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/* The Next Great Finite Element Library. */
/* Copyright (C) 2003 Benjamin S. Kirk */
/* This library is free software; you can redistribute it and/or */
/* modify it under the terms of the GNU Lesser General Public */
/* License as published by the Free Software Foundation; either */
/* version 2.1 of the License, or (at your option) any later version. */
/* This library is distributed in the hope that it will be useful, */
/* but WITHOUT ANY WARRANTY; without even the implied warranty of */
/* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU */
/* Lesser General Public License for more details. */
/* You should have received a copy of the GNU Lesser General Public */
/* License along with this library; if not, write to the Free Software */
/* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA */
// <h1>Miscellaneous Example 4 - Using a shell matrix</h1>
//
// This example solves the equation
//
// \f$-\Delta u+\int u = 1\f$
//
// with homogeneous Dirichlet boundary conditions. This system has
// a full system matrix which can be written as the sum of of sparse
// matrix and a rank 1 matrix. The shell matrix concept is used to
// solve this problem.
//
// The problem is solved in parallel on a non-uniform grid in order
// to demonstrate all the techniques that are required for this.
// The grid is fixed, however, i.e. no adaptive mesh refinement is
// used, so that the example remains simple.
//
// The example is 2d; extension to 3d is straight forward.
// C++ include files that we need
#include <iostream>
#include <algorithm>
#include <cstdlib> // *must* precede <cmath> for proper std:abs() on PGI, Sun Studio CC
#include <cmath>
// Basic include file needed for the mesh functionality.
#include "libmesh/libmesh.h"
#include "libmesh/mesh.h"
#include "libmesh/mesh_refinement.h"
#include "libmesh/vtk_io.h"
#include "libmesh/equation_systems.h"
#include "libmesh/fe.h"
#include "libmesh/quadrature_gauss.h"
#include "libmesh/dof_map.h"
#include "libmesh/sparse_matrix.h"
#include "libmesh/numeric_vector.h"
#include "libmesh/dense_matrix.h"
#include "libmesh/dense_vector.h"
#include "libmesh/mesh_generation.h"
#include "libmesh/sum_shell_matrix.h"
#include "libmesh/tensor_shell_matrix.h"
#include "libmesh/sparse_shell_matrix.h"
#include "libmesh/mesh_refinement.h"
#include "libmesh/getpot.h"
// This example will solve a linear transient system,
// so we need to include the \p TransientLinearImplicitSystem definition.
#include "libmesh/transient_system.h"
#include "libmesh/linear_implicit_system.h"
#include "libmesh/vector_value.h"
// The definition of a geometric element
#include "libmesh/elem.h"
// Bring in everything from the libMesh namespace
using namespace libMesh;
// Function prototype. This function will assemble the system matrix
// and right-hand-side.
void assemble (EquationSystems& es,
const std::string& system_name);
// Begin the main program. Note that the first
// statement in the program throws an error if
// you are in complex number mode, since this
// example is only intended to work with real
// numbers.
int main (int argc, char** argv)
{
// Initialize libMesh.
LibMeshInit init (argc, argv);
#if !defined(LIBMESH_ENABLE_AMR)
libmesh_example_assert(false, "--enable-amr");
#else
libmesh_example_assert(libMesh::default_solver_package() == PETSC_SOLVERS, "--enable-petsc");
// Brief message to the user regarding the program name
// and command line arguments.
std::cout << "Running: " << argv[0];
for (int i=1; i<argc; i++)
std::cout << " " << argv[i];
std::cout << std::endl << std::endl;
// Skip this 2D example if libMesh was compiled as 1D-only.
libmesh_example_assert(2 <= LIBMESH_DIM, "2D support");
// Create a mesh
Mesh mesh;
// Create an equation systems object.
