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// MFEM Example 10 - Parallel Version
//
// Compile with: make ex10p
//
// Sample runs:
// mpirun -np 4 ex10p -m ../data/beam-quad.mesh -s 3 -rs 2 -dt 3
// mpirun -np 4 ex10p -m ../data/beam-tri.mesh -s 3 -rs 2 -dt 3
// mpirun -np 4 ex10p -m ../data/beam-hex.mesh -s 2 -rs 1 -dt 3
// mpirun -np 4 ex10p -m ../data/beam-tet.mesh -s 2 -rs 1 -dt 3
// mpirun -np 4 ex10p -m ../data/beam-quad.mesh -s 14 -rs 2 -dt 0.03 -vs 20
// mpirun -np 4 ex10p -m ../data/beam-hex.mesh -s 14 -rs 1 -dt 0.05 -vs 20
// mpirun -np 4 ex10p -m ../data/beam-quad-amr.mesh -s 3 -rs 2 -dt 3
//
// Description: This examples solves a time dependent nonlinear elasticity
// problem of the form dv/dt = H(x) + S v, dx/dt = v, where H is a
// hyperelastic model and S is a viscosity operator of Laplacian
// type. The geometry of the domain is assumed to be as follows:
//
// +---------------------+
// boundary --->| |
// attribute 1 | |
// (fixed) +---------------------+
//
// The example demonstrates the use of nonlinear operators (the
// class HyperelasticOperator defining H(x)), as well as their
// implicit time integration using a Newton method for solving an
// associated reduced backward-Euler type nonlinear equation
// (class ReducedSystemOperator). Each Newton step requires the
// inversion of a Jacobian matrix, which is done through a
// (preconditioned) inner solver. Note that implementing the
// method HyperelasticOperator::ImplicitSolve is the only
// requirement for high-order implicit (SDIRK) time integration.
//
// We recommend viewing examples 2 and 9 before viewing this
// example.
#include "mfem.hpp"
#include <memory>
#include <iostream>
#include <fstream>
using namespace std;
using namespace mfem;
class ReducedSystemOperator;
/** After spatial discretization, the hyperelastic model can be written as a
* system of ODEs:
* dv/dt = -M^{-1}*(H(x) + S*v)
* dx/dt = v,
* where x is the vector representing the deformation, v is the velocity field,
* M is the mass matrix, S is the viscosity matrix, and H(x) is the nonlinear
* hyperelastic operator.
*
* Class HyperelasticOperator represents the right-hand side of the above
* system of ODEs. */
class HyperelasticOperator : public TimeDependentOperator
{
protected:
ParFiniteElementSpace &fespace;
Array<int> ess_tdof_list;
ParBilinearForm M, S;
ParNonlinearForm H;
double viscosity;
HyperelasticModel *model;
HypreParMatrix *Mmat; // Mass matrix from ParallelAssemble()
CGSolver M_solver; // Krylov solver for inverting the mass matrix M
HypreSmoother M_prec; // Preconditioner for the mass matrix M
/** Nonlinear operator defining the reduced backward Euler equation for the
velocity. Used in the implementation of method ImplicitSolve. */
ReducedSystemOperator *reduced_oper;
/// Newton solver for the reduced backward Euler equation
NewtonSolver newton_solver;
/// Solver for the Jacobian solve in the Newton method
Solver *J_solver;
/// Preconditioner for the Jacobian solve in the Newton method
Solver *J_prec;
mutable Vector z; // auxiliary vector
public:
HyperelasticOperator(ParFiniteElementSpace &f, Array<int> &ess_bdr,
double visc, double mu, double K);
/// Compute the right-hand side of the ODE system.
virtual void Mult(const Vector &vx, Vector &dvx_dt) const;
/** Solve the Backward-Euler equation: k = f(x + dt*k, t), for the unknown k.
