///////////////////////////////////////////////////////////////////////////////
/// Calculate the velocity
///
///\param para Pointer to FFD parameters
///\param var Pointer to FFD simulation variables
///\param BINDEX Pointer to boundary index
///
///\return 0 if no error occurred
///////////////////////////////////////////////////////////////////////////////
int vel_step(PARA_DATA *para, REAL **var,int **BINDEX) {
REAL *u = var[VX], *v = var[VY], *w = var[VZ];
REAL *u0 = var[TMP1], *v0 = var[TMP2], *w0 = var[TMP3];
int flag = 0;
flag = advect(para, var, VX, 0, u0, u, BINDEX);
if(flag!=0) {
ffd_log("vel_step(): Could not advect for velocity X.", FFD_ERROR);
return flag;
}
flag = advect(para, var, VY, 0, v0, v, BINDEX);
if(flag!=0) {
ffd_log("vel_step(): Could not advect for velocity Y.", FFD_ERROR);
return flag;
}
flag = advect(para, var, VZ, 0, w0, w, BINDEX);
if(flag!=0) {
ffd_log("vel_step(): Could not advect for velocity Z.", FFD_ERROR);
return flag;
}
flag = diffusion(para, var, VX, 0, u, u0, BINDEX);
if(flag!=0) {
ffd_log("vel_step(): Could not diffuse velocity X.", FFD_ERROR);
return flag;
}
flag = diffusion(para, var, VY, 0, v, v0, BINDEX);
if(flag!=0) {
ffd_log("vel_step(): Could not diffuse velocity Y.", FFD_ERROR);
return flag;
}
flag = diffusion(para, var, VZ, 0, w, w0, BINDEX);
if(flag!=0) {
ffd_log("vel_step(): Could not diffuse velocity Z.", FFD_ERROR);
return flag;
}
flag = project(para, var,BINDEX);
if(flag!=0) {
ffd_log("vel_step(): Could not project velocity.", FFD_ERROR);
return flag;
}
if(para->bc->nb_outlet!=0) flag = mass_conservation(para, var,BINDEX);
if(flag!=0) {
ffd_log("vel_step(): Could not conduct mass conservation correction.",
FFD_ERROR);
return flag;
}
return flag;
} // End of vel_step( )
void predcorr(double *x, double *v, double *w, int *ix, int *iw, int *pcd, double dt, params *p, gsl_rng *rg)
/* simplified weak order 2.0 adapted predictor-corrector scheme
( see E. Platen, N. Bruti-Liberati; Numerical Solution of Stochastic Differential Equations with Jumps in Finance; Springer 2010; p. 503, p. 532 )
*/
{
int i;
double l_xt, l_xtt, l_vt, l_vtt, l_wt, l_wtt, predl_x, predl_v, predl_w, l_x, l_v, l_w;
double basex = 1.0,
basew = PI2;
for (i = (p->paths)==1?0:(p->paths); i < (p->paths)*2; ++i){
l_x = x[i];
l_v = v[i];
l_w = w[i];
l_xt = l_v;
l_vt = drift(l_x, l_v, l_w, p);
l_wt = p->omega;
predl_x = l_x + l_xt*dt;
predl_v = l_v + l_vt*dt + diffusion(dt, p, rg);
predl_w = l_w + l_wt*dt;
l_xtt = predl_v;
l_vtt = drift(predl_x, predl_v, predl_w, p);
l_wtt = p->omega;
predl_x = l_x + 0.5*(l_xt + l_xtt)*dt;
predl_v = l_v + 0.5*(l_vt + l_vtt)*dt + diffusion(dt, p, rg);
predl_w = l_w + 0.5*(l_wt + l_wtt)*dt;
l_xtt = predl_v;
l_vtt = drift(predl_x, predl_v, predl_w, p);
//l_wtt = p->omega;
l_x += 0.5*(l_xt + l_xtt)*dt;
l_v += 0.5*(l_vt + l_vtt)*dt + diffusion(dt, p, rg) + adapted_jump(pcd, dt, p, rg);
l_w += 0.5*(l_wt + l_wtt)*dt;
//fold path parameters
//if (fabs(l_x) > basex){
// l_x -= floor(l_x/basex)*basex;
// ix[i]++;
//}
if (l_w > basew){
l_w -= floor(l_w/basew)*basew;
iw[i]++;
}
x[i] = l_x;
v[i] = l_v;
w[i] = l_w;
}
}
///////////////////////////////////////////////////////////////////////////////
/// Calculate the contaminant concentration
///
///\param para Pointer to FFD parameters
///\param var Pointer to FFD simulation variables
///\param BINDEX Pointer to boundary index
///
///\return 0 if no error occurred
///////////////////////////////////////////////////////////////////////////////
int den_step(PARA_DATA *para, REAL **var, int **BINDEX) {
REAL *den, *den0 = var[TMP1];
int i, flag = 0;
/****************************************************************************
| Solve the species
****************************************************************************/
for(i=0; i<para->bc->nb_Xi; i++) {
if(para->outp->version==DEBUG) {
sprintf(msg, "den_step(): start to solve Xi%d", i+1);
ffd_log(msg, FFD_NORMAL);
}
den = var[Xi1+i];
flag = advect(para, var, Xi1+i, i, den0, den, BINDEX);
if(flag!=0) {
sprintf(msg, "den_step(): Could not advect species %d", i+1);
ffd_log(msg, FFD_ERROR);
return flag;
}
flag = diffusion(para, var, Xi1+i, i, den, den0, BINDEX);
if(flag!=0) {
sprintf(msg, "den_step(): Could not diffuse species %d", i+1);
ffd_log(msg, FFD_ERROR);
return flag;
}
}
/****************************************************************************
| Solve the trace substances
****************************************************************************/
for(i=0; i<para->bc->nb_C; i++) {
if(para->outp->version==DEBUG) {
sprintf(msg, "den_step(): start to solve C%d", i+1);
ffd_log(msg, FFD_NORMAL);
}
den = var[C1+i];
flag = advect(para, var, Xi1, i, den0, den, BINDEX);
if(flag!=0) {
sprintf(msg, "den_step(): Could not advect trace substance %d", i+1);
ffd_log(msg, FFD_ERROR);
return flag;
}
flag = diffusion(para, var, Xi1, i, den, den0, BINDEX);
if(flag!=0) {
sprintf(msg, "den_step(): Could not diffuse trace substance %d", i+1);
ffd_log(msg, FFD_ERROR);
return flag;
}
}
return flag;
} // End of den_step( )
void FluidSimulator::step_velocity(float *u, float *v, float *u0,
float *v0, float viscosity){
add_source(u,u0);
add_source(v,v0);
swap(u0,u); diffusion(1, u, u0, viscosity);
swap(v0,v); diffusion(2, v, v0, viscosity);
project(u,v,u0,v0);
swap(u0,u); swap(v0,v);
advection(1,u,u0,u0,v0);
advection(2,v,v0,u0,v0);
project(u,v,u0,v0);
}
void StableSolver2D::anim_tex()
{
if(running == 0) return;
SWAP(tx0, tx);
SWAP(ty0, ty);
advection(tx, tx0, vx, vy, 0);
advection(ty, ty0, vx, vy, 0);
SWAP(tx0, tx);
SWAP(ty0, ty);
diffusion(tx, tx0, diff, 0);
diffusion(ty, ty0, diff, 0);
}
inline Disposable<Matrix> StochasticProcess1D::diffusion(
Time t, const Array& x) const {
#if defined(QL_EXTRA_SAFETY_CHECKS)
