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mfem/examples/ex19.cpp
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// MFEM Example 19
//
// Compile with: make ex19
//
// Sample runs:
// ex19 -m ../data/beam-quad.mesh
// ex19 -m ../data/beam-tri.mesh
// ex19 -m ../data/beam-hex.mesh
// ex19 -m ../data/beam-tet.mesh
// ex19 -m ../data/beam-wedge.mesh
// ex19 -m ../data/beam-quad-amr.mesh
//
// Description: This examples solves a quasi-static incompressible nonlinear
// elasticity problem of the form 0 = H(x), where H is an
// incompressible hyperelastic model and x is a block state vector
// containing displacement and pressure variables. The geometry of
// the domain is assumed to be as follows:
//
// +---------------------+
// boundary --->| |<--- boundary
// attribute 1 | | attribute 2
// (fixed) +---------------------+ (fixed, nonzero)
//
// The example demonstrates the use of block nonlinear operators
// (the class RubberOperator defining H(x)) as well as a nonlinear
// Newton solver for the quasi-static problem. Each Newton step
// requires the inversion of a Jacobian matrix, which is done
// through a (preconditioned) inner solver. The specialized block
// preconditioner is implemented as a user-defined solver.
//
// We recommend viewing examples 2, 5, and 10 before viewing this
// example.
#include "mfem.hpp"
#include <memory>
#include <iostream>
#include <fstream>
using namespace std;
using namespace mfem;
class GeneralResidualMonitor : public IterativeSolverMonitor
{
public:
GeneralResidualMonitor(const std::string& prefix_, int print_lvl)
: prefix(prefix_)
{
print_level = print_lvl;
}
void MonitorResidual(int it, real_t norm, const Vector &r, bool final) override;
private:
const std::string prefix;
int print_level;
mutable real_t norm0;
};
void GeneralResidualMonitor::MonitorResidual(int it, real_t norm,
const Vector &r, bool final)
{
if ((print_level == 1 && !final) || (print_level == 3 && (final || it == 0)))
{
mfem::out << prefix << " iteration " << setw(2) << it
<< " : ||r|| = " << norm;
if (it > 0)
{
mfem::out << ", ||r||/||r_0|| = " << norm/norm0;
}
else
{
norm0 = norm;
}
mfem::out << '\n';
}
}
// Custom block preconditioner for the Jacobian of the incompressible nonlinear
// elasticity operator. It has the form
//
// P^-1 = [ K^-1 0 ][ I -B^T ][ I 0 ]
// [ 0 I ][ 0 I ][ 0 -\gamma S^-1 ]
//
// where the original Jacobian has the form
//
// J = [ K B^T ]
// [ B 0 ]
//
// and K^-1 is an approximation of the inverse of the displacement part of the
// Jacobian and S^-1 is an approximation of the inverse of the Schur
// complement S = B K^-1 B^T. The Schur complement is approximated using
// a mass matrix of the pressure variables.
class JacobianPreconditioner : public Solver
{
protected:
// Finite element spaces for setting up preconditioner blocks
Array<FiniteElementSpace *> spaces;
// Offsets for extracting block vector segments
Array<int> &block_trueOffsets;
// Jacobian for block access
BlockOperator *jacobian;
// Scaling factor for the pressure mass matrix in the block preconditioner
real_t gamma;
// Objects for the block preconditioner application
SparseMatrix *pressure_mass;
Solver *mass_pcg;
Solver *mass_prec;
Solver *stiff_pcg;
Solver *stiff_prec;
public:
JacobianPreconditioner(Array<FiniteElementSpace *> &fes,
SparseMatrix &mass, Array<int> &offsets);
void Mult(const Vector &k, Vector &y) const override;
void SetOperator(const Operator &op) override;
~JacobianPreconditioner() override;
};
// After spatial discretization, the rubber model can be written as:
// 0 = H(x)
// where x is the block vector representing the deformation and pressure and
// H(x) is the nonlinear incompressible neo-Hookean operator.
