//Rotate by a random amount.
void Coordinates::RotateRand
(XYZArray & dest, uint & pStart, uint & pLen,
const uint m, const uint b, const double max)
{
//Rotate (-max, max) radians about a uniformly random vector
//Not uniformly random, but symmetrical wrt detailed balance
RotationMatrix matrix = RotationMatrix::FromAxisAngle(
prngRef.Sym(max), prngRef.PickOnUnitSphere());
XYZ center = comRef.Get(m);
uint stop = 0;
molRef.GetRange(pStart, stop, pLen, m);
//Copy coordinates
CopyRange(dest, pStart, 0, pLen);
boxDimRef.UnwrapPBC(dest, b, center);
//Do rotation
for (uint p = 0; p < pLen; p++) //Rotate each point.
{
dest.Add(p, -center);
dest.Set(p, matrix.Apply(dest.Get(p)));
dest.Add(p, center);
}
boxDimRef.WrapPBC(dest, b);
}
void DCFreeHedron::BuildNew(TrialMol& newMol, uint molIndex)
{
seed.BuildNew(newMol, 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
newMol.ShiftBasis(hed.Focus());
const XYZ center = newMol.AtomPosition(hed.Focus());
XYZArray* positions = data->multiPositions;
for (uint i = 0; i < hed.NumBond(); ++i)
{
positions[i].Set(0, newMol.RawRectCoords(hed.BondLength(i),
hed.Theta(i), hed.Phi(i)));
}
//add anchor atom
positions[hed.NumBond()].Set(0, newMol.RawRectCoords(anchorBond, 0, 0));
//counting backward to preserve prototype
for (uint lj = nLJTrials; lj-- > 0;)
{
//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)
{
data->axes.WrapPBC(positions[b], newMol.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, newMol.GetBox(), nLJTrials);
if(DoEwald){
data->calc.SwapSelf(self, molIndex, hed.Bonded(b), newMol.GetBox(), nLJTrials);
data->calc.SwapCorrection(corr, newMol, positions[b], hed.Bonded(b), newMol.GetBox(), nLJTrials);
}
}
calc.ParticleInter(inter, real, positions[hed.NumBond()], hed.Prev(),
molIndex, newMol.GetBox(), nLJTrials);
if(DoEwald){
data->calc.SwapSelf(self, molIndex, hed.Prev(), newMol.GetBox(), nLJTrials);
data->calc.SwapCorrection(corr, newMol, positions[hed.NumBond()], hed.Prev(), newMol.GetBox(), nLJTrials);
}
double stepWeight = 0;
for (uint lj = 0; lj < nLJTrials; ++lj)
{
ljWeights[lj] = exp(-ff.beta * inter[lj]);
stepWeight += ljWeights[lj];
}
uint winner = prng.PickWeighted(ljWeights, nLJTrials, stepWeight);
for(uint b = 0; b < hed.NumBond(); ++b)
{
newMol.AddAtom(hed.Bonded(b), positions[b][winner]);
}
newMol.AddAtom(hed.Prev(), positions[hed.NumBond()][winner]);
newMol.AddEnergy(Energy(hed.GetEnergy(), 0, inter[winner], real[winner], 0, self[winner], corr[winner]));
newMol.MultWeight(hed.GetWeight());
newMol.MultWeight(stepWeight);
}
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);
}
