ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/branches/new_design/OOPSE-3.0/src/primitives/Molecule.cpp
(Generate patch)

Comparing branches/new_design/OOPSE-3.0/src/primitives/Molecule.cpp (file contents):
Revision 1692 by tim, Mon Nov 1 20:15:58 2004 UTC vs.
Revision 1738 by tim, Sat Nov 13 05:08:12 2004 UTC

# Line 30 | Line 30
30   * @version 1.0
31   */
32  
33 – #include "primitives/Molecule.hpp"
33   #include <algorithm>
34 + #include <set>
35  
36 + #include "primitives/Molecule.hpp"
37 + #include "utils/MemoryUtils.hpp"
38 +
39   namespace oopse {
40 + Molecule::Molecule(int stampId, int globalIndex, const std::string& molName)
41 +    : stampId_(stampId), globalIndex_(globalIndex), moleculeName_(molName) {
42  
43 + }
44 +
45   Molecule::~Molecule() {
46  
47 <    deleteVectorOfPointer(atoms_);
48 <    deleteVectorOfPointer(bonds_);
49 <    deleteVectorOfPointer(bends_);
50 <    deleteVectorOfPointer(torsions_);
51 <    deleteVectorOfPointer(rigidbodies_);
52 <    deleteVectorOfPointer(cutoffGroups_);
47 >    MemoryUtils::deleteVectorOfPointer(atoms_);
48 >    MemoryUtils::deleteVectorOfPointer(bonds_);
49 >    MemoryUtils::deleteVectorOfPointer(bends_);
50 >    MemoryUtils::deleteVectorOfPointer(torsions_);
51 >    MemoryUtils::deleteVectorOfPointer(rigidBodies_);
52 >    MemoryUtils::deleteVectorOfPointer(cutoffGroups_);
53  
54 +    //integrableObjects_ don't own the objects
55      integrableObjects_.clear();
56      
57   }
58  
59   void Molecule::addAtom(Atom* atom) {
60 <    if (atoms_.find(atom) == atoms_.end()) {
60 >    if (std::find(atoms_.begin(), atoms_.end(), atom) == atoms_.end()) {
61          atoms_.push_back(atom);
62      }
63   }
64  
65   void Molecule::addBond(Bond* bond) {
66 <    if (bonds_.find(bond) == bonds_.end()) {
66 >    if (std::find(bonds_.begin(), bonds_.end(), bond) == bonds_.end()) {
67          bonds_.push_back(bond);
68      }
69   }
70  
71   void Molecule::addBend(Bend* bend) {
72 <    if (bends_.find(bend) == bends_.end()) {
72 >    if (std::find(bends_.begin(), bends_.end(), bend) == bends_.end()) {
73          bends_.push_back(bend);
74      }
75   }
76  
77   void Molecule::addTorsion(Torsion* torsion) {
78 <    if (torsions_.find(torsion) == torsions_.end()) {
78 >    if (std::find(torsions_.begin(), torsions_.end(), torsion) == torsions_.end()) {
79          torsions_.push_back(torsion);
80      }
81   }
82  
83   void Molecule::addRigidBody(RigidBody *rb) {
84 <    if (rigidBodies_.find(bond) == bonds_.end()) {
84 >    if (std::find(rigidBodies_.begin(), rigidBodies_.end(), rb) == rigidBodies_.end()) {
85          rigidBodies_.push_back(rb);
86      }
87   }
88  
89   void Molecule::addCutoffGroup(CutoffGroup* cp) {
90 <    if (cutoffGroups_.find(bond) == bonds_.end()) {
90 >    if (std::find(cutoffGroups_.begin(), cutoffGroups_.end(), cp) == cutoffGroups_.end()) {
91          cutoffGroups_.push_back(cp);
92      }
93  
# Line 92 | Line 100 | void Molecule::complete() {
100  
101      std::set<Atom*> rigidAtoms;
102      RigidBody* rb;
103 <    std::vector<RigidBody*> rbIter;
103 >    std::vector<RigidBody*>::iterator rbIter;
104  
105      
106      for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
107 <        rigidAtoms.insert(rb->beginAtomIter(), rb->endAtomIter());
107 >        rigidAtoms.insert(rb->getBeginAtomIter(), rb->getEndAtomIter());
108      }
109  
110      //find all free atoms (which do not belong to rigid bodies)  
# Line 104 | Line 112 | void Molecule::complete() {
112      //element that is contained in [allAtoms.begin(), allAtoms.end()) and not contained in
113      //[rigidAtoms.begin(), rigidAtoms.end()).
