat); CHKERRQ(ierr);
ierr = MatShellSetOperation(A,MATOP_GET_DIAGONAL,(void(*)())MatGetDiagonal_myMat); CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create the eigensolver and set various options
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Create eigensolver context
*/
ierr = EPSCreate(PETSC_COMM_WORLD,&eps); CHKERRQ(ierr);
/*
Set operators. In this case, it is a standard eigenvalue problem
*/
ierr = EPSSetOperators(eps,A,NULL); CHKERRQ(ierr);
ierr = EPSSetProblemType(eps,EPS_HEP); CHKERRQ(ierr);
ierr = EPSSetDimensions(eps, 5, 100, 100); CHKERRQ(ierr);
ierr = EPSSetTolerances(eps, (PetscScalar) 1e-1, (PetscInt) 100); CHKERRQ(ierr);
//Vec v0;
//MatGetVecs(A, &v0, NULL);
//VecSet(v0,1.0);
//EPSSetInitialSpace(eps,1,&v0);
/*
Set solver parameters at runtime
*/
ierr = EPSSetFromOptions(eps); CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Solve the eigensystem
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = EPSSolve(eps);CHKERRQ(ierr);
/*
Optional: Get some information from the solver and display it
*/
ierr = EPSGetType(eps,&type); CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," Solution method: %s\n\n",type); CHKERRQ(ierr);
ierr = EPSGetDimensions(eps,&nev,NULL,NULL); CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," Number of requested eigenvalues: %D\n",nev); CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Display solution and clean up
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = EPSPrintSolution(eps,NULL); CHKERRQ(ierr);
ierr = EPSDestroy(&eps); CHKERRQ(ierr);
ierr = MatDestroy(&A); CHKERRQ(ierr);
ierr = SlepcFinalize();
return 0;
}
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 implicit_solver(HashTable* El_Table, HashTable* NodeTable, double delta_t, double LapCoef,
TimeProps* timeprops_ptr) {
Vec x, b, xlocal; /* approx solution, RHS */
Mat A; /* linear system matrix */
KSP ksp; /* KSP context */
PetscReal norm; //,val1,val2; /* norm of solution error */
PetscErrorCode ierr;
PetscInt xsize, *num_elem_proc, *to, *from, its;
PetscMPIInt rank, size;
KSPConvergedReason reason;
VecScatter vscat;
IS globalis, tois;
MPI_Comm_rank(PETSC_COMM_WORLD, &rank);
MPI_Comm_size(PETSC_COMM_WORLD, &size);
/* -------------------------------------------------------------------
Compute the matrix and right-hand-side vector that define
the linear system, Ax = b.
------------------------------------------------------------------- */
ierr = PetscMalloc(size * sizeof(PetscInt), &num_elem_proc);
CHKERRQ(ierr);
num_elem_proc[rank] = num_nonzero_elem(El_Table);
if (rank > 0)
MPI_Send(&num_elem_proc[rank], 1, MPI_INT, 0, 22, PETSC_COMM_WORLD);
if (rank == 0)
for (int i = 1; i < size; i++)
MPI_Recv(&num_elem_proc[i], 1, MPI_INT, i, 22, PETSC_COMM_WORLD, MPI_STATUS_IGNORE);
MPI_Barrier(PETSC_COMM_WORLD);
MPI_Bcast(num_elem_proc, size, MPI_INT, 0, PETSC_COMM_WORLD);
//printf("Number of elements are (hi i am second)...........%d\n", num_nonzero_elem(Laplacian->El_Table));
int total_elem = 0, start_elem = 0;
//MPI_Allreduce(&num_elem, total_elem, 1, MPI_INT, MPI_SUM, PETSC_COMM_WORLD);
ierr = PetscMalloc(num_elem_proc[rank] * sizeof(PetscInt), &to);
CHKERRQ(ierr);
ierr = PetscMalloc(num_elem_proc[rank] * sizeof(PetscInt), &from);
CHKERRQ(ierr);
for (int i = 0; i < size; i++)
total_elem += num_elem_proc[i];
for (int i = 0; i < rank; i++)
start_elem += num_elem_proc[i];
for (int i = 0; i < num_elem_proc[rank]; i++) {
from[i] = i;
to[i] = i + start_elem;
}
ierr = ISCreateGeneral(PETSC_COMM_WORLD, num_elem_proc[rank], from, PETSC_COPY_VALUES, &tois);
CHKERRQ(ierr);
ierr = ISCreateGeneral(PETSC_COMM_WORLD, num_elem_proc[rank], to, PETSC_COPY_VALUES, &globalis);
CHKERRQ(ierr);
/*
Create parallel vectors
*/
ierr = VecCreate(PETSC_COMM_WORLD, &b);
CHKERRQ(ierr);
ierr = VecSetType(b, VECSTANDARD);
CHKERRQ(ierr);
ierr = VecSetSizes(b, num_elem_proc[rank], total_elem);
CHKERRQ(ierr);
ierr = VecSetFromOptions(b);
CHKERRQ(ierr);
ierr = VecGetSize(b, &xsize);
//cout<<"size b is "<<xsize<<endl;
ierr = VecCreateSeq(PETSC_COMM_SELF, num_elem_proc[rank], &xlocal);
CHKERRQ(ierr);
ierr = VecScatterCreate(xlocal, tois, b, globalis, &vscat);
CHKERRQ(ierr);
// we have to create a map between local and global vector
myctx.El_Table = El_Table;
myctx.Node_Table = NodeTable;
myctx.Scatter = vscat;
myctx.Total_elem = total_elem;
myctx.Num_elem_proc = num_elem_proc;
myctx.rank = rank;
myctx.size = size;
myctx.Timeptr = timeprops_ptr;
myctx.LapCoef = LapCoef;
myctx.delta_t = delta_t;
/*
right-hand-side vector.
*/
ierr = MakeRHS(&myctx, b);
CHKERRQ(ierr);
//ierr = VecView(b,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
ierr = VecDuplicate(b, &x);
CHKERRQ(ierr);
ierr = VecCopy(b, x);
CHKERRQ(ierr);
//ierr = VecView(x,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
ierr = VecGetSize(x, &xsize);
//cout<<"size x is "<<xsize<<endl;
/*
Create and assemble parallel matrix
*/
ierr = MatCreateShell(PETSC_COMM_WORLD, num_elem_proc[rank], num_elem_proc[rank], total_elem,
total_elem, &myctx, &A);
CHKERRQ(ierr);
ierr = MatShellSetOperation(A, MATOP_MULT, (void (*)(void))MatLaplacian2D_Mult);CHKERRQ
(ierr);
/*
Create linear solver context
*/
ierr = KSPCreate(PETSC_COMM_WORLD, &ksp);
CHKERRQ(ierr);
/*
Set operators. Here the matrix that defines the linear system
also serves as the preconditioning matrix.
*/
ierr = KSPSetOperators(ksp, A, A/*,DIFFERENT_NONZERO_PATTERN*/);
CHKERRQ(ierr);
ierr = KSPSetType(ksp, KSPFGMRES);
CHKERRQ(ierr);
/*
Set default preconditioner for this program to be block Jacobi.
This choice can be overridden at runtime with the option
-pc_type <type>
*/
// ierr = KSPSetTolerances(ksp,1.e-7,PETSC_DEFAULT,1.e9,3000);CHKERRQ(ierr);
ierr = KSPSetTolerances(ksp, PETSC_DEFAULT, PETSC_DEFAULT, PETSC_DEFAULT, 50000);
CHKERRQ(ierr);
/* -------------------------------------------------------------------
Solve the linear system
------------------------------------------------------------------- */
ierr = KSPSetInitialGuessNonzero(ksp, PETSC_TRUE);
CHKERRQ(ierr);
/*
Solve the linear system
*/
ierr = KSPSolve(ksp, b, x);
CHKERRQ(ierr);
/* -------------------------------------------------------------------
Check solution and clean up
------------------------------------------------------------------- */
/*
Check the error
*/
//ierr = VecNorm(x,NORM_2,&norm);CHKERRQ(ierr);
if (rank == 0) {
ierr = KSPGetIterationNumber(ksp, &its);
CHKERRQ(ierr);
ierr = KSPGetResidualNorm(ksp, &norm);
CHKERRQ(ierr);
ierr = PetscSynchronizedPrintf( MPI_COMM_SELF, "Norm of error %g iterations %D\n",
(double) norm, its);
CHKERRQ(ierr);
//PetscSynchronizedFlush(PETSC_COMM_WORLD);
ierr = KSPGetConvergedReason(ksp, &reason);
ierr = PetscSynchronizedPrintf( MPI_COMM_SELF, "kind of divergence is: ...........%D \n",
reason);
//PetscSynchronizedFlush(PETSC_COMM_WORLD);
}
/*
*/
//ierr = VecGetArray(x,&xx);CHKERRQ(ierr);
update_phi(El_Table, x, &myctx);
//ierr = VecRestoreArray(x, &xx);CHKERRQ(ierr);
/*
Free work space. All PETSc objects should be destroyed when they
are no longer needed.
