Fp operator-(const Fp& me, const Fp& rhs) {
mpz_class c = me.x - rhs.x;
if (c > 0) {
return c;
}
return Fp(c + Fp::p);
}
void LowMachNavierStokes<Mu,SH,TC>::assemble_mass_time_deriv( bool /*compute_jacobian*/,
AssemblyContext& context,
CachedValues& cache )
{
// The number of local degrees of freedom in each variable.
const unsigned int n_p_dofs = context.get_dof_indices(this->_p_var).size();
// Element Jacobian * quadrature weights for interior integration.
const std::vector<libMesh::Real> &JxW =
context.get_element_fe(this->_u_var)->get_JxW();
// The pressure shape functions at interior quadrature points.
const std::vector<std::vector<libMesh::Real> >& p_phi =
context.get_element_fe(this->_p_var)->get_phi();
libMesh::DenseSubVector<libMesh::Number> &Fp = context.get_elem_residual(this->_p_var); // R_{p}
unsigned int n_qpoints = context.get_element_qrule().n_points();
for (unsigned int qp=0; qp != n_qpoints; qp++)
{
libMesh::Number u, v, T;
u = cache.get_cached_values(Cache::X_VELOCITY)[qp];
v = cache.get_cached_values(Cache::Y_VELOCITY)[qp];
T = cache.get_cached_values(Cache::TEMPERATURE)[qp];
libMesh::Gradient grad_u = cache.get_cached_gradient_values(Cache::X_VELOCITY_GRAD)[qp];
libMesh::Gradient grad_v = cache.get_cached_gradient_values(Cache::Y_VELOCITY_GRAD)[qp];
libMesh::Gradient grad_T = cache.get_cached_gradient_values(Cache::TEMPERATURE_GRAD)[qp];
libMesh::NumberVectorValue U(u,v);
if (this->_dim == 3)
U(2) = cache.get_cached_values(Cache::Z_VELOCITY)[qp]; // w
libMesh::Number divU = grad_u(0) + grad_v(1);
if (this->_dim == 3)
{
libMesh::Gradient grad_w = cache.get_cached_gradient_values(Cache::Z_VELOCITY_GRAD)[qp];
divU += grad_w(2);
}
// Now a loop over the pressure degrees of freedom. This
// computes the contributions of the continuity equation.
for (unsigned int i=0; i != n_p_dofs; i++)
{
Fp(i) += (-U*grad_T/T + divU)*p_phi[i][qp]*JxW[qp];
}
}
return;
}
Expression* sintactico::Fp()
{
if(CurrentToken->tipo == PORCENTAJE)
{
CurrentToken = Lexer->NexToken();
Expression* izq = G();
Expression* der = Fp();
if(der != NULL)
return new exprMode(izq,der,Lexer->linea);
return izq;
}
return NULL;
}
void LowMachNavierStokesSPGSMStabilization<Mu,SH,TC>::assemble_continuity_time_deriv( bool /*compute_jacobian*/,
AssemblyContext& context )
{
// The number of local degrees of freedom in each variable.
const unsigned int n_p_dofs = context.get_dof_indices(this->_press_var.p()).size();
// Element Jacobian * quadrature weights for interior integration.
const std::vector<libMesh::Real> &JxW =
context.get_element_fe(this->_flow_vars.u())->get_JxW();
// The pressure shape functions at interior quadrature points.
const std::vector<std::vector<libMesh::RealGradient> >& p_dphi =
context.get_element_fe(this->_press_var.p())->get_dphi();
libMesh::DenseSubVector<libMesh::Number> &Fp = context.get_elem_residual(this->_press_var.p()); // R_{p}
unsigned int n_qpoints = context.get_element_qrule().n_points();
for (unsigned int qp=0; qp != n_qpoints; qp++)
{
libMesh::FEBase* fe = context.get_element_fe(this->_flow_vars.u());
libMesh::RealGradient g = this->_stab_helper.compute_g( fe, context, qp );
libMesh::RealTensor G = this->_stab_helper.compute_G( fe, context, qp );
libMesh::Real T = context.interior_value( this->_temp_vars.T(), qp );
libMesh::Real mu = this->_mu(T);
libMesh::Real rho = this->rho( T, this->get_p0_steady( context, qp ) );
libMesh::RealGradient U( context.interior_value( this->_flow_vars.u(), qp ),
context.interior_value( this->_flow_vars.v(), qp ) );
if( this->mesh_dim(context) == 3 )
U(2) = context.interior_value( this->_flow_vars.w(), qp );
libMesh::Real tau_M = this->_stab_helper.compute_tau_momentum( context, qp, g, G, rho, U, mu, this->_is_steady );
libMesh::RealGradient RM_s = this->compute_res_momentum_steady( context, qp );
// Now a loop over the pressure degrees of freedom. This
// computes the contributions of the continuity equation.
for (unsigned int i=0; i != n_p_dofs; i++)
{
Fp(i) += tau_M*RM_s*p_dphi[i][qp]*JxW[qp];
}
}
return;
}
// Right-hand side of the Lax-Wendroff discretization:
//
// ( q(t+dt) - q(t) )/dt = -F_{x} - G_{y}.
//
// This routine constructs the 'time-integrated' flux functions F and G using the
// Cauchy-Kowalewski procedure.
//
// First, consider time derivatives of q
//
// q^{n+1} = q^n + dt * (q^n_t + dt/2 * q^n_tt + dt^3/6 q^n_ttt ).
//
// Formally, these are given by
//
// q_{t} = ( -f(q) )_x + ( -g(q) )_y,
// q_{tt} = ( f'(q) * ( f_x + g_y )_x + ( g'(q) * ( f_x + g_y )_y
// q_{ttt} = ...
//
// Now, considering Taylor expansions of f and g, centered about t = t^n
//
// F = f^n + (t-t^n) \dot{f^n} + \cdots
// G = g^n + (t-t^n) \dot{g^n} + \cdots
//
// We have the following form, after integrating in time
//
// F: = ( f - dt/2 * ( f'(q)*( f_x+g_y )
// + dt^2/6 ( \pd2{f}{q} \cdot (f_x+g_y,f_x+g_y) +
// \pd{f}{q} ( f_x + g_y )_t ) + \cdots
//
// G: = ( g - dt/2 * ( g'(q)*( f_x+g_y )
// + dt^2/6 ( \pd2{g}{q} \cdot (f_x+g_y,f_x+g_y) +
// \pd{g}{q} ( f_x + g_y )_t ) + \cdots
//
// where the final ingredient is
//
// (f_x+g_y)_t = \pd2{f}{q} \cdot (q_x, f_x+g_y ) + \pd{f}{q} ( f_xx + g_xy ) +
// \pd2{g}{q} \cdot (q_y, f_x+g_y ) + \pd{g}{q} ( f_xy + g_yy ).
//
// At the end of the day, we set
//
// L(q) := -F_x - G_y.
//
// See also: ConstructL.
void LaxWendroff(double dt,
const dTensorBC4& aux, const dTensorBC4& q, // set bndy values modifies these
dTensorBC4& Lstar, dTensorBC3& smax)
{
printf("This call hasn't been tested \n");
if ( !dogParams.get_flux_term() )
{ return; }
const edge_data& edgeData = Legendre2d::get_edgeData();
const int space_order = dogParams.get_space_order();
const int mx = q.getsize(1);
const int my = q.getsize(2);
const int meqn = q.getsize(3);
const int kmax = q.getsize(4);
const int mbc = q.getmbc();
const int maux = aux.getsize(3);
// Flux values
//
// Space-order = number of quadrature points needed for 1D integration
// along cell edges.
//
dTensorBC4 Fm(mx, my, meqn, space_order, mbc);
dTensorBC4 Fp(mx, my, meqn, space_order, mbc);
dTensorBC4 Gm(mx, my, meqn, space_order, mbc);
dTensorBC4 Gp(mx, my, meqn, space_order, mbc);
// Flux function
void FluxFunc(const dTensor2& xpts,
const dTensor2& Q,
const dTensor2& Aux,
dTensor3& flux);
// Jacobian of the flux function:
void DFluxFunc(const dTensor2& xpts,
const dTensor2& Q,
const dTensor2& Aux,
dTensor4& Dflux );
// Hessian of the flux function:
void D2FluxFunc(const dTensor2& xpts,
const dTensor2& Q,
const dTensor2& Aux,
dTensor5& D2flux );
// Riemann solver that relies on the fact that we already have
// f(ql) and f(qr) already computed:
double RiemannSolveLxW(const dTensor1& nvec,
const dTensor1& xedge,
const dTensor1& Ql, const dTensor1& Qr,
const dTensor1& Auxl, const dTensor1& Auxr,
const dTensor1& ffl, const dTensor1& ffr,
dTensor1& Fl, dTensor1& Fr);
void LstarExtra(const dTensorBC4*,
const dTensorBC4*,
dTensorBC4*);
void ArtificialViscosity(const dTensorBC4* aux,
const dTensorBC4* q,
dTensorBC4* Lstar);
// Grid information
const double xlower = dogParamsCart2.get_xlow();
const double ylower = dogParamsCart2.get_ylow();
const double dx = dogParamsCart2.get_dx();
const double dy = dogParamsCart2.get_dy();
// --------------------------------------------------------------------- //
// Boundary data:
// --------------------------------------------------------------------- //
// TODO - call this routine before calling this function.
// void SetBndValues(dTensorBC4& q, dTensorBC4& aux);
// SetBndValues(q, aux);
// ---------------------------------------------------------
// --------------------------------------------------------------------- //
// Part 0: Compute the Lax-Wendroff "flux" function:
//
// Here, we include the extra information about time derivatives.
