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root/group/trunk/OOPSE/libmdtools/Molecule.cpp
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Comparing trunk/OOPSE/libmdtools/Molecule.cpp (file contents):
Revision 610 by gezelter, Tue Jul 15 15:50:55 2003 UTC vs.
Revision 1109 by gezelter, Wed Apr 14 16:32:15 2004 UTC

# Line 1 | Line 1
1 < #include <cstdlib>
1 > #include <stdlib.h>
2  
3  
4   #include "Molecule.hpp"
# Line 15 | Line 15 | Molecule::Molecule( void ){
15  
16   }
17  
18 –
19 –
18   Molecule::~Molecule( void ){
19    int i;
20    
# Line 40 | Line 38 | Molecule::~Molecule( void ){
38      delete[] myTorsions;
39    }
40  
43 –  if( myExcludes != NULL ){
44 –    for(i=0; i<nExcludes; i++) if(myExcludes[i] != NULL ) delete myExcludes[i];
45 –    delete[] myExcludes;
46 –  }
41   }
42  
43  
# Line 54 | Line 48 | void Molecule::initialize( molInit &theInit ){
48    nBonds = theInit.nBonds;
49    nBends = theInit.nBends;
50    nTorsions = theInit.nTorsions;
51 <  nExcludes = theInit.nExcludes;
51 >  nRigidBodies = theInit.nRigidBodies;
52    nOriented = theInit.nOriented;
53  
54    myAtoms = theInit.myAtoms;
55    myBonds = theInit.myBonds;
56    myBends = theInit.myBends;
57    myTorsions = theInit.myTorsions;
58 <  myExcludes = theInit.myExcludes;
58 >  myRigidBodies = theInit.myRigidBodies;
59 >
60 >  myIntegrableObjects = theInit.myIntegrableObjects;
61      
62   }
63  
# Line 69 | Line 65 | void Molecule::calcForces( void ){
65    
66    int i;
67  
68 +  for(i=0; i<myRigidBodies.size(); i++) {
69 +    myRigidBodies[i]->updateAtoms();
70 +  }
71 +
72    for(i=0; i<nBonds; i++){
73      myBonds[i]->calc_forces();
74    }
# Line 80 | Line 80 | void Molecule::calcForces( void ){
80    for(i=0; i<nTorsions; i++){
81      myTorsions[i]->calc_forces();
82    }
83 +
84 +  // Rigid Body forces and torques are done after the fortran force loop
85 +
86   }
87  
88  
# Line 87 | Line 90 | double Molecule::getPotential( void ){
90    
91    int i;
92    double myPot = 0.0;
93 +
94 +  for(i=0; i<myRigidBodies.size(); i++) {
95 +    myRigidBodies[i]->updateAtoms();
96 +  }
97    
98    for(i=0; i<nBonds; i++){
99      myPot += myBonds[i]->get_potential();
# Line 118 | Line 125 | void Molecule::printMe( void ){
125    for(i=0; i<nTorsions; i++){
126      myTorsions[i]->printMe();
127    }
128 +
129   }
130  
131   void Molecule::moveCOM(double delta[3]){
# Line 135 | Line 143 | void Molecule::moveCOM(double delta[3]){
143        myAtoms[i]->setPos( aPos );
144      }
145    }
146 +
147 +  for(i=0; i<myRigidBodies.size(); i++) {
148 +
149 +      myRigidBodies[i]->getPos( aPos );
150 +
151 +      for (j=0; j< 3; j++)
152 +        aPos[j] += delta[j];
153 +      
154 +      myRigidBodies[i]->setPos( aPos );
155 +    }
156   }
157  
158 + void Molecule::atoms2rigidBodies( void ) {
159 +  int i;
160 +  for (i = 0; i < myRigidBodies.size(); i++) {
161 +    myRigidBodies[i]->calcForcesAndTorques();  
162 +  }
163 + }
164 +
165   void Molecule::getCOM( double COM[3] ) {
166  
167    double mass, mtot;
# Line 198 | Line 223 | double Molecule::getCOMvel( double COMvel[3] ) {
223    return mtot;
224  
225   }
226 +
227 + double Molecule::getTotalMass()
228 + {
229 +  int natoms;
230 +  Atom** atoms;
231 +  double totalMass;
232 +  
233 +  natoms = getNAtoms();
234 +  atoms = getMyAtoms();
235 +  totalMass = 0;
236 +  for(int i =0; i < natoms; i++){
237 +    totalMass += atoms[i]->getMass();
238 +  }
239 +
240 +  return totalMass;
241 + }

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