*/
MPI_Barrier(PETSC_COMM_WORLD);
ierr = KSPDestroy(&ksp);
CHKERRQ(ierr); //ierr = PetscFree(phin);CHKERRQ(ierr);
ierr = VecDestroy(&x);
CHKERRQ(ierr); //ierr = PCDestroy(&pc);CHKERRQ(ierr);
ierr = VecDestroy(&b);
CHKERRQ(ierr);
ierr = MatDestroy(&A);
CHKERRQ(ierr);
ierr = VecScatterDestroy(&vscat);
CHKERRQ(ierr);
ierr = ISDestroy(&globalis);
CHKERRQ(ierr);
ierr = ISDestroy(&tois);
CHKERRQ(ierr);
PetscFree(num_elem_proc);
CHKERRQ(ierr);
PetscFree(to);
CHKERRQ(ierr);
PetscFree(from);
CHKERRQ(ierr);
return 0;
}
krylov_petsc_info_t
krylov_petsc_solve
(
p4est_t* p4est,
problem_data_t* vecs,
weakeqn_ptrs_t* fcns,
p4est_ghost_t** ghost,
element_data_t** ghost_data,
dgmath_jit_dbase_t* dgmath_jit_dbase,
krylov_petsc_params_t* krylov_params
)
{
krylov_petsc_info_t info;
KSP ksp;
Vec x,b;
PC pc;
/* double* u_temp; */
/* double* rhs_temp; */
KSPCreate(PETSC_COMM_WORLD,&ksp);
VecCreate(PETSC_COMM_WORLD,&x);//CHKERRQ(ierr);
VecSetSizes(x, vecs->local_nodes, PETSC_DECIDE);//CHKERRQ(ierr);
VecSetFromOptions(x);//CHKERRQ(ierr);
VecDuplicate(x,&b);//CHKERRQ(ierr);
/* VecGetArray(x,&u_temp); */
/* VecGetArray(b,&rhs_temp); */
krylov_pc_ctx_t kct;
kct.p4est = p4est;
kct.vecs = vecs;
kct.fcns = fcns;
kct.ghost = ghost;
kct.ghost_data = ghost_data;
kct.dgmath_jit_dbase = dgmath_jit_dbase;
kct.pc_data = krylov_params->pc_data;
if (krylov_params->ksp_monitor)
PetscOptionsSetValue(NULL,"-ksp_monitor","");
if (krylov_params->ksp_monitor)
PetscOptionsSetValue(NULL,"-ksp_view","");
/* KSPMonitorSet(ksp, KSPMonitorDefault, NULL, NULL); */
/* PetscOptionsSetValue(NULL,"-ksp_converged_reason",""); */
PetscOptionsSetValue(NULL,"-ksp_atol","1e-20");
/* PetscOptionsSetValue(NULL,"-with-debugging","1"); */
PetscOptionsSetValue(NULL,"-ksp_rtol","1e-20");
PetscOptionsSetValue(NULL,"-ksp_max_it","1000000");
KSPGetPC(ksp,&pc);
krylov_pc_t* kp = NULL;
if (krylov_params != NULL && krylov_params->user_defined_pc) {
PCSetType(pc,PCSHELL);//CHKERRQ(ierr);
kp = krylov_params->pc_create(&kct);
PCShellSetApply(pc, krylov_petsc_pc_apply);//CHKERRQ(ierr);
PCShellSetSetUp(pc, krylov_petsc_pc_setup);
PCShellSetContext(pc, kp);//CHKERRQ(ierr);
}
else {
PCSetType(pc,PCNONE);//CHKERRQ(ierr);
}
KSPSetType(ksp, krylov_params->krylov_type);
KSPSetFromOptions(ksp);
/* Create matrix-free shell for Aij */
Mat A;
MatCreateShell
(
PETSC_COMM_WORLD,
vecs->local_nodes,
vecs->local_nodes,
PETSC_DETERMINE,
PETSC_DETERMINE,
(void*)&kct,
&A
);
MatShellSetOperation(A,MATOP_MULT,(void(*)())krylov_petsc_apply_aij);
/* Set Amat and Pmat, where Pmat is the matrix the Preconditioner needs */
KSPSetOperators(ksp,A,A);
/* linalg_copy_1st_to_2nd(vecs->u, u_temp, vecs->local_nodes); */
/* linalg_copy_1st_to_2nd(vecs->rhs, rhs_temp, vecs->local_nodes); */
VecPlaceArray(b, vecs->rhs);
VecPlaceArray(x, vecs->u);
KSPSolve(ksp,b,x);
if (krylov_params != NULL && krylov_params->user_defined_pc) {
krylov_params->pc_destroy(kp);
}
KSPGetIterationNumber(ksp, &(info.iterations));
KSPGetResidualNorm(ksp, &(info.residual_norm));
/* linalg_copy_1st_to_2nd(u_temp, vecs->u, vecs->local_nodes); */
/* VecRestoreArray(x,&u_temp); */
/* VecRestoreArray(b,&rhs_temp); */
VecResetArray(b);
VecResetArray(x);
VecDestroy(&x);
VecDestroy(&b);
KSPDestroy(&ksp);
return info;
}
int main(int argc,char **args)
{
User user;
Mat A,S;
PetscScalar *data,diag = 1.3;
PetscReal tol = PETSC_SMALL;
PetscInt i,j,m = PETSC_DECIDE,n = PETSC_DECIDE,M = 17,N = 15,s1,s2;
PetscInt test, ntest = 2;
PetscMPIInt rank,size;
PetscBool nc = PETSC_FALSE, cong;
PetscBool ronl = PETSC_TRUE;
PetscBool randomize = PETSC_FALSE;
PetscBool keep = PETSC_FALSE;
PetscBool testzerorows = PETSC_TRUE, testdiagscale = PETSC_TRUE, testgetdiag = PETSC_TRUE;
PetscBool testshift = PETSC_TRUE, testscale = PETSC_TRUE, testdup = PETSC_TRUE, testreset = PETSC_TRUE;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-M",&M,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-N",&N,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-ml",&m,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-nl",&n,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,NULL,"-square_nc",&nc,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,NULL,"-rows_only",&ronl,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,NULL,"-randomize",&randomize,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,NULL,"-test_zerorows",&testzerorows,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,NULL,"-test_diagscale",&testdiagscale,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,NULL,"-test_getdiag",&testgetdiag,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,NULL,"-test_shift",&testshift,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,NULL,"-test_scale",&testscale,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,NULL,"-test_dup",&testdup,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,NULL,"-test_reset",&testreset,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-loop",&ntest,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetReal(NULL,NULL,"-tol",&tol,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetScalar(NULL,NULL,"-diag",&diag,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,NULL,"-keep",&keep,NULL);CHKERRQ(ierr);
/* This tests square matrices with different row/col layout */
if (nc && size > 1) {
M = PetscMax(PetscMax(N,M),1);
N = M;
m = n = 0;
if (rank == 0) { m = M-1; n = 1; }
else if (rank == 1) { m = 1; n = N-1; }
}
ierr = MatCreateDense(PETSC_COMM_WORLD,m,n,M,N,NULL,&A);CHKERRQ(ierr);
ierr = MatGetLocalSize(A,&m,&n);CHKERRQ(ierr);
ierr = MatGetSize(A,&M,&N);CHKERRQ(ierr);
ierr = MatHasCongruentLayouts(A,&cong);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(A,&s1,NULL);CHKERRQ(ierr);
s2 = 1;
while (s2 < M) s2 *= 10;
ierr = MatDenseGetArray(A,&data);CHKERRQ(ierr);
for (j = 0; j < N; j++) {
for (i = 0; i < m; i++) {
data[j*m + i] = s2*j + i + s1 + 1;
}
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatConvert(A,MATAIJ,MAT_INPLACE_MATRIX,&A);CHKERRQ(ierr);
ierr = MatSetOption(A,MAT_KEEP_NONZERO_PATTERN,keep);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)A,"initial");CHKERRQ(ierr);
ierr = MatViewFromOptions(A,NULL,"-view_mat");CHKERRQ(ierr);
ierr = PetscNew(&user);CHKERRQ(ierr);
ierr = MatCreateShell(PETSC_COMM_WORLD,m,n,M,N,user,&S);CHKERRQ(ierr);
ierr = MatShellSetOperation(S,MATOP_MULT,(void (*)(void))MatMult_User);CHKERRQ(ierr);
ierr = MatShellSetOperation(S,MATOP_MULT_TRANSPOSE,(void (*)(void))MatMultTranspose_User);CHKERRQ(ierr);
if (cong) {
ierr = MatShellSetOperation(S,MATOP_GET_DIAGONAL,(void (*)(void))MatGetDiagonal_User);CHKERRQ(ierr);
}
ierr = MatDuplicate(A,MAT_COPY_VALUES,&user->B);CHKERRQ(ierr);