QL_REQUIRE(x.size() == 1, "1-D array required");
#endif
Matrix m(1, 1, diffusion(t, x[0]));
return m;
}
//Animating Velocity
void StableSolver2D::anim_vel()
{
if(running == 0) return;
SWAP(vx0, vx);
SWAP(vy0, vy);
diffusion(vx, vx0, visc, 1);
diffusion(vy, vy0, visc, 2);
projection();
SWAP(vx0, vx);
SWAP(vy0, vy);
advection(vx, vx0, vx0, vy0, 1);
advection(vy, vy0, vx0, vy0, 2);
projection();
}
Real GeneralizedBlackScholesProcess::drift(Time t, Real x) const {
Real sigma = diffusion(t,x);
// we could be more anticipatory if we know the right dt
// for which the drift will be used
Time t1 = t + 0.0001;
return riskFreeRate_->forwardRate(t,t1,Continuous,NoFrequency,true)
- dividendYield_->forwardRate(t,t1,Continuous,NoFrequency,true)
- 0.5 * sigma * sigma;
}
//Animating Density
void StableSolver2D::anim_den()
{
if(running == 0) return;
SWAP(d0, d);
advection(d, d0, vx, vy, 0);
SWAP(d0, d);
diffusion(d, d0, diff, 0);
}
void Events::execute()
{
evolve();
newChoose:;
double chooseEvent = _random() * rates.total;
if (chooseEvent < rates.totalAds) {
int index = static_cast<int> (floor(chooseEvent / rates.ads));
adsorption(index, atomType::metal);
}
else if (chooseEvent < rates.totalAds + rates.totalDes) {
chooseEvent -= rates.totalAds;
double cumulateRates = 0;
unsigned ei = 0, ej = 0;
while (cumulateRates + rates.sumsofDes[ei] < chooseEvent) {
if (ei >= c::nDesTypes) {
goto newChoose;
}
cumulateRates += rates.sumsofDes[ei++];
}
ej = static_cast<int> (floor((chooseEvent - cumulateRates) / rates.des[ei]));
if (ej >= eventLists._desEvents[ei].size()) {
goto newChoose;
}/*
if (ei % c::nNeighCount == 0)
_nFreeDes++;
_nDesorbNeigh[ei % c::nNeighCount]++;*/
desorption(eventLists._desEvents[ei][ej]);
}
else {
chooseEvent -= rates.totalAds + rates.totalDes;
double cumulateRates = 0;
unsigned ei = 0, ej = 0;
while (cumulateRates + rates.sumsofDiff[ei] < chooseEvent) {
if (ei >= c::nDiffTypes) {
goto newChoose;
}
cumulateRates += rates.sumsofDiff[ei++];
}
ej = static_cast<int> (floor((chooseEvent - cumulateRates) / rates.diff[ei]));
if (ej >= eventLists._diffEvents[ei].size()) {
goto newChoose;
}
checkDiff(ei, eventLists._diffEvents[ei][ej]);
diffusion(eventLists._diffEvents[ei][ej]);
}
_nEvents++;
}
void Foam::pseudoSolidTetDecompositionMotionSolver::solve()
{
// Solve for mesh motion
if (!frozen_ && !firstMotion_)
{
Pout << "Correct mesh motion diffusion field." << endl;
diffusionPtr_->correct();
}
int iCorr = 0;
scalar initialResidual = 0;
do
{
Pout << "Correction: " << ++iCorr << endl;
tetFemVectorMatrix motionEqn
(
tetFem::laplacian(diffusion().motionGamma(), motionU())
+ tetFem::laplacianTranspose(diffusion().motionGamma(), motionU())
+ tetFem::laplacianTrace
(
(2*nu_/(1+2*nu_))*diffusion().motionGamma(),
motionU()
)
);
// Apply motion constraints
applyConstraints(motionEqn);
// Solve the motion equation
initialResidual = motionEqn.solve().initialResidual();
Pout << "Initial residual: " << initialResidual << endl;
}
while (initialResidual > convergenceTolerance_ && iCorr < nCorrectors_);
}
void yeseulWhitneyScene::draw(){
ofPushMatrix();
ofTranslate(dimensions.width/2, dimensions.height/2);
drawPattern();
diffusion();
ofPopMatrix();
}
void Foam::laplaceTetMotionSolver::solve()
{
// Solve for mesh motion
if (!frozen_ && !firstMotion_)
{
Info << "Correct mesh motion diffusion field." << endl;
diffusionPtr_->correct();
}
tetFemVectorMatrix motionEqn
(
tetFem::laplacian
(
diffusion().motionGamma(),
motionU()
)
);
// Apply motion constraints
applyConstraints(motionEqn);
// Solve the motion equation
if (firstMotion_)
{
firstMotion_ = false;
// In the first solution, solve the motion twice to avoid relative
// tolerance problem
for (label i = 0; i < 2; i++)
{
solverPerf_ = motionEqn.solve();
}
}
else
{
solverPerf_ = motionEqn.solve();
}
if (needTotDisplacement())
{
totDisplacement() += motionU()*tetMesh().time().deltaT();
}
}
///////////////////////////////////////////////////////////////////////////////
/// Calculate the temperature
///
///\param para Pointer to FFD parameters
///\param var Pointer to FFD simulation variables
///\param BINDEX Pointer to boundary index
///
///\return 0 if no error occurred
///////////////////////////////////////////////////////////////////////////////
int temp_step(PARA_DATA *para, REAL **var, int **BINDEX) {
REAL *T = var[TEMP], *T0 = var[TMP1];
int flag = 0;
flag = advect(para, var, TEMP, 0, T0, T, BINDEX);
if(flag!=0) {
ffd_log("temp_step(): Could not advect temperature.", FFD_ERROR);
return flag;
}
flag = diffusion(para, var, TEMP, 0, T, T0, BINDEX);
if(flag!=0) {
ffd_log("temp_step(): Could not diffuse temperature.", FFD_ERROR);
return flag;
}
return flag;
} // End of temp_step( )
/*
*************************************************************************
*
* Set initial conditions for CVODE solver
*
*************************************************************************
*/
void
CVODEModel::setInitialConditions(
SundialsAbstractVector* soln_init)
{
std::shared_ptr<SAMRAIVectorReal<double> > soln_init_samvect(
Sundials_SAMRAIVector::getSAMRAIVector(soln_init));
std::shared_ptr<PatchHierarchy> hierarchy(
soln_init_samvect->getPatchHierarchy());
for (int ln = 0; ln < hierarchy->getNumberOfLevels(); ++ln) {
std::shared_ptr<PatchLevel> level(hierarchy->getPatchLevel(ln));
for (int cn = 0; cn < soln_init_samvect->getNumberOfComponents(); ++cn) {
for (PatchLevel::iterator p(level->begin()); p != level->end(); ++p) {
const std::shared_ptr<Patch>& patch = *p;
/*
* Set initial conditions for y
*/
std::shared_ptr<CellData<double> > y_init(
SAMRAI_SHARED_PTR_CAST<CellData<double>, PatchData>(
soln_init_samvect->getComponentPatchData(cn, *patch)));
TBOX_ASSERT(y_init);
y_init->fillAll(d_initial_value);
/*
* Set initial diffusion coeff values.
