void DCDiatomic::BuildNew(TrialMol& newMol, uint molIndex)
{
PRNG& prng = data->prng;
XYZArray& positions = data->positions;
double beta = data->ff.beta;
uint nLJTrials = data->nLJTrialsNth;
double* inter = data->inter;
double* ljWeights = data->ljWeights;
prng.FillWithRandom(positions, nLJTrials,
data->axes.GetAxis(newMol.GetBox()));
data->axes.WrapPBC(positions, newMol.GetBox());
data->calc.ParticleInter(first, positions, inter, molIndex,
newMol.GetBox(), nLJTrials);
double stepWeight = 0;
for (uint trial = 0; trial < nLJTrials; ++trial)
{
ljWeights[trial] = exp(-1 * beta * inter[trial]);
stepWeight += ljWeights[trial];
}
uint winner = prng.PickWeighted(ljWeights, nLJTrials, stepWeight);
newMol.MultWeight(stepWeight);
newMol.AddEnergy(Energy(0, 0, inter[winner]));
newMol.AddAtom(first, positions[winner]);
prng.FillWithRandomOnSphere(positions, nLJTrials, bondLength,
newMol.AtomPosition(first));
data->axes.WrapPBC(positions, newMol.GetBox());
data->calc.ParticleInter(second, positions, inter, molIndex,
newMol.GetBox(), nLJTrials);
stepWeight = 0;
for (uint trial = 0; trial < nLJTrials; trial++)
{
ljWeights[trial] = exp(-1 * beta * inter[trial]);
stepWeight += ljWeights[trial];
}
winner = prng.PickWeighted(ljWeights, nLJTrials, stepWeight);
newMol.MultWeight(stepWeight);
newMol.AddEnergy(Energy(0, 0, inter[winner]));
newMol.AddAtom(second, positions[winner]);
}
void DCLinkNoDih::BuildNew(TrialMol& newMol, uint molIndex)
{
AlignBasis(newMol);
double* ljWeights = data->ljWeights;
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;
for (uint trial = 0, count = nLJTrials; trial < count; ++trial)
{
double phi = prng.rand(M_PI * 2);
positions.Set(trial, newMol.GetRectCoords(bondLength, theta, phi));
}
data->axes.WrapPBC(positions, newMol.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);
std::fill_n(ljWeights, nLJTrials, 0.0);
data->calc.ParticleInter(inter, real, positions, atom, molIndex,
newMol.GetBox(), nLJTrials);
if(DoEwald){
data->calc.SwapSelf(self, molIndex, atom, newMol.GetBox(), nLJTrials);
data->calc.SwapCorrection(corr, newMol, positions, atom, newMol.GetBox(), nLJTrials);
}
double stepWeight = 0.0;
for (uint trial = 0; trial < nLJTrials; trial++)
{
ljWeights[trial] = exp(-1 * data->ff.beta * (inter[trial] + real[trial] + self[trial] + corr[trial]));
if(ljWeights[trial] < 10e-200)
ljWeights[trial] = 0.0;
stepWeight += ljWeights[trial];
}
uint winner = prng.PickWeighted(ljWeights, nLJTrials, stepWeight);
double WinEnergy = inter[winner]+real[winner]+self[winner]+corr[winner];
if ( ( WinEnergy * data->ff.beta ) > (2.3*200.0) || WinEnergy * data->ff.beta < -2.303e308){
stepWeight = 0.0;
inter[winner] = 0.0;
real[winner] = 0.0;
self[winner] = 0.0;
corr[winner] = 0.0;
}
newMol.MultWeight(stepWeight * bendWeight);
newMol.AddAtom(atom, positions[winner]);
newMol.AddEnergy(Energy(bendEnergy, 0.0, inter[winner], real[winner], 0.0, self[winner], corr[winner]));
}
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::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);
}
void DCLinkNoDih::BuildNew(TrialMol& newMol, uint molIndex)
{//printf("DC Linked No dihhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh\n");
// printf("DCLinkNoDeh new\n");
AlignBasis(newMol);
double* ljWeights = data->ljWeights;
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;
for (uint trial = 0, count = nLJTrials; trial < count; ++trial)
{
double phi = prng.rand(M_PI * 2);
positions.Set(trial, newMol.GetRectCoords(bondLength, theta, phi));
}
data->axes.WrapPBC(positions, newMol.GetBox());
std::fill_n(inter, nLJTrials, 0);
std::fill_n(nonbonded_1_4, nLJTrials, 0);// v1
// data->calc.ParticleInter(inter, positions, atom, molIndex, newMol.GetBox(), nLJTrials);
// data->calc.GetParticleEnergyGPU(newMol.GetBox(), inter,positions, newMol.molLength, newMol.mOff, atom,newMol.molKindIndex);
data->calc.GetParticleEnergy(newMol.GetBox(), inter,positions, newMol.molLength, newMol.mOff, atom,newMol.molKindIndex,nLJTrials);
/* for (int trial = 0; trial < data->nLJTrials; ++trial)
{
printf("serial Trial %d energy=%f\n",trial,inter[trial] );
}
printf("\n\n");
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, newMol, positions, atom,
newMol.GetBox(), nLJTrials);// v1
double stepWeight = 0;
double beta = data->ff.beta;
for (uint trial = 0, count = nLJTrials; trial < count; ++trial)
{
ljWeights[trial] = exp(-data->ff.beta * (inter[trial] +
nonbonded_1_4[trial]));// v1
stepWeight += ljWeights[trial];
}
uint winner = prng.PickWeighted(ljWeights, nLJTrials, stepWeight);
newMol.MultWeight(stepWeight * bendWeight);
newMol.AddAtom(atom, positions[winner]);
newMol.AddEnergy(Energy(bendEnergy, nonbonded_1_4[winner],
inter[winner]));// v1
}
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
}