Real SimCalcs::calcIntraMolecularEnergy(int molIdx) {
int** moleculeData = sb->moleculeData;
int molStart = moleculeData[MOL_START][molIdx];
int molEnd = molStart + moleculeData[MOL_LEN][molIdx];
int molType = moleculeData[MOL_TYPE][molIdx];
Real** aCoords = GPUCopy::atomCoordinatesPtr();
Real** atomData = sb->atomData;
Real out = 0.0;
if (sb->hasFlexibleAngles) out += angleEnergy(molIdx);
if (sb->hasFlexibleBonds) out += bondEnergy(molIdx);
// Calculate intramolecular LJ and Coulomb energy if necessary
if (sb->hasFlexibleBonds || sb->hasFlexibleAngles) {
#pragma acc parallel loop deviceptr(aCoords) if (on_gpu)
for (int i = molStart; i < molEnd; i++) {
for (int j = i + 1; j < molEnd; j++) {
Real fudgeFactor = 1.0;
for (int k = 0; ; k++) {
int val = sb->excludeAtoms[molType][i - molStart][k];
if (val == -1) {
break;
} else if (val == j - molStart) {
fudgeFactor = 0.0;
break;
}
}
if (fudgeFactor > 0.0) {
for (int k = 0; ; k++) {
int val = sb->fudgeAtoms[molType][i - molStart][k];
if (val == -1) {
break;
} else if (val == j - molStart) {
fudgeFactor = 0.5;
break;
}
}
}
if (fudgeFactor > 0.0) {
Real r2 = calcAtomDistSquared(i, j, aCoords, sb->size);
Real r = sqrt(r2);
Real energy = calcLJEnergy(i, j, r2, atomData);
energy += calcChargeEnergy(i, j, r, atomData);
out += fudgeFactor * energy;
}
}
}
}
return out;
}
Real SimBox::calcIntraMolecularEnergy(int molIdx) {
int molStart = moleculeData[MOL_START][molIdx];
int molEnd = molStart + moleculeData[MOL_LEN][molIdx];
int molType = moleculeData[MOL_TYPE][molIdx];
Real out = 0.0;
out += angleEnergy(molIdx);
out += bondEnergy(molIdx);
for (int i = molStart; i < molEnd; i++) {
for (int j = i + 1; j < molEnd; j++) {
Real fudgeFactor = 1.0;
for (int k = 0; ; k++) {
int val = excludeAtoms[molType][i - molStart][k];
if (val == -1) {
break;
} else if (val == j - molStart) {
fudgeFactor = 0.0;
break;
}
}
if (fudgeFactor == 1.0) {
for (int k = 0; ; k++) {
int val = fudgeAtoms[molType][i - molStart][k];
if (val == -1) {
break;
} else if (val == j - molStart) {
fudgeFactor = 0.5;
break;
}
}
}
if (fudgeFactor > 0.0) {
Real r2 = calcAtomDistSquared(i, j, atomCoordinates, size);
Real r = sqrt(r2);
Real energy = calcLJEnergy(i, j, r2, atomData);
energy += calcChargeEnergy(i, j, r, atomData);
out += fudgeFactor * energy;
}
}
}
return out;
}
