int Box::changeMolecule(int molIdx)
{
Real maxTranslation = environment->maxTranslation;
Real maxRotation = environment->maxRotation;
saveChangedMol(molIdx);
//Pick an atom in the molecule about which to rotate
int atomIndex = randomReal(0, molecules[molIdx].numOfAtoms);
Atom vertex = molecules[molIdx].atoms[atomIndex];
const Real deltaX = randomReal(-maxTranslation, maxTranslation);
const Real deltaY = randomReal(-maxTranslation, maxTranslation);
const Real deltaZ = randomReal(-maxTranslation, maxTranslation);
const Real degreesX = randomReal(-maxRotation, maxRotation);
const Real degreesY = randomReal(-maxRotation, maxRotation);
const Real degreesZ = randomReal(-maxRotation, maxRotation);
moveMolecule(molecules[molIdx], vertex, deltaX, deltaY, deltaZ,
degreesX, degreesY, degreesZ);
keepMoleculeInBox(molIdx);
return molIdx;
}
void SimCalcs::intermolecularMove(int molIdx) {
Real maxT = sb->maxTranslate;
Real maxR = sb->maxRotate;
int molStart = sb->moleculeData[MOL_START][molIdx];
int molLen = sb->moleculeData[MOL_LEN][molIdx];
int vertexIdx = (int)randomReal(0, molLen);
const Real deltaX = randomReal(-maxT, maxT);
const Real deltaY = randomReal(-maxT, maxT);
const Real deltaZ = randomReal(-maxT, maxT);
const Real rotX = randomReal(-maxR, maxR);
const Real rotY = randomReal(-maxR, maxR);
const Real rotZ = randomReal(-maxR, maxR);
Real** rBCoords = GPUCopy::rollBackCoordinatesPtr();
Real** aCoords = GPUCopy::atomCoordinatesPtr();
Real* bSize = GPUCopy::sizePtr();
int* pIdxes = GPUCopy::primaryIndexesPtr();
int** molData = GPUCopy::moleculeDataPtr();
// Do the move here
#pragma acc parallel loop deviceptr(aCoords, rBCoords) \
if (on_gpu)
for (int i = 0; i < molLen; i++) {
for (int j = 0; j < NUM_DIMENSIONS; j++) {
rBCoords[j][i] = aCoords[j][molStart + i];
}
if (i == vertexIdx)
continue;
rotateAtom(molStart + i, molStart + vertexIdx, rotX, rotY, rotZ, aCoords);
translateAtom(molStart + i, deltaX, deltaY, deltaZ, aCoords);
}
#pragma acc parallel loop deviceptr(aCoords, molData, pIdxes, bSize) \
if (on_gpu)
for (int i = 0; i < 1; i++) {
aCoords[0][molStart + vertexIdx] += deltaX;
aCoords[1][molStart + vertexIdx] += deltaY;
aCoords[2][molStart + vertexIdx] += deltaZ;
keepMoleculeInBox(molIdx, aCoords, molData, pIdxes, bSize);
}
}