void DCDiatomic::BuildOld(TrialMol& oldMol, uint molIndex)
{
PRNG& prng = data->prng;
XYZArray& positions = data->positions;
uint nLJTrials = data->nLJTrialsNth;
double beta = data->ff.beta;
prng.FillWithRandom(data->positions, nLJTrials,
data->axes.GetAxis(oldMol.GetBox()));
positions.Set(0, oldMol.AtomPosition(first));
double* inter = data->inter;
double stepWeight = 0;
data->axes.WrapPBC(positions, oldMol.GetBox());
data->calc.ParticleInter(first, positions, inter, molIndex,
oldMol.GetBox(), nLJTrials);
for (uint trial = 0; trial < nLJTrials; ++trial)
{
stepWeight += exp(-1 * beta * inter[trial]);
}
oldMol.MultWeight(stepWeight);
oldMol.AddEnergy(Energy(0, 0, inter[0]));
oldMol.ConfirmOldAtom(first);
prng.FillWithRandomOnSphere(positions, nLJTrials, bondLength,
oldMol.AtomPosition(first));
positions.Set(0, oldMol.AtomPosition(second));
stepWeight = 0;
data->axes.WrapPBC(positions, oldMol.GetBox());
data->calc.ParticleInter(second, positions, inter, molIndex,
oldMol.GetBox(), nLJTrials);
for (uint trial = 0; trial < nLJTrials; trial++)
{
stepWeight += exp(-1 * beta * inter[trial]);
}
oldMol.MultWeight(stepWeight);
oldMol.AddEnergy(Energy(0, 0, inter[0]));
oldMol.ConfirmOldAtom(second);
}
void DCLinkNoDih::BuildOld(TrialMol& oldMol, uint molIndex)
{
AlignBasis(oldMol);
IncorporateOld(oldMol);
double* inter = data->inter;
double* real = data->real;
double *self = data->self;
double* corr = data->correction;
uint nLJTrials = data->nLJTrialsNth;
XYZArray& positions = data->positions;
PRNG& prng = data->prng;
positions.Set(0, oldMol.AtomPosition(atom));
for (uint trial = 1, count = nLJTrials; trial < count; ++trial)
{
double phi = prng.rand(M_PI * 2);
positions.Set(trial, oldMol.GetRectCoords(bondLength, theta, phi));
}
data->axes.WrapPBC(positions, oldMol.GetBox());
std::fill_n(inter, nLJTrials, 0.0);
std::fill_n(self, nLJTrials, 0.0);
std::fill_n(real, nLJTrials, 0.0);
std::fill_n(corr, nLJTrials, 0.0);
data->calc.ParticleInter(inter, real, positions, atom, molIndex,
oldMol.GetBox(), nLJTrials);
if(DoEwald){
data->calc.SwapSelf(self, molIndex, atom, oldMol.GetBox(), nLJTrials);
data->calc.SwapCorrection(corr, oldMol, positions, atom, oldMol.GetBox(), nLJTrials);
}
double stepWeight = 0.0;
for (uint trial = 0; trial < nLJTrials; ++trial)
{
stepWeight += exp(-1 * data->ff.beta * (inter[trial] + real[trial] + self[trial] + corr[trial]) );
if(stepWeight < 10e-200)
stepWeight = 0.0;
}
oldMol.MultWeight(stepWeight * bendWeight);
oldMol.ConfirmOldAtom(atom);
oldMol.AddEnergy(Energy(bendEnergy, 0.0, inter[0], real[0], 0.0, self[0], corr[0]));
}
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::BuildOld(TrialMol& oldMol, uint molIndex)
{//printf("DCLinkNoDeh old\n");
AlignBasis(oldMol);
IncorporateOld(oldMol);
double* nonbonded_1_4 = data->nonbonded_1_4;// v1
double* inter = data->inter;
uint nLJTrials = data->nLJTrialsNth;
XYZArray& positions = data->positions;
PRNG& prng = data->prng;
positions.Set(0, oldMol.AtomPosition(atom));
for (uint trial = 1, count = nLJTrials; trial < count; ++trial)
{
double phi = prng.rand(M_PI * 2);
positions.Set(trial, oldMol.GetRectCoords(bondLength, theta, phi));
}
data->axes.WrapPBC(positions, oldMol.GetBox());
std::fill_n(inter, nLJTrials, 0.0);
std::fill_n(nonbonded_1_4, nLJTrials, 0.0);//v1
//data->calc.ParticleInter(inter, positions, atom, molIndex, oldMol.GetBox(), nLJTrials);
//data->calc.GetParticleEnergyGPU(oldMol.GetBox(), inter,positions, oldMol.molLength, oldMol.mOff, atom,oldMol.molKindIndex);
data->calc.GetParticleEnergy(oldMol.GetBox(), inter,positions, oldMol.molLength, oldMol.mOff, atom,oldMol.molKindIndex,nLJTrials);
//printf("DC Linked No dihhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh\n");
/* for (int trial = 0; trial < data->nLJTrials; ++trial)
{
printf("serial Trial %d energy=%f\n",trial,inter[trial] );
}
printf("\n\n");
data->calc.GetParticleEnergyGPU(oldMol.GetBox(), data->nLJTrials, inter,positions, oldMol.molLength, oldMol.mOff, atom,oldMol.molKindIndex);
for (int trial = 0; trial < data->nLJTrials; ++trial)
{
printf("GPU Trial %d energy=%f\n",trial,inter[trial] );
}
printf("===================\n\n");*/
data->calc.ParticleNonbonded_1_4(nonbonded_1_4, oldMol, positions, atom,
oldMol.GetBox(), nLJTrials);// v1
double stepWeight = 0;
for (uint trial = 0, count = nLJTrials; trial < count; ++trial)
{
stepWeight += exp(-data->ff.beta * (inter[trial] +
nonbonded_1_4[trial]));//v1
}
oldMol.MultWeight(stepWeight * bendWeight);
oldMol.ConfirmOldAtom(atom);
oldMol.AddEnergy(Energy(bendEnergy, nonbonded_1_4[0], inter[0]));//v1
}