RealType GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2,
StuntDouble* sd3) {
bool usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions();
Vector3d v1;
Vector3d v2;
v1 = sd3->getPos() - sd1->getPos();
if (usePeriodicBoundaryConditions_)
currentSnapshot_->wrapVector(v1);
if (!sd2->isDirectional()) {
sprintf(painCave.errMsg,
"GofROmega: attempted to use a non-directional object: %s\n",
sd2->getType().c_str());
painCave.isFatal = 1;
simError();
}
if (sd2->isAtom()) {
AtomType* atype2 = static_cast<Atom*>(sd2)->getAtomType();
MultipoleAdapter ma2 = MultipoleAdapter(atype2);
if (ma2.isDipole() )
v2 = sd2->getDipole();
else
v2 = sd2->getA().transpose() * V3Z;
} else {
v2 = sd2->getA().transpose() * V3Z;
}
v1.normalize();
v2.normalize();
return dot(v1, v2);
}
void GofXyz::initializeHistogram() {
// Calculate the center of mass of the molecule of selected
// StuntDouble in selection1
if (!evaluator3_.isDynamic()) {
seleMan3_.setSelectionSet(evaluator3_.evaluate());
}
assert(seleMan1_.getSelectionCount() == seleMan3_.getSelectionCount());
bool usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions();
// The Dipole direction of selection3 and position of selection3 will
// be used to determine the y-z plane
// v1 = s3 -s1,
// z = origin.dipole
// x = v1 X z
// y = z X x
rotMats_.clear();
int i;
int j;
StuntDouble* sd1;
StuntDouble* sd3;
for (sd1 = seleMan1_.beginSelected(i), sd3 = seleMan3_.beginSelected(j);
sd1 != NULL || sd3 != NULL;
sd1 = seleMan1_.nextSelected(i), sd3 = seleMan3_.nextSelected(j)) {
Vector3d r3 = sd3->getPos();
Vector3d r1 = sd1->getPos();
Vector3d v1 = r3 - r1;
if (usePeriodicBoundaryConditions_)
info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1);
AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType();
MultipoleAdapter ma1 = MultipoleAdapter(atype1);
Vector3d zaxis;
if (ma1.isDipole())
zaxis = sd1->getDipole();
else
zaxis = sd1->getA().transpose() * V3Z;
Vector3d xaxis = cross(v1, zaxis);
Vector3d yaxis = cross(zaxis, xaxis);
xaxis.normalize();
yaxis.normalize();
zaxis.normalize();
RotMat3x3d rotMat;
rotMat.setRow(0, xaxis);
rotMat.setRow(1, yaxis);
rotMat.setRow(2, zaxis);
rotMats_.insert(std::map<int, RotMat3x3d>::value_type(sd1->getGlobalIndex(), rotMat));
}
}
RealType GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
Vector3d v1, v2;
if (!sd1->isDirectional()) {
sprintf(painCave.errMsg,
"GofROmega: attempted to use a non-directional object: %s\n",
sd1->getType().c_str());
painCave.isFatal = 1;
simError();
}
if (sd1->isAtom()){
AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType();
MultipoleAdapter ma1 = MultipoleAdapter(atype1);
if (ma1.isDipole() )
v1 = sd1->getDipole();
else
v1 = sd1->getA().transpose() * V3Z;
} else {
v1 = sd1->getA().transpose() * V3Z;
}
if (!sd2->isDirectional()) {
sprintf(painCave.errMsg,
"GofROmega attempted to use a non-directional object: %s\n",
sd2->getType().c_str());
painCave.isFatal = 1;
simError();
}
if (sd2->isAtom()) {
AtomType* atype2 = static_cast<Atom*>(sd2)->getAtomType();
MultipoleAdapter ma2 = MultipoleAdapter(atype2);
if (ma2.isDipole() )
v2 = sd2->getDipole();
else
v2 = sd2->getA().transpose() * V3Z;
} else {
v2 = sd2->getA().transpose() * V3Z;
}
v1.normalize();
v2.normalize();
return dot(v1, v2);
}
RealType GofRTheta::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
bool usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions();
Vector3d pos1 = sd1->getPos();
Vector3d pos2 = sd2->getPos();
Vector3d r12 = pos2 - pos1;
if (usePeriodicBoundaryConditions_)
currentSnapshot_->wrapVector(r12);
r12.normalize();
Vector3d vec;
if (!sd1->isDirectional()) {
sprintf(painCave.errMsg,
"GofRTheta: attempted to use a non-directional object: %s\n",
sd1->getType().c_str());
painCave.isFatal = 1;
simError();
}
if (sd1->isAtom()) {
AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType();
MultipoleAdapter ma1 = MultipoleAdapter(atype1);
if (ma1.isDipole() )
vec = sd1->getDipole();
else
vec = sd1->getA().transpose() * V3Z;
} else {
vec = sd1->getA().transpose() * V3Z;
}
vec.normalize();
return dot(r12, vec);
}
DirectionalAtom::DirectionalAtom(AtomType* dAtomType)
: Atom(dAtomType) {
objType_= otDAtom;
DirectionalAdapter da = DirectionalAdapter(dAtomType);
I_ = da.getI();
MultipoleAdapter ma = MultipoleAdapter(dAtomType);
if (ma.isDipole()) {
dipole_ = ma.getDipole();
}
if (ma.isQuadrupole()) {
quadrupole_ = ma.getQuadrupole();
}
// Check if one of the diagonal inertia tensor of this directional
// atom is zero:
int nLinearAxis = 0;
Mat3x3d inertiaTensor = getI();
for (int i = 0; i < 3; i++) {
if (fabs(inertiaTensor(i, i)) < OpenMD::epsilon) {
linear_ = true;
linearAxis_ = i;
++ nLinearAxis;
}
}
if (nLinearAxis > 1) {
sprintf( painCave.errMsg,
"Directional Atom warning.\n"
"\tOpenMD found more than one axis in this directional atom with a vanishing \n"
"\tmoment of inertia.");
painCave.isFatal = 0;
simError();
}
}
