void SimCalcs::stretchBond(int molIdx, int bondIdx, Real stretchDist) {
Real* bondLengths = GPUCopy::bondLengthsPtr();
int bondStart = sb->moleculeData[MOL_BOND_START][molIdx];
int bondEnd = bondStart + sb->moleculeData[MOL_BOND_COUNT][molIdx];
int startIdx = sb->moleculeData[MOL_START][molIdx];
int molSize = sb->moleculeData[MOL_LEN][molIdx];
int end1 = (int)sb->bondData[BOND_A1_IDX][bondStart + bondIdx];
int end2 = (int)sb->bondData[BOND_A2_IDX][bondStart + bondIdx];
Real** aCoords = GPUCopy::atomCoordinatesPtr();
for (int i = 0; i < molSize; i++) {
sb->unionFindParent[i] = i;
}
// Split the molecule atoms into two disjoint sets around the bond
for (int i = bondStart; i < bondEnd; i++) {
if (i == bondIdx + bondStart)
continue;
int a1 = (int)sb->bondData[BOND_A1_IDX][i] - startIdx;
int a2 = (int)sb->bondData[BOND_A2_IDX][i] - startIdx;
unionAtoms(a1, a2);
}
int side1 = find(end1 - startIdx);
int side2 = find(end2 - startIdx);
if (side1 == side2) {
// std::cerr << "ERROR: EXPANDING BOND IN A RING!" << std::endl;
return;
}
// Move each atom the appropriate distance for the bond stretch
Real v[NUM_DIMENSIONS];
Real denon = 0.0;
#pragma acc parallel loop deviceptr(aCoords) if (on_gpu)
for (int i = 0; i < NUM_DIMENSIONS; i++) {
v[i] = aCoords[i][end2] - aCoords[i][end1];
denon += v[i] * v[i];
}
denon = sqrt(denon);
for (int i = 0; i < NUM_DIMENSIONS; i++) {
v[i] = v[i] / denon / 2.0;
}
for (int i = 0; i < molSize; i++) {
if (find(i) == side2) {
#pragma acc parallel loop deviceptr(aCoords) if (on_gpu)
for (int j = 0; j < NUM_DIMENSIONS; j++) {
aCoords[j][i + startIdx] += v[j] * stretchDist;
}
} else {
#pragma acc parallel loop deviceptr(aCoords) if (on_gpu)
for (int j = 0; j < NUM_DIMENSIONS; j++) {
aCoords[j][i + startIdx] -= v[j] * stretchDist;
}
}
}
// Record the actual bond stretch
#pragma acc parallel deviceptr(bondLengths) if (on_gpu)
bondLengths[bondStart + bondIdx] += stretchDist;
}
void SimBox::stretchBond(int molIdx, int bondIdx, Real stretchDist) {
int bondStart = moleculeData[MOL_BOND_START][molIdx];
int bondEnd = bondStart + moleculeData[MOL_BOND_COUNT][molIdx];
changedBond = bondStart + bondIdx;
prevBond = bondLengths[bondStart + bondIdx];
int startIdx = moleculeData[MOL_START][molIdx];
int molSize = moleculeData[MOL_LEN][molIdx];
int end1 = (int) bondData[BOND_A1_IDX][bondStart + bondIdx];
int end2 = (int) bondData[BOND_A2_IDX][bondStart + bondIdx];
for (int i = 0; i < molSize; i++) {
unionFindParent[i] = i;
}
for (int i = bondStart; i < bondEnd; i++) {
if (i == bondIdx + bondStart)
continue;
int a1 = (int) bondData[BOND_A1_IDX][i] - startIdx;
int a2 = (int) bondData[BOND_A2_IDX][i] - startIdx;
unionAtoms(a1, a2);
}
int side1 = find(end1 - startIdx);
int side2 = find(end2 - startIdx);
if (side1 == side2) {
std::cout << "ERROR: EXPANDING BOND IN A RING!" << std::endl;
return;
}
Real v[NUM_DIMENSIONS];
Real denon;
for (int i = 0; i < NUM_DIMENSIONS; i++) {
v[i] = atomCoordinates[i][side2] - atomCoordinates[i][side1];
denon += v[i] * v[i];
}