/* Square and rows only scaling */
ronl = cong ? ronl : PETSC_TRUE;
for (test = 0; test < ntest; test++) {
PetscReal err;
if (testzerorows) {
Mat ST,B,C,BT,BTT;
IS zr;
Vec x = NULL, b1 = NULL, b2 = NULL;
PetscInt *idxs = NULL, nr = 0;
if (rank == (test%size)) {
nr = 1;
ierr = PetscMalloc1(nr,&idxs);CHKERRQ(ierr);
if (test%2) {
idxs[0] = (2*M - 1 - test/2)%M;
} else {
idxs[0] = (test/2)%M;
}
idxs[0] = PetscMax(idxs[0],0);
}
ierr = ISCreateGeneral(PETSC_COMM_WORLD,nr,idxs,PETSC_OWN_POINTER,&zr);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)zr,"ZR");CHKERRQ(ierr);
ierr = ISViewFromOptions(zr,NULL,"-view_is");CHKERRQ(ierr);
ierr = MatCreateVecs(A,&x,&b1);CHKERRQ(ierr);
if (randomize) {
ierr = VecSetRandom(x,NULL);CHKERRQ(ierr);
ierr = VecSetRandom(b1,NULL);CHKERRQ(ierr);
} else {
ierr = VecSet(x,11.4);CHKERRQ(ierr);
ierr = VecSet(b1,-14.2);CHKERRQ(ierr);
}
ierr = VecDuplicate(b1,&b2);CHKERRQ(ierr);
ierr = VecCopy(b1,b2);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)b1,"A_B1");CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)b2,"A_B2");CHKERRQ(ierr);
if (size > 1 && !cong) { /* MATMPIAIJ ZeroRows and ZeroRowsColumns are buggy in this case */
ierr = VecDestroy(&b1);CHKERRQ(ierr);
}
if (ronl) {
ierr = MatZeroRowsIS(A,zr,diag,x,b1);CHKERRQ(ierr);
ierr = MatZeroRowsIS(S,zr,diag,x,b2);CHKERRQ(ierr);
} else {
ierr = MatZeroRowsColumnsIS(A,zr,diag,x,b1);CHKERRQ(ierr);
ierr = MatZeroRowsColumnsIS(S,zr,diag,x,b2);CHKERRQ(ierr);
ierr = ISDestroy(&zr);CHKERRQ(ierr);
/* Mix zerorows and zerorowscols */
nr = 0;
idxs = NULL;
if (!rank) {
nr = 1;
ierr = PetscMalloc1(nr,&idxs);CHKERRQ(ierr);
if (test%2) {
idxs[0] = (3*M - 2 - test/2)%M;
} else {
idxs[0] = (test/2+1)%M;
}
idxs[0] = PetscMax(idxs[0],0);
}
ierr = ISCreateGeneral(PETSC_COMM_WORLD,nr,idxs,PETSC_OWN_POINTER,&zr);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)zr,"ZR2");CHKERRQ(ierr);
ierr = ISViewFromOptions(zr,NULL,"-view_is");CHKERRQ(ierr);
ierr = MatZeroRowsIS(A,zr,diag*2.0+PETSC_SMALL,NULL,NULL);CHKERRQ(ierr);
ierr = MatZeroRowsIS(S,zr,diag*2.0+PETSC_SMALL,NULL,NULL);CHKERRQ(ierr);
}
ierr = ISDestroy(&zr);CHKERRQ(ierr);
if (b1) {
Vec b;
ierr = VecViewFromOptions(b1,NULL,"-view_b");CHKERRQ(ierr);
ierr = VecViewFromOptions(b2,NULL,"-view_b");CHKERRQ(ierr);
ierr = VecDuplicate(b1,&b);CHKERRQ(ierr);
ierr = VecCopy(b1,b);CHKERRQ(ierr);
ierr = VecAXPY(b,-1.0,b2);CHKERRQ(ierr);
ierr = VecNorm(b,NORM_INFINITY,&err);CHKERRQ(ierr);
if (err >= tol) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"[test %D] Error b %g\n",test,(double)err);CHKERRQ(ierr);
}
ierr = VecDestroy(&b);CHKERRQ(ierr);
}
ierr = VecDestroy(&b1);CHKERRQ(ierr);
ierr = VecDestroy(&b2);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = MatConvert(S,MATDENSE,MAT_INITIAL_MATRIX,&B);CHKERRQ(ierr);
ierr = MatCreateTranspose(S,&ST);CHKERRQ(ierr);
ierr = MatComputeOperator(ST,MATDENSE,&BT);CHKERRQ(ierr);
ierr = MatTranspose(BT,MAT_INITIAL_MATRIX,&BTT);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)B,"S");CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)BTT,"STT");CHKERRQ(ierr);
ierr = MatConvert(A,MATDENSE,MAT_INITIAL_MATRIX,&C);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)C,"A");CHKERRQ(ierr);
ierr = MatViewFromOptions(C,NULL,"-view_mat");CHKERRQ(ierr);
ierr = MatViewFromOptions(B,NULL,"-view_mat");CHKERRQ(ierr);
ierr = MatViewFromOptions(BTT,NULL,"-view_mat");CHKERRQ(ierr);
ierr = MatAXPY(C,-1.0,B,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = MatNorm(C,NORM_FROBENIUS,&err);CHKERRQ(ierr);
if (err >= tol) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"[test %D] Error mat mult %g\n",test,(double)err);CHKERRQ(ierr);
}
ierr = MatConvert(A,MATDENSE,MAT_REUSE_MATRIX,&C);CHKERRQ(ierr);
ierr = MatAXPY(C,-1.0,BTT,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = MatNorm(C,NORM_FROBENIUS,&err);CHKERRQ(ierr);
if (err >= tol) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"[test %D] Error mat mult transpose %g\n",test,(double)err);CHKERRQ(ierr);
}
ierr = MatDestroy(&ST);CHKERRQ(ierr);
ierr = MatDestroy(&BTT);CHKERRQ(ierr);
ierr = MatDestroy(&BT);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = MatDestroy(&C);CHKERRQ(ierr);
}
if (testdiagscale) { /* MatDiagonalScale() */
Vec vr,vl;
ierr = MatCreateVecs(A,&vr,&vl);CHKERRQ(ierr);
if (randomize) {
ierr = VecSetRandom(vr,NULL);CHKERRQ(ierr);
ierr = VecSetRandom(vl,NULL);CHKERRQ(ierr);
} else {
ierr = VecSet(vr,test%2 ? 0.15 : 1.0/0.15);CHKERRQ(ierr);
ierr = VecSet(vl,test%2 ? -1.2 : 1.0/-1.2);CHKERRQ(ierr);
}
ierr = MatDiagonalScale(A,vl,vr);CHKERRQ(ierr);
ierr = MatDiagonalScale(S,vl,vr);CHKERRQ(ierr);
ierr = VecDestroy(&vr);CHKERRQ(ierr);
ierr = VecDestroy(&vl);CHKERRQ(ierr);
}
if (testscale) { /* MatScale() */
ierr = MatScale(A,test%2 ? 1.4 : 1.0/1.4);CHKERRQ(ierr);
ierr = MatScale(S,test%2 ? 1.4 : 1.0/1.4);CHKERRQ(ierr);
}
if (testshift && cong) { /* MatShift() : MATSHELL shift is broken when row/cols layout are not congruent and left/right scaling have been applied */
ierr = MatShift(A,test%2 ? -77.5 : 77.5);CHKERRQ(ierr);
ierr = MatShift(S,test%2 ? -77.5 : 77.5);CHKERRQ(ierr);
}
if (testgetdiag && cong) { /* MatGetDiagonal() */
Vec dA,dS;
ierr = MatCreateVecs(A,&dA,NULL);CHKERRQ(ierr);
ierr = MatCreateVecs(S,&dS,NULL);CHKERRQ(ierr);
ierr = MatGetDiagonal(A,dA);CHKERRQ(ierr);
ierr = MatGetDiagonal(S,dS);CHKERRQ(ierr);
ierr = VecAXPY(dA,-1.0,dS);CHKERRQ(ierr);
ierr = VecNorm(dA,NORM_INFINITY,&err);CHKERRQ(ierr);
if (err >= tol) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"[test %D] Error diag %g\n",test,(double)err);CHKERRQ(ierr);
}
ierr = VecDestroy(&dA);CHKERRQ(ierr);
ierr = VecDestroy(&dS);CHKERRQ(ierr);
}
if (testdup && !test) {
Mat A2, S2;
ierr = MatDuplicate(A,MAT_COPY_VALUES,&A2);CHKERRQ(ierr);
ierr = MatDuplicate(S,MAT_COPY_VALUES,&S2);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&S);CHKERRQ(ierr);
A = A2;
S = S2;
}
if (testreset && (ntest == 1 || test == ntest-2)) {
/* reset MATSHELL */
ierr = MatAssemblyBegin(S,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(S,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* reset A */
ierr = MatCopy(user->B,A,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
}
}
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&user->B);CHKERRQ(ierr);
ierr = MatDestroy(&S);CHKERRQ(ierr);
ierr = PetscFree(user);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
PetscErrorCode PEPSetUp_Linear(PEP pep)
{
PetscErrorCode ierr;
PEP_LINEAR *ctx = (PEP_LINEAR*)pep->data;
PetscInt i=0;
EPSWhich which;
PetscBool trackall,istrivial,flg;
PetscScalar sigma;
/* function tables */
PetscErrorCode (*fcreate[][2])(MPI_Comm,PEP_LINEAR*,Mat*) = {