* NOTE: in a "real" application, the diffusion coefficient is
* some function of y. Here, we just do a simple minded
* approach and set it to 1.
*/
std::shared_ptr<SideData<double> > diffusion(
SAMRAI_SHARED_PTR_CAST<SideData<double>, PatchData>(
patch->getPatchData(d_diff_id)));
TBOX_ASSERT(diffusion);
diffusion->fillAll(1.0);
}
}
}
}
void eulermaruyama(double *x, double *v, double *w, int *ix, int *iw, double dt, params *p, gsl_rng *rg)
/* simplified weak order 1.0 regular euler-maruyama scheme
( see E. Platen, N. Bruti-Liberati; Numerical Solution of Stochastic Differential Equations with Jumps in Finance; Springer 2010; p. 508,
C. Kim, E. Lee, P. Talkner, and P.Hanggi; Phys. Rev. E 76; 011109; 2007 )
*/
{
int i;
double l_xt, l_vt, l_wt, l_x, l_v, l_w;
double basex = 1.0,
basew = PI2;
for (i = (p->paths)==1?0:(p->paths); i < (p->paths)*2; ++i){
l_x = x[i];
l_v = v[i];
l_w = w[i];
l_xt = l_x + l_v*dt;
l_vt = l_v + drift(l_x, l_v, l_w, p)*dt
+ diffusion(dt, p, rg)
+ regular_jump(dt, p, rg);
l_wt = l_w + (p->omega)*dt;
//fold path parameters
//if (fabs(l_xt) > basex){
// l_xt -= floor(l_xt/basex)*basex;
// ix[i]++;
//}
if (l_wt > basew){
l_wt -= floor(l_wt/basew)*basew;
iw[i]++;
}
x[i] = l_xt;
v[i] = l_vt;
w[i] = l_wt;
}
}
double driftCorrected(double X, double t, double B)
{ // Corrected drift term
return drift(X,t) - B*diffusion(X,t)* diffusionDerivative(X, t);
}
void
UZRectMollerup::tick (const GeometryRect& geo,
const std::vector<size_t>& drain_cell,
const double drain_water_level,
const Soil& soil,
SoilWater& soil_water, const SoilHeat& soil_heat,
const Surface& surface, const Groundwater& groundwater,
const double dt, Treelog& msg)
{
daisy_assert (K_average.get ());
const size_t edge_size = geo.edge_size (); // number of edges
const size_t cell_size = geo.cell_size (); // number of cells
// Insert magic here.
ublas::vector<double> Theta (cell_size); // water content
ublas::vector<double> Theta_previous (cell_size); // at start of small t-step
ublas::vector<double> h (cell_size); // matrix pressure
ublas::vector<double> h_previous (cell_size); // at start of small timestep
ublas::vector<double> h_ice (cell_size); //
ublas::vector<double> S (cell_size); // sink term
ublas::vector<double> S_vol (cell_size); // sink term
#ifdef TEST_OM_DEN_ER_BRUGT
ublas::vector<double> S_macro (cell_size); // sink term
std::vector<double> S_drain (cell_size, 0.0); // matrix-> macro -> drain flow
std::vector<double> S_drain_sum (cell_size, 0.0); // For large timestep
const std::vector<double> S_matrix (cell_size, 0.0); // matrix -> macro
std::vector<double> S_matrix_sum (cell_size, 0.0); // for large timestep
#endif
ublas::vector<double> T (cell_size); // temperature
ublas::vector<double> Kold (edge_size); // old hydraulic conductivity
ublas::vector<double> Ksum (edge_size); // Hansen hydraulic conductivity
ublas::vector<double> Kcell (cell_size); // hydraulic conductivity
ublas::vector<double> Kold_cell (cell_size); // old hydraulic conductivity
ublas::vector<double> Ksum_cell (cell_size); // Hansen hydraulic conductivity
ublas::vector<double> h_lysimeter (cell_size);
std::vector<bool> active_lysimeter (cell_size);
const std::vector<size_t>& edge_above = geo.cell_edges (Geometry::cell_above);
const size_t edge_above_size = edge_above.size ();
ublas::vector<double> remaining_water (edge_above_size);
std::vector<bool> drain_cell_on (drain_cell.size (),false);
for (size_t i = 0; i < edge_above_size; i++)
{
const size_t edge = edge_above[i];
remaining_water (i) = surface.h_top (geo, edge);
}
ublas::vector<double> q; // Accumulated flux
q = ublas::zero_vector<double> (edge_size);
ublas::vector<double> dq (edge_size); // Flux in small timestep.
dq = ublas::zero_vector<double> (edge_size);
//Make Qmat area diagonal matrix
//Note: This only needs to be calculated once...
ublas::banded_matrix<double> Qmat (cell_size, cell_size, 0, 0);
for (int c = 0; c < cell_size; c++)
Qmat (c, c) = geo.cell_volume (c);
// make vectors
for (size_t cell = 0; cell != cell_size ; ++cell)
{
Theta (cell) = soil_water.Theta (cell);
h (cell) = soil_water.h (cell);
h_ice (cell) = soil_water.h_ice (cell);
S (cell) = soil_water.S_sum (cell);
S_vol (cell) = S (cell) * geo.cell_volume (cell);
if (use_forced_T)
T (cell) = forced_T;
else
T (cell) = soil_heat.T (cell);
h_lysimeter (cell) = geo.zplus (cell) - geo.cell_z (cell);
}
// Remember old value.
Theta_error = Theta;
// Start time loop
double time_left = dt; // How much of the large time step left.
double ddt = dt; // We start with small == large time step.
int number_of_time_step_reductions = 0;
int iterations_with_this_time_step = 0;
int n_small_time_steps = 0;
while (time_left > 0.0)
{
if (ddt > time_left)
ddt = time_left;
std::ostringstream tmp_ddt;
tmp_ddt << "Time t = " << (dt - time_left)
<< "; ddt = " << ddt
<< "; steps " << n_small_time_steps
<< "; time left = " << time_left;
Treelog::Open nest (msg, tmp_ddt.str ());
if (n_small_time_steps > 0
&& (n_small_time_steps%msg_number_of_small_time_steps) == 0)
{
msg.touch ();
msg.flush ();
}
n_small_time_steps++;
if (n_small_time_steps > max_number_of_small_time_steps)
{
msg.debug ("Too many small timesteps");
throw "Too many small timesteps";
}
// Initialization for each small time step.
if (debug > 0)
{
std::ostringstream tmp;
tmp << "h = " << h << "\n";
tmp << "Theta = " << Theta;
msg.message (tmp.str ());
}
int iterations_used = 0;
h_previous = h;
Theta_previous = Theta;
if (debug == 5)
{
std::ostringstream tmp;
tmp << "Remaining water at start: " << remaining_water;
msg.message (tmp.str ());
}
ublas::vector<double> h_conv;
for (size_t cell = 0; cell != cell_size ; ++cell)
active_lysimeter[cell] = h (cell) > h_lysimeter (cell);
for (size_t edge = 0; edge != edge_size ; ++edge)
{
Kold[edge] = find_K_edge (soil, geo, edge, h, h_ice, h_previous, T);
Ksum [edge] = 0.0;
}
std::vector<top_state> state (edge_above.size (), top_undecided);
// We try harder with smaller timesteps.