denon = sqrt(denon);
for (int i = 0; i < NUM_DIMENSIONS; i++) {
v[i] = v[i] / denon / 2.0;
}
for (int i = 0; i < molSize; i++) {
if(find(i) == side2) {
for (int j = 0; j < NUM_DIMENSIONS; j++) {
atomCoordinates[j][i + startIdx] += v[i];
}
} else {
for (int j = 0; j < NUM_DIMENSIONS; j++) {
atomCoordinates[j][i + startIdx] -= v[i];
}
}
}
bondLengths[bondStart + bondIdx] += stretchDist;
}
void SimBox::expandAngle(int molIdx, int angleIdx, Real expandDeg) {
int bondStart = moleculeData[MOL_BOND_START][molIdx];
int bondEnd = bondStart + moleculeData[MOL_BOND_COUNT][molIdx];
int angleStart = moleculeData[MOL_ANGLE_START][molIdx];
changedAngle = angleStart + angleIdx;
prevAngle = angleSizes[angleStart + angleIdx];
int startIdx = moleculeData[MOL_START][molIdx];
int molSize = moleculeData[MOL_LEN][molIdx];
int end1 = (int) angleData[ANGLE_A1_IDX][angleStart + angleIdx];
int end2 = (int) angleData[ANGLE_A2_IDX][angleStart + angleIdx];
int mid = (int) angleData[ANGLE_MID_IDX][angleStart + angleIdx];
for (int i = 0; i < molSize; i++) {
unionFindParent[i] = i;
}
for (int i = bondStart; i < bondEnd; i++) {
int a1 = (int) bondData[BOND_A1_IDX][i];
int a2 = (int) bondData[BOND_A2_IDX][i];
if (a1 == mid || a2 == mid)
continue;
unionAtoms(a1 - startIdx, a2 - startIdx);
}
int group1 = find(end1 - startIdx);
int group2 = find(end2 - startIdx);
if (group1 == group2) {
std::cout << "ERROR: EXPANDING ANGLE IN A RING!" << std::endl;
return;
}
Real DEG2RAD = 3.14159256358979323846264 / 180.0;
Real end1Mid[NUM_DIMENSIONS];
Real end2Mid[NUM_DIMENSIONS];
Real normal[NUM_DIMENSIONS];
Real mvector[NUM_DIMENSIONS];
for (int i = 0; i < NUM_DIMENSIONS; i++) {
end1Mid[i] = atomCoordinates[i][mid] - atomCoordinates[i][end1];
end2Mid[i] = atomCoordinates[i][mid] - atomCoordinates[i][end2];
mvector[i] = atomCoordinates[i][mid];
}
normal[0] = end1Mid[1] * end2Mid[2] - end2Mid[1] * end1Mid[2];
normal[1] = end2Mid[0] * end1Mid[2] - end1Mid[0] * end2Mid[2];
normal[2] = end1Mid[0] * end2Mid[1] - end2Mid[0] * end1Mid[1];
Real normLen = 0.0;
for (int i = 0; i < NUM_DIMENSIONS; i++) {
normLen += normal[i] * normal[i];
}
normLen = sqrt(normLen);
for (int i = 0; i < NUM_DIMENSIONS; i++) {
normal[i] = normal[i] / normLen;
}
for (int i = startIdx; i < startIdx + molSize; i++) {
Real theta;
Real point[NUM_DIMENSIONS];
Real dot = 0.0;
Real cross[NUM_DIMENSIONS];
if (find(i - startIdx) == group1) {
theta = expandDeg * -DEG2RAD;
} else if (find(i - startIdx) == group2) {
theta = expandDeg * DEG2RAD;
} else {
continue;
}
for (int j = 0; j < NUM_DIMENSIONS; j++) {
point[j] = atomCoordinates[j][i] - mvector[i];
dot += point[j] * normal[j];
}
cross[0] = normal[1] * point[2] - point[1] * normal[2];
cross[1] = point[0] * normal[2] - normal[0] * point[2];
cross[2] = normal[0] * point[1] - point[0] * normal[1];
for (int j = 0; j < NUM_DIMENSIONS; j++) {
point[j] = normal[j] * dot * (1 - cos(theta)) + point[j] * cos(theta) + cross[j] * sin(theta);
atomCoordinates[j][i] = point[j] + mvector[j];
}
}
angleSizes[angleStart + angleIdx] += expandDeg;
}
void SimCalcs::expandAngle(int molIdx, int angleIdx, Real expandDeg) {
int** moleculeData = sb->moleculeData;
Real* angleSizes = GPUCopy::angleSizesPtr();
int bondStart = moleculeData[MOL_BOND_START][molIdx];
int bondEnd = bondStart + moleculeData[MOL_BOND_COUNT][molIdx];
int angleStart = moleculeData[MOL_ANGLE_START][molIdx];
int startIdx = moleculeData[MOL_START][molIdx];
int molSize = moleculeData[MOL_LEN][molIdx];
int end1 = (int)sb->angleData[ANGLE_A1_IDX][angleStart + angleIdx];
int end2 = (int)sb->angleData[ANGLE_A2_IDX][angleStart + angleIdx];
int mid = (int)sb->angleData[ANGLE_MID_IDX][angleStart + angleIdx];
Real** aCoords = GPUCopy::atomCoordinatesPtr();
// Create a disjoint set of the atoms in the molecule
for (int i = 0; i < molSize; i++) {
sb->unionFindParent[i] = i;
}
// Union atoms connected by a bond
for (int i = bondStart; i < bondEnd; i++) {
int a1 = (int)sb->bondData[BOND_A1_IDX][i];
int a2 = (int)sb->bondData[BOND_A2_IDX][i];
if (a1 == mid || a2 == mid)
continue;
unionAtoms(a1 - startIdx, a2 - startIdx);
}
int group1 = find(end1 - startIdx);
int group2 = find(end2 - startIdx);
if (group1 == group2) {
// std::cout << "ERROR: EXPANDING ANGLE IN A RING!" << std::endl;
return;
}
Real DEG2RAD = 3.14159256358979323846264 / 180.0;
Real end1Mid[NUM_DIMENSIONS];
Real end2Mid[NUM_DIMENSIONS];
Real normal[NUM_DIMENSIONS];
Real mvector[NUM_DIMENSIONS];
#pragma acc parallel loop deviceptr(aCoords) if (on_gpu)
for (int i = 0; i < NUM_DIMENSIONS; i++) {
end1Mid[i] = aCoords[i][mid] - aCoords[i][end1];
end2Mid[i] = aCoords[i][mid] - aCoords[i][end2];
mvector[i] = aCoords[i][mid];
}
normal[0] = end1Mid[1] * end2Mid[2] - end2Mid[1] * end1Mid[2];
normal[1] = end2Mid[0] * end1Mid[2] - end1Mid[0] * end2Mid[2];
normal[2] = end1Mid[0] * end2Mid[1] - end2Mid[0] * end1Mid[1];
Real normLen = 0.0;
for (int i = 0; i < NUM_DIMENSIONS; i++) {
normLen += normal[i] * normal[i];
}
normLen = sqrt(normLen);
for (int i = 0; i < NUM_DIMENSIONS; i++) {
normal[i] = normal[i] / normLen;
}
for (int i = startIdx; i < startIdx + molSize; i++) {
Real theta;
Real point[NUM_DIMENSIONS];
Real dot = 0.0;
Real cross[NUM_DIMENSIONS];
if (find(i - startIdx) == group1) {
theta = expandDeg * -DEG2RAD;
} else if (find(i - startIdx) == group2) {
theta = expandDeg * DEG2RAD;
} else {
continue;
}
#pragma acc parallel loop deviceptr(aCoords) if (on_gpu)
for (int j = 0; j < NUM_DIMENSIONS; j++) {
point[j] = aCoords[j][i] - mvector[j];
dot += point[j] * normal[j];
}
cross[0] = normal[1] * point[2] - point[1] * normal[2];
cross[1] = point[0] * normal[2] - normal[0] * point[2];
cross[2] = normal[0] * point[1] - point[0] * normal[1];
#pragma acc parallel loop deviceptr(aCoords) if (on_gpu)
for (int j = 0; j < NUM_DIMENSIONS; j++) {
point[j] = (normal[j] * dot * (1 - cos(theta)) + point[j] * cos(theta) +
cross[j] * sin(theta));
aCoords[j][i] = point[j] + mvector[j];
}
}
#pragma acc parallel deviceptr(angleSizes) if (on_gpu)
angleSizes[angleStart + angleIdx] += expandDeg;
}