// --------------------------------------------------------------------- //
dTensorBC4 F(mx, my, meqn, kmax, mbc); F.setall(0.);
dTensorBC4 G(mx, my, meqn, kmax, mbc); G.setall(0.);
void L2ProjectLxW( const int mterms,
const double alpha, const double beta_dt, const double charlie_dt,
const int istart, const int iend,
const int jstart, const int jend,
const int QuadOrder,
const int BasisOrder_auxin,
const int BasisOrder_fout,
const dTensorBC4* qin,
const dTensorBC4* auxin,
dTensorBC4* F,
dTensorBC4* G,
void FluxFunc (const dTensor2& xpts,
const dTensor2& Q, const dTensor2& Aux, dTensor3& flux),
void DFluxFunc (const dTensor2& xpts,
const dTensor2& Q, const dTensor2& aux, dTensor4& Dflux),
void D2FluxFunc (const dTensor2& xpts,
const dTensor2& Q, const dTensor2& aux, dTensor5& D2flux) );
printf("hello\n");
L2ProjectLxW( 3, 1.0, 0.5*dt, dt*dt/6.0,
1-mbc, mx+mbc, 1-mbc, my+mbc,
space_order, space_order, space_order,
&q, &aux, &F, &G, &FluxFunc, &DFluxFunc, D2FluxFunc );
// ---------------------------------------------------------
// Part I: compute source term
// ---------------------------------------------------------
if( dogParams.get_source_term() > 0 )
{
// eprintf("error: have not implemented source term for LxW solver.");
printf("Source term has not been implemented for LxW solver. Terminating program.");
exit(1);
}
Lstar.setall( 0. );
// ---------------------------------------------------------
// Part II: compute inter-element interaction fluxes
//
// N = int( F(q,x,t) * phi_x, x ) / dA
//
// ---------------------------------------------------------
// 1-direction: loop over interior edges and solve Riemann problems
dTensor1 nvec(2);
nvec.set(1, 1.0e0 );
nvec.set(2, 0.0e0 );
#pragma omp parallel for
for (int i=(2-mbc); i<=(mx+mbc); i++)
{
dTensor1 Ql(meqn), Qr(meqn);
dTensor1 ffl(meqn), ffr(meqn);
dTensor1 Fl(meqn), Fr(meqn);
dTensor1 DFl(meqn), DFr(meqn);
dTensor1 Auxl(maux), Auxr(maux);
dTensor1 xedge(2);
for (int j=(2-mbc); j<=(my+mbc-1); j++)
{
// ell indexes Riemann point along the edge
for (int ell=1; ell<=space_order; ell++)
{
// Riemann data - q and f (from basis functions/q)
for (int m=1; m<=meqn; m++)
{
Ql.set (m, 0.0 );
Qr.set (m, 0.0 );
ffl.set(m, 0.0 );
ffr.set(m, 0.0 );
for (int k=1; k<=kmax; k++)
{
// phi_xl( xi=1.0, eta ), phi_xr( xi=-1.0, eta )
Ql.fetch(m) += edgeData.phi_xl->get(ell,k)*q.get(i-1, j, m, k );
Qr.fetch(m) += edgeData.phi_xr->get(ell,k)*q.get(i, j, m, k );
ffl.fetch(m) += edgeData.phi_xl->get(ell,k)*F.get(i-1, j, m, k );
ffr.fetch(m) += edgeData.phi_xr->get(ell,k)*F.get(i, j, m, k );
}
}
// Riemann data - aux
for (int m=1; m<=maux; m++)
{
Auxl.set(m, 0.0 );
Auxr.set(m, 0.0 );
for (int k=1; k<=kmax; k++)
{
Auxl.fetch(m) += edgeData.phi_xl->get(ell,k)*aux.get(i-1, j, m, k);
Auxr.fetch(m) += edgeData.phi_xr->get(ell,k)*aux.get(i, j, m, k);
}
}
// Solve Riemann problem
xedge.set(1, xlower + (double(i)-1.0)*dx );
xedge.set(2, ylower + (double(j)-0.5)*dy );
const double smax_edge = RiemannSolveLxW(
nvec, xedge, Ql, Qr, Auxl, Auxr, ffl, ffr, Fl, Fr);
smax.set(i-1, j, 1, Max(dy*smax_edge,smax.get(i-1, j, 1)) );
smax.set(i, j, 1, Max(dy*smax_edge,smax.get(i, j, 1)) );
// Construct fluxes
for (int m=1; m<=meqn; m++)
{
Fm.set(i , j, m, ell, Fr.get(m) );
Fp.set(i-1, j, m, ell, Fl.get(m) );
}
}
}
}
// 2-direction: loop over interior edges and solve Riemann problems
nvec.set(1, 0.0e0 );
nvec.set(2, 1.0e0 );
#pragma omp parallel for
for (int i=(2-mbc); i<=(mx+mbc-1); i++)
{
dTensor1 Ql(meqn), Qr(meqn);
dTensor1 Fl(meqn), Fr(meqn);
dTensor1 ffl(meqn), ffr(meqn);
dTensor1 Auxl(maux),Auxr(maux);
dTensor1 xedge(2);
for (int j=(2-mbc); j<=(my+mbc); j++)
for (int ell=1; ell<=space_order; ell++)
{
// Riemann data - q
for (int m=1; m<=meqn; m++)
{
Ql.set (m, 0.0 );
Qr.set (m, 0.0 );
ffl.set (m, 0.0 );
ffr.set (m, 0.0 );
for (int k=1; k<=kmax; k++)
{
Ql.fetch(m) += edgeData.phi_yl->get(ell, k)*q.get(i, j-1, m, k );
Qr.fetch(m) += edgeData.phi_yr->get(ell, k)*q.get(i, j, m, k );
ffl.fetch(m) += edgeData.phi_yl->get(ell, k)*G.get(i, j-1, m, k );
ffr.fetch(m) += edgeData.phi_yr->get(ell, k)*G.get(i, j, m, k );
}
}
// Riemann data - aux
for (int m=1; m<=maux; m++)
{
Auxl.set(m, 0.0 );
Auxr.set(m, 0.0 );
for (int k=1; k<=kmax; k++)
{
Auxl.fetch(m) += edgeData.phi_yl->get(ell,k)*aux.get(i,j-1,m,k);
Auxr.fetch(m) += edgeData.phi_yr->get(ell,k)*aux.get(i,j,m,k);
}
}
// Solve Riemann problem
xedge.set(1, xlower + (double(i)-0.5)*dx );
xedge.set(2, ylower + (double(j)-1.0)*dy );
const double smax_edge = RiemannSolveLxW(
nvec, xedge, Ql, Qr, Auxl, Auxr, ffl, ffr, Fl, Fr);
smax.set(i, j-1, 2, Max(dx*smax_edge, smax.get(i, j-1, 2)) );
smax.set(i, j, 2, Max(dx*smax_edge, smax.get(i, j, 2)) );
// Construct fluxes
for (int m=1; m<=meqn; m++)
{
Gm.set(i, j, m, ell, Fr.get(m) );
Gp.set(i, j-1, m, ell, Fl.get(m) );
}
}
}
// Compute ``flux differences'' dF and dG
const double half_dx_inv = 0.5/dx;
const double half_dy_inv = 0.5/dy;
const int mlength = Lstar.getsize(3); assert_eq( meqn, mlength );
// Use the four values, Gm, Gp, Fm, Fp to construct the boundary integral:
#pragma omp parallel for
for (int i=(2-mbc); i<=(mx+mbc-1); i++)
for (int j=(2-mbc); j<=(my+mbc-1); j++)
for (int m=1; m<=mlength; m++)
for (int k=1; k<=kmax; k++)
{
// 1-direction: dF
double F1 = 0.0;
double F2 = 0.0;
for (int ell=1; ell<=space_order; ell++)
{
F1 = F1 + edgeData.wght_phi_xr->get(ell,k)*Fm.get(i,j,m,ell);
F2 = F2 + edgeData.wght_phi_xl->get(ell,k)*Fp.get(i,j,m,ell);
}
// 2-direction: dG
double G1 = 0.0;
double G2 = 0.0;
for (int ell=1; ell<=space_order; ell++)
{
G1 = G1 + edgeData.wght_phi_yr->get(ell,k)*Gm.get(i,j,m,ell);
G2 = G2 + edgeData.wght_phi_yl->get(ell,k)*Gp.get(i,j,m,ell);
}
Lstar.fetch(i,j,m,k) -= (half_dx_inv*(F2-F1) + half_dy_inv*(G2-G1));
}
// ---------------------------------------------------------
// ---------------------------------------------------------
// Part III: compute intra-element contributions
// ---------------------------------------------------------
// No need to call this if first-order in space
if(dogParams.get_space_order()>1)
{
dTensorBC4 Ltmp( mx, my, meqn, kmax, mbc );
void L2ProjectGradAddLegendre(const int istart,
const int iend,
const int jstart,
const int jend,
const int QuadOrder,
const dTensorBC4* F,
const dTensorBC4* G,
dTensorBC4* fout );
L2ProjectGradAddLegendre( 1-mbc, mx+mbc, 1-mbc, my+mbc,
space_order, &F, &G, &Lstar );
}
// ---------------------------------------------------------
// ---------------------------------------------------------
// Part IV: add extra contributions to Lstar
// ---------------------------------------------------------
// Call LstarExtra
LstarExtra(&q,&aux,&Lstar);
// ---------------------------------------------------------
// ---------------------------------------------------------
// Part V: artificial viscosity limiter
// ---------------------------------------------------------
if (dogParams.get_space_order()>1 &&
dogParams.using_viscosity_limiter())
{ ArtificialViscosity(&aux,&q,&Lstar); }
// ---------------------------------------------------------
}
bool operator==(const Fp& me, const int rhs){
return me == Fp(rhs);
}
Fp operator*(const Fp& me, const Fp& rhs) {
return Fp(me.x * rhs.x);
}
Fp operator-(const Fp& me) {
return Fp(-me.x) + Fp::p;
}
void VelocityPenaltyAdjointStabilization<Mu>::element_constraint( bool compute_jacobian,
AssemblyContext& context,
CachedValues& /*cache*/ )
{
#ifdef GRINS_USE_GRVY_TIMERS
this->_timer->BeginTimer("VelocityPenaltyAdjointStabilization::element_constraint");
#endif
// The number of local degrees of freedom in each variable.
const unsigned int n_p_dofs = context.get_dof_indices(this->_press_var.p()).size();
const unsigned int n_u_dofs = context.get_dof_indices(this->_flow_vars.u()).size();
// Element Jacobian * quadrature weights for interior integration.
const std::vector<libMesh::Real> &JxW =
context.get_element_fe(this->_flow_vars.u())->get_JxW();
const std::vector<libMesh::Point>& u_qpoint =
context.get_element_fe(this->_flow_vars.u())->get_xyz();
const std::vector<std::vector<libMesh::Real> >& u_phi =
context.get_element_fe(this->_flow_vars.u())->get_phi();
const std::vector<std::vector<libMesh::RealGradient> >& p_dphi =
context.get_element_fe(this->_press_var.p())->get_dphi();
libMesh::DenseSubVector<libMesh::Number> &Fp = context.get_elem_residual(this->_press_var.p()); // R_{p}
libMesh::DenseSubMatrix<libMesh::Number> &Kpu =
context.get_elem_jacobian(this->_press_var.p(), this->_flow_vars.u()); // J_{pu}
libMesh::DenseSubMatrix<libMesh::Number> &Kpv =
context.get_elem_jacobian(this->_press_var.p(), this->_flow_vars.v()); // J_{pv}
libMesh::DenseSubMatrix<libMesh::Number> *Kpw = NULL;
if(this->mesh_dim(context) == 3)
{
Kpw = &context.get_elem_jacobian
(this->_press_var.p(), this->_flow_vars.w()); // J_{pw}
}
// Now we will build the element Jacobian and residual.