const int max_loop_iter
= max_iterations * (number_of_time_step_reductions
* max_iterations_timestep_reduction_factor + 1);
do // Start iteration loop
{
h_conv = h;
iterations_used++;
std::ostringstream tmp_conv;
tmp_conv << "Convergence " << iterations_used;
Treelog::Open nest (msg, tmp_conv.str ());
if (debug == 7)
msg.touch ();
// Calculate conductivity - The Hansen method
for (size_t e = 0; e < edge_size; e++)
{
Ksum[e] += find_K_edge (soil, geo, e, h, h_ice, h_previous, T);
Kedge[e] = (Ksum[e] / (iterations_used + 0.0)+ Kold[e]) / 2.0;
}
//Initialize diffusive matrix
Solver::Matrix diff (cell_size);
// diff = ublas::zero_matrix<double> (cell_size, cell_size);
diffusion (geo, Kedge, diff);
//Initialize gravitational matrix
ublas::vector<double> grav (cell_size); //ublass compatibility
grav = ublas::zero_vector<double> (cell_size);
gravitation (geo, Kedge, grav);
// Boundary matrices and vectors
ublas::banded_matrix<double> Dm_mat (cell_size, cell_size,
0, 0); // Dir bc
Dm_mat = ublas::zero_matrix<double> (cell_size, cell_size);
ublas::vector<double> Dm_vec (cell_size); // Dir bc
Dm_vec = ublas::zero_vector<double> (cell_size);
ublas::vector<double> Gm (cell_size); // Dir bc
Gm = ublas::zero_vector<double> (cell_size);
ublas::vector<double> B (cell_size); // Neu bc
B = ublas::zero_vector<double> (cell_size);
lowerboundary (geo, groundwater, active_lysimeter, h,
Kedge,
dq, Dm_mat, Dm_vec, Gm, B, msg);
upperboundary (geo, soil, T, surface, state, remaining_water, h,
Kedge,
dq, Dm_mat, Dm_vec, Gm, B, ddt, debug, msg, dt);
Darcy (geo, Kedge, h, dq); //for calculating drain fluxes
//Initialize water capacity matrix
ublas::banded_matrix<double> Cw (cell_size, cell_size, 0, 0);
for (size_t c = 0; c < cell_size; c++)
Cw (c, c) = soil.Cw2 (c, h[c]);
std::vector<double> h_std (cell_size);
//ublas vector -> std vector
std::copy(h.begin (), h.end (), h_std.begin ());
#ifdef TEST_OM_DEN_ER_BRUGT
for (size_t cell = 0; cell != cell_size ; ++cell)
{
S_macro (cell) = (S_matrix[cell] + S_drain[cell])
* geo.cell_volume (cell);
}
#endif
//Initialize sum matrix
Solver::Matrix summat (cell_size);
noalias (summat) = diff + Dm_mat;
//Initialize sum vector
ublas::vector<double> sumvec (cell_size);
sumvec = grav + B + Gm + Dm_vec - S_vol
#ifdef TEST_OM_DEN_ER_BRUGT
- S_macro
#endif
;
// QCw is shorthand for Qmatrix * Cw
Solver::Matrix Q_Cw (cell_size);
noalias (Q_Cw) = prod (Qmat, Cw);
//Initialize A-matrix
Solver::Matrix A (cell_size);
noalias (A) = (1.0 / ddt) * Q_Cw - summat;
// Q_Cw_h is shorthand for Qmatrix * Cw * h
const ublas::vector<double> Q_Cw_h = prod (Q_Cw, h);
//Initialize b-vector
ublas::vector<double> b (cell_size);
//b = sumvec + (1.0 / ddt) * (Qmatrix * Cw * h + Qmatrix *(Wxx-Wyy));
b = sumvec + (1.0 / ddt) * (Q_Cw_h
+ prod (Qmat, Theta_previous-Theta));
// Force active drains to zero h.
drain (geo, drain_cell, drain_water_level,
h, Theta_previous, Theta, S_vol,
#ifdef TEST_OM_DEN_ER_BRUGT
S_macro,
#endif
dq, ddt, drain_cell_on, A, b, debug, msg);
try {
solver->solve (A, b, h); // Solve Ah=b with regard to h.
} catch (const char *const error) {
std::ostringstream tmp;
tmp << "Could not solve equation system: " << error;
msg.warning (tmp.str ());
// Try smaller timestep.
iterations_used = max_loop_iter + 100;
break;
}
for (int c=0; c < cell_size; c++) // update Theta
Theta (c) = soil.Theta (c, h (c), h_ice (c));
if (debug > 1)
{
std::ostringstream tmp;
tmp << "Time left = " << time_left << ", ddt = " << ddt
<< ", iteration = " << iterations_used << "\n";
tmp << "B = " << B << "\n";
tmp << "h = " << h << "\n";
tmp << "Theta = " << Theta;
msg.message (tmp.str ());
}
for (int c=0; c < cell_size; c++)
{
if (h (c) < min_pressure_potential || h (c) > max_pressure_potential)
{
std::ostringstream tmp;
tmp << "Pressure potential out of realistic range, h["
<< c << "] = " << h (c);
msg.debug (tmp.str ());
iterations_used = max_loop_iter + 100;
break;
}
}
}
while (!converges (h_conv, h) && iterations_used <= max_loop_iter);
if (iterations_used > max_loop_iter)
{
number_of_time_step_reductions++;
if (number_of_time_step_reductions > max_time_step_reductions)
{
msg.debug ("Could not find solution");
throw "Could not find solution";
}
iterations_with_this_time_step = 0;
ddt /= time_step_reduction;
h = h_previous;
Theta = Theta_previous;
}
else
{
// Update dq for new h.
ublas::banded_matrix<double> Dm_mat (cell_size, cell_size,
0, 0); // Dir bc
Dm_mat = ublas::zero_matrix<double> (cell_size, cell_size);
ublas::vector<double> Dm_vec (cell_size); // Dir bc
Dm_vec = ublas::zero_vector<double> (cell_size);
ublas::vector<double> Gm (cell_size); // Dir bc
Gm = ublas::zero_vector<double> (cell_size);
ublas::vector<double> B (cell_size); // Neu bc
B = ublas::zero_vector<double> (cell_size);
lowerboundary (geo, groundwater, active_lysimeter, h,
Kedge,
dq, Dm_mat, Dm_vec, Gm, B, msg);
upperboundary (geo, soil, T, surface, state, remaining_water, h,
Kedge,
dq, Dm_mat, Dm_vec, Gm, B, ddt, debug, msg, dt);
Darcy (geo, Kedge, h, dq);
#ifdef TEST_OM_DEN_ER_BRUGT
// update macropore flow components
for (int c = 0; c < cell_size; c++)
{
S_drain_sum[c] += S_drain[c] * ddt/dt;
S_matrix_sum[c] += S_matrix[c] * ddt/dt;
}
#endif
std::vector<double> h_std_new (cell_size);
std::copy(h.begin (), h.end (), h_std_new.begin ());
// Update remaining_water.
for (size_t i = 0; i < edge_above.size (); i++)
{
const int edge = edge_above[i];
const int cell = geo.edge_other (edge, Geometry::cell_above);
const double out_sign = (cell == geo.edge_from (edge))
? 1.0 : -1.0;
remaining_water[i] += out_sign * dq (edge) * ddt;
daisy_assert (std::isfinite (dq (edge)));
}
if (debug == 5)
{
std::ostringstream tmp;
tmp << "Remaining water at end: " << remaining_water;
msg.message (tmp.str ());
}
// Contribution to large time step.
daisy_assert (std::isnormal (dt));
daisy_assert (std::isnormal (ddt));
q += dq * ddt / dt;
for (size_t e = 0; e < edge_size; e++)
{
daisy_assert (std::isfinite (dq (e)));
daisy_assert (std::isfinite (q (e)));
}
for (size_t e = 0; e < edge_size; e++)
{
daisy_assert (std::isfinite (dq (e)));
daisy_assert (std::isfinite (q (e)));
}
time_left -= ddt;
iterations_with_this_time_step++;
if (iterations_with_this_time_step > time_step_reduction)
{
number_of_time_step_reductions--;
iterations_with_this_time_step = 0;
ddt *= time_step_reduction;
}
}
// End of small time step.