{ MatCreateExplicit_Linear_N1A, MatCreateExplicit_Linear_N1B }, /* N1 */
{ MatCreateExplicit_Linear_N2A, MatCreateExplicit_Linear_N2B }, /* N2 */
{ MatCreateExplicit_Linear_S1A, MatCreateExplicit_Linear_S1B }, /* S1 */
{ MatCreateExplicit_Linear_S2A, MatCreateExplicit_Linear_S2B }, /* S2 */
{ MatCreateExplicit_Linear_H1A, MatCreateExplicit_Linear_H1B }, /* H1 */
{ MatCreateExplicit_Linear_H2A, MatCreateExplicit_Linear_H2B } /* H2 */
};
PetscErrorCode (*fmult[][2])(Mat,Vec,Vec) = {
{ MatMult_Linear_N1A, MatMult_Linear_N1B },
{ MatMult_Linear_N2A, MatMult_Linear_N2B },
{ MatMult_Linear_S1A, MatMult_Linear_S1B },
{ MatMult_Linear_S2A, MatMult_Linear_S2B },
{ MatMult_Linear_H1A, MatMult_Linear_H1B },
{ MatMult_Linear_H2A, MatMult_Linear_H2B }
};
PetscErrorCode (*fgetdiagonal[][2])(Mat,Vec) = {
{ MatGetDiagonal_Linear_N1A, MatGetDiagonal_Linear_N1B },
{ MatGetDiagonal_Linear_N2A, MatGetDiagonal_Linear_N2B },
{ MatGetDiagonal_Linear_S1A, MatGetDiagonal_Linear_S1B },
{ MatGetDiagonal_Linear_S2A, MatGetDiagonal_Linear_S2B },
{ MatGetDiagonal_Linear_H1A, MatGetDiagonal_Linear_H1B },
{ MatGetDiagonal_Linear_H2A, MatGetDiagonal_Linear_H2B }
};
PetscFunctionBegin;
if (!ctx->cform) ctx->cform = 1;
if (!pep->which) pep->which = PEP_LARGEST_MAGNITUDE;
if (pep->basis!=PEP_BASIS_MONOMIAL) SETERRQ(PetscObjectComm((PetscObject)pep),PETSC_ERR_SUP,"Solver not implemented for non-monomial bases");
if (pep->nmat!=3) SETERRQ(PetscObjectComm((PetscObject)pep),PETSC_ERR_SUP,"Solver only available for quadratic problems");
if (pep->scale==PEP_SCALE_DIAGONAL || pep->scale==PEP_SCALE_BOTH) SETERRQ(PetscObjectComm((PetscObject)pep),PETSC_ERR_SUP,"Diagonal scaling not allowed in PEP linear solver");
ierr = STGetTransform(pep->st,&flg);CHKERRQ(ierr);
if (flg) SETERRQ(PetscObjectComm((PetscObject)pep),PETSC_ERR_SUP,"ST transformation flag not allowed for PEP linear solver");
/* compute scale factor if no set by user */
ierr = PEPComputeScaleFactor(pep);CHKERRQ(ierr);
ierr = STGetOperators(pep->st,0,&ctx->K);CHKERRQ(ierr);
ierr = STGetOperators(pep->st,1,&ctx->C);CHKERRQ(ierr);
ierr = STGetOperators(pep->st,2,&ctx->M);CHKERRQ(ierr);
ctx->sfactor = pep->sfactor;
ierr = MatDestroy(&ctx->A);CHKERRQ(ierr);
ierr = MatDestroy(&ctx->B);CHKERRQ(ierr);
ierr = VecDestroy(&ctx->x1);CHKERRQ(ierr);
ierr = VecDestroy(&ctx->x2);CHKERRQ(ierr);
ierr = VecDestroy(&ctx->y1);CHKERRQ(ierr);
ierr = VecDestroy(&ctx->y2);CHKERRQ(ierr);
switch (pep->problem_type) {
case PEP_GENERAL: i = 0; break;
case PEP_HERMITIAN: i = 2; break;
case PEP_GYROSCOPIC: i = 4; break;
default: SETERRQ(PetscObjectComm((PetscObject)pep),1,"Wrong value of pep->problem_type");
}
i += ctx->cform-1;
if (ctx->explicitmatrix) {
ctx->x1 = ctx->x2 = ctx->y1 = ctx->y2 = NULL;
ierr = (*fcreate[i][0])(PetscObjectComm((PetscObject)pep),ctx,&ctx->A);CHKERRQ(ierr);
ierr = (*fcreate[i][1])(PetscObjectComm((PetscObject)pep),ctx,&ctx->B);CHKERRQ(ierr);
} else {
ierr = VecCreateMPIWithArray(PetscObjectComm((PetscObject)pep),1,pep->nloc,pep->n,NULL,&ctx->x1);CHKERRQ(ierr);
ierr = VecCreateMPIWithArray(PetscObjectComm((PetscObject)pep),1,pep->nloc,pep->n,NULL,&ctx->x2);CHKERRQ(ierr);
ierr = VecCreateMPIWithArray(PetscObjectComm((PetscObject)pep),1,pep->nloc,pep->n,NULL,&ctx->y1);CHKERRQ(ierr);
ierr = VecCreateMPIWithArray(PetscObjectComm((PetscObject)pep),1,pep->nloc,pep->n,NULL,&ctx->y2);CHKERRQ(ierr);
ierr = PetscLogObjectParent((PetscObject)pep,(PetscObject)ctx->x1);CHKERRQ(ierr);
ierr = PetscLogObjectParent((PetscObject)pep,(PetscObject)ctx->x2);CHKERRQ(ierr);
ierr = PetscLogObjectParent((PetscObject)pep,(PetscObject)ctx->y1);CHKERRQ(ierr);
ierr = PetscLogObjectParent((PetscObject)pep,(PetscObject)ctx->y2);CHKERRQ(ierr);
ierr = MatCreateShell(PetscObjectComm((PetscObject)pep),2*pep->nloc,2*pep->nloc,2*pep->n,2*pep->n,ctx,&ctx->A);CHKERRQ(ierr);
ierr = MatShellSetOperation(ctx->A,MATOP_MULT,(void(*)(void))fmult[i][0]);CHKERRQ(ierr);
ierr = MatShellSetOperation(ctx->A,MATOP_GET_DIAGONAL,(void(*)(void))fgetdiagonal[i][0]);CHKERRQ(ierr);
ierr = MatCreateShell(PetscObjectComm((PetscObject)pep),2*pep->nloc,2*pep->nloc,2*pep->n,2*pep->n,ctx,&ctx->B);CHKERRQ(ierr);
ierr = MatShellSetOperation(ctx->B,MATOP_MULT,(void(*)(void))fmult[i][1]);CHKERRQ(ierr);
ierr = MatShellSetOperation(ctx->B,MATOP_GET_DIAGONAL,(void(*)(void))fgetdiagonal[i][1]);CHKERRQ(ierr);
}
ierr = PetscLogObjectParent((PetscObject)pep,(PetscObject)ctx->A);CHKERRQ(ierr);
ierr = PetscLogObjectParent((PetscObject)pep,(PetscObject)ctx->B);CHKERRQ(ierr);
if (!ctx->eps) { ierr = PEPLinearGetEPS(pep,&ctx->eps);CHKERRQ(ierr); }
ierr = EPSSetOperators(ctx->eps,ctx->A,ctx->B);CHKERRQ(ierr);
if (pep->problem_type==PEP_HERMITIAN) {
ierr = EPSSetProblemType(ctx->eps,EPS_GHIEP);CHKERRQ(ierr);
} else {
ierr = EPSSetProblemType(ctx->eps,EPS_GNHEP);CHKERRQ(ierr);
}
switch (pep->which) {
case PEP_LARGEST_MAGNITUDE: which = EPS_LARGEST_MAGNITUDE; break;
case PEP_SMALLEST_MAGNITUDE: which = EPS_SMALLEST_MAGNITUDE; break;
case PEP_LARGEST_REAL: which = EPS_LARGEST_REAL; break;
case PEP_SMALLEST_REAL: which = EPS_SMALLEST_REAL; break;
case PEP_LARGEST_IMAGINARY: which = EPS_LARGEST_IMAGINARY; break;
case PEP_SMALLEST_IMAGINARY: which = EPS_SMALLEST_IMAGINARY; break;
case PEP_TARGET_MAGNITUDE: which = EPS_TARGET_MAGNITUDE; break;
case PEP_TARGET_REAL: which = EPS_TARGET_REAL; break;
case PEP_TARGET_IMAGINARY: which = EPS_TARGET_IMAGINARY; break;
default: SETERRQ(PetscObjectComm((PetscObject)pep),1,"Wrong value of which");
}
ierr = EPSSetWhichEigenpairs(ctx->eps,which);CHKERRQ(ierr);
ierr = EPSSetDimensions(ctx->eps,pep->nev,pep->ncv?pep->ncv:PETSC_DEFAULT,pep->mpd?pep->mpd:PETSC_DEFAULT);CHKERRQ(ierr);
ierr = EPSSetTolerances(ctx->eps,pep->tol==PETSC_DEFAULT?SLEPC_DEFAULT_TOL/10.0:pep->tol/10.0,pep->max_it?pep->max_it:PETSC_DEFAULT);CHKERRQ(ierr);
ierr = RGIsTrivial(pep->rg,&istrivial);CHKERRQ(ierr);
if (!istrivial) { ierr = EPSSetRG(ctx->eps,pep->rg);CHKERRQ(ierr); }
/* Transfer the trackall option from pep to eps */
ierr = PEPGetTrackAll(pep,&trackall);CHKERRQ(ierr);
ierr = EPSSetTrackAll(ctx->eps,trackall);CHKERRQ(ierr);
/* temporary change of target */
if (pep->sfactor!=1.0) {
ierr = EPSGetTarget(ctx->eps,&sigma);CHKERRQ(ierr);
ierr = EPSSetTarget(ctx->eps,sigma/pep->sfactor);CHKERRQ(ierr);
}
ierr = EPSSetUp(ctx->eps);CHKERRQ(ierr);
ierr = EPSGetDimensions(ctx->eps,NULL,&pep->ncv,&pep->mpd);CHKERRQ(ierr);
ierr = EPSGetTolerances(ctx->eps,NULL,&pep->max_it);CHKERRQ(ierr);
if (pep->nini>0) { ierr = PetscInfo(pep,"Ignoring initial vectors\n");CHKERRQ(ierr); }
ierr = PEPAllocateSolution(pep,0);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@C
MatCreateLMVM - Creates a limited memory matrix for lmvm algorithms.
