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b4eca8bbda6252ce549d5d05feec85e30eff7b03
mfem/examples/ex19p.cpp
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546 lines
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C++
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#include "mfem.hpp"
#include <memory>
#include <iostream>
#include <fstream>
using namespace std;
using namespace mfem;
class JacobianPreconditioner : public Solver
{
protected:
mutable BlockOperator *Jacobian;
mutable Operator *Pressure_mass;
mutable double gamma;
/// Newton solver for the hyperelastic operator
mutable Solver *mass_pcg;
mutable Solver *stiff_prec;
mutable Solver *mass_prec;
Array<int> &block_trueOffsets;
Array<Array<int> *> &ess_bdr;
public:
JacobianPreconditioner(Operator &mass, Array<int> &offsets,
Array<Array<int> *> &bdr);
virtual void Mult(const Vector &k, Vector &y) const;
virtual void SetOperator(const Operator &op);
virtual ~JacobianPreconditioner();
};
/** 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:
Array<ParFiniteElementSpace *> spaces;
ParBlockNonlinearForm *Hform;
mutable Operator *Jacobian;
const BlockVector *x;
Operator *Pressure_mass;
/// Newton solver for the hyperelastic operator
NewtonSolver newton_solver;
/// Solver for the Jacobian solve in the Newton method
Solver *J_solver;
Solver *J_solver_direct;
/// Preconditioner for the Jacobian
Solver *J_prec;
Coefficient &mu;
Array<int> &block_trueOffsets;
public:
RubberOperator(Array<ParFiniteElementSpace *> &fes, Array<Array<int> *>&ess_bdr,
Array<int> &block_trueOffsets, double rel_tol, double abs_tol, int iter,
Coefficient &mu);
/// Required to use the native newton solver
virtual Operator &GetGradient(const Vector &xp) const;
virtual void Mult(const Vector &k, Vector &y) const;
/// Driver for the newton solver
void Solve(Vector &xp) const;
virtual ~RubberOperator();
};
void visualize(ostream &out, ParMesh *mesh, ParGridFunction *deformed_nodes,
ParGridFunction *field, const char *field_name = NULL,
bool init_vis = false);
void ReferenceConfiguration(const Vector &x, Vector &y);
void InitialDeformation(const Vector &x, Vector &y);
int main(int argc, char *argv[])
{
// Initialize MPI.
int num_procs, myid;
MPI_Init(&argc, &argv);
MPI_Comm_size(MPI_COMM_WORLD, &num_procs);
MPI_Comm_rank(MPI_COMM_WORLD, &myid);
// Parse command-line options.
const char *mesh_file = "../data/beam-hex.mesh";
int ser_ref_levels = 0;
int par_ref_levels = 0;
int order = 2;
bool visualization = true;
double newton_rel_tol = 1.0e-6;
double newton_abs_tol = 1.0e-8;
int newton_iter = 500;
double mu = 1.0;
OptionsParser args(argc, argv);
args.AddOption(&mesh_file, "-m", "--mesh",
"Mesh file to use.");
args.AddOption(&ser_ref_levels, "-rs", "--refine-serial",
"Number of times to refine the mesh uniformly in serial.");
args.AddOption(&par_ref_levels, "-rp", "--refine-parallel",
"Number of times to refine the mesh uniformly in parallel.");
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())
{
if (myid == 0)
{
args.PrintUsage(cout);
}
MPI_Finalize();
return 1;
}
if (myid == 0)
{
args.PrintOptions(cout);
}
// Open the mesh
Mesh *mesh;
ifstream imesh(mesh_file);
if (!imesh)
{
if (myid == 0)
{
cerr << "\nCan not open mesh file: " << mesh_file << '\n' << endl;
}
MPI_Finalize();
return 2;
}
mesh = new Mesh(imesh, 1, 1);
imesh.close();
ParMesh *pmesh = NULL;
for (int lev = 0; lev < ser_ref_levels; lev++)
{
mesh->UniformRefinement();
}
pmesh = new ParMesh(MPI_COMM_WORLD, *mesh);
for (int lev = 0; lev < par_ref_levels; lev++)
{
pmesh->UniformRefinement();
}
