void DCFreeHedron::BuildOld(TrialMol& oldMol, uint molIndex)
{
seed.BuildOld(oldMol, molIndex);
PRNG& prng = data->prng;
const CalculateEnergy& calc = data->calc;
const Forcefield& ff = data->ff;
uint nLJTrials = data->nLJTrialsNth;
double* ljWeights = data->ljWeights;
double* inter = data->inter;
double* real = data->real;
double* self = data->self;
double* corr = data->correction;
//get info about existing geometry
oldMol.SetBasis(hed.Focus(), hed.Prev());
//Calculate OldMol Bond Energy &
//Calculate phi weight for nTrials using actual theta of OldMol
hed.ConstrainedAnglesOld(data->nAngleTrials - 1, oldMol);
const XYZ center = oldMol.AtomPosition(hed.Focus());
XYZArray* positions = data->multiPositions;
double prevPhi[MAX_BONDS];
for (uint i = 0; i < hed.NumBond(); ++i)
{
//get position and shift to origin
positions[i].Set(0, oldMol.AtomPosition(hed.Bonded(i)));
data->axes.UnwrapPBC(positions[i], 0, 1, oldMol.GetBox(), center);
positions[i].Add(0, -center);
}
//add anchor atom
positions[hed.NumBond()].Set(0, oldMol.AtomPosition(hed.Prev()));
data->axes.UnwrapPBC(positions[hed.NumBond()], 0, 1,
oldMol.GetBox(), center);
positions[hed.NumBond()].Add(0, -center);
//counting backward to preserve prototype
for (uint lj = nLJTrials; lj-- > 1;)
{
//convert chosen torsion to 3D positions
RotationMatrix spin =
RotationMatrix::UniformRandom(prng(), prng(), prng());
for (uint b = 0; b < hed.NumBond() + 1; ++b)
{
//find positions
positions[b].Set(lj, spin.Apply(positions[b][0]));
positions[b].Add(lj, center);
}
}
for (uint b = 0; b < hed.NumBond() + 1; ++b)
{
positions[b].Add(0, center);
data->axes.WrapPBC(positions[b], oldMol.GetBox());
}
std::fill_n(inter, nLJTrials, 0.0);
std::fill_n(real, nLJTrials, 0.0);
std::fill_n(self, nLJTrials, 0.0);
std::fill_n(corr, nLJTrials, 0.0);
for (uint b = 0; b < hed.NumBond(); ++b)
{
calc.ParticleInter(inter, real, positions[b], hed.Bonded(b),
molIndex, oldMol.GetBox(), nLJTrials);
if(DoEwald){
data->calc.SwapSelf(self, molIndex, hed.Bonded(b), oldMol.GetBox(), nLJTrials);
data->calc.SwapCorrection(corr, oldMol, positions[b], hed.Bonded(b), oldMol.GetBox(), nLJTrials);
}
}
double stepWeight = 0;
calc.ParticleInter(inter, real, positions[hed.NumBond()], hed.Prev(),
molIndex, oldMol.GetBox(), nLJTrials);
if(DoEwald){
data->calc.SwapSelf(self, molIndex, hed.Prev(), oldMol.GetBox(), nLJTrials);
data->calc.SwapCorrection(corr, oldMol, positions[hed.NumBond()], hed.Prev(), oldMol.GetBox(), nLJTrials);
}
for (uint lj = 0; lj < nLJTrials; ++lj)
{
stepWeight += exp(-ff.beta * inter[lj]);
}
for(uint b = 0; b < hed.NumBond(); ++b)
{
oldMol.ConfirmOldAtom(hed.Bonded(b));
}
oldMol.ConfirmOldAtom(hed.Prev());
oldMol.AddEnergy(Energy(hed.GetEnergy(), 0, inter[0], real[0], 0, self[0], corr[0]));
oldMol.MultWeight(hed.GetWeight());
oldMol.MultWeight(stepWeight);
}
void DCLinkNoDih::AlignBasis(TrialMol& mol)
{
mol.SetBasis(focus, prev);
}