Collective on A
Input Parameters:
+ comm - MPI Communicator
. n - local size of vectors
- N - global size of vectors
Output Parameters:
. A - New LMVM matrix
Level: developer
@*/
extern PetscErrorCode MatCreateLMVM(MPI_Comm comm, PetscInt n, PetscInt N, Mat *A)
{
MatLMVMCtx *ctx;
PetscErrorCode ierr;
PetscInt nhistory;
PetscFunctionBegin;
/* create data structure and populate with default values */
ierr = PetscNew(&ctx);CHKERRQ(ierr);
ctx->lm=5;
ctx->eps=0.0;
ctx->limitType=MatLMVM_Limit_None;
ctx->scaleType=MatLMVM_Scale_Broyden;
ctx->rScaleType = MatLMVM_Rescale_Scalar;
ctx->s_alpha = 1.0;
ctx->r_alpha = 1.0;
ctx->r_beta = 0.5;
ctx->mu = 1.0;
ctx->nu = 100.0;
ctx->phi = 0.125;
ctx->scalar_history = 1;
ctx->rescale_history = 1;
ctx->delta_min = 1e-7;
ctx->delta_max = 100.0;
/* Begin configuration */
ierr = PetscOptionsInt("-tao_lmm_vectors", "vectors to use for approximation", "", ctx->lm, &ctx->lm, 0);CHKERRQ(ierr);
ierr = PetscOptionsReal("-tao_lmm_limit_mu", "mu limiting factor", "", ctx->mu, &ctx->mu, 0);CHKERRQ(ierr);
ierr = PetscOptionsReal("-tao_lmm_limit_nu", "nu limiting factor", "", ctx->nu, &ctx->nu, 0);CHKERRQ(ierr);
ierr = PetscOptionsReal("-tao_lmm_broyden_phi", "phi factor for Broyden scaling", "", ctx->phi, &ctx->phi, 0);CHKERRQ(ierr);
ierr = PetscOptionsReal("-tao_lmm_scalar_alpha", "alpha factor for scalar scaling", "",ctx->s_alpha, &ctx->s_alpha, 0);CHKERRQ(ierr);
ierr = PetscOptionsReal("-tao_lmm_rescale_alpha", "alpha factor for rescaling diagonal", "", ctx->r_alpha, &ctx->r_alpha, 0);CHKERRQ(ierr);
ierr = PetscOptionsReal("-tao_lmm_rescale_beta", "beta factor for rescaling diagonal", "", ctx->r_beta, &ctx->r_beta, 0);CHKERRQ(ierr);
ierr = PetscOptionsInt("-tao_lmm_scalar_history", "amount of history for scalar scaling", "", ctx->scalar_history, &ctx->scalar_history, 0);CHKERRQ(ierr);
ierr = PetscOptionsInt("-tao_lmm_rescale_history", "amount of history for rescaling diagonal", "", ctx->rescale_history, &ctx->rescale_history, 0);CHKERRQ(ierr);
ierr = PetscOptionsReal("-tao_lmm_eps", "rejection tolerance", "", ctx->eps, &ctx->eps, 0);CHKERRQ(ierr);
ierr = PetscOptionsEList("-tao_lmm_scale_type", "scale type", "", Scale_Table, MatLMVM_Scale_Types, Scale_Table[ctx->scaleType], &ctx->scaleType, 0);CHKERRQ(ierr);
ierr = PetscOptionsEList("-tao_lmm_rescale_type", "rescale type", "", Rescale_Table, MatLMVM_Rescale_Types, Rescale_Table[ctx->rScaleType], &ctx->rScaleType, 0);CHKERRQ(ierr);
ierr = PetscOptionsEList("-tao_lmm_limit_type", "limit type", "", Limit_Table, MatLMVM_Limit_Types, Limit_Table[ctx->limitType], &ctx->limitType, 0);CHKERRQ(ierr);
ierr = PetscOptionsReal("-tao_lmm_delta_min", "minimum delta value", "", ctx->delta_min, &ctx->delta_min, 0);CHKERRQ(ierr);
ierr = PetscOptionsReal("-tao_lmm_delta_max", "maximum delta value", "", ctx->delta_max, &ctx->delta_max, 0);CHKERRQ(ierr);
/* Complete configuration */
ctx->rescale_history = PetscMin(ctx->rescale_history, ctx->lm);
ierr = PetscMalloc1(ctx->lm+1,&ctx->rho);CHKERRQ(ierr);
ierr = PetscMalloc1(ctx->lm+1,&ctx->beta);CHKERRQ(ierr);
nhistory = PetscMax(ctx->scalar_history,1);
ierr = PetscMalloc1(nhistory,&ctx->yy_history);CHKERRQ(ierr);
ierr = PetscMalloc1(nhistory,&ctx->ys_history);CHKERRQ(ierr);
ierr = PetscMalloc1(nhistory,&ctx->ss_history);CHKERRQ(ierr);
nhistory = PetscMax(ctx->rescale_history,1);
ierr = PetscMalloc1(nhistory,&ctx->yy_rhistory);CHKERRQ(ierr);
ierr = PetscMalloc1(nhistory,&ctx->ys_rhistory);CHKERRQ(ierr);
ierr = PetscMalloc1(nhistory,&ctx->ss_rhistory);CHKERRQ(ierr);
/* Finish initializations */
ctx->lmnow = 0;
ctx->iter = 0;
ctx->nupdates = 0;
ctx->nrejects = 0;
ctx->delta = 1.0;
ctx->Gprev = 0;
ctx->Xprev = 0;
ctx->scale = 0;
ctx->useScale = PETSC_FALSE;
ctx->H0 = 0;
ctx->useDefaultH0=PETSC_TRUE;
ierr = MatCreateShell(comm, n, n, N, N, ctx, A);CHKERRQ(ierr);
ierr = MatShellSetOperation(*A,MATOP_DESTROY,(void(*)(void))MatDestroy_LMVM);CHKERRQ(ierr);
ierr = MatShellSetOperation(*A,MATOP_VIEW,(void(*)(void))MatView_LMVM);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int Argc,char **Args)
{
PetscInt x_mesh = 15,levels = 3,cycles = 1,use_jacobi = 0;
PetscInt i,smooths = 1,*N,its;
PetscErrorCode ierr;
PCMGType am = PC_MG_MULTIPLICATIVE;
Mat cmat,mat[20],fmat;
KSP cksp,ksp[20],kspmg;
PetscReal e[3]; /* l_2 error,max error, residual */
char *shellname;
Vec x,solution,X[20],R[20],B[20];
PC pcmg,pc;
PetscTruth flg;
PetscInitialize(&Argc,&Args,(char *)0,help);
ierr = PetscOptionsGetInt(PETSC_NULL,"-x",&x_mesh,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-l",&levels,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-c",&cycles,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-smooths",&smooths,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsHasName(PETSC_NULL,"-a",&flg);CHKERRQ(ierr);
if (flg) {am = PC_MG_ADDITIVE;}
ierr = PetscOptionsHasName(PETSC_NULL,"-f",&flg);CHKERRQ(ierr);
if (flg) {am = PC_MG_FULL;}
ierr = PetscOptionsHasName(PETSC_NULL,"-j",&flg);CHKERRQ(ierr);
if (flg) {use_jacobi = 1;}
ierr = PetscMalloc(levels*sizeof(PetscInt),&N);CHKERRQ(ierr);
N[0] = x_mesh;
for (i=1; i<levels; i++) {
N[i] = N[i-1]/2;
if (N[i] < 1) {SETERRQ(1,"Too many levels");}
}
ierr = Create1dLaplacian(N[levels-1],&cmat);CHKERRQ(ierr);
ierr = KSPCreate(PETSC_COMM_WORLD,&kspmg);CHKERRQ(ierr);
ierr = KSPGetPC(kspmg,&pcmg);CHKERRQ(ierr);
ierr = KSPSetFromOptions(kspmg);CHKERRQ(ierr);
ierr = PCSetType(pcmg,PCMG);CHKERRQ(ierr);
ierr = PCMGSetLevels(pcmg,levels,PETSC_NULL);CHKERRQ(ierr);
ierr = PCMGSetType(pcmg,am);CHKERRQ(ierr);
ierr = PCMGGetCoarseSolve(pcmg,&cksp);CHKERRQ(ierr);
ierr = KSPSetOperators(cksp,cmat,cmat,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = KSPGetPC(cksp,&pc);CHKERRQ(ierr);
ierr = PCSetType(pc,PCLU);CHKERRQ(ierr);
ierr = KSPSetType(cksp,KSPPREONLY);CHKERRQ(ierr);
/* zero is finest level */
for (i=0; i<levels-1; i++) {
ierr = PCMGSetResidual(pcmg,levels - 1 - i,residual,(Mat)0);CHKERRQ(ierr);
ierr = MatCreateShell(PETSC_COMM_WORLD,N[i+1],N[i],N[i+1],N[i],(void*)0,&mat[i]);CHKERRQ(ierr);
ierr = MatShellSetOperation(mat[i],MATOP_MULT,(void(*)(void))restrct);CHKERRQ(ierr);
ierr = MatShellSetOperation(mat[i],MATOP_MULT_TRANSPOSE_ADD,(void(*)(void))interpolate);CHKERRQ(ierr);
ierr = PCMGSetInterpolation(pcmg,levels - 1 - i,mat[i]);CHKERRQ(ierr);
ierr = PCMGSetRestriction(pcmg,levels - 1 - i,mat[i]);CHKERRQ(ierr);
ierr = PCMGSetCyclesOnLevel(pcmg,levels - 1 - i,cycles);CHKERRQ(ierr);
/* set smoother */
ierr = PCMGGetSmoother(pcmg,levels - 1 - i,&ksp[i]);CHKERRQ(ierr);
ierr = KSPGetPC(ksp[i],&pc);CHKERRQ(ierr);
ierr = PCSetType(pc,PCSHELL);CHKERRQ(ierr);
ierr = PCShellSetName(pc,"user_precond");CHKERRQ(ierr);
ierr = PCShellGetName(pc,&shellname);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"level=%D, PCShell name is %s\n",i,shellname);CHKERRQ(ierr);
/* this is a dummy! since KSP requires a matrix passed in */
ierr = KSPSetOperators(ksp[i],mat[i],mat[i],DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
/*
We override the matrix passed in by forcing it to use Richardson with
a user provided application. This is non-standard and this practice
should be avoided.