// Constructing the residual requires the solution and its
// gradient from the previous timestep. This must be
// calculated at each quadrature point by summing the
// solution degree-of-freedom values by the appropriate
// weight functions.
unsigned int n_qpoints = context.get_element_qrule().n_points();
libMesh::FEBase* fe = context.get_element_fe(this->_flow_vars.u());
for (unsigned int qp=0; qp != n_qpoints; qp++)
{
libMesh::RealGradient g = this->_stab_helper.compute_g( fe, context, qp );
libMesh::RealTensor G = this->_stab_helper.compute_G( fe, context, qp );
libMesh::RealGradient U( context.interior_value( this->_flow_vars.u(), qp ),
context.interior_value( this->_flow_vars.v(), qp ) );
if( this->mesh_dim(context) == 3 )
{
U(2) = context.interior_value( this->_flow_vars.w(), qp );
}
// Compute the viscosity at this qp
libMesh::Real mu_qp = this->_mu(context, qp);
libMesh::Real tau_M;
libMesh::Real d_tau_M_d_rho;
libMesh::Gradient d_tau_M_dU;
if (compute_jacobian)
this->_stab_helper.compute_tau_momentum_and_derivs
( context, qp, g, G, this->_rho, U, mu_qp,
tau_M, d_tau_M_d_rho, d_tau_M_dU,
this->_is_steady );
else
tau_M = this->_stab_helper.compute_tau_momentum
( context, qp, g, G, this->_rho, U, mu_qp,
this->_is_steady );
libMesh::NumberVectorValue F;
libMesh::NumberTensorValue dFdU;
libMesh::NumberTensorValue* dFdU_ptr =
compute_jacobian ? &dFdU : NULL;
if (!this->compute_force(u_qpoint[qp], context, U, F, dFdU_ptr))
continue;
// First, an i-loop over the velocity degrees of freedom.
// We know that n_u_dofs == n_v_dofs so we can compute contributions
// for both at the same time.
for (unsigned int i=0; i != n_p_dofs; i++)
{
Fp(i) += -tau_M*F*p_dphi[i][qp]*JxW[qp];
if (compute_jacobian)
{
for (unsigned int j=0; j != n_u_dofs; ++j)
{
Kpu(i,j) += -d_tau_M_dU(0)*u_phi[j][qp]*F*p_dphi[i][qp]*JxW[qp]*context.get_elem_solution_derivative();
Kpv(i,j) += -d_tau_M_dU(1)*u_phi[j][qp]*F*p_dphi[i][qp]*JxW[qp]*context.get_elem_solution_derivative();
for (unsigned int d=0; d != 3; ++d)
{
Kpu(i,j) += -tau_M*dFdU(d,0)*u_phi[j][qp]*p_dphi[i][qp](d)*JxW[qp]*context.get_elem_solution_derivative();
Kpv(i,j) += -tau_M*dFdU(d,1)*u_phi[j][qp]*p_dphi[i][qp](d)*JxW[qp]*context.get_elem_solution_derivative();
}
}
if( this->mesh_dim(context) == 3 )
for (unsigned int j=0; j != n_u_dofs; ++j)
{
(*Kpw)(i,j) += -d_tau_M_dU(2)*u_phi[j][qp]*F*p_dphi[i][qp]*JxW[qp]*context.get_elem_solution_derivative();
for (unsigned int d=0; d != 3; ++d)
{
(*Kpw)(i,j) += -tau_M*dFdU(d,2)*u_phi[j][qp]*p_dphi[i][qp](d)*JxW[qp]*context.get_elem_solution_derivative();
}
}
}
}
} // End quadrature loop
#ifdef GRINS_USE_GRVY_TIMERS
this->_timer->EndTimer("VelocityPenaltyAdjointStabilization::element_constraint");
#endif
return;
}
void assemble_postvars_rhs (EquationSystems& es,
const std::string& system_name)
{
const Real E = es.parameters.get<Real>("E");
const Real NU = es.parameters.get<Real>("NU");
const Real KPERM = es.parameters.get<Real>("KPERM");
Real sum_jac_postvars=0;
Real av_pressure=0;
Real total_volume=0;
#include "assemble_preamble_postvars.cpp"
for ( ; el != end_el; ++el)
{
const Elem* elem = *el;
dof_map.dof_indices (elem, dof_indices);
dof_map.dof_indices (elem, dof_indices_u, u_var);
dof_map.dof_indices (elem, dof_indices_v, v_var);
dof_map.dof_indices (elem, dof_indices_p, p_var);
dof_map.dof_indices (elem, dof_indices_x, x_var);
dof_map.dof_indices (elem, dof_indices_y, y_var);
#if THREED
dof_map.dof_indices (elem, dof_indices_w, w_var);
dof_map.dof_indices (elem, dof_indices_z, z_var);
#endif
const unsigned int n_dofs = dof_indices.size();
const unsigned int n_u_dofs = dof_indices_u.size();
const unsigned int n_v_dofs = dof_indices_v.size();
const unsigned int n_p_dofs = dof_indices_p.size();
const unsigned int n_x_dofs = dof_indices_x.size();
const unsigned int n_y_dofs = dof_indices_y.size();
#if THREED
const unsigned int n_w_dofs = dof_indices_w.size();
const unsigned int n_z_dofs = dof_indices_z.size();
#endif
fe_disp->reinit (elem);
fe_vel->reinit (elem);
fe_pres->reinit (elem);
Ke.resize (n_dofs, n_dofs);
Fe.resize (n_dofs);
Kuu.reposition (u_var*n_u_dofs, u_var*n_u_dofs, n_u_dofs, n_u_dofs);
Kuv.reposition (u_var*n_u_dofs, v_var*n_u_dofs, n_u_dofs, n_v_dofs);
Kup.reposition (u_var*n_u_dofs, p_var*n_u_dofs, n_u_dofs, n_p_dofs);
Kux.reposition (u_var*n_u_dofs, p_var*n_u_dofs + n_p_dofs , n_u_dofs, n_x_dofs);
Kuy.reposition (u_var*n_u_dofs, p_var*n_u_dofs + n_p_dofs+n_x_dofs , n_u_dofs, n_y_dofs);
#if THREED
Kuw.reposition (u_var*n_u_dofs, w_var*n_u_dofs, n_u_dofs, n_w_dofs);
Kuz.reposition (u_var*n_u_dofs, p_var*n_u_dofs + n_p_dofs+2*n_x_dofs , n_u_dofs, n_z_dofs);
#endif
Kvu.reposition (v_var*n_v_dofs, u_var*n_v_dofs, n_v_dofs, n_u_dofs);
Kvv.reposition (v_var*n_v_dofs, v_var*n_v_dofs, n_v_dofs, n_v_dofs);
Kvp.reposition (v_var*n_v_dofs, p_var*n_v_dofs, n_v_dofs, n_p_dofs);
Kvx.reposition (v_var*n_v_dofs, p_var*n_u_dofs + n_p_dofs , n_v_dofs, n_x_dofs);
Kvy.reposition (v_var*n_v_dofs, p_var*n_u_dofs + n_p_dofs+n_x_dofs , n_v_dofs, n_y_dofs);
#if THREED
Kvw.reposition (v_var*n_u_dofs, w_var*n_u_dofs, n_v_dofs, n_w_dofs);
Kuz.reposition (v_var*n_u_dofs, p_var*n_u_dofs + n_p_dofs+2*n_x_dofs , n_u_dofs, n_z_dofs);
#endif
#if THREED
Kwu.reposition (w_var*n_w_dofs, u_var*n_v_dofs, n_v_dofs, n_u_dofs);
Kwv.reposition (w_var*n_w_dofs, v_var*n_v_dofs, n_v_dofs, n_v_dofs);
Kwp.reposition (w_var*n_w_dofs, p_var*n_v_dofs, n_v_dofs, n_p_dofs);
Kwx.reposition (w_var*n_w_dofs, p_var*n_u_dofs + n_p_dofs , n_v_dofs, n_x_dofs);
Kwy.reposition (w_var*n_w_dofs, p_var*n_u_dofs + n_p_dofs+n_x_dofs , n_v_dofs, n_y_dofs);
Kww.reposition (w_var*n_w_dofs, w_var*n_u_dofs, n_v_dofs, n_w_dofs);
Kwz.reposition (w_var*n_w_dofs, p_var*n_u_dofs + n_p_dofs+2*n_x_dofs , n_u_dofs, n_z_dofs);
#endif
Kpu.reposition (p_var*n_u_dofs, u_var*n_u_dofs, n_p_dofs, n_u_dofs);
Kpv.reposition (p_var*n_u_dofs, v_var*n_u_dofs, n_p_dofs, n_v_dofs);
Kpp.reposition (p_var*n_u_dofs, p_var*n_u_dofs, n_p_dofs, n_p_dofs);
Kpx.reposition (p_var*n_v_dofs, p_var*n_u_dofs + n_p_dofs , n_p_dofs, n_x_dofs);
Kpy.reposition (p_var*n_v_dofs, p_var*n_u_dofs + n_p_dofs+n_x_dofs , n_p_dofs, n_y_dofs);
#if THREED
Kpw.reposition (p_var*n_u_dofs, w_var*n_u_dofs, n_p_dofs, n_w_dofs);
Kpz.reposition (p_var*n_u_dofs, p_var*n_u_dofs + n_p_dofs+2*n_x_dofs , n_p_dofs, n_z_dofs);
#endif
Kxu.reposition (p_var*n_u_dofs + n_p_dofs, u_var*n_u_dofs, n_x_dofs, n_u_dofs);
Kxv.reposition (p_var*n_u_dofs + n_p_dofs, v_var*n_u_dofs, n_x_dofs, n_v_dofs);
Kxp.reposition (p_var*n_u_dofs + n_p_dofs, p_var*n_u_dofs, n_x_dofs, n_p_dofs);
Kxx.reposition (p_var*n_u_dofs + n_p_dofs, p_var*n_u_dofs + n_p_dofs , n_x_dofs, n_x_dofs);
Kxy.reposition (p_var*n_u_dofs + n_p_dofs, p_var*n_u_dofs + n_p_dofs+n_x_dofs , n_x_dofs, n_y_dofs);
#if THREED
Kxw.reposition (p_var*n_u_dofs + n_p_dofs, w_var*n_u_dofs, n_x_dofs, n_w_dofs);
Kxz.reposition (p_var*n_u_dofs + n_p_dofs, p_var*n_u_dofs + n_p_dofs+2*n_x_dofs , n_x_dofs, n_z_dofs);
#endif
Kyu.reposition (p_var*n_u_dofs + n_p_dofs+n_x_dofs, u_var*n_u_dofs, n_y_dofs, n_u_dofs);
Kyv.reposition (p_var*n_u_dofs + n_p_dofs+n_x_dofs, v_var*n_u_dofs, n_y_dofs, n_v_dofs);
Kyp.reposition (p_var*n_u_dofs + n_p_dofs+n_x_dofs, p_var*n_u_dofs, n_y_dofs, n_p_dofs);
Kyx.reposition (p_var*n_u_dofs + n_p_dofs+n_x_dofs, p_var*n_u_dofs + n_p_dofs , n_y_dofs, n_x_dofs);
Kyy.reposition (p_var*n_u_dofs + n_p_dofs+n_x_dofs, p_var*n_u_dofs + n_p_dofs+n_x_dofs , n_y_dofs, n_y_dofs);
#if THREED
Kyw.reposition (p_var*n_u_dofs + n_p_dofs+n_x_dofs, w_var*n_u_dofs, n_x_dofs, n_w_dofs);
Kyz.reposition (p_var*n_u_dofs + n_p_dofs+n_x_dofs, p_var*n_u_dofs + n_p_dofs+2*n_x_dofs , n_x_dofs, n_z_dofs);
#endif
#if THREED
Kzu.reposition (p_var*n_u_dofs + n_p_dofs+2*n_x_dofs, u_var*n_u_dofs, n_y_dofs, n_u_dofs);
Kzv.reposition (p_var*n_u_dofs + n_p_dofs+2*n_x_dofs, v_var*n_u_dofs, n_y_dofs, n_v_dofs);
Kzp.reposition (p_var*n_u_dofs + n_p_dofs+2*n_x_dofs, p_var*n_u_dofs, n_y_dofs, n_p_dofs);
Kzx.reposition (p_var*n_u_dofs + n_p_dofs+2*n_x_dofs, p_var*n_u_dofs + n_p_dofs , n_y_dofs, n_x_dofs);
Kzy.reposition (p_var*n_u_dofs + n_p_dofs+2*n_x_dofs, p_var*n_u_dofs + n_p_dofs+n_x_dofs , n_y_dofs, n_y_dofs);
Kzw.reposition (p_var*n_u_dofs + n_p_dofs+2*n_x_dofs, w_var*n_u_dofs, n_x_dofs, n_w_dofs);
Kzz.reposition (p_var*n_u_dofs + n_p_dofs+2*n_x_dofs, p_var*n_u_dofs + n_p_dofs+2*n_x_dofs , n_x_dofs, n_z_dofs);
#endif
Fu.reposition (u_var*n_u_dofs, n_u_dofs);
Fv.reposition (v_var*n_u_dofs, n_v_dofs);
Fp.reposition (p_var*n_u_dofs, n_p_dofs);
Fx.reposition (p_var*n_u_dofs + n_p_dofs, n_x_dofs);
Fy.reposition (p_var*n_u_dofs + n_p_dofs+n_x_dofs, n_y_dofs);
#if THREED
Fw.reposition (w_var*n_u_dofs, n_w_dofs);
Fz.reposition (p_var*n_u_dofs + n_p_dofs+2*n_x_dofs, n_y_dofs);
#endif
std::vector<unsigned int> undefo_index;
PoroelasticConfig material(dphi,psi);
// Now we will build the element matrix.