EquationSystems equation_systems (mesh);
MeshRefinement mesh_refinement (mesh);
MeshTools::Generation::build_square (mesh,
16,
16,
-1., 1.,
-1., 1.,
QUAD4);
LinearImplicitSystem & system =
equation_systems.add_system<LinearImplicitSystem>
("System");
// Adds the variable "u" to "System". "u"
// will be approximated using first-order approximation.
system.add_variable ("u", FIRST);
// Also, we need to add two vectors. The tensor matrix v*w^T of
// these two vectors will be part of the system matrix.
system.add_vector("v",false);
system.add_vector("w",false);
// We need an additional matrix to be used for preconditioning since
// a shell matrix is not suitable for that.
system.add_matrix("Preconditioner");
// Give the system a pointer to the matrix assembly function.
system.attach_assemble_function (assemble);
// Initialize the data structures for the equation system.
equation_systems.init ();
// Prints information about the system to the screen.
equation_systems.print_info();
equation_systems.parameters.set<unsigned int>
("linear solver maximum iterations") = 250;
equation_systems.parameters.set<Real>
("linear solver tolerance") = TOLERANCE;
// Refine arbitrarily some elements.
for(unsigned int i=0; i<2; i++)
{
MeshRefinement mesh_refinement(mesh);
MeshBase::element_iterator elem_it = mesh.elements_begin();
const MeshBase::element_iterator elem_end = mesh.elements_end();
for (; elem_it != elem_end; ++elem_it)
{
Elem* elem = *elem_it;
if(elem->active())
{
if((elem->id()%20)>8)
{
elem->set_refinement_flag(Elem::REFINE);
}
else
{
elem->set_refinement_flag(Elem::DO_NOTHING);
}
}
else
{
elem->set_refinement_flag(Elem::INACTIVE);
}
}
mesh_refinement.refine_elements();
equation_systems.reinit();
}
// Prints information about the system to the screen.
equation_systems.print_info();
// Before the assemblation of the matrix, we have to clear the two
// vectors that form the tensor matrix (since this is not performed
// automatically).
system.get_vector("v").init(system.n_dofs(), system.n_local_dofs());
system.get_vector("w").init(system.n_dofs(), system.n_local_dofs());
// We need a shell matrix to solve. There is currently no way to
// store the shell matrix in the system. We just create it locally
// here (a shell matrix does not occupy much memory).
SumShellMatrix<Number> shellMatrix;
TensorShellMatrix<Number> shellMatrix0(system.get_vector("v"),system.get_vector("w"));
shellMatrix.matrices.push_back(&shellMatrix0);
SparseShellMatrix<Number> shellMatrix1(*system.matrix);
shellMatrix.matrices.push_back(&shellMatrix1);
// Attach that to the system.
system.attach_shell_matrix(&shellMatrix);
// Reset the preconditioning matrix to zero (for the system matrix,
// the same thing is done automatically).
system.get_matrix("Preconditioner").zero();
// Assemble & solve the linear system
system.solve();
// Detach the shell matrix from the system since it will go out of
// scope. Nobody should solve the system outside this function.
system.detach_shell_matrix();
// Print a nice message.
std::cout << "Solved linear system in " << system.n_linear_iterations() << " iterations, residual norm is " << system.final_linear_residual() << "." << std::endl;
#if defined(LIBMESH_HAVE_VTK) && !defined(LIBMESH_ENABLE_PARMESH)
// Write result to file.
VTKIO(mesh).write_equation_systems ("out.pvtu", equation_systems);
#endif // #ifdef LIBMESH_HAVE_VTK
#endif // #ifndef LIBMESH_ENABLE_AMR
return 0;
}
// This function defines the assembly routine. It is responsible for
// computing the proper matrix entries for the element stiffness
// matrices and right-hand sides.
void assemble (EquationSystems& es,
const std::string& system_name)
{
#ifdef LIBMESH_ENABLE_AMR
// It is a good idea to make sure we are assembling
// the proper system.
libmesh_assert_equal_to (system_name, "System");
// Get a constant reference to the mesh object.
const MeshBase& mesh = es.get_mesh();
// The dimension that we are running
const unsigned int dim = mesh.mesh_dimension();
// Get a reference to the Convection-Diffusion system object.
