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root/group/trunk/OOPSE/libmdtools/Molecule.cpp
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Comparing trunk/OOPSE/libmdtools/Molecule.cpp (file contents):
Revision 438 by chuckv, Mon Mar 31 21:50:59 2003 UTC vs.
Revision 1113 by tim, Thu Apr 15 16:18:26 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 >  for (int i = 0; i < myRigidBodies.size(); i++)
63 >      myRigidBodies[i]->calcRefCoords();
64      
65   }
66  
# Line 69 | Line 68 | void Molecule::calcForces( void ){
68    
69    int i;
70  
71 +  for(i=0; i<myRigidBodies.size(); i++) {
72 +    myRigidBodies[i]->updateAtoms();
73 +  }
74 +
75    for(i=0; i<nBonds; i++){
76      myBonds[i]->calc_forces();
77    }
# Line 80 | Line 83 | void Molecule::calcForces( void ){
83    for(i=0; i<nTorsions; i++){
84      myTorsions[i]->calc_forces();
85    }
86 +
87 +  // Rigid Body forces and torques are done after the fortran force loop
88 +
89   }
90  
91  
# Line 87 | Line 93 | double Molecule::getPotential( void ){
93    
94    int i;
95    double myPot = 0.0;
96 +
97 +  for(i=0; i<myRigidBodies.size(); i++) {
98 +    myRigidBodies[i]->updateAtoms();
99 +  }
100    
101    for(i=0; i<nBonds; i++){
102      myPot += myBonds[i]->get_potential();
# Line 118 | Line 128 | void Molecule::printMe( void ){
128    for(i=0; i<nTorsions; i++){
129      myTorsions[i]->printMe();
130    }
131 +
132   }
133 +
134 + void Molecule::moveCOM(double delta[3]){
135 +  double aPos[3];
136 +  int i, j;
137 +
138 +  for(i=0; i<myIntegrableObjects.size(); i++) {
139 +    if(myIntegrableObjects[i] != NULL ) {
140 +      
141 +      myIntegrableObjects[i]->getPos( aPos );
142 +      
143 +      for (j=0; j< 3; j++)
144 +        aPos[j] += delta[j];
145 +
146 +      myIntegrableObjects[i]->setPos( aPos );
147 +    }
148 +  }
149 +
150 +  for(i=0; i<myRigidBodies.size(); i++) {
151 +
152 +      myRigidBodies[i]->getPos( aPos );
153 +
154 +      for (j=0; j< 3; j++)
155 +        aPos[j] += delta[j];
156 +      
157 +      myRigidBodies[i]->setPos( aPos );
158 +    }
159 + }
160 +
161 + void Molecule::atoms2rigidBodies( void ) {
162 +  int i;
163 +  for (i = 0; i < myRigidBodies.size(); i++) {
164 +    myRigidBodies[i]->calcForcesAndTorques();  
165 +  }
166 + }
167 +
168 + void Molecule::getCOM( double COM[3] ) {
169 +
170 +  double mass, mtot;
171 +  double aPos[3];
172 +  int i, j;
173 +
174 +  for (j=0; j<3; j++)
175 +    COM[j] = 0.0;
176 +
177 +  mtot   = 0.0;
178 +
179 +  for (i=0; i < myIntegrableObjects.size(); i++) {
180 +    if (myIntegrableObjects[i] != NULL) {
181 +
182 +      mass = myIntegrableObjects[i]->getMass();
183 +      mtot   += mass;
184 +      
185 +      myIntegrableObjects[i]->getPos( aPos );
186 +
187 +      for( j = 0; j < 3; j++)
188 +        COM[j] += aPos[j] * mass;
189 +
190 +    }
191 +  }
192 +
193 +  for (j = 0; j < 3; j++)
194 +    COM[j] /= mtot;
195 + }
196 +
197 + double Molecule::getCOMvel( double COMvel[3] ) {
198 +
199 +  double mass, mtot;
200 +  double aVel[3];
201 +  int i, j;
202 +
203 +
204 +  for (j=0; j<3; j++)
205 +    COMvel[j] = 0.0;
206 +
207 +  mtot   = 0.0;
208 +
209 +  for (i=0; i < myIntegrableObjects.size(); i++) {
210 +    if (myIntegrableObjects[i] != NULL) {
211 +
212 +      mass = myIntegrableObjects[i]->getMass();
213 +      mtot   += mass;
214 +
215 +      myIntegrableObjects[i]->getVel(aVel);
216 +
217 +      for (j=0; j<3; j++)
218 +        COMvel[j] += aVel[j]*mass;
219 +
220 +    }
221 +  }
222 +
223 +  for (j=0; j<3; j++)
224 +    COMvel[j] /= mtot;
225 +
226 +  return mtot;
227 +
228 + }
229 +
230 + double Molecule::getTotalMass()
231 + {
232 +
233 +  double totalMass;
234 +  
235 +  totalMass = 0;
236 +  for(int i =0; i < myIntegrableObjects.size(); i++){
237 +    totalMass += myIntegrableObjects[i]->getMass();
238 +  }
239 +
240 +  return totalMass;
241 + }

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