ComputeFullJacobianThread::ComputeFullJacobianThread(FEProblem & fe_problem, NonlinearSystem & sys, SparseMatrix<Number> & jacobian) :
ComputeJacobianThread(fe_problem, sys, jacobian),
_integrated_bcs(sys.getIntegratedBCWarehouse()),
_dg_kernels(sys.getDGKernelWarehouse()),
_kernels(sys.getKernelWarehouse())
{
}
ComputeJacobianThread::ComputeJacobianThread(FEProblem & fe_problem, NonlinearSystem & sys, SparseMatrix<Number> & jacobian) :
ThreadedElementLoop<ConstElemRange>(fe_problem, sys),
_jacobian(jacobian),
_sys(sys),
_num_cached(0),
_integrated_bcs(sys.getIntegratedBCWarehouse()),
_dg_kernels(sys.getDGKernelWarehouse()),
_interface_kernels(sys.getInterfaceKernelWarehouse()),
_kernels(sys.getKernelWarehouse())
{
}
void petscSetupDM (NonlinearSystem & nl) {
#if !PETSC_VERSION_LESS_THAN(3,3,0)
PetscErrorCode ierr;
// Initialize the part of the DM package that's packaged with Moose; in the PETSc source tree this call would be in DMInitializePackage()
ierr = DMMooseRegisterAll();
CHKERRABORT(nl.comm().get(),ierr);
// Create and set up the DM that will consume the split options and deal with block matrices.
PetscNonlinearSolver<Number> *petsc_solver = dynamic_cast<PetscNonlinearSolver<Number> *>(nl.sys().nonlinear_solver.get());
SNES snes = petsc_solver->snes();
/* FIXME: reset the DM, do not recreate it anew every time? */
DM dm = PETSC_NULL;
ierr = DMCreateMoose(nl.comm().get(), nl, &dm);
CHKERRABORT(nl.comm().get(),ierr);
ierr = DMSetFromOptions(dm);
CHKERRABORT(nl.comm().get(),ierr);
ierr = DMSetUp(dm);
CHKERRABORT(nl.comm().get(),ierr);
ierr = SNESSetDM(snes,dm);
CHKERRABORT(nl.comm().get(),ierr);
ierr = DMDestroy(&dm);
CHKERRABORT(nl.comm().get(),ierr);
ierr = SNESSetUpdate(snes,SNESUpdateDMMoose);
CHKERRABORT(nl.comm().get(),ierr);
#endif
}
ComputeDampingThread::ComputeDampingThread(FEProblem & feproblem,
NonlinearSystem & sys) :
ThreadedElementLoop<ConstElemRange>(feproblem, sys),
_damping(1.0),
_nl(sys),
_dampers(sys.getDamperWarehouse())
{
}
void
petscSetupDM (NonlinearSystem & nl) {
#if !PETSC_VERSION_LESS_THAN(3,3,0)
PetscErrorCode ierr;
PetscBool ismoose;
DM dm = PETSC_NULL;
// Initialize the part of the DM package that's packaged with Moose; in the PETSc source tree this call would be in DMInitializePackage()
ierr = DMMooseRegisterAll();
CHKERRABORT(nl.comm().get(),ierr);
// Create and set up the DM that will consume the split options and deal with block matrices.
PetscNonlinearSolver<Number> *petsc_solver = dynamic_cast<PetscNonlinearSolver<Number> *>(nl.sys().nonlinear_solver.get());
SNES snes = petsc_solver->snes();
// if there exists a DMMoose object, not to recreate a new one
ierr = SNESGetDM(snes, &dm);
CHKERRABORT(nl.comm().get(), ierr);
if (dm)
{
ierr = PetscObjectTypeCompare((PetscObject)dm, DMMOOSE, &ismoose);
CHKERRABORT(nl.comm().get(), ierr);
if (ismoose)
return;
}
ierr = DMCreateMoose(nl.comm().get(), nl, &dm);
CHKERRABORT(nl.comm().get(),ierr);
ierr = DMSetFromOptions(dm);
CHKERRABORT(nl.comm().get(),ierr);
ierr = DMSetUp(dm);
CHKERRABORT(nl.comm().get(),ierr);
ierr = SNESSetDM(snes,dm);
CHKERRABORT(nl.comm().get(),ierr);
ierr = DMDestroy(&dm);
CHKERRABORT(nl.comm().get(),ierr);
// We temporarily comment out this updating function because
// we lack an approach to check if the problem
// structure has been changed from the last iteration.
// The indices will be rebuilt for every timestep.
// TODO: figure out a way to check the structure changes of the
// matrix
// ierr = SNESSetUpdate(snes,SNESUpdateDMMoose);
// CHKERRABORT(nl.comm().get(),ierr);
#endif
}
ComputeResidualThread::ComputeResidualThread(FEProblem & fe_problem, NonlinearSystem & sys, Moose::KernelType type) :
ThreadedElementLoop<ConstElemRange>(fe_problem, sys),
_sys(sys),
_kernel_type(type),
_num_cached(0),
_integrated_bcs(sys.getIntegratedBCWarehouse()),
_dg_kernels(sys.getDGKernelWarehouse()),
_interface_kernels(sys.getInterfaceKernelWarehouse()),
_kernels(sys.getKernelWarehouse()),
_time_kernels(sys.getTimeKernelWarehouse()),
_non_time_kernels(sys.getNonTimeKernelWarehouse())
{
}
int main( )
{
const size_t systemSize = 2;
// Declare equations of system.
NonlinearSystem<systemSize> sys;
equation_type eq1 = []( const vector_type& x) {
return 1.0 - x[0];
};
sys.assign_equation( eq1, 0);
equation_type eq2 = []( const vector_type& x) {
return 10 * (x[1] - x[0] * x[0] );
};
sys.assign_equation( eq2, 1 );
// Now intialize the system with initial input vector x..
array<double, systemSize> init = { -10, -5 };
sys.initialize( init );
cout << sys.to_string() << endl;
sys.find_roots_gnewton( );
cout << sys.to_string() << endl;
// Another system
eq1 = []( const vector_type& x) {
return 1.0 - sin(x[0]);
};
sys.assign_equation( eq1, 0);
eq2 = []( const vector_type& x) {
return 10 * cos(x[1]);
};
sys.assign_equation( eq2, 1 );
// Now intialize the system with initial input vector x..
init = { -10, -5 };
sys.initialize( init );
cout << sys.to_string() << endl;
sys.find_roots_gnewton( );
cout << sys.to_string() << endl;
cerr << " A system with 3-dimen" << endl;
NonlinearSystem<3> sys3;
equation_type e1 = []( const vector_type& x) {
return 3*x[0] - cos( x[1] * x[2] ) - 1.5;
};
equation_type e2 = []( const vector_type& x) {
return 4*x[0]*x[0] - 625* x[1] * x[1] + 2*x[1]- 1;
};
equation_type e3 = []( const vector_type& x) {
return exp(- x[0] * x[1]) + 20 * x[2] + (31.1416 - 3)/3 ;
};
sys3.assign_equation( e1, 0 );
sys3.assign_equation( e2, 1 );
sys3.assign_equation( e3, 2 );
array< double, 3> init3 = {{ 0.0, 0.0, 0.0 }};
sys3.initialize( init3 );
sys3.find_roots_gnewton( );
cout << sys3.to_string() << endl;
// Another system
NonlinearSystem<2> sA;
return 0;
}