}
// Mass balance.
// New = Old - S * dt + q_in * dt - q_out * dt + Error =>
// 0 = Old - New - S * dt + q_in * dt - q_out * dt + Error
Theta_error -= Theta; // Old - New
Theta_error -= S * dt;
#ifdef TEST_OM_DEN_ER_BRUGT
for (size_t c = 0; c < cell_size; c++)
Theta_error (c) -= (S_matrix_sum[c] + S_drain_sum[c]) * dt;
#endif
for (size_t edge = 0; edge != edge_size; ++edge)
{
const int from = geo.edge_from (edge);
const int to = geo.edge_to (edge);
const double flux = q (edge) * geo.edge_area (edge) * dt;
if (geo.cell_is_internal (from))
Theta_error (from) -= flux / geo.cell_volume (from);
if (geo.cell_is_internal (to))
Theta_error (to) += flux / geo.cell_volume (to);
}
// Find drain sink from mass balance.
#ifdef TEST_OM_DEN_ER_BRUGT
std::fill(S_drain.begin (), S_drain.end (), 0.0);
#else
std::vector<double> S_drain (cell_size);
#endif
for (size_t i = 0; i < drain_cell.size (); i++)
{
const size_t cell = drain_cell[i];
S_drain[cell] = Theta_error (cell) / dt;
Theta_error (cell) -= S_drain[cell] * dt;
}
if (debug == 2)
{
double total_error = 0.0;
double total_abs_error = 0.0;
double max_error = 0.0;
int max_cell = -1;
for (size_t cell = 0; cell != cell_size; ++cell)
{
const double volume = geo.cell_volume (cell);
const double error = Theta_error (cell);
total_error += volume * error;
total_abs_error += std::fabs (volume * error);
if (std::fabs (error) > std::fabs (max_error))
{
max_error = error;
max_cell = cell;
}
}
std::ostringstream tmp;
tmp << "Total error = " << total_error << " [cm^3], abs = "
<< total_abs_error << " [cm^3], max = " << max_error << " [] in cell "
<< max_cell;
msg.message (tmp.str ());
}
// Make it official.
for (size_t cell = 0; cell != cell_size; ++cell)
soil_water.set_content (cell, h (cell), Theta (cell));
#ifdef TEST_OM_DEN_ER_BRUGT
soil_water.add_tertiary_sink (S_matrix_sum);
soil_water.drain (S_drain_sum, msg);
#endif
for (size_t edge = 0; edge != edge_size; ++edge)
{
daisy_assert (std::isfinite (q[edge]));
soil_water.set_flux (edge, q[edge]);
}
soil_water.drain (S_drain, msg);
// End of large time step.
}
double DiffusionProcess::variance(double t0, double x0, double dt) const
{
double dSigma = diffusion(t0, x0);
return dSigma * dSigma * dt;
}
int main(){
bool deposit = true;
printf("Enter value for diffusion rate D: ");
scanf(" %f", &D);
printf("Enter value for deposition rate F: ");
scanf(" %f", &F);
printf("Enter total number of steps: ");
scanf(" %d", &steps);
FILE *file = fopen("Output.txt", "w");
fclose(file);
int deposition_ct=0;
create_lattice();
//sets inverse pointer array to -1
for(i=0;i<L;i++){
for(j=0;j<L;j++){
ipointa[i][j]=-1;
}}
//initialize ip and im arrays to take care to pbc's easilyn
for(i=0;i<L;i++){
ip[i]=i+1;
im[i]=i-1;
}
ip[L-1]=0;
im[0]=L-1;
//initialize nbxa[L][4] and nbya[L][4] for the 4 directions
for(i=0;i<L;i++){
nbxa[i][0]=ip[i];
nbya[i][0]=i;
nbxa[i][1]=i;
nbya[i][1]=im[i];
nbxa[i][2]=im[i];
nbya[i][2]=i;
nbxa[i][3]=i;
nbya[i][3]=ip[i];
}
for(int i = 0; i <steps; i++){
float Rdep = F*(L^2);
float Rdiff = monomer_ct * D;
P_d = Rdep / (Rdep + Rdiff);
P_f = 1 - P_d;
float random = (rand() % 10000)/10000.0;
fprintf(debug, "P_d %f, random %f\n", P_d, random);
fprintf(debug, "monomer_ct %d\n", monomer_ct);
if((random < P_d) /*&& (deposit)*/){
deposition();
fprintf(debug, "Deposition \n");
deposition_ct++;
}
else{
fprintf(debug, "Carrying out diffusion\n");
diffusion();
//printf("Diffusion \n");
}
pbc();
print_walkers();
output();
//draw();
}
}
int main(int argc, char* argv[])
{
acc_set_device_num(0, acc_device_nvidia);
// read command line arguments
readcmdline(&options, argc, argv);
int nx = options.nx;
int ny = options.ny;
int N = options.N;
int nt = options.nt;
printf("========================================================================\n");
printf(" Welcome to mini-stencil!\n");
printf("mesh :: %d * %d, dx = %f\n", nx, ny, options.dx);
printf("time :: %d, time steps from 0 .. %f\n", nt, options.nt * options.dt);
printf("========================================================================\n");
// allocate global fields
x_new = (double*) malloc(sizeof(double)*nx*ny);
x_old = (double*) malloc(sizeof(double)*nx*ny);
bndN = (double*) malloc(sizeof(double)*nx);
bndS = (double*) malloc(sizeof(double)*nx);
bndE = (double*) malloc(sizeof(double)*ny);
bndW = (double*) malloc(sizeof(double)*ny);
double* b = (double*) malloc(N*sizeof(double));
double* deltax = (double*) malloc(N*sizeof(double));
// set dirichlet boundary conditions to 0 all around
memset(x_old, 0, sizeof(double) * nx * ny);
memset(bndN, 0, sizeof(double) * nx);
memset(bndS, 0, sizeof(double) * nx);
memset(bndE, 0, sizeof(double) * ny);
memset(bndW, 0, sizeof(double) * ny);
memset(deltax, 0, sizeof(double) * N);
// set the initial condition
// a circle of concentration 0.1 centred at (xdim/4, ydim/4) with radius
// no larger than 1/8 of both xdim and ydim
memset(x_new, 0, sizeof(double) * nx * ny);
double xc = 1.0 / 4.0;
double yc = (ny - 1) * options.dx / 4;
double radius = fmin(xc, yc) / 2.0;
int i,j;
//
for (j = 0; j < ny; j++)
{
double y = (j - 1) * options.dx;
for (i = 0; i < nx; i++)
{
double x = (i - 1) * options.dx;
if ((x - xc) * (x - xc) + (y - yc) * (y - yc) < radius * radius)
//((double(*)[nx])x_new)[j][i] = 0.1;
x_new[i+j*nx] = 0.1;
}
}
flops_bc = 0;
flops_diff = 0;
flops_blas1 = 0;
verbose_output = 0;
iters_cg = 0;
iters_newton = 0;
// initialize temporary storage fields used by the cg solver
// I do this here so that the fields are persistent between calls
// to the CG solver. This is useful if we want to avoid malloc/free calls
// on the device for the OpenACC implementation (feel free to suggest a better
// method for doing this)
printf("INITIALIZING CG STATE\n");
Ap = (double*) malloc(N*sizeof(double));
r = (double*) malloc(N*sizeof(double));
p = (double*) malloc(N*sizeof(double));
Fx = (double*) malloc(N*sizeof(double));
Fxold = (double*) malloc(N*sizeof(double));
v = (double*) malloc(N*sizeof(double));
xold = (double*) malloc(N*sizeof(double));
int cg_converged = 1;
double timespent;
// start timer
timespent = -omp_get_wtime();
// main timeloop
double tolerance = 1.e-6;
int timestep;
for (timestep = 1; timestep <= nt; timestep++)
{
// set x_new and x_old to be the solution
ss_copy(x_old, x_new, N);
double residual;
int converged = 0;
int it = 1;
for ( ; it <= 50; it++)
{
// compute residual : requires both x_new and x_old
diffusion(x_new, b);
residual = ss_norm2(b, N);
// check for convergence
if (residual < tolerance)
{
converged = 1;
break;
}
// solve linear system to get -deltax
ss_cg(deltax, b, 200, tolerance, &cg_converged);
// check that the CG solver converged