This is the only requirement for high-order SDIRK implicit integration.*/
virtual void ImplicitSolve(const double dt, const Vector &x, Vector &k);
double ElasticEnergy(const ParGridFunction &x) const;
double KineticEnergy(const ParGridFunction &v) const;
void GetElasticEnergyDensity(const ParGridFunction &x,
ParGridFunction &w) const;
virtual ~HyperelasticOperator();
};
/** Nonlinear operator of the form:
k --> (M + dt*S)*k + H(x + dt*v + dt^2*k) + S*v,
where M and S are given BilinearForms, H is a given NonlinearForm, v and x
are given vectors, and dt is a scalar. */
class ReducedSystemOperator : public Operator
{
private:
ParBilinearForm *M, *S;
ParNonlinearForm *H;
mutable HypreParMatrix *Jacobian;
double dt;
const Vector *v, *x;
mutable Vector w, z;
const Array<int> &ess_tdof_list;
public:
ReducedSystemOperator(ParBilinearForm *M_, ParBilinearForm *S_,
ParNonlinearForm *H_, const Array<int> &ess_tdof_list);
/// Set current dt, v, x values - needed to compute action and Jacobian.
void SetParameters(double dt_, const Vector *v_, const Vector *x_);
/// Compute y = H(x + dt (v + dt k)) + M k + S (v + dt k).
virtual void Mult(const Vector &k, Vector &y) const;
/// Compute J = M + dt S + dt^2 grad_H(x + dt (v + dt k)).
virtual Operator &GetGradient(const Vector &k) const;
virtual ~ReducedSystemOperator();
};
/** Function representing the elastic energy density for the given hyperelastic
model+deformation. Used in HyperelasticOperator::GetElasticEnergyDensity. */
class ElasticEnergyCoefficient : public Coefficient
{
private:
HyperelasticModel &model;
const ParGridFunction &x;
DenseMatrix J;
public:
ElasticEnergyCoefficient(HyperelasticModel &m, const ParGridFunction &x_)
: model(m), x(x_) { }
virtual double Eval(ElementTransformation &T, const IntegrationPoint &ip);
virtual ~ElasticEnergyCoefficient() { }
};
void InitialDeformation(const Vector &x, Vector &y);
void InitialVelocity(const Vector &x, Vector &v);
void visualize(ostream &out, ParMesh *mesh, ParGridFunction *deformed_nodes,
ParGridFunction *field, const char *field_name = NULL,
bool init_vis = false);
int main(int argc, char *argv[])
{
// 1. 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);
// 2. Parse command-line options.
const char *mesh_file = "../data/beam-quad.mesh";
int ser_ref_levels = 2;
int par_ref_levels = 0;
int order = 2;
int ode_solver_type = 3;
double t_final = 300.0;
double dt = 3.0;
double visc = 1e-2;
double mu = 0.25;
double K = 5.0;
bool visualization = true;
int vis_steps = 1;
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(&ode_solver_type, "-s", "--ode-solver",
"ODE solver: 1 - Backward Euler, 2 - SDIRK2, 3 - SDIRK3,\n\t"
" 11 - Forward Euler, 12 - RK2,\n\t"
" 13 - RK3 SSP, 14 - RK4.");
args.AddOption(&t_final, "-tf", "--t-final",
"Final time; start time is 0.");
args.AddOption(&dt, "-dt", "--time-step",
"Time step.");
args.AddOption(&visc, "-v", "--viscosity",
"Viscosity coefficient.");
args.AddOption(&mu, "-mu", "--shear-modulus",
"Shear modulus in the Neo-Hookean hyperelastic model.");
args.AddOption(&K, "-K", "--bulk-modulus",
"Bulk modulus in the Neo-Hookean hyperelastic model.");
args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
"--no-visualization",
"Enable or disable GLVis visualization.");
args.AddOption(&vis_steps, "-vs", "--visualization-steps",
"Visualize every n-th timestep.");
args.Parse();
if (!args.Good())
{
if (myid == 0)
{
args.PrintUsage(cout);
}
MPI_Finalize();
return 1;
}
if (myid == 0)
{
args.PrintOptions(cout);
}
// 3. Read the serial mesh from the given mesh file on all processors. 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();
// 4. Define the ODE solver used for time integration. Several implicit
// singly diagonal implicit Runge-Kutta (SDIRK) methods, as well as
// explicit Runge-Kutta methods are available.