for (unsigned int qp=0; qp<qrule.n_points(); qp++)
{
Number p_solid = 0.;
grad_u_mat(0) = grad_u_mat(1) = grad_u_mat(2) = 0;
for (unsigned int d = 0; d < dim; ++d) {
std::vector<Number> u_undefo;
std::vector<Number> u_undefo_ref;
//Fills the vector di with the global degree of freedom indices for the element. :dof_indicies
Last_non_linear_soln.get_dof_map().dof_indices(elem, undefo_index,d);
Last_non_linear_soln.current_local_solution->get(undefo_index, u_undefo);
reference.current_local_solution->get(undefo_index, u_undefo_ref);
for (unsigned int l = 0; l != n_u_dofs; l++){
grad_u_mat(d).add_scaled(dphi[l][qp], u_undefo[l]+u_undefo_ref[l]);
}
}
for (unsigned int l=0; l<n_p_dofs; l++)
{
p_solid += psi[l][qp]*Last_non_linear_soln.current_local_solution->el(dof_indices_p[l]);
}
Point rX;
material.init_for_qp(rX,grad_u_mat, p_solid, qp,0, p_solid,es);
Real J=material.J;
Real I_1=material.I_1;
Real I_2=material.I_2;
Real I_3=material.I_3;
RealTensor sigma=material.sigma;
av_pressure=av_pressure + p_solid*JxW[qp];
/*
std::cout<<"grad_u_mat(0)" << grad_u_mat(0) <<std::endl;
std::cout<<" J " << J <<std::endl;
std::cout<<" sigma " << sigma <<std::endl;
*/
Real sigma_sum_sq=pow(sigma(0,0)*sigma(0,0)+sigma(0,1)*sigma(0,1)+sigma(0,2)*sigma(0,2)+sigma(1,0)*sigma(1,0)+sigma(1,1)*sigma(1,1)+sigma(1,2)*sigma(1,2)+sigma(2,0)*sigma(2,0)+sigma(2,1)*sigma(2,1)+sigma(2,2)*sigma(2,2),0.5);
// std::cout<<" J " << J <<std::endl;
sum_jac_postvars=sum_jac_postvars+JxW[qp];
for (unsigned int i=0; i<n_u_dofs; i++){
Fu(i) += I_1*JxW[qp]*phi[i][qp];
Fv(i) += I_2*JxW[qp]*phi[i][qp];
Fw(i) += I_3*JxW[qp]*phi[i][qp];
Fx(i) += sigma_sum_sq*JxW[qp]*phi[i][qp];
Fy(i) += J*JxW[qp]*phi[i][qp];
Fz(i) += 0*JxW[qp]*phi[i][qp];
}
for (unsigned int i=0; i<n_p_dofs; i++){
Fp(i) += J*JxW[qp]*psi[i][qp];
}
} // end qp
system.rhs->add_vector(Fe, dof_indices);
system.matrix->add_matrix (Ke, dof_indices);
} // end of element loop
system.matrix->close();
system.rhs->close();
std::cout<<"Assemble postvars rhs->l2_norm () "<<system.rhs->l2_norm ()<<std::endl;
std::cout<<"sum_jac "<< sum_jac_postvars <<std::endl;
std::cout<<"av_pressure "<< av_pressure/sum_jac_postvars <<std::endl;
return;
}
void testGeometry() {
cout << "running testGeometry" << endl;
cout << "Creating Variables" << endl;
// Variable Declarations
// Points
const Point a = Point(0, 0), b = Point(100, 100), c = Point(0, 100);
const Point e = Point(200, 0), d = Point(100, 0), f = Point(100, 200);
// Poly's
const cnt tri {a, e, b}; // non-equal sides
const cnt square {a, c, b, d};
const cnt rect {a, c*2, f, d};
const cnt bigSquare {a*2-b, c*2-b, b*2-b, d*2-b};
// Fp's
const Fp testFp1 = Fp({bigSquare, square});
const Fp testFp2 = Fp({bigSquare}); // not a valid Fp
const Fp testFp3 = Fp({square}); // not a valid Fp
cout << "Creating Vectors" << endl;
// Vectors
// Poly's
const vector<cnt> vpoly1 {tri, square, bigSquare};
const vector<cnt> vpoly2 {tri, square};
const vector<cnt> vpoly3 {square, bigSquare};
const vector<cnt> vpoly4 {tri, bigSquare};
const vector<cnt> vpoly5 {tri};
const vector<cnt> vpoly6 {square};
const vector<cnt> vpoly7 {bigSquare};
// Fp's
const vector<Fp> vfp1 {testFp1, testFp2, testFp3};
const vector<Fp> vfp2 {testFp1, testFp2};
const vector<Fp> vfp3 {testFp2, testFp3};
const vector<Fp> vfp4 {testFp1, testFp3};
const vector<Fp> vfp5 {testFp1};
const vector<Fp> vfp6 {testFp2};
const vector<Fp> vfp7 {testFp3};
cout << "Test Methods..." << endl;
// Test Methods
// Centroid
Point tric = centroid(tri);
Point squarec = centroid(square);
Point bigsc = centroid(bigSquare);
cout << "Triangle" << tostr(tri) << tostr(tric) << endl;
cout << "Square" << tostr(square) << tostr(squarec) << endl;
cout << "Big Square" << tostr(bigSquare) << tostr(bigsc) << endl;
cout << "Square & BigSquare Centroid: " << tostr(centroid(vpoly3)) << endl;
// Dist & Angs
vector<double> dts = dists(tri);
vector<double> ans = angles(tri);
cout << "Triangle lengths: " << vtostr(dts) << endl;
cout << "Triangle angles: " << vtostr(ans) << endl;
cout << "Unit Angle: " << "Origin - " << tostr(a) << "; Point - " << tostr(b) << "; Ang - " << angle(a,b) << endl;
// All same length
cout << "Triangle all same length? " << allSameLength(tri, (double)0.0) << endl;
cout << "Square all same length? " << allSameLength(square, (double)0.0) << endl;
// isPoly
bool test1 = isPoly(tri, 3, false, false, 0, 0); // True
bool test2 = isPoly(tri, 3, true, true, 0, 0); // False
bool test3 = isPoly(tri, 4, false, false, 0, 0); // False
bool test4 = isRectangle(rect, false, 0, 0); // True
bool test5 = isRectangle(rect, true, 0, 0); // False
bool test6 = isSquare(square, 0, 0); // True
cout << test1 << test2 << test3 << test4 << test5 << test6 << endl;
}
int main(int argc, char* argv[])
{
programname = copystring(Basename(argv[0]));
argc--, argv++;
while (argc && argv[0][0] == '-') {
while (*++*argv)
switch(**argv) {
case 'p':
pflag++;
break;
case 'e':
eflag++;
epsfwidth = WidthInPoints(*argv + 1);
goto nextarg;
case 'd':
dflag++;
goto nextarg;
case 'i':
switch( *(*argv + 1) ) {
case '-':
iflag = -1;
case '+':
default:
iflag = 1;
}
goto nextarg;
case 'g':
gflag++;
goto nextarg;
case 'y':
yflag++;
goto nextarg;
case 'b':
bflag++;
goto nextarg;
case 's':
sflag++;
goto nextarg;
case 'm':
mflag++;
TWENTY = atoi(*argv + 1);
if (TWENTY > DEFAULT_TWENTY)
Usage(*argv-1);
goto nextarg;
case 't':
tflag++;
THRESHOLD_PERCENT = (floatish) atof(*argv + 1);
if (THRESHOLD_PERCENT < 0 || THRESHOLD_PERCENT > 5)
Usage(*argv-1);
goto nextarg;
case 'c':
cflag++;
goto nextarg;
case '?':
default:
Usage(*argv-1);
}
nextarg: ;
argc--, argv++;
}
hpfile = "stdin";
psfile = "stdout";
hpfp = stdin;
psfp = stdout;
filter = argc < 1;
if (!filter) {
pathName = copystring(argv[0]);
DropSuffix(pathName, ".hp");
baseName = copystring(Basename(pathName));
hpfp = Fp(pathName, &hpfile, ".hp", "r");
// I changed these two lines to use 'pathName' instead of
// 'baseName'. This means that the .ps and .aux files get put in
// the same directory as the .hp file. This solved Valgrind bugt
// #117686. --njn
// psfp = Fp(baseName, &psfile, ".ps", "w");
psfp = Fp(pathName, &psfile, ".ps", "w");
// if (pflag) auxfp = Fp(baseName, &auxfile, ".aux", "r");
if (pflag) auxfp = Fp(pathName, &auxfile, ".aux", "r");
}
GetHpFile(hpfp);
if (!filter && pflag) GetAuxFile(auxfp);
TraceElement(); /* Orders on total, Removes trace elements (tflag) */
if (dflag) Deviation(); /* ReOrders on deviation */
if (iflag) Identorder(iflag); /* ReOrders on identifier */
if (pflag) Reorder(); /* ReOrders on aux file */
if (TWENTY) TopTwenty(); /* Selects top twenty (mflag) */
Dimensions();
areabelow = AreaBelow();
Scale();
PutPsFile();
if (!filter) {
auxfp = Fp(baseName, &auxfile, ".aux", "w");
PutAuxFile(auxfp);
}
return(0);
}
// The matrix assembly function to be called at each time step to
// prepare for the linear solve.
