12 |
|
myBonds = NULL; |
13 |
|
myBends = NULL; |
14 |
|
myTorsions = NULL; |
15 |
– |
myRigidBodies = NULL; |
15 |
|
|
16 |
|
} |
17 |
|
|
19 |
– |
|
20 |
– |
|
18 |
|
Molecule::~Molecule( void ){ |
19 |
|
int i; |
20 |
|
|
38 |
|
delete[] myTorsions; |
39 |
|
} |
40 |
|
|
44 |
– |
if( myRigidBodies != NULL ){ |
45 |
– |
for(i=0; i<nRigidBodies; i++) if(myRigidBodies[i] != NULL ) |
46 |
– |
delete myRigidBodies[i]; |
47 |
– |
delete[] myRigidBodies; |
48 |
– |
} |
49 |
– |
|
41 |
|
} |
42 |
|
|
43 |
|
|
56 |
|
myBends = theInit.myBends; |
57 |
|
myTorsions = theInit.myTorsions; |
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 |
|
|
68 |
|
|
69 |
|
int i; |
70 |
|
|
71 |
< |
for(i=0; i<nRigidBodies; i++) { |
71 |
> |
for(i=0; i<myRigidBodies.size(); i++) { |
72 |
|
myRigidBodies[i]->updateAtoms(); |
73 |
|
} |
74 |
|
|
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(); |
135 |
|
double aPos[3]; |
136 |
|
int i, j; |
137 |
|
|
138 |
< |
for(i=0; i<nAtoms; i++) { |
139 |
< |
if(myAtoms[i] != NULL ) { |
138 |
> |
for(i=0; i<myIntegrableObjects.size(); i++) { |
139 |
> |
if(myIntegrableObjects[i] != NULL ) { |
140 |
|
|
141 |
< |
myAtoms[i]->getPos( aPos ); |
141 |
> |
myIntegrableObjects[i]->getPos( aPos ); |
142 |
|
|
143 |
|
for (j=0; j< 3; j++) |
144 |
|
aPos[j] += delta[j]; |
145 |
|
|
146 |
< |
myAtoms[i]->setPos( aPos ); |
146 |
> |
myIntegrableObjects[i]->setPos( aPos ); |
147 |
|
} |
148 |
|
} |
149 |
|
|
150 |
< |
for(i=0; i<nRigidBodies; i++) { |
150 |
> |
for(i=0; i<myRigidBodies.size(); i++) { |
151 |
|
|
152 |
– |
if (myRigidBodies[i] != NULL) { |
153 |
– |
|
152 |
|
myRigidBodies[i]->getPos( aPos ); |
153 |
|
|
154 |
|
for (j=0; j< 3; j++) |
156 |
|
|
157 |
|
myRigidBodies[i]->setPos( aPos ); |
158 |
|
} |
161 |
– |
} |
159 |
|
} |
160 |
|
|
161 |
|
void Molecule::atoms2rigidBodies( void ) { |
162 |
|
int i; |
163 |
< |
for (i = 0; i < nRigidBodies; i++) { |
164 |
< |
if (myRigidBodies[i] != NULL) { |
168 |
< |
myRigidBodies[i]->calcForcesAndTorques(); |
169 |
< |
} |
163 |
> |
for (i = 0; i < myRigidBodies.size(); i++) { |
164 |
> |
myRigidBodies[i]->calcForcesAndTorques(); |
165 |
|
} |
166 |
|
} |
167 |
|
|
176 |
|
|
177 |
|
mtot = 0.0; |
178 |
|
|
179 |
< |
for (i=0; i < nAtoms; i++) { |
180 |
< |
if (myAtoms[i] != NULL) { |
179 |
> |
for (i=0; i < myIntegrableObjects.size(); i++) { |
180 |
> |
if (myIntegrableObjects[i] != NULL) { |
181 |
|
|
182 |
< |
mass = myAtoms[i]->getMass(); |
182 |
> |
mass = myIntegrableObjects[i]->getMass(); |
183 |
|
mtot += mass; |
184 |
|
|
185 |
< |
myAtoms[i]->getPos( aPos ); |
185 |
> |
myIntegrableObjects[i]->getPos( aPos ); |
186 |
|
|
187 |
|
for( j = 0; j < 3; j++) |
188 |
|
COM[j] += aPos[j] * mass; |
206 |
|
|
207 |
|
mtot = 0.0; |
208 |
|
|
209 |
< |
for (i=0; i < nAtoms; i++) { |
210 |
< |
if (myAtoms[i] != NULL) { |
209 |
> |
for (i=0; i < myIntegrableObjects.size(); i++) { |
210 |
> |
if (myIntegrableObjects[i] != NULL) { |
211 |
|
|
212 |
< |
mass = myAtoms[i]->getMass(); |
212 |
> |
mass = myIntegrableObjects[i]->getMass(); |
213 |
|
mtot += mass; |
214 |
|
|
215 |
< |
myAtoms[i]->getVel(aVel); |
215 |
> |
myIntegrableObjects[i]->getVel(aVel); |
216 |
|
|
217 |
|
for (j=0; j<3; j++) |
218 |
|
COMvel[j] += aVel[j]*mass; |
229 |
|
|
230 |
|
double Molecule::getTotalMass() |
231 |
|
{ |
232 |
< |
int natoms; |
238 |
< |
Atom** atoms; |
232 |
> |
|
233 |
|
double totalMass; |
234 |
|
|
241 |
– |
natoms = getNAtoms(); |
242 |
– |
atoms = getMyAtoms(); |
235 |
|
totalMass = 0; |
236 |
< |
for(int i =0; i < natoms; i++){ |
237 |
< |
totalMass += atoms[i]->getMass(); |
236 |
> |
for(int i =0; i < myIntegrableObjects.size(); i++){ |
237 |
> |
totalMass += myIntegrableObjects[i]->getMass(); |
238 |
|
} |
239 |
|
|
240 |
|
return totalMass; |