if (!cg_converged) break;
// update solution
ss_axpy(x_new, -1.0, deltax, N);
}
iters_newton += it;
// output some statistics
//if (converged && verbose_output)
if (converged && verbose_output)
printf("step %d required %d iterations for residual %E\n", timestep, it, residual);
if (!converged)
{
fprintf(stderr, "step %d ERROR : nonlinear iterations failed to converge\n", timestep);
break;
}
}
// get times
timespent += omp_get_wtime();
unsigned long long flops_total = flops_diff + flops_blas1;
////////////////////////////////////////////////////////////////////
// write final solution to BOV file for visualization
////////////////////////////////////////////////////////////////////
// binary data
{
FILE* output = fopen("output.bin", "w");
fwrite(x_new, sizeof(double), nx * ny, output);
fclose(output);
}
// metadata
{
FILE* output = fopen("output.bov", "wb");
fprintf(output, "TIME: 0.0\n");
fprintf(output, "DATA_FILE: output.bin\n");
fprintf(output, "DATA_SIZE: %d, %d, 1\n", nx, ny);
fprintf(output, "DATA_FORMAT: DOUBLE\n");
fprintf(output, "VARIABLE: phi\n");
fprintf(output, "DATA_ENDIAN: LITTLE\n");
fprintf(output, "CENTERING: nodal\n");
//fprintf(output, "BYTE_OFFSET: 4\n");
fprintf(output, "BRICK_SIZE: 1.0 %f 1.0\n", (ny - 1) * options.dx);
fclose(output);
}
// print table sumarizing results
printf("--------------------------------------------------------------------------------\n");
printf("simulation took %f seconds (%f GFLOP/s)\n", timespent, flops_total / 1e9 / timespent);
printf("%u conjugate gradient iterations\n", iters_cg);
printf("%u newton iterations\n", iters_newton);
printf("--------------------------------------------------------------------------------\n");
// deallocate global fields
free (x_new);
free (x_old);
free (bndN);
free (bndS);
free (bndE);
free (bndW);
printf("Goodbye!\n");
return 0;
}
Real VarianceGammaProcess::omega(Time t, Real x) const {
Real sigma = diffusion(t, x);
return 1 / nu() * std::log(1 - theta() * nu() - sigma * sigma * nu() * 0.5);
}
int main(int argc, char *argv[])
{
int step, ie, iside, i, j, k;
double mflops, tmax, nelt_tot = 0.0;
char Class;
logical ifmortar = false, verified;
double t2, trecs[t_last+1];
char *t_names[t_last+1];
//--------------------------------------------------------------------
// Initialize NUMA control
//--------------------------------------------------------------------
numa_initialize_env(NUMA_MIGRATE_EXISTING);
//---------------------------------------------------------------------
// Read input file (if it exists), else take
// defaults from parameters
//---------------------------------------------------------------------
FILE *fp;
if ((fp = fopen("timer.flag", "r")) != NULL) {
timeron = true;
t_names[t_total] = "total";
t_names[t_init] = "init";
t_names[t_convect] = "convect";
t_names[t_transfb_c] = "transfb_c";
t_names[t_diffusion] = "diffusion";
t_names[t_transf] = "transf";
t_names[t_transfb] = "transfb";
t_names[t_adaptation] = "adaptation";
t_names[t_transf2] = "transf+b";
t_names[t_add2] = "add2";
fclose(fp);
} else {
timeron = false;
}
printf("\n\n NAS Parallel Benchmarks (NPB3.3-OMP-C) - UA Benchmark\n\n");
if ((fp = fopen("inputua.data", "r")) != NULL) {
int result;
printf(" Reading from input file inputua.data\n");
result = fscanf(fp, "%d", &fre);
while (fgetc(fp) != '\n');
result = fscanf(fp, "%d", &niter);
while (fgetc(fp) != '\n');
result = fscanf(fp, "%d", &nmxh);
while (fgetc(fp) != '\n');
result = fscanf(fp, "%lf", &alpha);
Class = 'U';
fclose(fp);
} else {
printf(" No input file inputua.data. Using compiled defaults\n");
fre = FRE_DEFAULT;
niter = NITER_DEFAULT;
nmxh = NMXH_DEFAULT;
alpha = ALPHA_DEFAULT;
Class = CLASS_DEFAULT;
}
dlmin = pow(0.5, REFINE_MAX);
dtime = 0.04*dlmin;
printf(" Levels of refinement: %8d\n", REFINE_MAX);
printf(" Adaptation frequency: %8d\n", fre);
printf(" Time steps: %8d dt: %15.6E\n", niter, dtime);
printf(" CG iterations: %8d\n", nmxh);
printf(" Heat source radius: %8.4f\n", alpha);
printf(" Number of available threads: %8d\n", omp_get_max_threads());
printf("\n");
top_constants();
for (i = 1; i <= t_last; i++) {
timer_clear(i);
}
if (timeron) timer_start(t_init);
// set up initial mesh (single element) and solution (all zero)
create_initial_grid();
r_init_omp((double *)ta1, ntot, 0.0);
nr_init_omp((int *)sje, 4*6*nelt, -1);
init_locks();
// compute tables of coefficients and weights
coef();
geom1();
// compute the discrete laplacian operators
setdef();
// prepare for the preconditioner
setpcmo_pre();
// refine initial mesh and do some preliminary work
time = 0.0;
mortar();
prepwork();
adaptation(&ifmortar, 0);
if (timeron) timer_stop(t_init);
timer_clear(1);
time = 0.0;
for (step = 0; step <= niter; step++) {
if (step == 1) {
// reset the solution and start the timer, keep track of total no elms
r_init((double *)ta1, ntot, 0.0);
time = 0.0;
nelt_tot = 0.0;
for (i = 1; i <= t_last; i++) {
if (i != t_init) timer_clear(i);
}
timer_start(1);
}
// advance the convection step
convect(ifmortar);
if (timeron) timer_start(t_transf2);
// prepare the intital guess for cg
transf(tmort, (double *)ta1);
// compute residual for diffusion term based on intital guess
// compute the left hand side of equation, lapacian t
#pragma omp parallel default(shared) private(ie,k,j,i)
{
#pragma omp for
for (ie = 0; ie < nelt; ie++) {
laplacian(ta2[ie], ta1[ie], size_e[ie]);
}
// compute the residual
#pragma omp for
for (ie = 0; ie < nelt; ie++) {
for (k = 0; k < LX1; k++) {
for (j = 0; j < LX1; j++) {
for (i = 0; i < LX1; i++) {
trhs[ie][k][j][i] = trhs[ie][k][j][i] - ta2[ie][k][j][i];
}
}
}
}
} //end parallel
// get the residual on mortar
transfb(rmor, (double *)trhs);
if (timeron) timer_stop(t_transf2);
// apply boundary condition: zero out the residual on domain boundaries
// apply boundary conidtion to trhs
#pragma omp parallel for default(shared) private(ie,iside)
for (ie = 0; ie < nelt; ie++) {
for (iside = 0; iside < NSIDES; iside++) {
if (cbc[ie][iside] == 0) {
facev(trhs[ie], iside, 0.0);
}
}
}
// apply boundary condition to rmor
col2(rmor, tmmor, nmor);
// call the conjugate gradient iterative solver
diffusion(ifmortar);
// add convection and diffusion
if (timeron) timer_start(t_add2);
add2((double *)ta1, (double *)t, ntot);
if (timeron) timer_stop(t_add2);
// perform mesh adaptation
time = time + dtime;
if ((step != 0) && (step/fre*fre == step)) {
if (step != niter) {
adaptation(&ifmortar, step);
}
} else {
ifmortar = false;
}
nelt_tot = nelt_tot + (double)(nelt);
}
timer_stop(1);
tmax = timer_read(1);
verify(&Class, &verified);
// compute millions of collocation points advanced per second.