void assemble_solid (EquationSystems& es,
const std::string& system_name)
{
//es.print_info();
#if LOG_ASSEMBLE_PERFORMANCE
PerfLog perf_log("Assemble");
perf_log.push("assemble stiffness");
#endif
// Get a reference to the auxiliary system
//TransientExplicitSystem& aux_system = es.get_system<TransientExplicitSystem>("Newton-update");
// It is a good idea to make sure we are assembling
// the proper system.
libmesh_assert (system_name == "Newton-update");
// 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 Stokes system object.
TransientLinearImplicitSystem & newton_update =
es.get_system<TransientLinearImplicitSystem> ("Newton-update");
// New
TransientLinearImplicitSystem & last_non_linear_soln =
es.get_system<TransientLinearImplicitSystem> ("Last-non-linear-soln");
TransientLinearImplicitSystem & fluid_system_vel =
es.get_system<TransientLinearImplicitSystem> ("fluid-system-vel");
#if VELOCITY
TransientLinearImplicitSystem& velocity = es.get_system<TransientLinearImplicitSystem>("velocity-system");
#endif
#if UN_MINUS_ONE
TransientLinearImplicitSystem & unm1 =
es.get_system<TransientLinearImplicitSystem> ("unm1-system");
#endif
test(62);
const System & ref_sys = es.get_system("Reference-Configuration");
test(63);
// Numeric ids corresponding to each variable in the system
const unsigned int u_var = last_non_linear_soln .variable_number ("u");
const unsigned int v_var = last_non_linear_soln .variable_number ("v");
const unsigned int w_var = last_non_linear_soln .variable_number ("w");
#if INCOMPRESSIBLE
const unsigned int p_var = last_non_linear_soln .variable_number ("p");
#endif
#if FLUID_P_CONST
const unsigned int m_var = fluid_system_vel.variable_number ("fluid_M");
std::vector<unsigned int> dof_indices_m;
#endif
// Get the Finite Element type for "u". Note this will be
// the same as the type for "v".
FEType fe_vel_type = last_non_linear_soln.variable_type(u_var);
test(64);
#if INCOMPRESSIBLE
// Get the Finite Element type for "p".
FEType fe_pres_type = last_non_linear_soln .variable_type(p_var);
#endif
// Build a Finite Element object of the specified type for
// the velocity variables.
AutoPtr<FEBase> fe_vel (FEBase::build(dim, fe_vel_type));
#if INCOMPRESSIBLE
// Build a Finite Element object of the specified type for
// the pressure variables.
AutoPtr<FEBase> fe_pres (FEBase::build(dim, fe_pres_type));
#endif
// A Gauss quadrature rule for numerical integration.
// Let the \p FEType object decide what order rule is appropriate.
QGauss qrule (dim, fe_vel_type.default_quadrature_order());
// Tell the finite element objects to use our quadrature rule.
fe_vel->attach_quadrature_rule (&qrule);
test(65);
// AutoPtr<QBase> qrule2(fe_vel_type.default_quadrature_rule(dim));
// fe_vel->attach_quadrature_rule (qrule2.get());
#if INCOMPRESSIBLE
fe_pres->attach_quadrature_rule (&qrule);
#endif
// The element Jacobian * quadrature weight at each integration point.
const std::vector<Real>& JxW = fe_vel->get_JxW();
// The element shape functions evaluated at the quadrature points.
const std::vector<std::vector<Real> >& phi = fe_vel->get_phi();
// The element shape function gradients for the velocity
// variables evaluated at the quadrature points.
const std::vector<std::vector<RealGradient> >& dphi = fe_vel->get_dphi();
test(66);
#if INCOMPRESSIBLE
// The element shape functions for the pressure variable
// evaluated at the quadrature points.
const std::vector<std::vector<Real> >& psi = fe_pres->get_phi();
#endif
const std::vector<Point>& coords = fe_vel->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 = last_non_linear_soln .get_dof_map();
#if FLUID_P_CONST
const DofMap & dof_map_fluid = fluid_system_vel .get_dof_map();
#endif
// K will be the jacobian
// F will be the Residual
DenseMatrix<Number> Ke;
DenseVector<Number> Fe;
DenseSubMatrix<Number>
Kuu(Ke), Kuv(Ke), Kuw(Ke),
Kvu(Ke), Kvv(Ke), Kvw(Ke),
Kwu(Ke), Kwv(Ke), Kww(Ke);
#if INCOMPRESSIBLE
DenseSubMatrix<Number> Kup(Ke),Kvp(Ke),Kwp(Ke), Kpu(Ke), Kpv(Ke), Kpw(Ke), Kpp(Ke);
#endif;
DenseSubVector<Number>
Fu(Fe), Fv(Fe), Fw(Fe);
#if INCOMPRESSIBLE
DenseSubVector<Number> Fp(Fe);
#endif
// 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;
std::vector<unsigned int> dof_indices_u;
std::vector<unsigned int> dof_indices_v;
std::vector<unsigned int> dof_indices_w;
#if INCOMPRESSIBLE
std::vector<unsigned int> dof_indices_p;
#endif
#if INERTIA
test(67);
const unsigned int a_var = last_non_linear_soln.variable_number ("a");
const unsigned int b_var = last_non_linear_soln.variable_number ("b");
const unsigned int c_var = last_non_linear_soln.variable_number ("c");
//B block
DenseSubMatrix<Number>
Kua(Ke), Kub(Ke), Kuc(Ke),
Kva(Ke), Kvb(Ke), Kvc(Ke),
Kwa(Ke), Kwb(Ke), Kwc(Ke);
//C block
DenseSubMatrix<Number>
Kau(Ke), Kav(Ke), Kaw(Ke),
Kbu(Ke), Kbv(Ke), Kbw(Ke),
Kcu(Ke), Kcv(Ke), Kcw(Ke);
//D block
DenseSubMatrix<Number>
Kaa(Ke), Kab(Ke), Kac(Ke),
Kba(Ke), Kbb(Ke), Kbc(Ke),
Kca(Ke), Kcb(Ke), Kcc(Ke);
DenseSubVector<Number>
Fa(Fe), Fb(Fe), Fc(Fe);
std::vector<unsigned int> dof_indices_a;
std::vector<unsigned int> dof_indices_b;
std::vector<unsigned int> dof_indices_c;
test(68);
#endif
DenseMatrix<Real> stiff;
DenseVector<Real> res;
VectorValue<Gradient> grad_u_mat;
VectorValue<Gradient> grad_u_mat_old;
const Real dt = es.parameters.get<Real>("dt");
const Real progress = es.parameters.get<Real>("progress");
#if PORO
DenseVector<Real> p_stiff;
DenseVector<Real> p_res;
PoroelasticConfig material(dphi,psi);
#endif
// Just calculate jacobian contribution when we need to
material.calculate_linearized_stiffness = true;
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)
{
test(69);
const Elem* elem = *el;
dof_map.dof_indices (elem, dof_indices);
dof_map.dof_indices (elem, dof_indices_u, u_var);
dof_map.dof_indices (elem, dof_indices_v, v_var);
dof_map.dof_indices (elem, dof_indices_w, w_var);
#if INCOMPRESSIBLE
dof_map.dof_indices (elem, dof_indices_p, p_var);
#endif
const unsigned int n_dofs = dof_indices.size();
const unsigned int n_u_dofs = dof_indices_u.size();
const unsigned int n_v_dofs = dof_indices_v.size();
const unsigned int n_w_dofs = dof_indices_w.size();
#if INCOMPRESSIBLE
const unsigned int n_p_dofs = dof_indices_p.size();
#endif
#if FLUID_P_CONST
dof_map_fluid.dof_indices (elem, dof_indices_m, m_var);
#endif
//elem->print_info();
fe_vel->reinit (elem);
#if INCOMPRESSIBLE
fe_pres->reinit (elem);
#endif
Ke.resize (n_dofs, n_dofs);
Fe.resize (n_dofs);
Kuu.reposition (u_var*n_u_dofs, u_var*n_u_dofs, n_u_dofs, n_u_dofs);
Kuv.reposition (u_var*n_u_dofs, v_var*n_u_dofs, n_u_dofs, n_v_dofs);
Kuw.reposition (u_var*n_u_dofs, w_var*n_u_dofs, n_u_dofs, n_w_dofs);
#if INCOMPRESSIBLE
Kup.reposition (u_var*n_u_dofs, p_var*n_u_dofs, n_u_dofs, n_p_dofs);
#endif
Kvu.reposition (v_var*n_v_dofs, u_var*n_v_dofs, n_v_dofs, n_u_dofs);
Kvv.reposition (v_var*n_v_dofs, v_var*n_v_dofs, n_v_dofs, n_v_dofs);
Kvw.reposition (v_var*n_v_dofs, w_var*n_v_dofs, n_v_dofs, n_w_dofs);
#if INCOMPRESSIBLE
Kvp.reposition (v_var*n_v_dofs, p_var*n_v_dofs, n_v_dofs, n_p_dofs);
#endif
Kwu.reposition (w_var*n_w_dofs, u_var*n_w_dofs, n_w_dofs, n_u_dofs);
Kwv.reposition (w_var*n_w_dofs, v_var*n_w_dofs, n_w_dofs, n_v_dofs);
Kww.reposition (w_var*n_w_dofs, w_var*n_w_dofs, n_w_dofs, n_w_dofs);
#if INCOMPRESSIBLE
Kwp.reposition (w_var*n_w_dofs, p_var*n_w_dofs, n_w_dofs, n_p_dofs);
Kpu.reposition (p_var*n_u_dofs, u_var*n_u_dofs, n_p_dofs, n_u_dofs);
Kpv.reposition (p_var*n_u_dofs, v_var*n_u_dofs, n_p_dofs, n_v_dofs);
Kpw.reposition (p_var*n_u_dofs, w_var*n_u_dofs, n_p_dofs, n_w_dofs);
Kpp.reposition (p_var*n_u_dofs, p_var*n_u_dofs, n_p_dofs, n_p_dofs);
#endif
Fu.reposition (u_var*n_u_dofs, n_u_dofs);