114      std::set_difference(allAtoms.begin(), allAtoms.end(), rigidAtoms.begin(), rigidAtoms.end(),
115 <                            std::back_inserter(integrableObjects_));
115 >                            std::back_inserter(integrableObjects_.end()));
116  
117      if (integrableObjects_.size() != allAtoms.size() - rigidAtoms.size()) {
118          //Some atoms in rigidAtoms are not in allAtoms, something must be wrong
119 +        sprintf(painCave.errMsg, "Atoms in rigidbody are not in the atom list of the same molecule");
120 +
121 +        painCave.isFatal = 1;
122 +        simError();        
123      }
124  
125      integrableObjects_.insert(integrableObjects_.end(), rigidBodies_.begin(), rigidBodies_.end());
# Line 184 | Line 196 | CutoffGroup* Molecule::nextCutoffGroup(std::vector<Cut
196      ++i;
197      return (i == cutoffGroups_.end()) ? NULL : *i;    
198   }
187 –
188 – void Molecule::calcForces() {
189 –    RigidBody* rb;
190 –    Bond* bond;
191 –    Bend* bend;
192 –    Torsion* torsion;
193 –    std::vector<RigidBody*> rbIter;
194 –    std::vector<Bond*> bondIter;;
195 –    std::vector<Bend*> bendIter;
196 –    std::vector<Torsion*> torsionIter;
197 –
198 –    for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
199 –        rb->updateAtoms();
200 –    }
199  
202 –    for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) {
203 –        bond->calcForce();
204 –    }
200  
206 –    for (bend = beginBend(bendIter); bend != NULL; bend = nextBend(bendIter)) {
207 –        bend->calcForce();
208 –    }
209 –
210 –    for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion = nextTorsion(torsionIter)) {
211 –        torsion->calcForce();
212 –    }
213 –    
214 – }
215 –
216 – double Molecule::getPotential() {
217 –    //RigidBody* rb;
218 –    Bond* bond;
219 –    Bend* bend;
220 –    Torsion* torsion;
221 –    //std::vector<RigidBody*> rbIter;
222 –    std::vector<Bond*> bondIter;;
223 –    std::vector<Bend*> bendIter;
224 –    std::vector<Torsion*> torsionIter;
225 –
226 –    double potential = 0;
227 –    
228 –    //for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) {
229 –    //    rb->updateAtoms();
230 –    //}
231 –
232 –    for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) {
233 –        potential += bond->getPotential();
234 –    }
235 –
236 –    for (bend = beginBend(bendIter); bend != NULL; bend = nextBend(bendIter)) {
237 –        potential += bend->getPotential();
238 –    }
239 –
240 –    for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion = nextTorsion(torsionIter)) {
241 –        potential += torsion->getPotential();
242 –    }
243 –    
244 –    return potential;
245 – }
246 –
201   Vector3d Molecule::getCom() {
202      StuntDouble* sd;
203      std::vector<StuntDouble*>::iterator i;
# Line 262 | Line 216 | void Molecule::moveCom(const Vetor3d& delta) {
216      return com;
217   }
218  
219 < void Molecule::moveCom(const Vetor3d& delta) {
219 > void Molecule::moveCom(const Vector3d& delta) {
220      StuntDouble* sd;
221      std::vector<StuntDouble*>::iterator i;
222      
223      for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
224 <        s->setPos(sd->getPos() + delta);
224 >        sd->setPos(sd->getPos() + delta);
225      }
226  
227   }
# Line 290 | Line 244 | std::ostream& operator <<(std::ostream& o, const Molec
244      return velCom;
245   }
246  
247 < std::ostream& operator <<(std::ostream& o, const Molecule& mol) {
247 > std::ostream& operator <<(std::ostream& o, Molecule& mol) {
248      o << std::endl;
249      o << "Molecule " << mol.getGlobalIndex() << "has: " << std::endl;
250      o << mol.getNAtoms() << " atoms" << std::endl;

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines