double InterMolecularTorsions::compute( const unsigned& tindex, multicolvar::AtomValuePack& myatoms ) const {
Vector v1, v2, dv1, dv2, dconn, conn = getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );
// Retrieve vectors
std::vector<double> orient0( 5 ), orient1( 5 );
getInputData( 0, true, myatoms, orient0 );
getInputData( 1, true, myatoms, orient1 );
for(unsigned i=0; i<3; ++i) { v1[i]=orient0[2+i]; v2[i]=orient1[2+i]; }
if( getBaseMultiColvar(0)->getNumberOfQuantities()<3 ) return 1.0;
// Evaluate angle
Torsion t; double angle = t.compute( v1, conn, v2, dv1, dconn, dv2 );
for(unsigned i=0; i<3; ++i) { orient0[i+2]=dv1[i]; orient1[i+2]=dv2[i]; }
// And accumulate derivatives
if( !doNotCalculateDerivatives() ) {
MultiValue& myder0=getInputDerivatives( 0, true, myatoms );
mergeInputDerivatives( 1, 2, orient1.size(), 0, orient0, myder0, myatoms );
MultiValue& myder1=getInputDerivatives( 1, true, myatoms );
mergeInputDerivatives( 1, 2, orient0.size(), 1, orient1, myder1, myatoms );
addAtomDerivatives( 1, 0, -dconn, myatoms ); addAtomDerivatives( 1, 1, dconn, myatoms );
myatoms.addBoxDerivatives( 1, -extProduct( conn, dconn ) );
}
return angle;
}
double Molecule::getPotential() {
//RigidBody* rb;
Bond* bond;
Bend* bend;
Torsion* torsion;
//std::vector<RigidBody*> rbIter;
std::vector<Bond*> bondIter;;
std::vector<Bend*> bendIter;
std::vector<Torsion*> torsionIter;
double potential = 0;
//for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
// rb->updateAtoms();
//}
for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) {
potential += bond->getPotential();
}
for (bend = beginBend(bendIter); bend != NULL; bend = nextBend(bendIter)) {
potential += bend->getPotential();
}
for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion = nextTorsion(torsionIter)) {
potential += torsion->getPotential();
}
return potential;
}
void Molecule::calcForces() {
RigidBody* rb;
Bond* bond;
Bend* bend;
Torsion* torsion;
std::vector<RigidBody*> rbIter;
std::vector<Bond*> bondIter;;
std::vector<Bend*> bendIter;
std::vector<Torsion*> torsionIter;
for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
rb->updateAtoms();
}
for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) {
bond->calcForce();
}
for (bend = beginBend(bendIter); bend != NULL; bend = nextBend(bendIter)) {
bend->calcForce();
}
for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion = nextTorsion(torsionIter)) {
torsion->calcForce();
}
}
DistanceFinder::DistanceFinder(SimInfo* info) : info_(info) {
nObjects_.push_back(info_->getNGlobalAtoms()+info_->getNGlobalRigidBodies());
nObjects_.push_back(info_->getNGlobalBonds());
nObjects_.push_back(info_->getNGlobalBends());
nObjects_.push_back(info_->getNGlobalTorsions());
nObjects_.push_back(info_->getNGlobalInversions());
stuntdoubles_.resize(nObjects_[STUNTDOUBLE]);
bonds_.resize(nObjects_[BOND]);
bends_.resize(nObjects_[BEND]);
torsions_.resize(nObjects_[TORSION]);
inversions_.resize(nObjects_[INVERSION]);
SimInfo::MoleculeIterator mi;
Molecule::AtomIterator ai;
Molecule::RigidBodyIterator rbIter;
Molecule::BondIterator bondIter;
Molecule::BendIterator bendIter;
Molecule::TorsionIterator torsionIter;
Molecule::InversionIterator inversionIter;
Molecule* mol;
Atom* atom;
RigidBody* rb;
Bond* bond;
Bend* bend;
Torsion* torsion;
Inversion* inversion;
for (mol = info_->beginMolecule(mi); mol != NULL;
mol = info_->nextMolecule(mi)) {
for(atom = mol->beginAtom(ai); atom != NULL;
atom = mol->nextAtom(ai)) {
stuntdoubles_[atom->getGlobalIndex()] = atom;
}
for (rb = mol->beginRigidBody(rbIter); rb != NULL;
rb = mol->nextRigidBody(rbIter)) {
stuntdoubles_[rb->getGlobalIndex()] = rb;
}
for (bond = mol->beginBond(bondIter); bond != NULL;
bond = mol->nextBond(bondIter)) {
bonds_[bond->getGlobalIndex()] = bond;
}
for (bend = mol->beginBend(bendIter); bend != NULL;
bend = mol->nextBend(bendIter)) {
bends_[bend->getGlobalIndex()] = bend;
}
for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
torsion = mol->nextTorsion(torsionIter)) {
torsions_[torsion->getGlobalIndex()] = torsion;
}
for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
inversion = mol->nextInversion(inversionIter)) {
inversions_[inversion->getGlobalIndex()] = inversion;
}
}
}
void IndexFinder::init() {
SimInfo::MoleculeIterator mi;
Molecule::AtomIterator ai;
Molecule::RigidBodyIterator rbIter;
Molecule::BondIterator bondIter;
Molecule::BendIterator bendIter;
Molecule::TorsionIterator torsionIter;
Molecule::InversionIterator inversionIter;
Molecule* mol;
Atom* atom;
RigidBody* rb;
Bond* bond;
Bend* bend;
Torsion* torsion;
Inversion* inversion;
for (mol = info_->beginMolecule(mi); mol != NULL;
mol = info_->nextMolecule(mi)) {
SelectionSet ss(nObjects_);
ss.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
ss.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
}
for (rb = mol->beginRigidBody(rbIter); rb != NULL;
rb = mol->nextRigidBody(rbIter)) {
ss.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex());
}
for (bond = mol->beginBond(bondIter); bond != NULL;
bond = mol->nextBond(bondIter)) {
ss.bitsets_[BOND].setBitOn(bond->getGlobalIndex());
}
for (bend = mol->beginBend(bendIter); bend != NULL;
bend = mol->nextBend(bendIter)) {
ss.bitsets_[BEND].setBitOn(bend->getGlobalIndex());
}
for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
torsion = mol->nextTorsion(torsionIter)) {
ss.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex());
}
for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
inversion = mol->nextInversion(inversionIter)) {
ss.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex());
}
selectionSets_[mol->getGlobalIndex()] = ss;
}
}
