//Calculate OldMol Bond Energy &
//Calculate phi weight for nTrials using actual theta of OldMol
void DCHedron::ConstrainedAnglesOld(uint nTrials, TrialMol& oldMol,
uint molIndex)
{
IncorporateOld(oldMol, molIndex);
for (uint b = 1; b < nBonds; ++b) {
double stepWeight = 0.0;
//pick "twist" angles
for (uint i = 0; i < nTrials; ++i) {
double angles = data->prng.rand(M_PI * 2);
double energies = 0.0;
double nonbondedEng = 0.0;
//compare to angles determined in previous iterations
for (uint c = 0; c < b; ++c) {
if(!data->ff.angles->AngleFixed(angleKinds[b][c])) {
double cosTerm = cos(theta[b]) * cos(theta[c]);
double sinTerm = sin(theta[b]) * sin(theta[c]);
double bfcTheta = acos(sinTerm * cos(angles - phi[c])
+ cosTerm);
double distSq = oldMol.AngleDist(bondLengthOld[b],
bondLengthOld[c], bfcTheta);
nonbondedEng += data->calc.IntraEnergy_1_3(distSq, bonded[b],
bonded[c], molIndex);
energies += data->ff.angles->Calc(angleKinds[b][c], bfcTheta);
} else {
double cosTerm = cos(theta[b]) * cos(theta[c]);
double sinTerm = sin(theta[b]) * sin(theta[c]);
double bfcTheta = data->ff.angles->Angle(angleKinds[b][c]);
angles = acos((cos(bfcTheta) - cosTerm) / sinTerm) + phi[c];
double distSq = oldMol.AngleDist(bondLengthOld[b],
bondLengthOld[c], bfcTheta);
nonbondedEng += data->calc.IntraEnergy_1_3(distSq, bonded[b],
bonded[c], molIndex);
energies += data->ff.angles->Calc(angleKinds[b][c],
bfcTheta);
if(abs(angles) > 2.0 * M_PI) {
std::cout << "Error: Cannot constrain fix angle for " <<
oldMol.GetKind().atomTypeNames[bonded[b]] << " " <<
oldMol.GetKind().atomTypeNames[focus] << " " <<
oldMol.GetKind().atomTypeNames[bonded[c]] << " !\n";
exit(EXIT_FAILURE);
}
}
}
//calculate weights from combined energy
double weights = exp(-1 * data->ff.beta * (energies + nonbondedEng));
stepWeight += weights;
}
phiWeight[b] += stepWeight;
}
}
void DCHedron::GenerateAnglesOld(TrialMol& oldMol, uint molIndex,
uint kind, uint nTrials, uint bType)
{
double* nonbonded_1_3 = data->nonbonded_1_3;
int i;
double distSq, thetaFix;
bool angleFix = false;
std::fill_n(nonbonded_1_3, nTrials, 0.0);
if(data->ff.angles->AngleFixed(kind)) {
angleFix = true;
thetaFix = data->ff.angles->Angle(kind);
}
for (i = 0; i < nTrials; ++i) {
if(angleFix)
data->angles[i] = thetaFix;
else
data->angles[i] = data->prng.rand(M_PI);
}
#ifdef _OPENMP
#pragma omp parallel for default(shared) private(i, distSq)
#endif
for (i = 0; i < nTrials; ++i) {
data->angleEnergy[i] = data->ff.angles->Calc(kind, data->angles[i]);
distSq = oldMol.AngleDist(anchorBondOld, bondLengthOld[bType],
data->angles[i]);
nonbonded_1_3[i] =
data->calc.IntraEnergy_1_3(distSq, prev, bonded[bType], molIndex);
data->angleWeights[i] = exp((data->angleEnergy[i] + nonbonded_1_3[i])
* -data->ff.beta);
}
}
void DCHedron::ConstrainedAngles(TrialMol& newMol, uint molIndex, uint nTrials)
{
double* angles = data->angles;
double* energies = data->angleEnergy;
double* weights = data->angleWeights;
double* nonbonded_1_3 = data->nonbonded_1_3;
std::fill_n(nonbonded_1_3, nTrials, 0.0);
phi[0] = 0.0;
for (uint b = 1; b < nBonds; ++b) {
//pick "twist" angles
for (uint i = 0; i < nTrials; ++i) {
angles[i] = data->prng.rand(M_PI * 2);
energies[i] = 0.0;
nonbonded_1_3[i] = 0.0;
}
//compare to angles determined in previous iterations
for (uint c = 0; c < b; ++c) {
double cosTerm = cos(theta[b]) * cos(theta[c]);
double sinTerm = sin(theta[b]) * sin(theta[c]);
for (uint i = 0; i < nTrials; ++i) {
if(!data->ff.angles->AngleFixed(angleKinds[b][c])) {
double bfcTheta = acos(sinTerm * cos(angles[i] - phi[c]) +
cosTerm);
double distSq = newMol.AngleDist(bondLength[b], bondLength[c],
bfcTheta);
double tempEn = data->calc.IntraEnergy_1_3(distSq, bonded[b],
bonded[c],
molIndex);
nonbonded_1_3[i] += tempEn;
energies[i] += data->ff.angles->Calc(angleKinds[b][c],
bfcTheta);
} else {
double bfcTheta = data->ff.angles->Angle(angleKinds[b][c]);
angles[i] = acos((cos(bfcTheta) - cosTerm) / sinTerm) + phi[c];
double distSq = newMol.AngleDist(bondLength[b], bondLength[c],
bfcTheta);
double tempEn = data->calc.IntraEnergy_1_3(distSq, bonded[b],
bonded[c],
molIndex);
nonbonded_1_3[i] += tempEn;
energies[i] += data->ff.angles->Calc(angleKinds[b][c],
bfcTheta);
if(abs(angles[i]) > 2.0 * M_PI) {
std::cout << "Error: Cannot constrain fix angle for " <<
newMol.GetKind().atomTypeNames[bonded[b]] << " " <<
newMol.GetKind().atomTypeNames[focus] << " " <<
newMol.GetKind().atomTypeNames[bonded[c]] << " !\n";
exit(EXIT_FAILURE);
}
}
}
}
//calculate weights from combined energy
double stepWeight = 0.0;
int i;
#ifdef _OPENMP
#pragma omp parallel for default(shared) private(i) reduction(+:stepWeight)
#endif
for (i = 0; i < nTrials; ++i) {
weights[i] = exp(-1 * data->ff.beta * (energies[i] +
nonbonded_1_3[i]));
stepWeight += weights[i];
}
uint winner = data->prng.PickWeighted(weights, nTrials, stepWeight);
phi[b] = angles[winner];
bendEnergy += energies[winner];
oneThree += nonbonded_1_3[winner];
phiWeight[b] = stepWeight;
}
}