LinearImplicitSystem & system =
es.get_system<LinearImplicitSystem> ("System");
// Get the Finite Element type for the first (and only)
// variable in the system.
FEType fe_type = system.variable_type(0);
// Build a Finite Element object of the specified type. Since the
// \p FEBase::build() member dynamically creates memory we will
// store the object as an \p AutoPtr<FEBase>. This can be thought
// of as a pointer that will clean up after itself.
AutoPtr<FEBase> fe (FEBase::build(dim, fe_type));
AutoPtr<FEBase> fe_face (FEBase::build(dim, fe_type));
// A Gauss quadrature rule for numerical integration.
// Let the \p FEType object decide what order rule is appropriate.
QGauss qrule (dim, fe_type.default_quadrature_order());
QGauss qface (dim-1, fe_type.default_quadrature_order());
// Tell the finite element object to use our quadrature rule.
fe->attach_quadrature_rule (&qrule);
fe_face->attach_quadrature_rule (&qface);
// Here we define some references to cell-specific data that
// will be used to assemble the linear system. We will start
// with the element Jacobian * quadrature weight at each integration point.
const std::vector<Real>& JxW = fe->get_JxW();
const std::vector<Real>& JxW_face = fe_face->get_JxW();
// The element shape functions evaluated at the quadrature points.
const std::vector<std::vector<Real> >& phi = fe->get_phi();
const std::vector<std::vector<Real> >& psi = fe_face->get_phi();
// The element shape function gradients evaluated at the quadrature
// points.
const std::vector<std::vector<RealGradient> >& dphi = fe->get_dphi();
// The XY locations of the quadrature points used for face integration
//const std::vector<Point>& qface_points = fe_face->get_xyz();
// A reference to the \p DofMap object for this system. The \p DofMap
// object handles the index translation from node and element numbers
// to degree of freedom numbers. We will talk more about the \p DofMap
// in future examples.
const DofMap& dof_map = system.get_dof_map();
// Define data structures to contain the element matrix
// and right-hand-side vector contribution. Following
// basic finite element terminology we will denote these
// "Ke" and "Fe".
DenseMatrix<Number> Ke;
DenseVector<Number> Fe;
// Analogous data structures for thw two vectors v and w that form
// the tensor shell matrix.
DenseVector<Number> Ve;
DenseVector<Number> We;
// This vector will hold the degree of freedom indices for
// the element. These define where in the global system
// the element degrees of freedom get mapped.
std::vector<unsigned int> dof_indices;
// Now we will loop over all the elements in the mesh that
// live on the local processor. We will compute the element
// matrix and right-hand-side contribution. Since the mesh
// will be refined we want to only consider the ACTIVE elements,
// hence we use a variant of the \p active_elem_iterator.
MeshBase::const_element_iterator el = mesh.active_local_elements_begin();
const MeshBase::const_element_iterator end_el = mesh.active_local_elements_end();
for ( ; el != end_el; ++el)
{
// Store a pointer to the element we are currently
// working on. This allows for nicer syntax later.
const Elem* elem = *el;
// Get the degree of freedom indices for the
// current element. These define where in the global
// matrix and right-hand-side this element will
// contribute to.
dof_map.dof_indices (elem, dof_indices);
// Compute the element-specific data for the current
// element. This involves computing the location of the
// quadrature points (q_point) and the shape functions
// (phi, dphi) for the current element.
fe->reinit (elem);
// Zero the element matrix and right-hand side before
// summing them. We use the resize member here because
// the number of degrees of freedom might have changed from
// the last element. Note that this will be the case if the
// element type is different (i.e. the last element was a
// triangle, now we are on a quadrilateral).
Ke.resize (dof_indices.size(),
dof_indices.size());
Fe.resize (dof_indices.size());
Ve.resize (dof_indices.size());
We.resize (dof_indices.size());
// Now we will build the element matrix and right-hand-side.
// Constructing the RHS requires the solution and its
// gradient from the previous timestep. This myst be
// calculated at each quadrature point by summing the
// solution degree-of-freedom values by the appropriate
// weight functions.
for (unsigned int qp=0; qp<qrule.n_points(); qp++)
{
// Now compute the element matrix and RHS contributions.
for (unsigned int i=0; i<phi.size(); i++)
{
// The RHS contribution
Fe(i) += JxW[qp]*(
phi[i][qp]
);
for (unsigned int j=0; j<phi.size(); j++)
{
// The matrix contribution
Ke(i,j) += JxW[qp]*(
// Stiffness matrix
(dphi[i][qp]*dphi[j][qp])
);
}
// V and W are the same for this example.
Ve(i) += JxW[qp]*(
phi[i][qp]
);
We(i) += JxW[qp]*(
phi[i][qp]
);
}
}
// At this point the interior element integration has
// been completed. However, we have not yet addressed
// boundary conditions. For this example we will only
// consider simple Dirichlet boundary conditions imposed
// via the penalty method.
//
// The following loops over the sides of the element.
// If the element has no neighbor on a side then that
// side MUST live on a boundary of the domain.
{
// The penalty value.
const Real penalty = 1.e10;
// The following loops over the sides of the element.
// If the element has no neighbor on a side then that
// side MUST live on a boundary of the domain.
for (unsigned int s=0; s<elem->n_sides(); s++)
if (elem->neighbor(s) == NULL)
{
fe_face->reinit(elem,s);
for (unsigned int qp=0; qp<qface.n_points(); qp++)
{
// Matrix contribution
for (unsigned int i=0; i<psi.size(); i++)
for (unsigned int j=0; j<psi.size(); j++)
Ke(i,j) += penalty*JxW_face[qp]*psi[i][qp]*psi[j][qp];
}
}
}
// We have now built the element matrix and RHS vector in terms
// of the element degrees of freedom. However, it is possible
// that some of the element DOFs are constrained to enforce
// solution continuity, i.e. they are not really "free". We need
// to constrain those DOFs in terms of non-constrained DOFs to
// ensure a continuous solution. The
// \p DofMap::constrain_element_matrix_and_vector() method does
// just that.
// However, constraining both the sparse matrix (and right hand
// side) plus the rank 1 matrix is tricky. The dof_indices
// vector has to be backuped for that because the constraining
// functions modify it.
std::vector<unsigned int> dof_indices_backup(dof_indices);
dof_map.constrain_element_matrix_and_vector (Ke, Fe, dof_indices);
dof_indices = dof_indices_backup;
dof_map.constrain_element_dyad_matrix(Ve,We,dof_indices);
// The element matrix and right-hand-side are now built
// for this element. Add them to the global matrix and
// right-hand-side vector. The \p SparseMatrix::add_matrix()
// and \p NumericVector::add_vector() members do this for us.
system.matrix->add_matrix (Ke, dof_indices);
system.get_matrix("Preconditioner").add_matrix (Ke, dof_indices);
system.rhs->add_vector (Fe, dof_indices);
system.get_vector("v").add_vector(Ve,dof_indices);
system.get_vector("w").add_vector(We,dof_indices);
}
// Finished computing the sytem matrix and right-hand side.
// Matrices and vectors must be closed manually. This is necessary
// because the matrix is not directly used as the system matrix (in
// which case the solver closes it) but as a part of a shell matrix.
system.matrix->close();
system.get_matrix("Preconditioner").close();
system.rhs->close();
system.get_vector("v").close();
system.get_vector("w").close();
#endif // #ifdef LIBMESH_ENABLE_AMR
}
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