class RubberOperator : public Operator
{
protected:
// Finite element spaces
Array<FiniteElementSpace *> spaces;
// Block nonlinear form
BlockNonlinearForm *Hform;
// Pressure mass matrix for the preconditioner
SparseMatrix *pressure_mass;
// Newton solver for the hyperelastic operator
NewtonSolver newton_solver;
GeneralResidualMonitor newton_monitor;
// Solver for the Jacobian solve in the Newton method
Solver *j_solver;
GeneralResidualMonitor j_monitor;
// Preconditioner for the Jacobian
Solver *j_prec;
// Shear modulus coefficient
Coefficient &mu;
// Block offsets for variable access
Array<int> &block_trueOffsets;
public:
RubberOperator(Array<FiniteElementSpace *> &fes, Array<Array<int> *>&ess_bdr,
Array<int> &block_trueOffsets, real_t rel_tol, real_t abs_tol,
int iter, Coefficient &mu);
// Required to use the native newton solver
Operator &GetGradient(const Vector &xp) const override;
void Mult(const Vector &k, Vector &y) const override;
// Driver for the newton solver
void Solve(Vector &xp) const;
~RubberOperator() override;
};
// Visualization driver
void visualize(ostream &os, Mesh *mesh, GridFunction *deformed_nodes,
GridFunction *field, const char *field_name = NULL,
bool init_vis = false);
// Configuration definition functions
void ReferenceConfiguration(const Vector &x, Vector &y);
void InitialDeformation(const Vector &x, Vector &y);
int main(int argc, char *argv[])
{
// 1. Parse command-line options
const char *mesh_file = "../data/beam-tet.mesh";
int ref_levels = 0;
int order = 2;
bool visualization = true;
real_t newton_rel_tol = 1e-4;
real_t newton_abs_tol = 1e-6;
int newton_iter = 500;
real_t mu = 1.0;
OptionsParser args(argc, argv);
args.AddOption(&mesh_file, "-m", "--mesh",
"Mesh file to use.");
args.AddOption(&ref_levels, "-r", "--refine",
"Number of times to refine the mesh uniformly.");
args.AddOption(&order, "-o", "--order",
"Order (degree) of the finite elements.");
args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
"--no-visualization",
"Enable or disable GLVis visualization.");
args.AddOption(&newton_rel_tol, "-rel", "--relative-tolerance",
"Relative tolerance for the Newton solve.");
args.AddOption(&newton_abs_tol, "-abs", "--absolute-tolerance",
"Absolute tolerance for the Newton solve.");
args.AddOption(&newton_iter, "-it", "--newton-iterations",
"Maximum iterations for the Newton solve.");
args.AddOption(&mu, "-mu", "--shear-modulus",
"Shear modulus for the neo-Hookean material.");
args.Parse();
if (!args.Good())
{
args.PrintUsage(cout);
return 1;
}
args.PrintOptions(cout);
// 2. Read the mesh from the given mesh file. We can handle triangular,
// quadrilateral, tetrahedral and hexahedral meshes with the same code.
Mesh *mesh = new Mesh(mesh_file, 1, 1);
int dim = mesh->Dimension();
// 3. Refine the mesh to increase the resolution. In this example we do
// 'ref_levels' of uniform refinement, where 'ref_levels' is a
// command-line parameter.
for (int lev = 0; lev < ref_levels; lev++)
{
mesh->UniformRefinement();
}
// 4. Define the shear modulus for the incompressible Neo-Hookean material
ConstantCoefficient c_mu(mu);
// 5. Define the finite element spaces for displacement and pressure
// (Taylor-Hood elements). By default, the displacement (u/x) is a second
// order vector field, while the pressure (p) is a linear scalar function.
