[ViewVC] Diff of: OpenMD/trunk/test/brains/Molecule.cpp

Comparing trunk/test/brains/Molecule.cpp (file contents):
Revision 192 by tim, Fri Oct 29 20:54:04 2004 UTC vs.
Revision 196 by tim, Fri Oct 29 22:37:59 2004 UTC

+ */
+/**
-<
+ * @file Molecule.hpp
->
+ * @file Molecule.cpp
+ * @author    tlin
-<
+ * @date  10/25/2004
->
+ * @date  10/28/2004
+ * @version 1.0
+ */
+#include "primitives/Molecule.hpp"
-+
+#include <algorithm>
+namespace oopse {
-+
+void Molecule::addAtom(Atom* atom) {
-+
+    if (atoms_.find(atom) == atoms_.end()) {
-+
+        atoms_.push_back(atom);
-+
+    }
-+
+}
-+
+void Molecule::addBond(Bond* bond) {
-+
+    if (bonds_.find(bond) == bonds_.end()) {
-+
+        bonds_.push_back(bond);
-+
+    }
-+
+}
-+
-+
+void Molecule::addBend(Bend* bend) {
-+
+    if (bends_.find(bend) == bends_.end()) {
-+
+        bends_.push_back(bend);
-+
+    }
-+
+}
-+
-+
+void Molecule::addTorsion(Torsion* torsion) {
-+
+    if (torsions_.find(torsion) == torsions_.end()) {
-+
+        torsions_.push_back(torsion);
-+
+    }
-+
+}
-+
-+
+void Molecule::addRigidBody(RigidBody *rb) {
-+
+    if (rigidBodies_.find(bond) == bonds_.end()) {
-+
+        rigidBodies_.push_back(rb);
-+
+    }
-+
+}
-+
-+
+void Molecule::addCutoffGroup(CutoffGroup* cp) {
-+
+    if (cutoffGroups_.find(bond) == bonds_.end()) {
-+
+        cutoffGroups_.push_back(cp);
-+
+    }
-+
-+
+}
-+
-+
+void Molecule::complete() {
-+
-+
+    std::set<Atom*> allAtoms;
-+
+    allAtoms.insert(atoms_.begin(), atoms_.end());
-+
-+
+    std::set<Atom*> rigidAtoms;
-+
+    RigidBody* rb;
-+
+    std::vector<RigidBody*> rbIter;
-+
-+
-+
+    for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
-+
+        rigidAtoms.insert(rb->beginAtomIter(), rb->endAtomIter());
-+
+    }
-+
-+
+    //find all free atoms (which do not belong to rigid bodies)
-+
+    //performs the "difference" operation from set theory,  the output range contains a copy of every
-+
+    //element that is contained in [allAtoms.begin(), allAtoms.end()) and not contained in
-+
+    //[rigidAtoms.begin(), rigidAtoms.end()).
-+
+    std::set_difference(allAtoms.begin(), allAtoms.end(), rigidAtoms.begin(), rigidAtoms.end(),
-+
+                            std::back_inserter(integrableObjects_));
-+
-+
+    if (integrableObjects_.size() != allAtoms.size() - rigidAtoms.size()) {
-+
+        //Some atoms in rigidAtoms are not in allAtoms, something must be wrong
-+
+    }
-+
-+
+    integrableObjects_.insert(integrableObjects_.end(), rigidBodies_.begin(), rigidBodies_.end());
-+
+}
-+
+Atom* Molecule::beginAtom(std::vector<Atom*>::iterator& i) {
+    i = atoms_.begin();
+    return (i == atoms_.end()) ? NULL : *i;
-+
+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;
-+
+}
-+
-+
+Vector3d Molecule::getCom() {
-+
+    StuntDouble* sd;
-+
+    std::vector<StuntDouble*>::iterator i;
-+
+    Vector3d com;
-+
+    double totalMass = 0;
-+
+    double mass;
-+
-+
+    for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
-+
+        mass = sd->getMass();
-+
+        totalMass += mass;
-+
+        com += sd->getPos() * mass;
-+
+    }
-+
-+
+    com /= totalMass;
-+
-+
+    return com;
-+
+}
-+
-+
+void Molecule::moveCom(const Vetor3d& delta) {
-+
+    StuntDouble* sd;
-+
+    std::vector<StuntDouble*>::iterator i;
-+
-+
+    for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
-+
+        s->setPos(sd->getPos() + delta);
-+
+    }
-+
-+
+}
-+
-+
+Vector3d Molecule::getComVel() {
-+
+    StuntDouble* sd;
-+
+    std::vector<StuntDouble*>::iterator i;
-+
+    Vector3d velCom;
-+
+    double totalMass = 0;
-+
+    double mass;
-+
-+
+    for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
-+
+        mass = sd->getMass();
-+
+        totalMass += mass;
-+
+        velCom += sd->getVel() * mass;
-+
+    }
-+
-+
+    velCom /= totalMass;
-+
-+
+    return velCom;
-+
+}
-+
-+
+std::ostream& operator <<(std::ostream& o, const Molecule& mol) {
-+
+    o << std::endl;
-+
+    o << "Molecule " << mol.getGlobalIndex() << "has: " << std::endl;
-+
+    o << mol.getNAtoms() << " atoms" << std::endl;
-+
+    o << mol.getNBonds() << " bonds" << std::endl;
-+
+    o << mol.getNBends() << " bends" << std::endl;
-+
+    o << mol.getNTorsions() << " torsions" << std::endl;
-+
+    o << mol.getNRigidBodies() << " rigid bodies" << std::endl;
-+
+    o << mol.getNIntegrableObjects() << "integrable objects" << std::endl;
-+
+    o << mol.getNCutoffGroups() << "cutoff groups" << std::endl;
-+
-+
+    return o;
-+
+}
-+
+}//end namespace oopse

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Comparing trunk/test/brains/Molecule.cpp (file contents): Revision 192 by tim, Fri Oct 29 20:54:04 2004 UTC vs. Revision 196 by tim, Fri Oct 29 22:37:59 2004 UTC

Diff Legend

Comparing trunk/test/brains/Molecule.cpp (file contents):
Revision 192 by tim, Fri Oct 29 20:54:04 2004 UTC vs.
Revision 196 by tim, Fri Oct 29 22:37:59 2004 UTC