Fv.reposition (v_var*n_u_dofs, n_v_dofs);
Fw.reposition (w_var*n_u_dofs, n_w_dofs);
#if INCOMPRESSIBLE
Fp.reposition (p_var*n_u_dofs, n_p_dofs);
#endif
#if INERTIA
//B block
Kua.reposition (u_var*n_u_dofs, 3*n_u_dofs + n_p_dofs, n_u_dofs, n_u_dofs);
Kub.reposition (u_var*n_u_dofs, 4*n_u_dofs + n_p_dofs, n_u_dofs, n_v_dofs);
Kuc.reposition (u_var*n_u_dofs, 5*n_u_dofs + n_p_dofs, n_u_dofs, n_w_dofs);
Kva.reposition (v_var*n_v_dofs, 3*n_u_dofs + n_p_dofs, n_v_dofs, n_u_dofs);
Kvb.reposition (v_var*n_v_dofs, 4*n_u_dofs + n_p_dofs, n_v_dofs, n_v_dofs);
Kvc.reposition (v_var*n_v_dofs, 5*n_u_dofs + n_p_dofs, n_v_dofs, n_w_dofs);
Kwa.reposition (w_var*n_w_dofs, 3*n_u_dofs + n_p_dofs, n_w_dofs, n_u_dofs);
Kwb.reposition (w_var*n_w_dofs, 4*n_u_dofs + n_p_dofs, n_w_dofs, n_v_dofs);
Kwc.reposition (w_var*n_w_dofs, 5*n_u_dofs + n_p_dofs, n_w_dofs, n_w_dofs);
test(701);
//C block
Kau.reposition (3*n_u_dofs + n_p_dofs, u_var*n_u_dofs, n_u_dofs, n_u_dofs);
Kav.reposition (3*n_u_dofs + n_p_dofs, v_var*n_u_dofs, n_u_dofs, n_v_dofs);
Kaw.reposition (3*n_u_dofs + n_p_dofs, w_var*n_u_dofs, n_u_dofs, n_w_dofs);
Kbu.reposition (4*n_u_dofs + n_p_dofs, u_var*n_v_dofs, n_v_dofs, n_u_dofs);
Kbv.reposition (4*n_u_dofs + n_p_dofs, v_var*n_v_dofs, n_v_dofs, n_v_dofs);
Kbw.reposition (4*n_u_dofs + n_p_dofs, w_var*n_v_dofs, n_v_dofs, n_w_dofs);
Kcu.reposition (5*n_u_dofs + n_p_dofs, u_var*n_w_dofs, n_w_dofs, n_u_dofs);
Kcv.reposition (5*n_u_dofs + n_p_dofs, v_var*n_w_dofs, n_w_dofs, n_v_dofs);
Kcw.reposition (5*n_u_dofs + n_p_dofs, w_var*n_w_dofs, n_w_dofs, n_w_dofs);
//D block
Kaa.reposition (3*n_u_dofs + n_p_dofs, 3*n_u_dofs + n_p_dofs, n_u_dofs, n_u_dofs);
Kab.reposition (3*n_u_dofs + n_p_dofs, 4*n_u_dofs + n_p_dofs, n_u_dofs, n_v_dofs);
Kac.reposition (3*n_u_dofs + n_p_dofs, 5*n_u_dofs + n_p_dofs, n_u_dofs, n_w_dofs);
Kba.reposition (4*n_u_dofs + n_p_dofs, 3*n_u_dofs + n_p_dofs, n_v_dofs, n_u_dofs);
Kbb.reposition (4*n_u_dofs + n_p_dofs, 4*n_u_dofs + n_p_dofs, n_v_dofs, n_v_dofs);
Kbc.reposition (4*n_u_dofs + n_p_dofs, 5*n_u_dofs + n_p_dofs, n_v_dofs, n_w_dofs);
Kca.reposition (5*n_u_dofs + n_p_dofs, 3*n_u_dofs + n_p_dofs, n_w_dofs, n_u_dofs);
Kcb.reposition (5*n_u_dofs + n_p_dofs, 4*n_u_dofs + n_p_dofs, n_w_dofs, n_v_dofs);
Kcc.reposition (5*n_u_dofs + n_p_dofs, 5*n_u_dofs + n_p_dofs, n_w_dofs, n_w_dofs);
Fa.reposition (3*n_u_dofs + n_p_dofs, n_u_dofs);
Fb.reposition (4*n_u_dofs + n_p_dofs, n_v_dofs);
Fc.reposition (5*n_u_dofs + n_p_dofs, n_w_dofs);
dof_map.dof_indices (elem, dof_indices_a, a_var);
dof_map.dof_indices (elem, dof_indices_b, b_var);
dof_map.dof_indices (elem, dof_indices_c, c_var);
test(71);
#endif
System& aux_system = es.get_system<System>("Reference-Configuration");
std::vector<unsigned int> undefo_index;
std::vector<unsigned int> vel_index;
for (unsigned int qp=0; qp<qrule.n_points(); qp++)
{
Point rX;
for (unsigned int l=0; l<n_u_dofs; l++)
{
rX(0) += phi[l][qp]*ref_sys.current_local_solution->el(dof_indices_u[l]);
rX(1) += phi[l][qp]*ref_sys.current_local_solution->el(dof_indices_v[l]);
rX(2) += phi[l][qp]*ref_sys.current_local_solution->el(dof_indices_w[l]);
}
#if INERTIA || DT
test(72);
Real rho_s=15;
Point current_x;
for (unsigned int l=0; l<n_u_dofs; l++)
{
current_x(0) += phi[l][qp]*last_non_linear_soln.current_local_solution->el(dof_indices_u[l]);
current_x(1) += phi[l][qp]*last_non_linear_soln.current_local_solution->el(dof_indices_v[l]);
current_x(2) += phi[l][qp]*last_non_linear_soln.current_local_solution->el(dof_indices_w[l]);
}
Point old_x;
for (unsigned int l=0; l<n_u_dofs; l++)
{
old_x(0) += phi[l][qp]*last_non_linear_soln.old_local_solution->el(dof_indices_u[l]);
old_x(1) += phi[l][qp]*last_non_linear_soln.old_local_solution->el(dof_indices_v[l]);
old_x(2) += phi[l][qp]*last_non_linear_soln.old_local_solution->el(dof_indices_w[l]);
}
#if INERTIA
Point old_vel;
for (unsigned int l=0; l<n_u_dofs; l++)
{
old_vel(0) += phi[l][qp]*last_non_linear_soln.old_local_solution->el(dof_indices_a[l]);
old_vel(1) += phi[l][qp]*last_non_linear_soln.old_local_solution->el(dof_indices_b[l]);
old_vel(2) += phi[l][qp]*last_non_linear_soln.old_local_solution->el(dof_indices_c[l]);
}
Point current_vel;
for (unsigned int l=0; l<n_u_dofs; l++)
{
current_vel(0) += phi[l][qp]*last_non_linear_soln.current_local_solution->el(dof_indices_a[l]);
current_vel(1) += phi[l][qp]*last_non_linear_soln.current_local_solution->el(dof_indices_b[l]);
current_vel(2) += phi[l][qp]*last_non_linear_soln.current_local_solution->el(dof_indices_c[l]);
}
#endif
#if UN_MINUS_ONE
Point unm1_x;
for (unsigned int l=0; l<n_u_dofs; l++)
{
unm1_x(0) += phi[l][qp]*unm1.old_local_solution->el(dof_indices_u[l]);
unm1_x(1) += phi[l][qp]*unm1.old_local_solution->el(dof_indices_v[l]);
unm1_x(2) += phi[l][qp]*unm1.old_local_solution->el(dof_indices_w[l]);
}
#endif
Point value_acc;
Point value_acc_alt;
#if DT
for (unsigned int d = 0; d < dim; ++d) {
value_acc_alt(d) = (rho_s)*( ((current_x(d)-rX(d))-(old_x(d)-rX(d)))-((old_x(d)-rX(d))- (unm1_x(d)-rX(d))) );
value_acc(d) = (rho_s)*((current_x(d))-2*(old_x(d))+ (unm1_x(d)));
value_acc(d) = (rho_s)*((current_x(d))-(old_x(d)));
}
#endif
Point res_1;
Point res_2;
#if INERTIA
for (unsigned int d = 0; d < dim; ++d) {
res_1(d) = (rho_s)*((current_vel(d))-(old_vel(d)));
res_2(d) = current_x(d)-dt*current_vel(d)-old_x(d);
}
/*
std::cout<<" current_vel "<<current_vel<<std::endl;
std::cout<<" res_1 "<<res_1<<std::endl;
std::cout<<" res_2 "<<res_2<<std::endl;
*/
#endif
test(73);
#endif
Number p_solid = 0.;
#if MOVING_MESH
grad_u_mat(0) = grad_u_mat(1) = grad_u_mat(2) = 0;
for (unsigned int d = 0; d < dim; ++d) {
std::vector<Number> u_undefo;
//Fills the vector di with the global degree of freedom indices for the element. :dof_indicies
aux_system.get_dof_map().dof_indices(elem, undefo_index,d);
aux_system.current_local_solution->get(undefo_index, u_undefo);
for (unsigned int l = 0; l != n_u_dofs; l++)
grad_u_mat(d).add_scaled(dphi[l][qp], u_undefo[l]);
}
#endif
//#include "fixed_mesh_in_solid_assemble_code.txt"
#if INCOMPRESSIBLE
for (unsigned int l=0; l<n_p_dofs; l++)
{
p_solid += psi[l][qp]*last_non_linear_soln.current_local_solution->el(dof_indices_p[l]);
}
#endif
#if INCOMPRESSIBLE
Real m=0;
Real p_fluid=0;
#if FLUID_VEL
for (unsigned int l=0; l<n_p_dofs; l++)
{
p_fluid += psi[l][qp]*fluid_system_vel.current_local_solution->el(dof_indices_p[l]);
}
//As outlined in Chappel p=(p_curr-p_old)/2
Real p_fluid_old=0;
for (unsigned int l=0; l<n_p_dofs; l++)
{
p_fluid_old += psi[l][qp]*fluid_system_vel.old_local_solution->el(dof_indices_p[l]);
}
p_fluid=0.5*p_fluid+0.5*p_fluid_old;
Real m_old=0;
#if FLUID_P_CONST
for (unsigned int l=0; l<n_p_dofs; l++)
{
m += psi[l][qp]*fluid_system_vel.current_local_solution->el(dof_indices_m[l]);
}
for (unsigned int l=0; l<n_p_dofs; l++)
{
m_old += psi[l][qp]*fluid_system_vel.old_local_solution->el(dof_indices_m[l]);
}
#endif
material.init_for_qp(grad_u_mat, p_solid, qp, 1.0*m+0.0*m_old, p_fluid);
#endif
#endif //#if INCOMPRESSIBLE
#if INCOMPRESSIBLE && ! PORO
material.init_for_qp(grad_u_mat, p_solid, qp);
#endif
for (unsigned int i=0; i<n_u_dofs; i++)
{
res.resize(dim);
material.get_residual(res, i);
res.scale(JxW[qp]);
#if INERTIA
res.scale(dt);
#endif
#if DT
res.scale(dt);
#endif
//std::cout<< "res "<<res<<std::endl;
Fu(i) += res(0);
Fv(i) += res(1) ;
Fw(i) += res(2);
#if GRAVITY
Real grav=0.0;
Fu(i) += progress*grav*JxW[qp]*phi[i][qp];
#endif
#if INERTIA
Fu(i) += JxW[qp]*phi[i][qp]*res_1(0);
Fv(i) += JxW[qp]*phi[i][qp]*res_1(1);
Fw(i) += JxW[qp]*phi[i][qp]*res_1(2);
Fa(i) += JxW[qp]*phi[i][qp]*res_2(0);
Fb(i) += JxW[qp]*phi[i][qp]*res_2(1);
Fc(i) += JxW[qp]*phi[i][qp]*res_2(2);
#endif
// Matrix contributions for the uu and vv couplings.
for (unsigned int j=0; j<n_u_dofs; j++)
{
material.get_linearized_stiffness(stiff, i, j);
stiff.scale(JxW[qp]);
#if DT
res.scale(dt);
#endif
#if INERTIA
stiff.scale(dt);
Kua(i,j)+= rho_s*JxW[qp]*phi[i][qp]*phi[j][qp];
Kvb(i,j)+= rho_s*JxW[qp]*phi[i][qp]*phi[j][qp];
Kwc(i,j)+= rho_s*JxW[qp]*phi[i][qp]*phi[j][qp];
Kau(i,j)+= JxW[qp]*phi[i][qp]*phi[j][qp];
Kbv(i,j)+= JxW[qp]*phi[i][qp]*phi[j][qp];
Kcw(i,j)+= JxW[qp]*phi[i][qp]*phi[j][qp];
Kaa(i,j)+= -dt*JxW[qp]*phi[i][qp]*phi[j][qp];
Kbb(i,j)+= -dt*JxW[qp]*phi[i][qp]*phi[j][qp];
Kcc(i,j)+= -dt*JxW[qp]*phi[i][qp]*phi[j][qp];
#endif
Kuu(i,j)+= stiff(u_var, u_var);
Kuv(i,j)+= stiff(u_var, v_var);
Kuw(i,j)+= stiff(u_var, w_var);
Kvu(i,j)+= stiff(v_var, u_var);
Kvv(i,j)+= stiff(v_var, v_var);
Kvw(i,j)+= stiff(v_var, w_var);
Kwu(i,j)+= stiff(w_var, u_var);
Kwv(i,j)+= stiff(w_var, v_var);
Kww(i,j)+= stiff(w_var, w_var);
#if GRAVITY
Kuu(i,j)+= 1*JxW[qp]*phi[i][qp]*phi[j][qp];
#endif
}
}
#if INCOMPRESSIBLE && FLUID_P_CONST
for (unsigned int i = 0; i < n_p_dofs; i++) {
material.get_p_residual(p_res, i);
p_res.scale(JxW[qp]);
Fp(i) += p_res(0);
}
for (unsigned int i = 0; i < n_u_dofs; i++) {
for (unsigned int j = 0; j < n_p_dofs; j++) {
material.get_linearized_uvw_p_stiffness(p_stiff, i, j);
p_stiff.scale(JxW[qp]);
Kup(i, j) += p_stiff(0);
Kvp(i, j) += p_stiff(1);
Kwp(i, j) += p_stiff(2);
}
}
for (unsigned int i = 0; i < n_p_dofs; i++) {
for (unsigned int j = 0; j < n_u_dofs; j++) {
material.get_linearized_p_uvw_stiffness(p_stiff, i, j);
p_stiff.scale(JxW[qp]);
Kpu(i, j) += p_stiff(0);
Kpv(i, j) += p_stiff(1);
Kpw(i, j) += p_stiff(2);
}
}
#endif
#if CHAP && ! FLUID_P_CONST
for (unsigned int i = 0; i < n_p_dofs; i++) {
Fp(i) += 0*JxW[qp]*psi[i][qp];
}
for (unsigned int i = 0; i < n_p_dofs; i++) {
for (unsigned int j = 0; j < n_p_dofs; j++) {
Kpp(i, j) += 1*JxW[qp]*psi[i][qp]*psi[j][qp];
}
}
#endif
}//end of qp loop
newton_update.matrix->add_matrix (Ke, dof_indices);
newton_update.rhs->add_vector (Fe, dof_indices);
} // end of element loop
// dof_map.constrain_element_matrix_and_vector (Ke, Fe, dof_indices);
newton_update.rhs->close();
newton_update.matrix->close();
#if LOG_ASSEMBLE_PERFORMANCE
perf_log.pop("assemble stiffness");
#endif
#if LOG_ASSEMBLE_PERFORMANCE
perf_log.push("assemble bcs");
#endif
//Assemble the boundary conditions.
assemble_bcs(es);
#if LOG_ASSEMBLE_PERFORMANCE
perf_log.pop("assemble bcs");
#endif
std::ofstream lhs_out("lhsoutS3.dat");
Ke.print(lhs_out);
lhs_out.close();
return;
}
void BoussinesqBuoyancyAdjointStabilization<Mu>::element_constraint( bool compute_jacobian,
AssemblyContext& context,
CachedValues& /*cache*/ )
{
#ifdef GRINS_USE_GRVY_TIMERS
this->_timer->BeginTimer("BoussinesqBuoyancyAdjointStabilization::element_constraint");
#endif
// The number of local degrees of freedom in each variable.
const unsigned int n_p_dofs = context.get_dof_indices(_flow_vars.p_var()).size();
const unsigned int n_u_dofs = context.get_dof_indices(_flow_vars.u_var()).size();
const unsigned int n_T_dofs = context.get_dof_indices(_temp_vars.T_var()).size();
// Element Jacobian * quadrature weights for interior integration.
const std::vector<libMesh::Real> &JxW =
context.get_element_fe(_flow_vars.u_var())->get_JxW();
const std::vector<std::vector<libMesh::Real> >& T_phi =
context.get_element_fe(this->_temp_vars.T_var())->get_phi();
const std::vector<std::vector<libMesh::Real> >& u_phi =
context.get_element_fe(this->_flow_vars.u_var())->get_phi();
const std::vector<std::vector<libMesh::RealGradient> >& p_dphi =
context.get_element_fe(this->_flow_vars.p_var())->get_dphi();
libMesh::DenseSubVector<libMesh::Number> &Fp = context.get_elem_residual(this->_flow_vars.p_var()); // R_{p}
libMesh::DenseSubMatrix<libMesh::Number> &KpT =
context.get_elem_jacobian(_flow_vars.p_var(), _temp_vars.T_var()); // J_{pT}
libMesh::DenseSubMatrix<libMesh::Number> &Kpu =
context.get_elem_jacobian(_flow_vars.p_var(), _flow_vars.u_var()); // J_{pu}
libMesh::DenseSubMatrix<libMesh::Number> &Kpv =
context.get_elem_jacobian(_flow_vars.p_var(), _flow_vars.v_var()); // J_{pv}
libMesh::DenseSubMatrix<libMesh::Number> *Kpw = NULL;
if(this->_dim == 3)
{
Kpw = &context.get_elem_jacobian
(_flow_vars.p_var(), _flow_vars.w_var()); // J_{pw}
}
// Now we will build the element Jacobian and residual.
// Constructing the residual requires the solution and its
// gradient from the previous timestep. This must be
// calculated at each quadrature point by summing the
// solution degree-of-freedom values by the appropriate
// weight functions.
unsigned int n_qpoints = context.get_element_qrule().n_points();
libMesh::FEBase* fe = context.get_element_fe(this->_flow_vars.u_var());
for (unsigned int qp=0; qp != n_qpoints; qp++)
{
libMesh::RealGradient g = this->_stab_helper.compute_g( fe, context, qp );
libMesh::RealTensor G = this->_stab_helper.compute_G( fe, context, qp );
libMesh::RealGradient U( context.interior_value( this->_flow_vars.u_var(), qp ),
context.interior_value( this->_flow_vars.v_var(), qp ) );
if( this->_dim == 3 )
{
U(2) = context.interior_value( this->_flow_vars.w_var(), qp );
}
// Compute the viscosity at this qp
libMesh::Real mu_qp = this->_mu(context, qp);
libMesh::Real tau_M;
libMesh::Real d_tau_M_d_rho;
libMesh::Gradient d_tau_M_dU;
if (compute_jacobian)
this->_stab_helper.compute_tau_momentum_and_derivs
( context, qp, g, G, this->_rho, U, mu_qp,
tau_M, d_tau_M_d_rho, d_tau_M_dU,
this->_is_steady );
else
tau_M = this->_stab_helper.compute_tau_momentum
( context, qp, g, G, this->_rho, U, mu_qp,
this->_is_steady );
// Compute the solution & its gradient at the old Newton iterate.
libMesh::Number T;
T = context.interior_value(_temp_vars.T_var(), qp);
libMesh::RealGradient d_residual_dT = _rho_ref*_beta_T*_g;
// d_residual_dU = 0
libMesh::RealGradient residual = (T-_T_ref)*d_residual_dT;
// First, an i-loop over the velocity degrees of freedom.
