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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 1104 by gezelter, Tue Apr 13 16:26:03 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 14 | Line 15 | Molecule::Molecule( void ){
15  
16   }
17  
17 –
18 –
18   Molecule::~Molecule( void ){
19    int i;
20    
# Line 39 | Line 38 | Molecule::~Molecule( void ){
38      delete[] myTorsions;
39    }
40  
42 –  if( myExcludes != NULL ){
43 –    for(i=0; i<nExcludes; i++) if(myExcludes[i] != NULL ) delete myExcludes[i];
44 –    delete[] myExcludes;
45 –  }
41   }
42  
43  
# Line 53 | 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.myExcludses;
58 >  myRigidBodies = theInit.myRigidBodies;
59 >
60 >  myIntegrableObjects = theInit.myIntegrableObjects;
61      
62   }
63  
# Line 68 | 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 79 | 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  
89 < void Molecule::getPotential( void ){
89 > double Molecule::getPotential( void ){
90    
91    int i;
92    double myPot = 0.0;
# Line 101 | Line 105 | void Molecule::getPotential( void ){
105  
106    return myPot;
107   }
108 +
109 + void Molecule::printMe( void ){
110 +  
111 +  int i;
112 +
113 +  for(i=0; i<nBonds; i++){
114 +    myBonds[i]->printMe();
115 +  }
116 +
117 +  for(i=0; i<nBends; i++){
118 +    myBends[i]->printMe();
119 +  }
120 +
121 +  for(i=0; i<nTorsions; i++){
122 +    myTorsions[i]->printMe();
123 +  }
124 +
125 + }
126 +
127 + void Molecule::moveCOM(double delta[3]){
128 +  double aPos[3];
129 +  int i, j;
130 +
131 +  for(i=0; i<nAtoms; i++) {
132 +    if(myAtoms[i] != NULL ) {
133 +      
134 +      myAtoms[i]->getPos( aPos );
135 +      
136 +      for (j=0; j< 3; j++)
137 +        aPos[j] += delta[j];
138 +
139 +      myAtoms[i]->setPos( aPos );
140 +    }
141 +  }
142 +
143 +  for(i=0; i<myRigidBodies.size(); i++) {
144 +
145 +      myRigidBodies[i]->getPos( aPos );
146 +
147 +      for (j=0; j< 3; j++)
148 +        aPos[j] += delta[j];
149 +      
150 +      myRigidBodies[i]->setPos( aPos );
151 +    }
152 + }
153 +
154 + void Molecule::atoms2rigidBodies( void ) {
155 +  int i;
156 +  for (i = 0; i < myRigidBodies.size(); i++) {
157 +    myRigidBodies[i]->calcForcesAndTorques();  
158 +  }
159 + }
160 +
161 + void Molecule::getCOM( double COM[3] ) {
162 +
163 +  double mass, mtot;
164 +  double aPos[3];
165 +  int i, j;
166 +
167 +  for (j=0; j<3; j++)
168 +    COM[j] = 0.0;
169 +
170 +  mtot   = 0.0;
171 +
172 +  for (i=0; i < nAtoms; i++) {
173 +    if (myAtoms[i] != NULL) {
174 +
175 +      mass = myAtoms[i]->getMass();
176 +      mtot   += mass;
177 +      
178 +      myAtoms[i]->getPos( aPos );
179 +
180 +      for( j = 0; j < 3; j++)
181 +        COM[j] += aPos[j] * mass;
182 +
183 +    }
184 +  }
185 +
186 +  for (j = 0; j < 3; j++)
187 +    COM[j] /= mtot;
188 + }
189 +
190 + double Molecule::getCOMvel( double COMvel[3] ) {
191 +
192 +  double mass, mtot;
193 +  double aVel[3];
194 +  int i, j;
195 +
196 +
197 +  for (j=0; j<3; j++)
198 +    COMvel[j] = 0.0;
199 +
200 +  mtot   = 0.0;
201 +
202 +  for (i=0; i < nAtoms; i++) {
203 +    if (myAtoms[i] != NULL) {
204 +
205 +      mass = myAtoms[i]->getMass();
206 +      mtot   += mass;
207 +
208 +      myAtoms[i]->getVel(aVel);
209 +
210 +      for (j=0; j<3; j++)
211 +        COMvel[j] += aVel[j]*mass;
212 +
213 +    }
214 +  }
215 +
216 +  for (j=0; j<3; j++)
217 +    COMvel[j] /= mtot;
218 +
219 +  return mtot;
220 +
221 + }
222 +
223 + double Molecule::getTotalMass()
224 + {
225 +  int natoms;
226 +  Atom** atoms;
227 +  double totalMass;
228 +  
229 +  natoms = getNAtoms();
230 +  atoms = getMyAtoms();
231 +  totalMass = 0;
232 +  for(int i =0; i < natoms; i++){
233 +    totalMass += atoms[i]->getMass();
234 +  }
235 +
236 +  return totalMass;
237 + }

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