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root/group/trunk/OOPSE/libmdtools/Molecule.cpp
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Comparing trunk/OOPSE/libmdtools/Molecule.cpp (file contents):
Revision 427 by mmeineke, Thu Mar 27 20:48:37 2003 UTC vs.
Revision 1234 by tim, Fri Jun 4 03:15:31 2004 UTC

# Line 1 | Line 1
1 < #include <cstdlib>
1 > #include <stdlib.h>
2  
3  
4   #include "Molecule.hpp"
5 + #include "simError.h"
6  
7  
8  
# Line 11 | Line 12 | Molecule::Molecule( void ){
12    myBonds = NULL;
13    myBends = NULL;
14    myTorsions = NULL;
14 –
15   }
16  
17 –
18 –
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 39 | Line 39 | Molecule::~Molecule( void ){
39      delete[] myTorsions;
40    }
41  
42 <  if( myExcludes != NULL ){
43 <    for(i=0; i<nExcludes; i++) if(myExcludes[i] != NULL ) delete myExcludes[i];
44 <    delete[] myExcludes;
45 <  }
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;
60    nBends = theInit.nBends;
61    nTorsions = theInit.nTorsions;
62 <  nExcludes = theInit.nExcludes;
62 >  nRigidBodies = theInit.nRigidBodies;
63    nOriented = theInit.nOriented;
64  
65    myAtoms = theInit.myAtoms;
66    myBonds = theInit.myBonds;
67    myBends = theInit.myBends;
68    myTorsions = theInit.myTorsions;
69 <  myExcludes = theInit.myExcludses;
70 <    
69 >  myRigidBodies = theInit.myRigidBodies;
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<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 79 | Line 106 | void Molecule::calcForces( void ){
106    for(i=0; i<nTorsions; i++){
107      myTorsions[i]->calc_forces();
108    }
109 +
110 +  // Rigid Body forces and torques are done after the fortran force loop
111 +
112   }
113  
114  
115 < void Molecule::getPotential( void ){
115 > 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 101 | Line 135 | void Molecule::getPotential( void ){
135  
136    return myPot;
137   }
138 +
139 + void Molecule::printMe( void ){
140 +  
141 +  int i;
142 +
143 +  for(i=0; i<nBonds; i++){
144 +    myBonds[i]->printMe();
145 +  }
146 +
147 +  for(i=0; i<nBends; i++){
148 +    myBends[i]->printMe();
149 +  }
150 +
151 +  for(i=0; i<nTorsions; i++){
152 +    myTorsions[i]->printMe();
153 +  }
154 +
155 + }
156 +
157 + void Molecule::moveCOM(double delta[3]){
158 +  double aPos[3];
159 +  int i, j;
160 +
161 +  for(i=0; i<myIntegrableObjects.size(); i++) {
162 +    if(myIntegrableObjects[i] != NULL ) {
163 +      
164 +      myIntegrableObjects[i]->getPos( aPos );
165 +      
166 +      for (j=0; j< 3; j++)
167 +        aPos[j] += delta[j];
168 +
169 +      myIntegrableObjects[i]->setPos( aPos );
170 +    }
171 +  }
172 +
173 +  for(i=0; i<myRigidBodies.size(); i++) {
174 +
175 +      myRigidBodies[i]->getPos( aPos );
176 +
177 +      for (j=0; j< 3; j++)
178 +        aPos[j] += delta[j];
179 +      
180 +      myRigidBodies[i]->setPos( aPos );
181 +    }
182 + }
183 +
184 + void Molecule::atoms2rigidBodies( void ) {
185 +  int i;
186 +  for (i = 0; i < myRigidBodies.size(); i++) {
187 +    myRigidBodies[i]->calcForcesAndTorques();  
188 +  }
189 + }
190 +
191 + void Molecule::getCOM( double COM[3] ) {
192 +
193 +  double mass, mtot;
194 +  double aPos[3];
195 +  int i, j;
196 +
197 +  for (j=0; j<3; j++)
198 +    COM[j] = 0.0;
199 +
200 +  mtot   = 0.0;
201 +
202 +  for (i=0; i < myIntegrableObjects.size(); i++) {
203 +    if (myIntegrableObjects[i] != NULL) {
204 +
205 +      mass = myIntegrableObjects[i]->getMass();
206 +      mtot   += mass;
207 +      
208 +      myIntegrableObjects[i]->getPos( aPos );
209 +
210 +      for( j = 0; j < 3; j++)
211 +        COM[j] += aPos[j] * mass;
212 +
213 +    }
214 +  }
215 +
216 +  for (j = 0; j < 3; j++)
217 +    COM[j] /= mtot;
218 + }
219 +
220 + double Molecule::getCOMvel( double COMvel[3] ) {
221 +
222 +  double mass, mtot;
223 +  double aVel[3];
224 +  int i, j;
225 +
226 +
227 +  for (j=0; j<3; j++)
228 +    COMvel[j] = 0.0;
229 +
230 +  mtot   = 0.0;
231 +
232 +  for (i=0; i < myIntegrableObjects.size(); i++) {
233 +    if (myIntegrableObjects[i] != NULL) {
234 +
235 +      mass = myIntegrableObjects[i]->getMass();
236 +      mtot   += mass;
237 +
238 +      myIntegrableObjects[i]->getVel(aVel);
239 +
240 +      for (j=0; j<3; j++)
241 +        COMvel[j] += aVel[j]*mass;
242 +
243 +    }
244 +  }
245 +
246 +  for (j=0; j<3; j++)
247 +    COMvel[j] /= mtot;
248 +
249 +  return mtot;
250 +
251 + }
252 +
253 + double Molecule::getTotalMass()
254 + {
255 +
256 +  double totalMass;
257 +  
258 +  totalMass = 0;
259 +  for(int i =0; i < myIntegrableObjects.size(); i++){
260 +    totalMass += myIntegrableObjects[i]->getMass();
261 +  }
262 +
263 +  return totalMass;
264 + }

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