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root/group/trunk/OOPSE/libmdtools/Molecule.cpp
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Comparing trunk/OOPSE/libmdtools/Molecule.cpp (file contents):
Revision 1097 by gezelter, Mon Apr 12 20:32:20 2004 UTC vs.
Revision 1234 by tim, Fri Jun 4 03:15:31 2004 UTC

# Line 12 | Line 12 | Molecule::Molecule( void ){
12    myBonds = NULL;
13    myBends = NULL;
14    myTorsions = NULL;
15 –  myRigidBodies = NULL;
16 –
15   }
16  
19 –
20 –
17   Molecule::~Molecule( void ){
18    int i;
19 +  CutoffGroup* cg;
20 +  vector<CutoffGroup*>::iterator iter;
21    
22    if( myAtoms != NULL ){
23      for(i=0; i<nAtoms; i++) if(myAtoms[i] != NULL ) delete myAtoms[i];
# Line 41 | Line 39 | Molecule::~Molecule( void ){
39      delete[] myTorsions;
40    }
41  
42 <  if( myRigidBodies != NULL ){
43 <    for(i=0; i<nRigidBodies; i++) if(myRigidBodies[i] != NULL )
44 <      delete myRigidBodies[i];
47 <    delete[] myRigidBodies;
48 <  }
42 >  for(cg = beginCutoffGroup(iter);  cg != NULL; cg = nextCutoffGroup(iter))
43 >    delete cg;
44 >  myCutoffGroups.clear();
45    
46   }
47  
48  
49   void Molecule::initialize( molInit &theInit ){
50  
51 +  CutoffGroup* curCutoffGroup;
52 +  vector<CutoffGroup*>::iterator iterCutoff;
53 +  Atom* cutoffAtom;
54 +  vector<Atom*>::iterator iterAtom;
55 +  int atomIndex;
56 +  
57    nAtoms = theInit.nAtoms;
58    nMembers = nAtoms;
59    nBonds = theInit.nBonds;
# Line 65 | Line 67 | void Molecule::initialize( molInit &theInit ){
67    myBends = theInit.myBends;
68    myTorsions = theInit.myTorsions;
69    myRigidBodies = theInit.myRigidBodies;
70 <    
70 >
71 >  myIntegrableObjects = theInit.myIntegrableObjects;
72 >
73 >  for (int i = 0; i < myRigidBodies.size(); i++)
74 >      myRigidBodies[i]->calcRefCoords();
75 >
76 >  myCutoffGroups = theInit.myCutoffGroups;
77 >  nCutoffGroups = myCutoffGroups.size();
78 >
79 >  myConstraintPairs = theInit.myConstraintPairs;
80 >  
81   }
82  
83   void Molecule::calcForces( void ){
84    
85    int i;
86 +  double com[3];
87  
88 <  for(i=0; i<nRigidBodies; i++) {
88 >  for(i=0; i<myRigidBodies.size(); i++) {
89      myRigidBodies[i]->updateAtoms();
90    }
91  
92 +  //calculate the center of mass of the molecule
93 +  //getCOM(com);  
94 +  //for(int i = 0; i < nAtoms; i ++)
95 +  //  myAtoms[i]->setRc(com);  
96 +  
97 +
98    for(i=0; i<nBonds; i++){
99      myBonds[i]->calc_forces();
100    }
# Line 97 | Line 116 | double Molecule::getPotential( void ){
116    
117    int i;
118    double myPot = 0.0;
119 +
120 +  for(i=0; i<myRigidBodies.size(); i++) {
121 +    myRigidBodies[i]->updateAtoms();
122 +  }
123    
124    for(i=0; i<nBonds; i++){
125      myPot += myBonds[i]->get_potential();
# Line 135 | Line 158 | void Molecule::moveCOM(double delta[3]){
158    double aPos[3];
159    int i, j;
160  
161 <  for(i=0; i<nAtoms; i++) {
162 <    if(myAtoms[i] != NULL ) {
161 >  for(i=0; i<myIntegrableObjects.size(); i++) {
162 >    if(myIntegrableObjects[i] != NULL ) {
163        
164 <      myAtoms[i]->getPos( aPos );
164 >      myIntegrableObjects[i]->getPos( aPos );
165        
166        for (j=0; j< 3; j++)
167          aPos[j] += delta[j];
168  
169 <      myAtoms[i]->setPos( aPos );
169 >      myIntegrableObjects[i]->setPos( aPos );
170      }
171    }
172  
173 <  for(i=0; i<nRigidBodies; i++) {
173 >  for(i=0; i<myRigidBodies.size(); i++) {
174  
152 –    if (myRigidBodies[i] != NULL) {
153 –      
175        myRigidBodies[i]->getPos( aPos );
176  
177        for (j=0; j< 3; j++)
# Line 158 | Line 179 | void Molecule::moveCOM(double delta[3]){
179        
180        myRigidBodies[i]->setPos( aPos );
181      }
161 –  }  
182   }
183  
184   void Molecule::atoms2rigidBodies( void ) {
185    int i;
186 <  for (i = 0; i < nRigidBodies; i++) {
187 <    if (myRigidBodies[i] != NULL) {
168 <      myRigidBodies[i]->calcForcesAndTorques();  
169 <    }
186 >  for (i = 0; i < myRigidBodies.size(); i++) {
187 >    myRigidBodies[i]->calcForcesAndTorques();  
188    }
189   }
190  
# Line 181 | Line 199 | void Molecule::getCOM( double COM[3] ) {
199  
200    mtot   = 0.0;
201  
202 <  for (i=0; i < nAtoms; i++) {
203 <    if (myAtoms[i] != NULL) {
202 >  for (i=0; i < myIntegrableObjects.size(); i++) {
203 >    if (myIntegrableObjects[i] != NULL) {
204  
205 <      mass = myAtoms[i]->getMass();
205 >      mass = myIntegrableObjects[i]->getMass();
206        mtot   += mass;
207        
208 <      myAtoms[i]->getPos( aPos );
208 >      myIntegrableObjects[i]->getPos( aPos );
209  
210        for( j = 0; j < 3; j++)
211          COM[j] += aPos[j] * mass;
# Line 211 | Line 229 | double Molecule::getCOMvel( double COMvel[3] ) {
229  
230    mtot   = 0.0;
231  
232 <  for (i=0; i < nAtoms; i++) {
233 <    if (myAtoms[i] != NULL) {
232 >  for (i=0; i < myIntegrableObjects.size(); i++) {
233 >    if (myIntegrableObjects[i] != NULL) {
234  
235 <      mass = myAtoms[i]->getMass();
235 >      mass = myIntegrableObjects[i]->getMass();
236        mtot   += mass;
237  
238 <      myAtoms[i]->getVel(aVel);
238 >      myIntegrableObjects[i]->getVel(aVel);
239  
240        for (j=0; j<3; j++)
241          COMvel[j] += aVel[j]*mass;
# Line 234 | Line 252 | double Molecule::getTotalMass()
252  
253   double Molecule::getTotalMass()
254   {
255 <  int natoms;
238 <  Atom** atoms;
255 >
256    double totalMass;
257    
241 –  natoms = getNAtoms();
242 –  atoms = getMyAtoms();
258    totalMass = 0;
259 <  for(int i =0; i < natoms; i++){
260 <    totalMass += atoms[i]->getMass();
259 >  for(int i =0; i < myIntegrableObjects.size(); i++){
260 >    totalMass += myIntegrableObjects[i]->getMass();
261    }
262  
263    return totalMass;

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