// diffusion: nmxh advancements, convection: 1 advancement
mflops = nelt_tot*(double)(LX1*LX1*LX1*(nmxh+1))/(tmax*1.e6);
print_results("UA", Class, REFINE_MAX, 0, 0, niter,
tmax, mflops, " coll. point advanced",
verified, NPBVERSION, COMPILETIME, CS1, CS2, CS3, CS4, CS5,
CS6, "(none)");
//---------------------------------------------------------------------
// More timers
//---------------------------------------------------------------------
if (timeron) {
for (i = 1; i <= t_last; i++) {
trecs[i] = timer_read(i);
}
if (tmax == 0.0) tmax = 1.0;
printf(" SECTION Time (secs)\n");
for (i = 1; i <= t_last; i++) {
printf(" %-10s:%9.3f (%6.2f%%)\n",
t_names[i], trecs[i], trecs[i]*100./tmax);
if (i == t_transfb_c) {
t2 = trecs[t_convect] - trecs[t_transfb_c];
printf(" --> %11s:%9.3f (%6.2f%%)\n",
"sub-convect", t2, t2*100./tmax);
} else if (i == t_transfb) {
t2 = trecs[t_diffusion] - trecs[t_transf] - trecs[t_transfb];
printf(" --> %11s:%9.3f (%6.2f%%)\n",
"sub-diffuse", t2, t2*100./tmax);
}
}
}
//--------------------------------------------------------------------
// Teardown NUMA control
//--------------------------------------------------------------------
numa_shutdown();
return 0;
}
//--------------------------------------------------------------
void Rd::step(int numSteps){
for(int i = 0; i < numSteps; i++){
diffusion();
reaction();
}
}
int CVODEModel::CVSpgmrPrecondSet(
double t,
SundialsAbstractVector* y,
SundialsAbstractVector* fy,
int jok,
int* jcurPtr,
double gamma,
SundialsAbstractVector* vtemp1,
SundialsAbstractVector* vtemp2,
SundialsAbstractVector* vtemp3)
{
#ifndef USE_FAC_PRECONDITIONER
NULL_USE(t);
NULL_USE(y);
NULL_USE(gamma);
#endif
NULL_USE(fy);
NULL_USE(jok);
NULL_USE(jcurPtr);
NULL_USE(vtemp1);
NULL_USE(vtemp2);
NULL_USE(vtemp3);
#ifdef USE_FAC_PRECONDITIONER
/*
* Convert passed-in CVODE vectors into SAMRAI vectors
*/
std::shared_ptr<SAMRAIVectorReal<double> > y_samvect(
Sundials_SAMRAIVector::getSAMRAIVector(y));
std::shared_ptr<PatchHierarchy> hierarchy(
y_samvect->getPatchHierarchy());
int y_indx = y_samvect->getComponentDescriptorIndex(0);
/*
* Construct refine algorithm to fill boundaries of solution vector
*/
RefineAlgorithm fill_soln_vector_bounds;
std::shared_ptr<RefineOperator> refine_op(d_grid_geometry->
lookupRefineOperator(d_soln_var,
"CONSERVATIVE_LINEAR_REFINE"));
fill_soln_vector_bounds.registerRefine(d_soln_scr_id,
y_samvect->getComponentDescriptorIndex(0),
d_soln_scr_id,
refine_op);
/*
* Construct coarsen algorithm to fill interiors on coarser levels
* with solution on finer level.
*/
CoarsenAlgorithm fill_soln_interior_on_coarser(d_dim);
std::shared_ptr<CoarsenOperator> coarsen_op(d_grid_geometry->
lookupCoarsenOperator(d_soln_var,
"CONSERVATIVE_COARSEN"));
fill_soln_interior_on_coarser.registerCoarsen(y_indx,
y_indx,
coarsen_op);
/*
* Step through levels - largest to smallest
*/
for (int amr_level = hierarchy->getFinestLevelNumber();
amr_level >= 0;
--amr_level) {
std::shared_ptr<PatchLevel> level(
hierarchy->getPatchLevel(amr_level));
std::shared_ptr<RefineSchedule> fill_soln_vector_bounds_sched =
fill_soln_vector_bounds.createSchedule(level,
amr_level - 1,
hierarchy,
this);
if (!level->checkAllocated(d_soln_scr_id)) {
level->allocatePatchData(d_soln_scr_id);
}
fill_soln_vector_bounds_sched->fillData(t);
/*
* Construct a coarsen schedule for all levels larger than coarsest,
* and fill interiors of solution vector on coarser levels using fine
* data.