*/
ierr = PCShellSetApplyRichardson(pc,gauss_seidel);CHKERRQ(ierr);
if (use_jacobi) {
ierr = PCShellSetApplyRichardson(pc,jacobi);CHKERRQ(ierr);
}
ierr = KSPSetType(ksp[i],KSPRICHARDSON);CHKERRQ(ierr);
ierr = KSPSetInitialGuessNonzero(ksp[i],PETSC_TRUE);CHKERRQ(ierr);
ierr = KSPSetTolerances(ksp[i],PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT,smooths);CHKERRQ(ierr);
ierr = VecCreateSeq(PETSC_COMM_SELF,N[i],&x);CHKERRQ(ierr);
X[levels - 1 - i] = x;
if (i > 0) {
ierr = PCMGSetX(pcmg,levels - 1 - i,x);CHKERRQ(ierr);
}
ierr = VecCreateSeq(PETSC_COMM_SELF,N[i],&x);CHKERRQ(ierr);
B[levels -1 - i] = x;
if (i > 0) {
ierr = PCMGSetRhs(pcmg,levels - 1 - i,x);CHKERRQ(ierr);
}
ierr = VecCreateSeq(PETSC_COMM_SELF,N[i],&x);CHKERRQ(ierr);
R[levels - 1 - i] = x;
ierr = PCMGSetR(pcmg,levels - 1 - i,x);CHKERRQ(ierr);
}
/* create coarse level vectors */
ierr = VecCreateSeq(PETSC_COMM_SELF,N[levels-1],&x);CHKERRQ(ierr);
ierr = PCMGSetX(pcmg,0,x);CHKERRQ(ierr); X[0] = x;
ierr = VecCreateSeq(PETSC_COMM_SELF,N[levels-1],&x);CHKERRQ(ierr);
ierr = PCMGSetRhs(pcmg,0,x);CHKERRQ(ierr); B[0] = x;
/* create matrix multiply for finest level */
ierr = MatCreateShell(PETSC_COMM_WORLD,N[0],N[0],N[0],N[0],(void*)0,&fmat);CHKERRQ(ierr);
ierr = MatShellSetOperation(fmat,MATOP_MULT,(void(*)(void))amult);CHKERRQ(ierr);
ierr = KSPSetOperators(kspmg,fmat,fmat,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = CalculateSolution(N[0],&solution);CHKERRQ(ierr);
ierr = CalculateRhs(B[levels-1]);CHKERRQ(ierr);
ierr = VecSet(X[levels-1],0.0);CHKERRQ(ierr);
ierr = residual((Mat)0,B[levels-1],X[levels-1],R[levels-1]);CHKERRQ(ierr);
ierr = CalculateError(solution,X[levels-1],R[levels-1],e);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF,"l_2 error %G max error %G resi %G\n",e[0],e[1],e[2]);CHKERRQ(ierr);
ierr = KSPSolve(kspmg,B[levels-1],X[levels-1]);CHKERRQ(ierr);
ierr = KSPGetIterationNumber(kspmg,&its);CHKERRQ(ierr);
ierr = residual((Mat)0,B[levels-1],X[levels-1],R[levels-1]);CHKERRQ(ierr);
ierr = CalculateError(solution,X[levels-1],R[levels-1],e);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF,"its %D l_2 error %G max error %G resi %G\n",its,e[0],e[1],e[2]);CHKERRQ(ierr);
ierr = PetscFree(N);CHKERRQ(ierr);
ierr = VecDestroy(solution);CHKERRQ(ierr);
/* note we have to keep a list of all vectors allocated, this is
not ideal, but putting it in MGDestroy is not so good either*/
for (i=0; i<levels; i++) {
ierr = VecDestroy(X[i]);CHKERRQ(ierr);
ierr = VecDestroy(B[i]);CHKERRQ(ierr);
if(i){ierr = VecDestroy(R[i]);CHKERRQ(ierr);}
}
for (i=0; i<levels-1; i++) {
ierr = MatDestroy(mat[i]);CHKERRQ(ierr);
}
ierr = MatDestroy(cmat);CHKERRQ(ierr);
ierr = MatDestroy(fmat);CHKERRQ(ierr);
ierr = KSPDestroy(kspmg);CHKERRQ(ierr);
ierr = PetscFinalize();CHKERRQ(ierr);
return 0;
}
int main(int argc,char **argv)
{
Mat A; /* eigenvalue problem matrix */
EPS eps; /* eigenproblem solver context */
EPSType type;
PetscScalar delta1,delta2,L,h,value[3];
PetscInt N=30,n,i,col[3],Istart,Iend,nev;
PetscBool FirstBlock=PETSC_FALSE,LastBlock=PETSC_FALSE;
CTX_BRUSSEL *ctx;
PetscErrorCode ierr;
SlepcInitialize(&argc,&argv,(char*)0,help);
ierr = PetscOptionsGetInt(NULL,"-n",&N,NULL);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"\nBrusselator wave model, n=%D\n\n",N);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Generate the matrix
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Create shell matrix context and set default parameters
*/
ierr = PetscNew(&ctx);CHKERRQ(ierr);
ctx->alpha = 2.0;
ctx->beta = 5.45;
delta1 = 0.008;
delta2 = 0.004;
L = 0.51302;
/*
Look the command line for user-provided parameters
*/
ierr = PetscOptionsGetScalar(NULL,"-L",&L,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetScalar(NULL,"-alpha",&ctx->alpha,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetScalar(NULL,"-beta",&ctx->beta,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetScalar(NULL,"-delta1",&delta1,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetScalar(NULL,"-delta2",&delta2,NULL);CHKERRQ(ierr);
/*
Create matrix T
*/
ierr = MatCreate(PETSC_COMM_WORLD,&ctx->T);CHKERRQ(ierr);
ierr = MatSetSizes(ctx->T,PETSC_DECIDE,PETSC_DECIDE,N,N);CHKERRQ(ierr);
ierr = MatSetFromOptions(ctx->T);CHKERRQ(ierr);
ierr = MatSetUp(ctx->T);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(ctx->T,&Istart,&Iend);CHKERRQ(ierr);
if (Istart==0) FirstBlock=PETSC_TRUE;
if (Iend==N) LastBlock=PETSC_TRUE;
value[0]=1.0; value[1]=-2.0; value[2]=1.0;
for (i=(FirstBlock? Istart+1: Istart); i<(LastBlock? Iend-1: Iend); i++) {
col[0]=i-1; col[1]=i; col[2]=i+1;
ierr = MatSetValues(ctx->T,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr);
}
if (LastBlock) {
i=N-1; col[0]=N-2; col[1]=N-1;
ierr = MatSetValues(ctx->T,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);
}
if (FirstBlock) {
i=0; col[0]=0; col[1]=1; value[0]=-2.0; value[1]=1.0;
ierr = MatSetValues(ctx->T,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(ctx->T,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(ctx->T,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatGetLocalSize(ctx->T,&n,NULL);CHKERRQ(ierr);
/*
Fill the remaining information in the shell matrix context
and create auxiliary vectors
*/
h = 1.0 / (PetscReal)(N+1);
ctx->tau1 = delta1 / ((h*L)*(h*L));
ctx->tau2 = delta2 / ((h*L)*(h*L));
ctx->sigma = 0.0;
ierr = VecCreateMPIWithArray(PETSC_COMM_WORLD,1,n,PETSC_DECIDE,NULL,&ctx->x1);CHKERRQ(ierr);
ierr = VecCreateMPIWithArray(PETSC_COMM_WORLD,1,n,PETSC_DECIDE,NULL,&ctx->x2);CHKERRQ(ierr);
ierr = VecCreateMPIWithArray(PETSC_COMM_WORLD,1,n,PETSC_DECIDE,NULL,&ctx->y1);CHKERRQ(ierr);
ierr = VecCreateMPIWithArray(PETSC_COMM_WORLD,1,n,PETSC_DECIDE,NULL,&ctx->y2);CHKERRQ(ierr);
/*
Create the shell matrix
*/
ierr = MatCreateShell(PETSC_COMM_WORLD,2*n,2*n,2*N,2*N,(void*)ctx,&A);CHKERRQ(ierr);
ierr = MatShellSetOperation(A,MATOP_MULT,(void(*)())MatMult_Brussel);CHKERRQ(ierr);
ierr = MatShellSetOperation(A,MATOP_SHIFT,(void(*)())MatShift_Brussel);CHKERRQ(ierr);
