void HFPlanner::computeHF(gridVertex vgoal)
{
//initialize potential to -1 and goal to 0
setPotential(vgoal, _goalPotential);
//relax potential
int numneighs = _wkSpace->getDimension()*2;
graph_traits<gridGraph>::vertex_iterator vi, vend;
graph_traits<gridGraph>::adjacency_iterator avi, avi_end;
for(int i=0; i<_hfiter; i++)
{
for(tie(vi,vend)=vertices(*g); vi!=vend; ++vi)
{
if(getPotential(*vi) == _goalPotential ||
getPotential(*vi) == _obstaclePotential) continue;
//cout << "cell "<<*vi<< " neighs = ";
KthReal p=0;
int count=0;
int totalcount=0;
for(tie(avi,avi_end)=adjacent_vertices(*vi, *g); avi!=avi_end; ++avi)
{
totalcount++;
//cout<<*avi<<" ";
if(_dirichlet != 0)
{
//dirichlet
count++;
p+=getPotential(*avi);
}
else {
//neumann
//cout<<"("<<getPotential(*avi)<<") ";
if(getPotential(*avi) != _obstaclePotential)
{
count++;
p+=getPotential(*avi);
}
}
}
//the borders of the cspace fixed to high
for(;totalcount<numneighs;totalcount++)
{
count++;
p+=_obstaclePotential;
}
//cout<<" POT= "<<p<<"/"<<count<<"= "<<p/count<<endl;
if(count) setPotential(*vi, p/count);
}
}
}
CXXSpace::CXXSpace(float probeRadius, float gridSpacing,
float xMin, float xMax, float yMin, float yMax,
float zMin, float zMax):SolventMap(gridSpacing, probeRadius,
xMin, xMax, yMin, yMax, zMin, zMax) {
saltConc = 0.0;
temp = 300;
// WARNING dummy value - if this is not set by defineBondaryConditions will raise and Exception...
dielectricBoundary = -1;
// constructor calls base class constructor (solvent map constructor) generating fftw optimised conservative
// discrete grid - now need to make sure the chargeGrid uses the same dimensions and is consistent with the
// optimised solvnetMap grid.
try {
chargeGrid = new double[dim[0]*dim[1]*dim[2]];
solvationGrid = new double[dim[0]*dim[1]*dim[2]];
potentialGrid = new double[dim[0]*dim[1]*dim[2]];
dielGrid = new CXXCoord[dim[0]*dim[1]*dim[2]];
epsilonKappaSq = new double[dim[0]*dim[1]*dim[2]];
if ((chargeGrid == 0) || (potentialGrid == 0) | (dielGrid == 0)) {
CXXException theException = CXXException(" ERROR: (CXXSpace::CXXSpace()) :Could not reserve suffiecent memory !\n");
throw theException;
}
// set all values in chargeGrid / potentialGrid and dielectric Grids to 0
for (int i = 0; i < dim[0]; i++) {
for (int j = 0; j < dim[1]; j++) {
for (int k = 0; k < dim[2]; k++) {
setChargeGrid(i, j, k, 0.);
setPotential(i,j,k,0.);
setDielGrid(i,j,k,0,0.);
setDielGrid(i,j,k,1,0.);
setDielGrid(i,j,k,2,0.);
setSolvationGrid(i,j,k,0);
}
}
}
// If we got here no problems where identified so now give a simple status report about what is happening
std::cout << "Generated Space: \nReal origin x: " << originOfGrid[0] << " y: " << originOfGrid[1] << " z: " << originOfGrid[2];
std::cout << " \nGrid dimensions i: " << dim[0] << " j: " << dim[1] << " k: " << dim[2];
std::cout << " \nGrid spacing: " << gridSpacing << " \nProbeRadius: " << probeRadius << "\n";
}
catch (CXXException theExeption) {
theExeption.Report();
throw theExeption;
}
}