H1_FECollection quad_coll(order, dim);
H1_FECollection lin_coll(order-1, dim);
FiniteElementSpace R_space(mesh, &quad_coll, dim, Ordering::byVDIM);
FiniteElementSpace W_space(mesh, &lin_coll);
Array<FiniteElementSpace *> spaces(2);
spaces[0] = &R_space;
spaces[1] = &W_space;
int R_size = R_space.GetTrueVSize();
int W_size = W_space.GetTrueVSize();
// 6. Define the Dirichlet conditions (set to boundary attribute 1 and 2)
Array<Array<int> *> ess_bdr(2);
Array<int> ess_bdr_u(R_space.GetMesh()->bdr_attributes.Max());
Array<int> ess_bdr_p(W_space.GetMesh()->bdr_attributes.Max());
ess_bdr_p = 0;
ess_bdr_u = 0;
ess_bdr_u[0] = 1;
ess_bdr_u[1] = 1;
ess_bdr[0] = &ess_bdr_u;
ess_bdr[1] = &ess_bdr_p;
// 7. Print the mesh statistics
std::cout << "***********************************************************\n";
std::cout << "dim(u) = " << R_size << "\n";
std::cout << "dim(p) = " << W_size << "\n";
std::cout << "dim(u+p) = " << R_size + W_size << "\n";
std::cout << "***********************************************************\n";
// 8. Define the block structure of the solution vector (u then p)
Array<int> block_trueOffsets(3);
block_trueOffsets[0] = 0;
block_trueOffsets[1] = R_space.GetTrueVSize();
block_trueOffsets[2] = W_space.GetTrueVSize();
block_trueOffsets.PartialSum();
BlockVector xp(block_trueOffsets);
// 9. Define grid functions for the current configuration, reference
// configuration, final deformation, and pressure
GridFunction x_gf(&R_space);
GridFunction x_ref(&R_space);
GridFunction x_def(&R_space);
GridFunction p_gf(&W_space);
x_gf.MakeTRef(&R_space, xp.GetBlock(0), 0);
p_gf.MakeTRef(&W_space, xp.GetBlock(1), 0);
VectorFunctionCoefficient deform(dim, InitialDeformation);
VectorFunctionCoefficient refconfig(dim, ReferenceConfiguration);
x_gf.ProjectCoefficient(deform);
x_ref.ProjectCoefficient(refconfig);
p_gf = 0.0;
x_gf.SetTrueVector();
p_gf.SetTrueVector();
// 10. Initialize the incompressible neo-Hookean operator
RubberOperator oper(spaces, ess_bdr, block_trueOffsets,
newton_rel_tol, newton_abs_tol, newton_iter, c_mu);
// 11. Solve the Newton system
oper.Solve(xp);
// 12. Compute the final deformation
x_gf.SetFromTrueVector();
p_gf.SetFromTrueVector();
subtract(x_gf, x_ref, x_def);
// 13. Visualize the results if requested
socketstream vis_u, vis_p;
if (visualization)
{
char vishost[] = "localhost";
int visport = 19916;
vis_u.open(vishost, visport);
vis_u.precision(8);
visualize(vis_u, mesh, &x_gf, &x_def, "Deformation", true);
vis_p.open(vishost, visport);
vis_p.precision(8);
visualize(vis_p, mesh, &x_gf, &p_gf, "Pressure", true);
}
// 14. Save the displaced mesh, the final deformation, and the pressure
{
GridFunction *nodes = &x_gf;
int owns_nodes = 0;
mesh->SwapNodes(nodes, owns_nodes);
ofstream mesh_ofs("deformed.mesh");
mesh_ofs.precision(8);
mesh->Print(mesh_ofs);
ofstream pressure_ofs("pressure.sol");
pressure_ofs.precision(8);
p_gf.Save(pressure_ofs);
ofstream deformation_ofs("deformation.sol");
deformation_ofs.precision(8);
x_def.Save(deformation_ofs);
}
// 15. Free the used memory
