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 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 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
}