*/
if (amr_level > 0) {
std::shared_ptr<PatchLevel> coarser_level(
hierarchy->getPatchLevel(amr_level - 1));
std::shared_ptr<CoarsenSchedule> fill_soln_interior_on_coarser_sched(
fill_soln_interior_on_coarser.createSchedule(coarser_level,
level));
fill_soln_interior_on_coarser_sched->coarsenData();
}
for (PatchLevel::iterator p(level->begin()); p != level->end(); ++p) {
const std::shared_ptr<Patch>& patch = *p;
const Index ifirst(patch->getBox().lower());
const Index ilast(patch->getBox().upper());
std::shared_ptr<SideData<double> > diffusion(
SAMRAI_SHARED_PTR_CAST<SideData<double>, PatchData>(
patch->getPatchData(d_diff_id)));
TBOX_ASSERT(diffusion);
diffusion->fillAll(1.0);
TBOX_ASSERT((t - d_current_soln_time) >= 0.);
/*
* Set Neumann fluxes and flag array (if desired)
*/
if (d_use_neumann_bcs) {
std::shared_ptr<OuterfaceData<int> > flag_data(
SAMRAI_SHARED_PTR_CAST<OuterfaceData<int>, PatchData>(
patch->getPatchData(d_flag_id)));
std::shared_ptr<OuterfaceData<double> > neuf_data(
SAMRAI_SHARED_PTR_CAST<OuterfaceData<double>, PatchData>(
patch->getPatchData(d_neuf_id)));
TBOX_ASSERT(flag_data);
TBOX_ASSERT(neuf_data);
/*
* Outerface data access:
* neuf_data->getPointer(axis,face);
* where axis specifies X, Y, or Z (0,1,2 respectively)
* and face specifies lower or upper (0,1 respectively)
*/
if (d_dim == Dimension(2)) {
SAMRAI_F77_FUNC(setneufluxvalues2d, SETNEUFLUXVALUES2D) (
ifirst(0), ilast(0),
ifirst(1), ilast(1),
d_bdry_types,
&d_bdry_edge_val[0],
flag_data->getPointer(0, 0), // x lower
flag_data->getPointer(0, 1), // x upper
flag_data->getPointer(1, 0), // y lower
flag_data->getPointer(1, 1), // y upper
neuf_data->getPointer(0, 0), // x lower
neuf_data->getPointer(0, 1), // x upper
neuf_data->getPointer(1, 0), // y lower
neuf_data->getPointer(1, 1)); // y upper
} else if (d_dim == Dimension(3)) {
SAMRAI_F77_FUNC(setneufluxvalues3d, SETNEUFLUXVALUES3D) (
ifirst(0), ilast(0),
ifirst(1), ilast(1),
ifirst(2), ilast(2),
d_bdry_types,
&d_bdry_face_val[0],
flag_data->getPointer(0, 0), // x lower
flag_data->getPointer(0, 1), // x upper
flag_data->getPointer(1, 0), // y lower
flag_data->getPointer(1, 1), // y upper
flag_data->getPointer(2, 0), // z lower
flag_data->getPointer(2, 1), // z lower
neuf_data->getPointer(0, 0), // x lower
neuf_data->getPointer(0, 1), // x upper
neuf_data->getPointer(1, 0), // y lower
neuf_data->getPointer(1, 1), // y upper
neuf_data->getPointer(2, 0), // z lower
neuf_data->getPointer(2, 1)); // z upper
}
}
} // patch loop
level->deallocatePatchData(d_soln_scr_id);
} // level loop
/*
* Set boundaries. The "bdry_types" array holds a set of integers
* where 0 = dirichlet and 1 = neumann boundary conditions.
*/
if (d_use_neumann_bcs) {
d_FAC_solver->setBoundaries("Mixed", d_neuf_id, d_flag_id, d_bdry_types);
} else {
d_FAC_solver->setBoundaries("Dirichlet");
}
d_FAC_solver->setCConstant(1.0 / gamma);
d_FAC_solver->setDPatchDataId(d_diff_id);
/*
* increment counter for number of precond setup calls
*/
++d_number_precond_setup;
#endif
/*
* We return 0 or 1 here - 0 if it passes, 1 if it fails. For now,
* just be optimistic and return 0. Eventually we should add some
* assertion handling above to set what this value should be.
*/
return 0;
}
void FluidSimulator::step_density(float *x, float *x0, float*u,
float *v, float diffusion_rate){
add_source(x, x0);
swap(x0, x); diffusion(0, x, x0, diffusion_rate);
swap(x0, x); advection(0, x, x0, u, v);
}
// returns the variance of the process after a time reversal
// returns Var(x_{t_0 + Delta t} | x_{t_0} = x_0)
// By default, it returns the Euler approximation defined by
// sigma(t_0, x_0)^2 \Delta t
virtual double variance(Time t0, double x0, Time dt) const {
double sigma = diffusion(t0, x0);
return sigma * sigma * dt;
}
void tetDecompositionEngineMesh::move()
{
scalar deltaZ = engineDB_.pistonDisplacement().value();
Info<< "deltaZ = " << deltaZ << endl;
// Position of the top of the static mesh layers above the piston
scalar pistonPlusLayers = pistonPosition_.value() + pistonLayers_.value();
pointField newPoints = points();
tetPolyMesh tetMesh(*this);
// Select the set of boundary condition types. For symmetry planes
// and wedge boundaries, the slip condition should be used;
// otherwise, use the fixedValue
wordList boundaryTypes
(
boundary().size(),
fixedValueTetPolyPatchScalarField::typeName
);
forAll (boundary(), patchI)
{
if
(
isType<symmetryFvPatch>(boundary()[patchI])
|| isType<wedgeFvPatch>(boundary()[patchI])
|| isType<emptyFvPatch>(boundary()[patchI])
)
{
boundaryTypes[patchI] = slipTetPolyPatchScalarField::typeName;
}
}
tetPointScalarField motionUz
(
IOobject
(
"motionUz",
engineDB_.timeName(),
engineDB_,
IOobject::NO_READ,
IOobject::NO_WRITE
),
tetMesh,
dimensionedScalar("0", dimLength, 0),
boundaryTypes
);
motionUz.boundaryField()[pistonIndex_] == deltaZ;
{
scalarField linerPoints =
motionUz.boundaryField()[linerIndex_].patch()
.localPoints().component(vector::Z);
motionUz.boundaryField()[linerIndex_] ==
deltaZ*pos(deckHeight_.value() - linerPoints)
*(deckHeight_.value() - linerPoints)
/(deckHeight_.value() - pistonPlusLayers);
}
elementScalarField diffusion
(
IOobject
(
"motionDiffusion",
engineDB_.timeName(),
engineDB_,
IOobject::NO_READ,
IOobject::NO_WRITE
),
tetMesh,
dimensionedScalar("d", dimless, 1.0)
);
const fvPatchList& patches = boundary();
forAll (patches, patchI)
{
const unallocLabelList& fc = patches[patchI].faceCells();
forAll (fc, fcI)
{
diffusion[fc[fcI]] = 2;
}
}
solve(tetFem::laplacian(diffusion, motionUz));
newPoints.replace
(
vector::Z,
newPoints.component(vector::Z)
+ scalarField::subField
(
motionUz.internalField(),
newPoints.size()
)
);
if (engineDB_.foundObject<surfaceScalarField>("phi"))
{
surfaceScalarField& phi =
const_cast<surfaceScalarField&>
(engineDB_.lookupObject<surfaceScalarField>("phi"));
const volScalarField& rho =
engineDB_.lookupObject<volScalarField>("rho");
const volVectorField& U =
engineDB_.lookupObject<volVectorField>("U");
bool absolutePhi = false;
if (moving())
{
phi += fvc::interpolate(rho)*fvc::meshPhi(rho, U);
absolutePhi = true;
}
movePoints(newPoints);
if (absolutePhi)
{
phi -= fvc::interpolate(rho)*fvc::meshPhi(rho, U);
}
}
pistonPosition_.value() += deltaZ;
scalar pistonSpeed = deltaZ/engineDB_.deltaT().value();
Info<< "clearance: " << deckHeight_.value() - pistonPosition_.value() << nl
<< "Piston speed = " << pistonSpeed << " m/s" << endl;
}