delete mesh;
return 0;
}
JacobianPreconditioner::JacobianPreconditioner(Array<FiniteElementSpace *> &fes,
SparseMatrix &mass,
Array<int> &offsets)
: Solver(offsets[2]), block_trueOffsets(offsets), pressure_mass(&mass)
{
fes.Copy(spaces);
gamma = 0.00001;
// The mass matrix and preconditioner do not change every Newton cycle, so we
// only need to define them once
GSSmoother *mass_prec_gs = new GSSmoother(*pressure_mass);
mass_prec = mass_prec_gs;
CGSolver *mass_pcg_iter = new CGSolver();
mass_pcg_iter->SetRelTol(1e-12);
mass_pcg_iter->SetAbsTol(1e-12);
mass_pcg_iter->SetMaxIter(200);
mass_pcg_iter->SetPrintLevel(0);
mass_pcg_iter->SetPreconditioner(*mass_prec);
mass_pcg_iter->SetOperator(*pressure_mass);
mass_pcg_iter->iterative_mode = false;
mass_pcg = mass_pcg_iter;
// The stiffness matrix does change every Newton cycle, so we will define it
// during SetOperator
stiff_pcg = NULL;
stiff_prec = NULL;
}
void JacobianPreconditioner::Mult(const Vector &k, Vector &y) const
{
// Extract the blocks from the input and output vectors
Vector disp_in(k.GetData() + block_trueOffsets[0],
block_trueOffsets[1]-block_trueOffsets[0]);
Vector pres_in(k.GetData() + block_trueOffsets[1],
block_trueOffsets[2]-block_trueOffsets[1]);
Vector disp_out(y.GetData() + block_trueOffsets[0],
block_trueOffsets[1]-block_trueOffsets[0]);
Vector pres_out(y.GetData() + block_trueOffsets[1],
block_trueOffsets[2]-block_trueOffsets[1]);
Vector temp(block_trueOffsets[1]-block_trueOffsets[0]);
Vector temp2(block_trueOffsets[1]-block_trueOffsets[0]);
// Perform the block elimination for the preconditioner
mass_pcg->Mult(pres_in, pres_out);
pres_out *= -gamma;
jacobian->GetBlock(0,1).Mult(pres_out, temp);
subtract(disp_in, temp, temp2);
stiff_pcg->Mult(temp2, disp_out);
}
void JacobianPreconditioner::SetOperator(const Operator &op)
{
jacobian = (BlockOperator *) &op;
// Initialize the stiffness preconditioner and solver
if (stiff_prec == NULL)
{
GSSmoother *stiff_prec_gs = new GSSmoother();
stiff_prec = stiff_prec_gs;
GMRESSolver *stiff_pcg_iter = new GMRESSolver();
stiff_pcg_iter->SetRelTol(1e-8);
stiff_pcg_iter->SetAbsTol(1e-8);
stiff_pcg_iter->SetMaxIter(200);
stiff_pcg_iter->SetPrintLevel(0);
stiff_pcg_iter->SetPreconditioner(*stiff_prec);
stiff_pcg_iter->iterative_mode = false;
stiff_pcg = stiff_pcg_iter;
}
// At each Newton cycle, compute the new stiffness preconditioner by updating
// the iterative solver which, in turn, updates its preconditioner
stiff_pcg->SetOperator(jacobian->GetBlock(0,0));
}
JacobianPreconditioner::~JacobianPreconditioner()
{
delete mass_pcg;
delete mass_prec;
delete stiff_prec;
delete stiff_pcg;
}
RubberOperator::RubberOperator(Array<FiniteElementSpace *> &fes,
Array<Array<int> *> &ess_bdr,
Array<int> &offsets,
real_t rel_tol,
real_t abs_tol,
int iter,
Coefficient &c_mu)
: Operator(fes[0]->GetTrueVSize() + fes[1]->GetTrueVSize()),
newton_solver(), newton_monitor("Newton", 1),
j_monitor(" GMRES", 3), mu(c_mu), block_trueOffsets(offsets)
{
Array<Vector *> rhs(2);
rhs = NULL; // Set all entries in the array