delete mesh;
int dim = pmesh->Dimension();
ConstantCoefficient c_mu(mu);
// Definie the finite element spaces for displacement and pressure (Stokes elements)
H1_FECollection quad_coll(order, dim);
H1_FECollection lin_coll(order-1, dim);
ParFiniteElementSpace R_space(pmesh, &quad_coll, dim);
ParFiniteElementSpace W_space(pmesh, &lin_coll);
Array<ParFiniteElementSpace *> spaces(2);
spaces[0] = &R_space;
spaces[1] = &W_space;
HYPRE_Int glob_R_size = R_space.GlobalTrueVSize();
HYPRE_Int glob_W_size = W_space.GlobalTrueVSize();
// Define the Dirichlet conditions (set to boundary attribute 1)
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;
// Print the mesh statistics
if (myid == 0)
{
std::cout << "***********************************************************\n";
std::cout << "dim(u) = " << glob_R_size << "\n";
std::cout << "dim(p) = " << glob_W_size << "\n";
std::cout << "dim(u+p) = " << glob_R_size + glob_W_size << "\n";
std::cout << "***********************************************************\n";
}
// Define the block structure of the solution vector (u then p)
Array<int> block_offsets(3);
block_offsets[0] = 0;
block_offsets[1] = R_space.GetVSize();
block_offsets[2] = W_space.GetVSize();
block_offsets.PartialSum();
Array<int> block_trueOffsets(3);
block_trueOffsets[0] = 0;
block_trueOffsets[1] = R_space.TrueVSize();
block_trueOffsets[2] = W_space.TrueVSize();
block_trueOffsets.PartialSum();
BlockVector xp(block_trueOffsets);
// Define grid functions for the current configuration, reference configuration,
// final deformation, and pressure
ParGridFunction x_gf(&R_space);
ParGridFunction x_ref(&R_space);
ParGridFunction x_def(&R_space);
ParGridFunction p_gf(&W_space);
// Project the initial and reference configuration functions onto the appropriate grid functions
VectorFunctionCoefficient deform(dim, InitialDeformation);
VectorFunctionCoefficient refconfig(dim, ReferenceConfiguration);
x_gf.ProjectCoefficient(deform);
x_ref.ProjectCoefficient(refconfig);
// Set up the block solution vectors
x_gf.GetTrueDofs(xp.GetBlock(0));
p_gf.GetTrueDofs(xp.GetBlock(1));
// Initialize the incompressible neo-Hookean operator
RubberOperator oper(spaces, ess_bdr, block_trueOffsets,
newton_rel_tol, newton_abs_tol, newton_iter, c_mu);
// Solve the Newton system
oper.Solve(xp);
// Distribute the ghost dofs
x_gf.Distribute(xp.GetBlock(0));
p_gf.Distribute(xp.GetBlock(1));
// Set the final deformation
subtract(x_gf, x_ref, x_def);
// 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, pmesh, &x_gf, &x_def, "Deformation", true);
// Make sure all ranks have sent their 'u' solution before initiating
// another set of GLVis connections (one from each rank):
MPI_Barrier(pmesh->GetComm());
vis_p.open(vishost, visport);
vis_p.precision(8);
visualize(vis_p, pmesh, &x_gf, &p_gf, "Pressure", true);
}
// Save the displaced mesh, the final deformation, and the pressure
{
GridFunction *nodes = &x_gf;
int owns_nodes = 0;
pmesh->SwapNodes(nodes, owns_nodes);
ostringstream mesh_name, pressure_name, deformation_name;
mesh_name << "mesh." << setfill('0') << setw(6) << myid;
pressure_name << "pressure." << setfill('0') << setw(6) << myid;
deformation_name << "deformation." << setfill('0') << setw(6) << myid;
ofstream mesh_ofs(mesh_name.str().c_str());
mesh_ofs.precision(8);
pmesh->Print(mesh_ofs);
ofstream pressure_ofs(pressure_name.str().c_str());
pressure_ofs.precision(8);
p_gf.Save(pressure_ofs);
ofstream deformation_ofs(deformation_name.str().c_str());
deformation_ofs.precision(8);
x_def.Save(deformation_ofs);
}
// Free the used memory.