ODESolver *ode_solver;
switch (ode_solver_type)
{
// Implicit L-stable methods
case 1: ode_solver = new BackwardEulerSolver; break;
case 2: ode_solver = new SDIRK23Solver(2); break;
case 3: ode_solver = new SDIRK33Solver; break;
// Explicit methods
case 11: ode_solver = new ForwardEulerSolver; break;
case 12: ode_solver = new RK2Solver(0.5); break; // midpoint method
case 13: ode_solver = new RK3SSPSolver; break;
case 14: ode_solver = new RK4Solver; break;
case 15: ode_solver = new GeneralizedAlphaSolver(0.5); break;
// Implicit A-stable methods (not L-stable)
case 22: ode_solver = new ImplicitMidpointSolver; break;
case 23: ode_solver = new SDIRK23Solver; break;
case 24: ode_solver = new SDIRK34Solver; break;
default:
if (myid == 0)
{
cout << "Unknown ODE solver type: " << ode_solver_type << '\n';
}
delete mesh;
MPI_Finalize();
return 3;
}
// 5. Refine the mesh in serial to increase the resolution. In this example
// we do 'ser_ref_levels' of uniform refinement, where 'ser_ref_levels' is
// a command-line parameter.
for (int lev = 0; lev < ser_ref_levels; lev++)
{
mesh->UniformRefinement();
}
// 6. Define a parallel mesh by a partitioning of the serial mesh. Refine
// this mesh further in parallel to increase the resolution. Once the
// parallel mesh is defined, the serial mesh can be deleted.
ParMesh *pmesh = new ParMesh(MPI_COMM_WORLD, *mesh);
delete mesh;
for (int lev = 0; lev < par_ref_levels; lev++)
{
pmesh->UniformRefinement();
}
// 7. Define the parallel vector finite element spaces representing the mesh
// deformation x_gf, the velocity v_gf, and the initial configuration,
// x_ref. Define also the elastic energy density, w_gf, which is in a
// discontinuous higher-order space. Since x and v are integrated in time
// as a system, we group them together in block vector vx, on the unique
// parallel degrees of freedom, with offsets given by array true_offset.
H1_FECollection fe_coll(order, dim);
ParFiniteElementSpace fespace(pmesh, &fe_coll, dim);
HYPRE_Int glob_size = fespace.GlobalTrueVSize();
if (myid == 0)
{
cout << "Number of velocity/deformation unknowns: " << glob_size << endl;
}
int true_size = fespace.TrueVSize();
Array<int> true_offset(3);
true_offset[0] = 0;
true_offset[1] = true_size;
true_offset[2] = 2*true_size;
BlockVector vx(true_offset);
ParGridFunction v_gf, x_gf;
v_gf.MakeTRef(&fespace, vx, true_offset[0]);
x_gf.MakeTRef(&fespace, vx, true_offset[1]);
ParGridFunction x_ref(&fespace);
pmesh->GetNodes(x_ref);
L2_FECollection w_fec(order + 1, dim);
ParFiniteElementSpace w_fespace(pmesh, &w_fec);
ParGridFunction w_gf(&w_fespace);
// 8. Set the initial conditions for v_gf, x_gf and vx, and define the
// boundary conditions on a beam-like mesh (see description above).
VectorFunctionCoefficient velo(dim, InitialVelocity);
v_gf.ProjectCoefficient(velo);
v_gf.SetTrueVector();
VectorFunctionCoefficient deform(dim, InitialDeformation);
x_gf.ProjectCoefficient(deform);
x_gf.SetTrueVector();
v_gf.SetFromTrueVector(); x_gf.SetFromTrueVector();
Array<int> ess_bdr(fespace.GetMesh()->bdr_attributes.Max());
ess_bdr = 0;
ess_bdr[0] = 1; // boundary attribute 1 (index 0) is fixed
// 9. Initialize the hyperelastic operator, the GLVis visualization and print
// the initial energies.
HyperelasticOperator oper(fespace, ess_bdr, visc, mu, K);
socketstream vis_v, vis_w;
if (visualization)
{
char vishost[] = "localhost";
int visport = 19916;
vis_v.open(vishost, visport);
vis_v.precision(8);
visualize(vis_v, pmesh, &x_gf, &v_gf, "Velocity", true);
// Make sure all ranks have sent their 'v' solution before initiating
// another set of GLVis connections (one from each rank):
MPI_Barrier(pmesh->GetComm());
vis_w.open(vishost, visport);
if (vis_w)
{
oper.GetElasticEnergyDensity(x_gf, w_gf);
vis_w.precision(8);
visualize(vis_w, pmesh, &x_gf, &w_gf, "Elastic energy density", true);
}
}
double ee0 = oper.ElasticEnergy(x_gf);
double ke0 = oper.KineticEnergy(v_gf);
if (myid == 0)
{
cout << "initial elastic energy (EE) = " << ee0 << endl;
cout << "initial kinetic energy (KE) = " << ke0 << endl;
cout << "initial total energy (TE) = " << (ee0 + ke0) << endl;
}
double t = 0.0;
oper.SetTime(t);
ode_solver->Init(oper);
// 10. Perform time-integration
// (looping over the time iterations, ti, with a time-step dt).
bool last_step = false;
for (int ti = 1; !last_step; ti++)
{
double dt_real = min(dt, t_final - t);
ode_solver->Step(vx, t, dt_real);
last_step = (t >= t_final - 1e-8*dt);
if (last_step || (ti % vis_steps) == 0)
{
v_gf.SetFromTrueVector(); x_gf.SetFromTrueVector();
double ee = oper.ElasticEnergy(x_gf);
double ke = oper.KineticEnergy(v_gf);
if (myid == 0)
{
cout << "step " << ti << ", t = " << t << ", EE = " << ee
<< ", KE = " << ke << ", ΔTE = " << (ee+ke)-(ee0+ke0) << endl;
}
if (visualization)
{
visualize(vis_v, pmesh, &x_gf, &v_gf);
if (vis_w)
{
oper.GetElasticEnergyDensity(x_gf, w_gf);
visualize(vis_w, pmesh, &x_gf, &w_gf);
}
}
}
}
// 11. Save the displaced mesh, the velocity and elastic energy.
{
v_gf.SetFromTrueVector(); x_gf.SetFromTrueVector();
GridFunction *nodes = &x_gf;
int owns_nodes = 0;
pmesh->SwapNodes(nodes, owns_nodes);
ostringstream mesh_name, velo_name, ee_name;
mesh_name << "deformed." << setfill('0') << setw(6) << myid;
velo_name << "velocity." << setfill('0') << setw(6) << myid;
ee_name << "elastic_energy." << setfill('0') << setw(6) << myid;
ofstream mesh_ofs(mesh_name.str().c_str());
mesh_ofs.precision(8);
pmesh->Print(mesh_ofs);
pmesh->SwapNodes(nodes, owns_nodes);
ofstream velo_ofs(velo_name.str().c_str());
velo_ofs.precision(8);
v_gf.Save(velo_ofs);
ofstream ee_ofs(ee_name.str().c_str());
ee_ofs.precision(8);
oper.GetElasticEnergyDensity(x_gf, w_gf);
w_gf.Save(ee_ofs);
}
// 12. Free the used memory.