ierr = MatShellSetOperation(A,MATOP_GET_DIAGONAL,(void(*)())MatGetDiagonal_Brussel);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create the eigensolver and set various options
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Create eigensolver context
*/
ierr = EPSCreate(PETSC_COMM_WORLD,&eps);CHKERRQ(ierr);
/*
Set operators. In this case, it is a standard eigenvalue problem
*/
ierr = EPSSetOperators(eps,A,NULL);CHKERRQ(ierr);
ierr = EPSSetProblemType(eps,EPS_NHEP);CHKERRQ(ierr);
/*
Ask for the rightmost eigenvalues
*/
ierr = EPSSetWhichEigenpairs(eps,EPS_LARGEST_REAL);CHKERRQ(ierr);
/*
Set other solver options at runtime
*/
ierr = EPSSetFromOptions(eps);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Solve the eigensystem
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = EPSSolve(eps);CHKERRQ(ierr);
/*
Optional: Get some information from the solver and display it
*/
ierr = EPSGetType(eps,&type);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," Solution method: %s\n\n",type);CHKERRQ(ierr);
ierr = EPSGetDimensions(eps,&nev,NULL,NULL);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," Number of requested eigenvalues: %D\n",nev);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Display solution and clean up
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = EPSPrintSolution(eps,NULL);CHKERRQ(ierr);
ierr = EPSDestroy(&eps);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&ctx->T);CHKERRQ(ierr);
ierr = VecDestroy(&ctx->x1);CHKERRQ(ierr);
ierr = VecDestroy(&ctx->x2);CHKERRQ(ierr);
ierr = VecDestroy(&ctx->y1);CHKERRQ(ierr);
ierr = VecDestroy(&ctx->y2);CHKERRQ(ierr);
ierr = PetscFree(ctx);CHKERRQ(ierr);
ierr = SlepcFinalize();
return 0;
}
void IBImplicitStaggeredHierarchyIntegrator::integrateHierarchy(const double current_time,
const double new_time,
const int cycle_num)
{
IBHierarchyIntegrator::integrateHierarchy(current_time, new_time, cycle_num);
Pointer<INSStaggeredHierarchyIntegrator> ins_hier_integrator = d_ins_hier_integrator;
TBOX_ASSERT(ins_hier_integrator);
PetscErrorCode ierr;
int n_local;
const int coarsest_ln = 0;
const int finest_ln = d_hierarchy->getFinestLevelNumber();
// const double half_time = current_time+0.5*(new_time-current_time);
VariableDatabase<NDIM>* var_db = VariableDatabase<NDIM>::getDatabase();
Pointer<VariableContext> current_ctx = ins_hier_integrator->getCurrentContext();
Pointer<VariableContext> scratch_ctx = ins_hier_integrator->getScratchContext();
Pointer<VariableContext> new_ctx = ins_hier_integrator->getNewContext();
const int wgt_cc_idx = d_hier_math_ops->getCellWeightPatchDescriptorIndex();
const int wgt_sc_idx = d_hier_math_ops->getSideWeightPatchDescriptorIndex();
Pointer<Variable<NDIM> > u_var = ins_hier_integrator->getVelocityVariable();
// const int u_current_idx = var_db->mapVariableAndContextToIndex(u_var, current_ctx);
const int u_scratch_idx = var_db->mapVariableAndContextToIndex(u_var, scratch_ctx);
// const int u_new_idx = var_db->mapVariableAndContextToIndex(u_var, new_ctx);
Pointer<Variable<NDIM> > p_var = ins_hier_integrator->getPressureVariable();
// const int p_current_idx = var_db->mapVariableAndContextToIndex(p_var, current_ctx);
const int p_scratch_idx = var_db->mapVariableAndContextToIndex(p_var, scratch_ctx);
// const int p_new_idx = var_db->mapVariableAndContextToIndex(p_var, new_ctx);
// Skip all cycles in the INS solver --- we advance the state data here.
ins_hier_integrator->skipCycle(current_time, new_time, cycle_num);
// Setup Eulerian vectors used in solving the implicit IB equations.
Pointer<SAMRAIVectorReal<NDIM, double> > eul_sol_vec = new SAMRAIVectorReal<NDIM, double>(
d_object_name + "::eulerian_sol_vec", d_hierarchy, coarsest_ln, finest_ln);
eul_sol_vec->addComponent(u_var, u_scratch_idx, wgt_sc_idx, d_hier_velocity_data_ops);
eul_sol_vec->addComponent(p_var, p_scratch_idx, wgt_cc_idx, d_hier_pressure_data_ops);
Pointer<SAMRAIVectorReal<NDIM, double> > eul_rhs_vec =
eul_sol_vec->cloneVector(d_object_name + "::eulerian_rhs_vec");
eul_rhs_vec->allocateVectorData(current_time);
d_u_scratch_vec = eul_sol_vec->cloneVector(d_object_name + "::u_scratch_vec");
d_f_scratch_vec = eul_rhs_vec->cloneVector(d_object_name + "::f_scratch_vec");
d_u_scratch_vec->allocateVectorData(current_time);
d_f_scratch_vec->allocateVectorData(current_time);
ins_hier_integrator->setupSolverVectors(
eul_sol_vec, eul_rhs_vec, current_time, new_time, cycle_num);
d_stokes_solver = ins_hier_integrator->getStokesSolver();
Pointer<KrylovLinearSolver> p_stokes_solver = d_stokes_solver;
TBOX_ASSERT(p_stokes_solver);
d_stokes_op = p_stokes_solver->getOperator();
TBOX_ASSERT(d_stokes_op);
// Setup Lagrangian vectors used in solving the implicit IB equations.
Vec lag_sol_petsc_vec, lag_rhs_petsc_vec;
d_ib_implicit_ops->createSolverVecs(lag_sol_petsc_vec, lag_rhs_petsc_vec);
d_ib_implicit_ops->setupSolverVecs(lag_sol_petsc_vec, lag_rhs_petsc_vec);
// Indicate that the current approximation to position of the structure
// should be used for Lagrangian-Eulerian coupling.
d_ib_implicit_ops->updateFixedLEOperators();
// Setup multi-vec objects to store the composite solution and
// right-hand-side vectors.
Vec eul_sol_petsc_vec =
PETScSAMRAIVectorReal::createPETScVector(eul_sol_vec, PETSC_COMM_WORLD);
Vec eul_rhs_petsc_vec =
PETScSAMRAIVectorReal::createPETScVector(eul_rhs_vec, PETSC_COMM_WORLD);
Vec sol_petsc_vecs[] = { eul_sol_petsc_vec, lag_sol_petsc_vec };
Vec rhs_petsc_vecs[] = { eul_rhs_petsc_vec, lag_rhs_petsc_vec };
Vec composite_sol_petsc_vec, composite_rhs_petsc_vec, composite_res_petsc_vec;
ierr = VecCreateMultiVec(PETSC_COMM_WORLD, 2, sol_petsc_vecs, &composite_sol_petsc_vec);
IBTK_CHKERRQ(ierr);
ierr = VecCreateMultiVec(PETSC_COMM_WORLD, 2, rhs_petsc_vecs, &composite_rhs_petsc_vec);
IBTK_CHKERRQ(ierr);
ierr = VecDuplicate(composite_rhs_petsc_vec, &composite_res_petsc_vec);
IBTK_CHKERRQ(ierr);
// Solve the implicit IB equations.