// We know that n_u_dofs == n_v_dofs so we can compute contributions
// for both at the same time.
for (unsigned int i=0; i != n_p_dofs; i++)
{
Fp(i) += tau_M*residual*p_dphi[i][qp]*JxW[qp];
if (compute_jacobian)
{
for (unsigned int j=0; j != n_T_dofs; ++j)
{
KpT(i,j) += tau_M*d_residual_dT*T_phi[j][qp]*p_dphi[i][qp]*JxW[qp] * context.get_elem_solution_derivative();
}
for (unsigned int j=0; j != n_u_dofs; ++j)
{
Kpu(i,j) += d_tau_M_dU(0)*u_phi[j][qp]*residual*p_dphi[i][qp]*JxW[qp] * context.get_elem_solution_derivative();
Kpv(i,j) += d_tau_M_dU(1)*u_phi[j][qp]*residual*p_dphi[i][qp]*JxW[qp] * context.get_elem_solution_derivative();
}
if( this->_dim == 3 )
for (unsigned int j=0; j != n_u_dofs; ++j)
{
(*Kpw)(i,j) += d_tau_M_dU(2)*u_phi[j][qp]*residual*p_dphi[i][qp]*JxW[qp] * context.get_elem_solution_derivative();
}
}
}
} // End quadrature loop
#ifdef GRINS_USE_GRVY_TIMERS
this->_timer->EndTimer("BoussinesqBuoyancyAdjointStabilization::element_constraint");
#endif
return;
}
void DislocationDensity<EvalT, Traits>::
evaluateFields(typename Traits::EvalData workset)
{
Teuchos::SerialDenseMatrix<int, double> A;
Teuchos::SerialDenseMatrix<int, double> X;
Teuchos::SerialDenseMatrix<int, double> B;
Teuchos::SerialDenseSolver<int, double> solver;
A.shape(numNodes,numNodes);
X.shape(numNodes,numNodes);
B.shape(numNodes,numNodes);
// construct Identity for RHS
for (int i = 0; i < numNodes; ++i)
B(i,i) = 1.0;
for (int i=0; i < G.size() ; i++) G[i] = 0.0;
// construct the node --> point operator
for (std::size_t cell=0; cell < workset.numCells; ++cell)
{
for (std::size_t node=0; node < numNodes; ++node)
for (std::size_t qp=0; qp < numQPs; ++qp)
A(qp,node) = BF(cell,node,qp);
X = 0.0;
solver.setMatrix( Teuchos::rcp( &A, false) );
solver.setVectors( Teuchos::rcp( &X, false ), Teuchos::rcp( &B, false ) );
// Solve the system A X = B to find A_inverse
int status = 0;
status = solver.factor();
status = solver.solve();
// compute nodal Fp
nodalFp.initialize(0.0);
for (std::size_t node=0; node < numNodes; ++node)
for (std::size_t qp=0; qp < numQPs; ++qp)
for (std::size_t i=0; i < numDims; ++i)
for (std::size_t j=0; j < numDims; ++j)
nodalFp(node,i,j) += X(node,qp) * Fp(cell,qp,i,j);
// compute the curl using nodalFp
curlFp.initialize(0.0);
for (std::size_t node=0; node < numNodes; ++node)
{
for (std::size_t qp=0; qp < numQPs; ++qp)
{
curlFp(qp,0,0) += nodalFp(node,0,2) * GradBF(cell,node,qp,1) - nodalFp(node,0,1) * GradBF(cell,node,qp,2);
curlFp(qp,0,1) += nodalFp(node,1,2) * GradBF(cell,node,qp,1) - nodalFp(node,1,1) * GradBF(cell,node,qp,2);
curlFp(qp,0,2) += nodalFp(node,2,2) * GradBF(cell,node,qp,1) - nodalFp(node,2,1) * GradBF(cell,node,qp,2);
curlFp(qp,1,0) += nodalFp(node,0,0) * GradBF(cell,node,qp,2) - nodalFp(node,0,2) * GradBF(cell,node,qp,0);
curlFp(qp,1,1) += nodalFp(node,1,0) * GradBF(cell,node,qp,2) - nodalFp(node,1,2) * GradBF(cell,node,qp,0);
curlFp(qp,1,2) += nodalFp(node,2,0) * GradBF(cell,node,qp,2) - nodalFp(node,2,2) * GradBF(cell,node,qp,0);
curlFp(qp,2,0) += nodalFp(node,0,1) * GradBF(cell,node,qp,0) - nodalFp(node,0,0) * GradBF(cell,node,qp,1);
curlFp(qp,2,1) += nodalFp(node,1,1) * GradBF(cell,node,qp,0) - nodalFp(node,1,0) * GradBF(cell,node,qp,1);
curlFp(qp,2,2) += nodalFp(node,2,1) * GradBF(cell,node,qp,0) - nodalFp(node,2,0) * GradBF(cell,node,qp,1);
}
}
for (std::size_t qp=0; qp < numQPs; ++qp)
for (std::size_t i=0; i < numDims; ++i)
for (std::size_t j=0; j < numDims; ++j)
for (std::size_t k=0; k < numDims; ++k)
G(cell,qp,i,j) += Fp(cell,qp,i,k) * curlFp(qp,k,j);
}
}
int main()
{
SystemInit();
const Ec1 g1(-1, 1);
const Ec2 g2(
Fp2(Fp(g2c.aa), Fp(g2c.ab)),
Fp2(Fp(g2c.ba), Fp(g2c.bb))
);
// assertBool g2 and g1 on curve
assertBool("g1 is on EC", g1.isValid());
assertBool("g2 is on twist EC", g2.isValid());
puts("order of group");
const Mpz& r = GetParamR();
PUT(r);
{
Ec1 t = g1;
t.mul(r);
assertBool("orgder of g1 == r", t.isZero());
}
{
Ec2 t = g2;
t.mul(r);
assertBool("order of g2 == r", t.isZero());
}
const Mpz a("123456789012345");
const Mpz b("998752342342342342424242421");
// scalar-multiplication sample
{
Mpz c = a;
c.add(b);
Ec1 Pa = g1; Pa.mul(a);
Ec1 Pb = g1; Pb.mul(b);
Ec1 Pc = g1; Pc.mul(c);
Ec1 out = Pa;
out.add(Pb);
assertEqual("check g1 * c = g1 * a + g1 * b", Pc, out);
}
Fp12 e;
// calc e : G2 x G1 -> G3 pairing
e.pairing(g2, g1); // e = e(g2, g1)
PUT(e);
{
Fp12 t = e;
t.power(r);
assertEqual("order of e == r", t, Fp12(1));
}
Ec2 g2a = g2;
g2a.mul(a);
Fp12 ea1;
ea1.pairing(g2a, g1);
Fp12 ea2 = e;
ea2.power(a); // ea2 = e^a
assertEqual("e(g2 * a, g1) = e(g2, g1)^a", ea1, ea2);
Ec1 g1b = g1;
g1b.mul(b);
Fp12 eb1;
eb1.pairing(g2, g1b); // eb1 = e(g2, g1b)
Fp12 eb2 = e;
eb2.power(b); // eb2 = e^b
assertEqual("e(g2a, g1 * b) = e(g2, g1)^b", eb1, eb2);
Ec1 q1 = g1;
q1.mul(12345);
assertBool("q1 is on EC", q1.isValid());
Fp12 e1, e2;
e1.pairing(g2, g1); // e1 = e(g2, g1)
e2.pairing(g2, q1); // e2 = e(g2, q1)
Ec1 q2 = g1;
q2.add(q1);
e.pairing(g2, q2); // e = e(g2, q2)
e1.mul(e2);
assertEqual("e = e1 * e2", e, e1);
/*
reduce one copy as the following
*/
g2a = g2;
g2a.mul(a);
g1b = g1;
g1b.mul(b);
Ec2 g2at = g2; g2at.mul(a);
Ec1 g1bt = g1; g1bt.mul(b);
assertEqual("g2a == g2 * a", g2a, g2at);
assertEqual("g1b == g1 * b", g1b, g1bt);
printf("errNum = %d\n", errNum);
}
Fp PublicParams::getFp(long x) const {
return Fp(x);
}
Fp operator+(const Fp& me, const Fp& rhs) {
return Fp(me.x + rhs.x);
}
int main(int argc, char *argv[])
{
programname = copystring(Basename(argv[0]));
argc--, argv++;
while (argc && argv[0][0] == '-') {
while (*++*argv)
switch(**argv) {
case 'p':
pflag++;
break;
case 'e':
eflag++;
epsfwidth = WidthInPoints(*argv + 1);
goto nextarg;
case 'd':
dflag++;
goto nextarg;
case 'i':
switch( *(*argv + 1) ) {
case '-':
iflag = -1;
break;
case '+':
default:
iflag = 1;
}
goto nextarg;
case 'g':
gflag++;
goto nextarg;
case 'y':
yflag++;
goto nextarg;
case 'b':
bflag++;
goto nextarg;
case 's':
sflag++;
goto nextarg;
case 'm':
mflag++;
TWENTY = atoi(*argv + 1);
// only 20 keys fit on a page
if (TWENTY > DEFAULT_TWENTY)
multipageflag++;
goto nextarg;
case 'M':
multipageflag++;
goto nextarg;
case 't':
tflag++;
THRESHOLD_PERCENT = (floatish) atof(*argv + 1);
if (THRESHOLD_PERCENT < 0 || THRESHOLD_PERCENT > 5)
Usage(*argv-1);
goto nextarg;
case 'c':
cflag++;
goto nextarg;
case '?':
default:
Usage(*argv-1);
}
nextarg: ;
argc--, argv++;
}
hpfile = "stdin";
psfile = "stdout";
hpfp = stdin;
psfp = stdout;
filter = argc < 1;
if (!filter) {
pathName = copystring(argv[0]);
DropSuffix(pathName, ".hp");
#if defined(_WIN32)
DropSuffix(pathName, ".exe");
#endif
baseName = copystring(Basename(pathName));
hpfp = Fp(pathName, &hpfile, ".hp", "r");
psfp = Fp(baseName, &psfile, ".ps", "w");
if (pflag) auxfp = Fp(baseName, &auxfile, ".aux", "r");
}
GetHpFile(hpfp);
if (!filter && pflag) GetAuxFile(auxfp);
TraceElement(); /* Orders on total, Removes trace elements (tflag) */
if (dflag) Deviation(); /* ReOrders on deviation */
if (iflag) Identorder(iflag); /* ReOrders on identifier */
if (pflag) Reorder(); /* ReOrders on aux file */
/* Selects top bands (mflag) - can be more than 20 now */
if (TWENTY != 0) TopTwenty();
Dimensions();
areabelow = AreaBelow();
Scale();
PutPsFile();
if (!filter) {
auxfp = Fp(baseName, &auxfile, ".aux", "w");
PutAuxFile(auxfp);
}
return(0);
}