delete ode_solver;
delete pmesh;
MPI_Finalize();
return 0;
}
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;
}
ReducedSystemOperator::ReducedSystemOperator(
ParBilinearForm *M_, ParBilinearForm *S_, ParNonlinearForm *H_,
const Array<int> &ess_tdof_list_)
: Operator(M_->ParFESpace()->TrueVSize()), M(M_), S(S_), H(H_),
Jacobian(NULL), dt(0.0), v(NULL), x(NULL), w(height), z(height),
ess_tdof_list(ess_tdof_list_)
{ }
void ReducedSystemOperator::SetParameters(double dt_, const Vector *v_,
const Vector *x_)
{
dt = dt_; v = v_; x = x_;
}
void ReducedSystemOperator::Mult(const Vector &k, Vector &y) const
{
// compute: y = H(x + dt*(v + dt*k)) + M*k + S*(v + dt*k)
add(*v, dt, k, w);
add(*x, dt, w, z);
H->Mult(z, y);
M->TrueAddMult(k, y);
S->TrueAddMult(w, y);
y.SetSubVector(ess_tdof_list, 0.0);
}
Operator &ReducedSystemOperator::GetGradient(const Vector &k) const
{
delete Jacobian;
SparseMatrix *localJ = Add(1.0, M->SpMat(), dt, S->SpMat());
add(*v, dt, k, w);
add(*x, dt, w, z);
localJ->Add(dt*dt, H->GetLocalGradient(z));
Jacobian = M->ParallelAssemble(localJ);
delete localJ;
HypreParMatrix *Je = Jacobian->EliminateRowsCols(ess_tdof_list);
delete Je;
return *Jacobian;
}
ReducedSystemOperator::~ReducedSystemOperator()
{
delete Jacobian;
}
HyperelasticOperator::HyperelasticOperator(ParFiniteElementSpace &f,
Array<int> &ess_bdr, double visc,
double mu, double K)
: TimeDependentOperator(2*f.TrueVSize(), 0.0), fespace(f),
M(&fespace), S(&fespace), H(&fespace),
viscosity(visc), M_solver(f.GetComm()), newton_solver(f.GetComm()),
z(height/2)
{
const double rel_tol = 1e-8;
const int skip_zero_entries = 0;
const double ref_density = 1.0; // density in the reference configuration
ConstantCoefficient rho0(ref_density);
M.AddDomainIntegrator(new VectorMassIntegrator(rho0));
M.Assemble(skip_zero_entries);
M.Finalize(skip_zero_entries);
Mmat = M.ParallelAssemble();
fespace.GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
HypreParMatrix *Me = Mmat->EliminateRowsCols(ess_tdof_list);
delete Me;
M_solver.iterative_mode = false;
M_solver.SetRelTol(rel_tol);
M_solver.SetAbsTol(0.0);
M_solver.SetMaxIter(30);
M_solver.SetPrintLevel(0);
M_prec.SetType(HypreSmoother::Jacobi);
M_solver.SetPreconditioner(M_prec);
M_solver.SetOperator(*Mmat);
model = new NeoHookeanModel(mu, K);
H.AddDomainIntegrator(new HyperelasticNLFIntegrator(model));
H.SetEssentialTrueDofs(ess_tdof_list);
ConstantCoefficient visc_coeff(viscosity);
S.AddDomainIntegrator(new VectorDiffusionIntegrator(visc_coeff));
S.Assemble(skip_zero_entries);
S.Finalize(skip_zero_entries);
reduced_oper = new ReducedSystemOperator(&M, &S, &H, ess_tdof_list);
HypreSmoother *J_hypreSmoother = new HypreSmoother;
J_hypreSmoother->SetType(HypreSmoother::l1Jacobi);
J_hypreSmoother->SetPositiveDiagonal(true);
J_prec = J_hypreSmoother;
MINRESSolver *J_minres = new MINRESSolver(f.GetComm());
J_minres->SetRelTol(rel_tol);
J_minres->SetAbsTol(0.0);