fes.Copy(spaces);
// Define the block nonlinear form
Hform = new BlockNonlinearForm(spaces);
// Add the incompressible neo-Hookean integrator
Hform->AddDomainIntegrator(new IncompressibleNeoHookeanIntegrator(mu));
// Set the essential boundary conditions
Hform->SetEssentialBC(ess_bdr, rhs);
// Compute the pressure mass stiffness matrix
BilinearForm *a = new BilinearForm(spaces[1]);
ConstantCoefficient one(1.0);
a->AddDomainIntegrator(new MassIntegrator(one));
a->Assemble();
a->Finalize();
OperatorPtr op;
Array<int> p_ess_tdofs;
a->FormSystemMatrix(p_ess_tdofs, op);
pressure_mass = a->LoseMat();
delete a;
// Initialize the Jacobian preconditioner
JacobianPreconditioner *jac_prec =
new JacobianPreconditioner(fes, *pressure_mass, block_trueOffsets);
j_prec = jac_prec;
// Set up the Jacobian solver
GMRESSolver *j_gmres = new GMRESSolver();
j_gmres->iterative_mode = false;
j_gmres->SetRelTol(1e-12);
j_gmres->SetAbsTol(1e-12);
j_gmres->SetMaxIter(300);
j_gmres->SetPrintLevel(-1);
j_gmres->SetMonitor(j_monitor);
j_gmres->SetPreconditioner(*j_prec);
j_solver = j_gmres;
// Set the newton solve parameters
newton_solver.iterative_mode = true;
newton_solver.SetSolver(*j_solver);
newton_solver.SetOperator(*this);
newton_solver.SetPrintLevel(-1);
newton_solver.SetMonitor(newton_monitor);
newton_solver.SetRelTol(rel_tol);
newton_solver.SetAbsTol(abs_tol);
newton_solver.SetMaxIter(iter);
}
// Solve the Newton system
void RubberOperator::Solve(Vector &xp) const
{
Vector zero;
newton_solver.Mult(zero, xp);
MFEM_VERIFY(newton_solver.GetConverged(),
"Newton Solver did not converge.");
}
// compute: y = H(x,p)
void RubberOperator::Mult(const Vector &k, Vector &y) const
{
Hform->Mult(k, y);
}
// Compute the Jacobian from the nonlinear form
Operator &RubberOperator::GetGradient(const Vector &xp) const
{
return Hform->GetGradient(xp);
}
RubberOperator::~RubberOperator()
{
delete Hform;
delete pressure_mass;
delete j_solver;
delete j_prec;
}
// Inline visualization
void visualize(ostream &os, Mesh *mesh, GridFunction *deformed_nodes,
GridFunction *field, const char *field_name, bool init_vis)
{
if (!os)
{
return;
}
GridFunction *nodes = deformed_nodes;
int owns_nodes = 0;
mesh->SwapNodes(nodes, owns_nodes);
os << "solution\n" << *mesh << *field;
mesh->SwapNodes(nodes, owns_nodes);
if (init_vis)
{
os << "window_size 800 800\n";
os << "window_title '" << field_name << "'\n";
if (mesh->SpaceDimension() == 2)
{
os << "view 0 0\n"; // view from top
// turn off perspective and light, +anti-aliasing
os << "keys jlA\n";
}
os << "keys cmA\n"; // show colorbar and mesh, +anti-aliasing
// update value-range; keep mesh-extents fixed
os << "autoscale value\n";
}
os << flush;
}
void ReferenceConfiguration(const Vector &x, Vector &y)
{
// Set the reference, stress free, configuration
y = x;
}
void InitialDeformation(const Vector &x, Vector &y)
{
// Set the initial configuration. Having this different from the reference
// configuration can help convergence
y = x;
y[1] = x[1] + 0.25*x[0];
}
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