d_ib_implicit_ops->preprocessSolveFluidEquations(current_time, new_time, cycle_num);
SNES snes;
ierr = SNESCreate(PETSC_COMM_WORLD, &snes);
IBTK_CHKERRQ(ierr);
ierr = SNESSetFunction(snes, composite_res_petsc_vec, compositeIBFunction_SAMRAI, this);
IBTK_CHKERRQ(ierr);
ierr = SNESSetOptionsPrefix(snes, "ib_");
IBTK_CHKERRQ(ierr);
Mat jac;
ierr = VecGetLocalSize(composite_sol_petsc_vec, &n_local);
IBTK_CHKERRQ(ierr);
ierr = MatCreateShell(
PETSC_COMM_WORLD, n_local, n_local, PETSC_DETERMINE, PETSC_DETERMINE, this, &jac);
IBTK_CHKERRQ(ierr);
ierr = MatShellSetOperation(
jac, MATOP_MULT, reinterpret_cast<void (*)(void)>(compositeIBJacobianApply_SAMRAI));
IBTK_CHKERRQ(ierr);
ierr = SNESSetJacobian(snes, jac, jac, compositeIBJacobianSetup_SAMRAI, this);
IBTK_CHKERRQ(ierr);
Mat schur;
ierr = VecGetLocalSize(lag_sol_petsc_vec, &n_local);
IBTK_CHKERRQ(ierr);
ierr = MatCreateShell(
PETSC_COMM_WORLD, n_local, n_local, PETSC_DETERMINE, PETSC_DETERMINE, this, &schur);
IBTK_CHKERRQ(ierr);
ierr = MatShellSetOperation(
schur, MATOP_MULT, reinterpret_cast<void (*)(void)>(lagrangianSchurApply_SAMRAI));
IBTK_CHKERRQ(ierr);
ierr = KSPCreate(PETSC_COMM_WORLD, &d_schur_solver);
IBTK_CHKERRQ(ierr);
ierr = KSPSetOptionsPrefix(d_schur_solver, "ib_schur_");
IBTK_CHKERRQ(ierr);
ierr = KSPSetOperators(d_schur_solver, schur, schur, SAME_PRECONDITIONER);
IBTK_CHKERRQ(ierr);
PC schur_pc;
ierr = KSPGetPC(d_schur_solver, &schur_pc);
IBTK_CHKERRQ(ierr);
ierr = PCSetType(schur_pc, PCNONE);
IBTK_CHKERRQ(ierr);
ierr = KSPSetFromOptions(d_schur_solver);
IBTK_CHKERRQ(ierr);
KSP snes_ksp;
ierr = SNESGetKSP(snes, &snes_ksp);
IBTK_CHKERRQ(ierr);
ierr = KSPSetType(snes_ksp, KSPFGMRES);
IBTK_CHKERRQ(ierr);
PC snes_pc;
ierr = KSPGetPC(snes_ksp, &snes_pc);
IBTK_CHKERRQ(ierr);
ierr = PCSetType(snes_pc, PCSHELL);
IBTK_CHKERRQ(ierr);
ierr = PCShellSetContext(snes_pc, this);
IBTK_CHKERRQ(ierr);
ierr = PCShellSetApply(snes_pc, compositeIBPCApply_SAMRAI);
IBTK_CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes);
IBTK_CHKERRQ(ierr);
ierr = SNESSolve(snes, composite_rhs_petsc_vec, composite_sol_petsc_vec);
IBTK_CHKERRQ(ierr);
ierr = SNESDestroy(&snes);
IBTK_CHKERRQ(ierr);
ierr = MatDestroy(&jac);
IBTK_CHKERRQ(ierr);
ierr = MatDestroy(&schur);
IBTK_CHKERRQ(ierr);
ierr = KSPDestroy(&d_schur_solver);
IBTK_CHKERRQ(ierr);
d_ib_implicit_ops->postprocessSolveFluidEquations(current_time, new_time, cycle_num);
// Reset Eulerian solver vectors and Eulerian state data.
ins_hier_integrator->resetSolverVectors(
eul_sol_vec, eul_rhs_vec, current_time, new_time, cycle_num);
// Interpolate the Eulerian velocity to the curvilinear mesh.
d_ib_implicit_ops->setUpdatedPosition(lag_sol_petsc_vec);
#if 0
d_hier_velocity_data_ops->linearSum(d_u_idx, 0.5, u_current_idx, 0.5, u_new_idx);
if (d_enable_logging) plog << d_object_name << "::integrateHierarchy(): interpolating Eulerian velocity to the Lagrangian mesh\n";
d_ib_implicit_ops->interpolateVelocity(d_u_idx, getCoarsenSchedules(d_object_name+"::u::CONSERVATIVE_COARSEN"), getGhostfillRefineSchedules(d_object_name+"::u"), half_time);
// Compute the final value of the updated positions of the Lagrangian
// structure.
d_ib_implicit_ops->midpointStep(current_time, new_time);
#endif
// Deallocate temporary data.
ierr = VecDestroy(&composite_sol_petsc_vec);
IBTK_CHKERRQ(ierr);
ierr = VecDestroy(&composite_rhs_petsc_vec);
IBTK_CHKERRQ(ierr);
ierr = VecDestroy(&composite_res_petsc_vec);
IBTK_CHKERRQ(ierr);
PETScSAMRAIVectorReal::destroyPETScVector(eul_sol_petsc_vec);
PETScSAMRAIVectorReal::destroyPETScVector(eul_rhs_petsc_vec);
eul_rhs_vec->freeVectorComponents();
d_u_scratch_vec->freeVectorComponents();
d_f_scratch_vec->freeVectorComponents();
ierr = VecDestroy(&lag_sol_petsc_vec);
IBTK_CHKERRQ(ierr);
ierr = VecDestroy(&lag_rhs_petsc_vec);
IBTK_CHKERRQ(ierr);
// Execute any registered callbacks.
executeIntegrateHierarchyCallbackFcns(current_time, new_time, cycle_num);
return;
} // integrateHierarchy
int main(int argc,char **args)
{
const PetscScalar xvals[] = {11,13},yvals[] = {17,19},zvals[] = {23,29};
const PetscInt inds[] = {0,1};
PetscScalar avals[] = {2,3,5,7};
Mat A,S,D[4],N;
Vec X,Y,Z;
User user;
PetscInt i;
PetscErrorCode ierr;
PetscInitialize(&argc,&args,(char*)0,help);
ierr = MatCreateSeqAIJ(PETSC_COMM_WORLD,2,2,2,NULL,&A);
CHKERRQ(ierr);
ierr = MatSetUp(A);
CHKERRQ(ierr);
ierr = MatSetValues(A,2,inds,2,inds,avals,INSERT_VALUES);
CHKERRQ(ierr);
ierr = VecCreateSeq(PETSC_COMM_WORLD,2,&X);
CHKERRQ(ierr);
ierr = VecDuplicate(X,&Y);
CHKERRQ(ierr);
ierr = VecDuplicate(X,&Z);
CHKERRQ(ierr);
ierr = VecSetValues(X,2,inds,xvals,INSERT_VALUES);
CHKERRQ(ierr);
ierr = VecSetValues(Y,2,inds,yvals,INSERT_VALUES);
CHKERRQ(ierr);
ierr = VecSetValues(Z,2,inds,zvals,INSERT_VALUES);
CHKERRQ(ierr);
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
ierr = VecAssemblyBegin(X);
CHKERRQ(ierr);
ierr = VecAssemblyBegin(Y);
CHKERRQ(ierr);
ierr = VecAssemblyBegin(Z);
CHKERRQ(ierr);
ierr = VecAssemblyEnd(X);
CHKERRQ(ierr);
ierr = VecAssemblyEnd(Y);
CHKERRQ(ierr);
ierr = VecAssemblyEnd(Z);
CHKERRQ(ierr);
ierr = PetscNew(struct _n_User,&user);
CHKERRQ(ierr);
user->B = A;
ierr = MatCreateShell(PETSC_COMM_WORLD,2,2,2,2,user,&S);
CHKERRQ(ierr);
ierr = MatSetUp(S);
CHKERRQ(ierr);
ierr = MatShellSetOperation(S,MATOP_MULT,(void (*)(void))MatMult_User);
CHKERRQ(ierr);
ierr = MatShellSetOperation(S,MATOP_MULT_TRANSPOSE,(void (*)(void))MatMultTranspose_User);
CHKERRQ(ierr);
ierr = MatShellSetOperation(S,MATOP_GET_DIAGONAL,(void (*)(void))MatGetDiagonal_User);
CHKERRQ(ierr);
for (i=0; i<4; i++) {
ierr = MatCreateSeqDense(PETSC_COMM_WORLD,1,1,&avals[i],&D[i]);
CHKERRQ(ierr);
}
ierr = MatCreateNest(PETSC_COMM_WORLD,2,NULL,2,NULL,D,&N);
CHKERRQ(ierr);
ierr = MatSetUp(N);
CHKERRQ(ierr);
ierr = TestMatrix(S,X,Y,Z);
CHKERRQ(ierr);
ierr = TestMatrix(A,X,Y,Z);
CHKERRQ(ierr);
ierr = TestMatrix(N,X,Y,Z);
CHKERRQ(ierr);
for (i=0; i<4; i++) {
ierr = MatDestroy(&D[i]);
CHKERRQ(ierr);
}
ierr = MatDestroy(&A);
CHKERRQ(ierr);
ierr = MatDestroy(&S);
CHKERRQ(ierr);
ierr = MatDestroy(&N);
CHKERRQ(ierr);
ierr = VecDestroy(&X);
CHKERRQ(ierr);
ierr = VecDestroy(&Y);
CHKERRQ(ierr);
ierr = VecDestroy(&Z);
CHKERRQ(ierr);
ierr = PetscFree(user);
CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