J_minres->SetMaxIter(300);
J_minres->SetPrintLevel(-1);
J_minres->SetPreconditioner(*J_prec);
J_solver = J_minres;
newton_solver.iterative_mode = false;
newton_solver.SetSolver(*J_solver);
newton_solver.SetOperator(*reduced_oper);
newton_solver.SetPrintLevel(1); // print Newton iterations
newton_solver.SetRelTol(rel_tol);
newton_solver.SetAbsTol(0.0);
newton_solver.SetMaxIter(10);
}
void HyperelasticOperator::Mult(const Vector &vx, Vector &dvx_dt) const
{
// Create views to the sub-vectors v, x of vx, and dv_dt, dx_dt of dvx_dt
int sc = height/2;
Vector v(vx.GetData() + 0, sc);
Vector x(vx.GetData() + sc, sc);
Vector dv_dt(dvx_dt.GetData() + 0, sc);
Vector dx_dt(dvx_dt.GetData() + sc, sc);
H.Mult(x, z);
if (viscosity != 0.0)
{
S.TrueAddMult(v, z);
z.SetSubVector(ess_tdof_list, 0.0);
}
z.Neg(); // z = -z
M_solver.Mult(z, dv_dt);
dx_dt = v;
}
void HyperelasticOperator::ImplicitSolve(const double dt,
const Vector &vx, Vector &dvx_dt)
{
int sc = height/2;
Vector v(vx.GetData() + 0, sc);
Vector x(vx.GetData() + sc, sc);
Vector dv_dt(dvx_dt.GetData() + 0, sc);
Vector dx_dt(dvx_dt.GetData() + sc, sc);
// By eliminating kx from the coupled system:
// kv = -M^{-1}*[H(x + dt*kx) + S*(v + dt*kv)]
// kx = v + dt*kv
// we reduce it to a nonlinear equation for kv, represented by the
// reduced_oper. This equation is solved with the newton_solver
// object (using J_solver and J_prec internally).
reduced_oper->SetParameters(dt, &v, &x);
Vector zero; // empty vector is interpreted as zero r.h.s. by NewtonSolver
newton_solver.Mult(zero, dv_dt);
MFEM_VERIFY(newton_solver.GetConverged(), "Newton solver did not converge.");
add(v, dt, dv_dt, dx_dt);
}
double HyperelasticOperator::ElasticEnergy(const ParGridFunction &x) const
{
return H.GetEnergy(x);
}
double HyperelasticOperator::KineticEnergy(const ParGridFunction &v) const
{
double loc_energy = 0.5*M.InnerProduct(v, v);
double energy;
MPI_Allreduce(&loc_energy, &energy, 1, MPI_DOUBLE, MPI_SUM,
fespace.GetComm());
return energy;
}
void HyperelasticOperator::GetElasticEnergyDensity(
const ParGridFunction &x, ParGridFunction &w) const
{
ElasticEnergyCoefficient w_coeff(*model, x);
w.ProjectCoefficient(w_coeff);
}
HyperelasticOperator::~HyperelasticOperator()
{
delete J_solver;
delete J_prec;
delete reduced_oper;
delete model;
delete Mmat;
}
double ElasticEnergyCoefficient::Eval(ElementTransformation &T,
const IntegrationPoint &ip)
{
model.SetTransformation(T);
x.GetVectorGradient(T, J);
// return model.EvalW(J); // in reference configuration
return model.EvalW(J)/J.Det(); // in deformed configuration
}
void InitialDeformation(const Vector &x, Vector &y)
{
// set the initial configuration to be the same as the reference, stress
// free, configuration
y = x;
}
void InitialVelocity(const Vector &x, Vector &v)
{
const int dim = x.Size();
const double s = 0.1/64.;
v = 0.0;
v(dim-1) = s*x(0)*x(0)*(8.0-x(0));
v(0) = -s*x(0)*x(0);
}