void
calc_cluster_volume_and_store_with_cluster_rep(
Triangulation &triang,
map<int, cell_cluster> &cluster_set,
vector<double> &cluster_volume_vector,
vector<int> &cluster_rep_vector )
{
for(FCI cit = triang.finite_cells_begin();
cit != triang.finite_cells_end(); cit ++)
{
if( ! cluster_set[cit->id].in_cluster )
continue;
if( ! cluster_set[cit->id].outside )
continue;
double volume = cell_volume(cit);
// see if we already computed some of the cluster volume.
// in other words see if the 'rep' is there in the cluster_rep_vector.
int rep = cluster_set[cit->id].find();
bool found = false;
int pos = -1;
for(int i = 0; i < (int)cluster_rep_vector.size(); i ++)
if(cluster_rep_vector[i] == rep)
{
found = true;
pos = i;
break;
}
if(found)
cluster_volume_vector[pos] += volume;
else
{
cluster_volume_vector.push_back(volume);
cluster_rep_vector.push_back(rep);
}
}
CGAL_assertion(cluster_volume_vector.size() == cluster_rep_vector.size());
}
void TopologyMatrix::calculateForThreeAtoms( const unsigned& iat, const Vector& d1, const double& d1_len,
HistogramBead& bead, multicolvar::AtomValuePack& myatoms ) const {
// Calculate if there are atoms in the cylinder (can use delta here as pbc are done in atom setup)
Vector d2 = getSeparation( myatoms.getPosition(0), myatoms.getPosition(iat) );
// Now calculate projection of d2 on d1
double proj=dotProduct(d2,d1);
// This tells us if we are outside the end of the cylinder
double excess = proj - d1_len;
// Return if we are outside of the cylinder as calculated based on excess
if( excess>low_sf( getBaseColvarNumber( myatoms.getIndex(0) ), getBaseColvarNumber( myatoms.getIndex(1) ) ).get_dmax() ) return;
// Find the length of the cylinder
double binw = binw_mat( getBaseColvarNumber( myatoms.getIndex(0) ), getBaseColvarNumber( myatoms.getIndex(1) ) );
double lcylinder = (std::floor( d1_len / binw ) + 1)*binw;
// Return if the projection is outside the length of interest
if( proj<-bead.getCutoff() || proj>(lcylinder+bead.getCutoff()) ) return;
// Calculate the excess swiching function
double edf, eval = low_sf( getBaseColvarNumber( myatoms.getIndex(0) ), getBaseColvarNumber( myatoms.getIndex(1) ) ).calculate( excess, edf );
// Calculate the projection on the perpendicular distance from the center of the tube
double cm = d2.modulo2() - proj*proj;
// Now calculate the density in the cylinder
if( cm<cylinder_sw( getBaseColvarNumber( myatoms.getIndex(0) ), getBaseColvarNumber( myatoms.getIndex(1) ) ).get_dmax2() ) {
double dfuncr, val = cylinder_sw( getBaseColvarNumber( myatoms.getIndex(0) ),
getBaseColvarNumber( myatoms.getIndex(1) ) ).calculateSqr( cm, dfuncr );
double cellv = cell_volume( getBaseColvarNumber( myatoms.getIndex(0) ), getBaseColvarNumber( myatoms.getIndex(1) ) );
Vector dc1, dc2, dc3, dd1, dd2, dd3, de1, de2, de3;
if( !doNotCalculateDerivatives() ) {
Tensor d1_a1;
// Derivative of director connecting atom1 - atom2 wrt the position of atom 1
d1_a1(0,0) = ( -(d1[1]*d1[1]+d1[2]*d1[2])/d1_len ); // dx/dx
d1_a1(0,1) = ( d1[0]*d1[1]/d1_len ); // dx/dy
d1_a1(0,2) = ( d1[0]*d1[2]/d1_len ); // dx/dz
d1_a1(1,0) = ( d1[1]*d1[0]/d1_len ); // dy/dx
d1_a1(1,1) = ( -(d1[0]*d1[0]+d1[2]*d1[2])/d1_len ); // dy/dy
d1_a1(1,2) = ( d1[1]*d1[2]/d1_len );
d1_a1(2,0) = ( d1[2]*d1[0]/d1_len );
d1_a1(2,1) = ( d1[2]*d1[1]/d1_len );
d1_a1(2,2) = ( -(d1[1]*d1[1]+d1[0]*d1[0])/d1_len );
// Calculate derivatives of dot product
dd1 = matmul(d2, d1_a1) - d1;
dd2 = matmul(d2, -d1_a1);
dd3 = d1;
// Calculate derivatives of cross product
dc1 = dfuncr*( -d2 - proj*dd1 );
dc2 = dfuncr*( -proj*dd2 );
dc3 = dfuncr*( d2 - proj*dd3 );
// Calculate derivatives of excess
de1 = edf*excess*( dd1 + d1 );
de2 = edf*excess*( dd2 - d1 );
de3 = edf*excess*dd3;
}
Vector pos1 = myatoms.getPosition(0) + d1_len*d1;
Vector pos2 = myatoms.getPosition(0) + d2;
Vector g1derivf,g2derivf,lderivf; Tensor vir;
for(unsigned bin=0; bin<maxbins; ++bin) {
bead.set( bin*binw, (bin+1)*binw, sigma );
if( proj<(bin*binw-bead.getCutoff()) || proj>binw*(bin+1)+bead.getCutoff() ) continue;
double der, contr=bead.calculateWithCutoff( proj, der ) / cellv; der /= cellv;
myatoms.addValue( 2+bin, contr*val*eval );
if( !doNotCalculateDerivatives() ) {
g1derivf=contr*eval*dc1 + val*eval*der*dd1 + contr*val*de1;
addAtomDerivatives( 2+bin, 0, g1derivf, myatoms );
g2derivf=contr*eval*dc2 + val*eval*der*dd2 + contr*val*de2;
addAtomDerivatives( 2+bin, 1, g2derivf, myatoms );
lderivf=contr*eval*dc3 + val*eval*der*dd3 + contr*val*de3;
addAtomDerivatives( 2+bin, iat, lderivf, myatoms );
// Virial
vir = -Tensor( myatoms.getPosition(0), g1derivf ) - Tensor( pos1, g2derivf ) - Tensor( pos2, lderivf );
myatoms.addBoxDerivatives( 2+bin, vir );
}
}
}
}