delete pmesh;
MPI_Finalize();
return 0;
}
JacobianPreconditioner::JacobianPreconditioner(Operator &mass,
Array<int> &offsets,
Array<Array<int> *> &bdr)
: Solver(offsets[2]), block_trueOffsets(offsets), Pressure_mass(&mass),
ess_bdr(bdr)
{
gamma = .00001;
#ifdef MFEM_USE_SUPERLU
SuperLUSolver *mass_slu = new SuperLUSolver(MPI_COMM_WORLD);
mass_slu->SetPrintStatistics(false);
mass_slu->SetSymmetricPattern(false);
mass_slu->SetColumnPermutation(superlu::PARMETIS);
mass_slu->SetOperator(*Pressure_mass);
mass_pcg = mass_slu;
#else
HypreBoomerAMG *mass_prec_amg = new HypreBoomerAMG();
mass_prec_amg->SetOperator(*Pressure_mass);
mass_prec_amg->SetPrintLevel(0);
CGSolver *mass_pcg_amg = new CGSolver();
mass_pcg_amg->SetOperator(*Pressure_mass);
mass_pcg_amg->SetRelTol(1e-12);
mass_pcg_amg->SetAbsTol(1e-12);
mass_pcg_amg->SetMaxIter(20000);
mass_pcg_amg->SetPrintLevel(0);
mass_pcg_amg->SetPreconditioner(*mass_prec_amg);
mass_pcg = mass_pcg_amg;
mass_prec = mass_prec_amg;
#endif
}
void JacobianPreconditioner::Mult(const Vector &k, Vector &y) const
{
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]);
pres_in *= -1.0 * gamma;
mass_pcg->Mult(pres_in, pres_out);
Jacobian->GetBlock(0,1).Mult(pres_out, temp);
subtract(disp_in, temp, temp2);
stiff_prec->Mult(temp2, disp_out);
}
void JacobianPreconditioner::SetOperator(const Operator &op)
{
Jacobian = (BlockOperator *) &op;
#ifdef MFEM_USE_SUPERLU
SuperLUSolver *stiff_prec_slu = new SuperLUSolver(MPI_COMM_WORLD);
stiff_prec_slu->SetPrintStatistics(false);
stiff_prec_slu->SetSymmetricPattern(false);
stiff_prec_slu->SetColumnPermutation(superlu::PARMETIS);
stiff_prec_slu->SetOperator(Jacobian->GetBlock(0,0));
stiff_prec = stiff_prec_slu;
#else
HypreBoomerAMG *stiff_prec_amg = new HypreBoomerAMG();
stiff_prec_amg->SetOperator(Jacobian->GetBlock(0,0));
stiff_prec_amg->SetPrintLevel(0);
stiff_prec = stiff_prec_amg;
#endif
}
JacobianPreconditioner::~JacobianPreconditioner()
{
delete mass_pcg;
delete mass_prec;
delete stiff_prec;
}
RubberOperator::RubberOperator(Array<ParFiniteElementSpace *> &fes,
Array<Array<int> *> &ess_bdr,
Array<int> &trueOffsets,
double rel_tol,
double abs_tol,
int iter,
Coefficient &c_mu)
: Operator(fes[0]->TrueVSize() + fes[1]->TrueVSize()),
newton_solver(fes[0]->GetComm()), mu(c_mu), block_trueOffsets(trueOffsets)
{
Array<Vector *> rhs(2);
rhs[0] = NULL;
rhs[1] = NULL;
fes.Copy(spaces);
// Define the mixed nonlinear form
Hform = new ParBlockNonlinearForm(spaces);
// Add the passive stress integrator
Hform->AddDomainIntegrator(new IncompressibleNeoHookeanIntegrator(mu));
// Set the essential boundary conditions
Hform->SetEssentialBC(ess_bdr, rhs);
ParBilinearForm *a = new ParBilinearForm(spaces[1]);
ConstantCoefficient one(1.0);
OperatorHandle mass(Operator::Hypre_ParCSR);
a->AddDomainIntegrator(new MassIntegrator(one));
a->Assemble();
a->Finalize();
a->ParallelAssemble(mass);
mass.SetOperatorOwner(false);
Pressure_mass = mass.Ptr();
JacobianPreconditioner *Jac_prec = new JacobianPreconditioner(*Pressure_mass,
block_trueOffsets, ess_bdr);
J_prec = Jac_prec;
GMRESSolver *J_gmres = new GMRESSolver(spaces[0]->GetComm());
J_gmres->SetRelTol(1.0e-12);
J_gmres->SetAbsTol(0.0);
J_gmres->SetMaxIter(3000);
J_gmres->SetPrintLevel(0);
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.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
{
Jacobian = &Hform->GetGradient(xp);
return *Jacobian;
}
RubberOperator::~RubberOperator()
{
delete J_solver;
if (J_prec != NULL)
{
delete J_prec;
}
}
// In line visualization
void visualize(ostream &out, ParMesh *mesh, ParGridFunction *deformed_nodes,
ParGridFunction *field, const char *field_name, bool init_vis)
{
if (!out)
{
return;
}
GridFunction *nodes = deformed_nodes;
int owns_nodes = 0;
mesh->SwapNodes(nodes, owns_nodes);
out << "parallel " << mesh->GetNRanks() << " " << mesh->GetMyRank() << "\n";
out << "solution\n" << *mesh << *field;
mesh->SwapNodes(nodes, owns_nodes);
if (init_vis)
{
out << "window_size 800 800\n";
out << "window_title '" << field_name << "'\n";
if (mesh->SpaceDimension() == 2)
{
out << "view 0 0\n"; // view from top
out << "keys jl\n"; // turn off perspective and light
}
out << "keys cm\n"; // show colorbar and mesh
out << "autoscale value\n"; // update value-range; keep mesh-extents fixed
out << "pause\n";
}
out << 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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