| 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 |
|
|
| 44 |
|
void Molecule::initialize( molInit &theInit ){ |
| 45 |
< |
|
| 45 |
> |
double totMass; |
| 46 |
> |
|
| 47 |
|
nAtoms = theInit.nAtoms; |
| 48 |
|
nMembers = nAtoms; |
| 49 |
|
nBonds = theInit.nBonds; |
| 57 |
|
myBends = theInit.myBends; |
| 58 |
|
myTorsions = theInit.myTorsions; |
| 59 |
|
myRigidBodies = theInit.myRigidBodies; |
| 60 |
< |
|
| 60 |
> |
|
| 61 |
> |
myIntegrableObjects = theInit.myIntegrableObjects; |
| 62 |
> |
|
| 63 |
> |
for (int i = 0; i < myRigidBodies.size(); i++) |
| 64 |
> |
myRigidBodies[i]->calcRefCoords(); |
| 65 |
> |
|
| 66 |
> |
|
| 67 |
> |
//the mass ratio will never change during the simulation. Thus, we could |
| 68 |
> |
//just calculate it at the begining of the simulation |
| 69 |
> |
totMass = getTotalMass(); |
| 70 |
> |
for(int i = 0; i < nAtoms; i ++) |
| 71 |
> |
myAtoms[i]->setMassRatio(myAtoms[i]->getMass()/totMass); |
| 72 |
|
} |
| 73 |
|
|
| 74 |
|
void Molecule::calcForces( void ){ |
| 75 |
|
|
| 76 |
|
int i; |
| 77 |
+ |
double com[3]; |
| 78 |
|
|
| 79 |
< |
for(i=0; i<nRigidBodies; i++) { |
| 79 |
> |
for(i=0; i<myRigidBodies.size(); i++) { |
| 80 |
|
myRigidBodies[i]->updateAtoms(); |
| 81 |
|
} |
| 82 |
|
|
| 83 |
+ |
//calculate the center of mass of the molecule |
| 84 |
+ |
getCOM(com); |
| 85 |
+ |
for(int i = 0; i < nAtoms; i ++) |
| 86 |
+ |
myAtoms[i]->setRc(com); |
| 87 |
+ |
|
| 88 |
+ |
|
| 89 |
|
for(i=0; i<nBonds; i++){ |
| 90 |
|
myBonds[i]->calc_forces(); |
| 91 |
|
} |
| 107 |
|
|
| 108 |
|
int i; |
| 109 |
|
double myPot = 0.0; |
| 110 |
+ |
|
| 111 |
+ |
for(i=0; i<myRigidBodies.size(); i++) { |
| 112 |
+ |
myRigidBodies[i]->updateAtoms(); |
| 113 |
+ |
} |
| 114 |
|
|
| 115 |
|
for(i=0; i<nBonds; i++){ |
| 116 |
|
myPot += myBonds[i]->get_potential(); |
| 149 |
|
double aPos[3]; |
| 150 |
|
int i, j; |
| 151 |
|
|
| 152 |
< |
for(i=0; i<nAtoms; i++) { |
| 153 |
< |
if(myAtoms[i] != NULL ) { |
| 152 |
> |
for(i=0; i<myIntegrableObjects.size(); i++) { |
| 153 |
> |
if(myIntegrableObjects[i] != NULL ) { |
| 154 |
|
|
| 155 |
< |
myAtoms[i]->getPos( aPos ); |
| 155 |
> |
myIntegrableObjects[i]->getPos( aPos ); |
| 156 |
|
|
| 157 |
|
for (j=0; j< 3; j++) |
| 158 |
|
aPos[j] += delta[j]; |
| 159 |
|
|
| 160 |
< |
myAtoms[i]->setPos( aPos ); |
| 160 |
> |
myIntegrableObjects[i]->setPos( aPos ); |
| 161 |
|
} |
| 162 |
|
} |
| 163 |
|
|
| 164 |
< |
for(i=0; i<nRigidBodies; i++) { |
| 164 |
> |
for(i=0; i<myRigidBodies.size(); i++) { |
| 165 |
|
|
| 152 |
– |
if (myRigidBodies[i] != NULL) { |
| 153 |
– |
|
| 166 |
|
myRigidBodies[i]->getPos( aPos ); |
| 167 |
|
|
| 168 |
|
for (j=0; j< 3; j++) |
| 170 |
|
|
| 171 |
|
myRigidBodies[i]->setPos( aPos ); |
| 172 |
|
} |
| 161 |
– |
} |
| 173 |
|
} |
| 174 |
|
|
| 175 |
|
void Molecule::atoms2rigidBodies( void ) { |
| 176 |
|
int i; |
| 177 |
< |
for (i = 0; i < nRigidBodies; i++) { |
| 178 |
< |
if (myRigidBodies[i] != NULL) { |
| 168 |
< |
myRigidBodies[i]->calcForcesAndTorques(); |
| 169 |
< |
} |
| 177 |
> |
for (i = 0; i < myRigidBodies.size(); i++) { |
| 178 |
> |
myRigidBodies[i]->calcForcesAndTorques(); |
| 179 |
|
} |
| 180 |
|
} |
| 181 |
|
|
| 190 |
|
|
| 191 |
|
mtot = 0.0; |
| 192 |
|
|
| 193 |
< |
for (i=0; i < nAtoms; i++) { |
| 194 |
< |
if (myAtoms[i] != NULL) { |
| 193 |
> |
for (i=0; i < myIntegrableObjects.size(); i++) { |
| 194 |
> |
if (myIntegrableObjects[i] != NULL) { |
| 195 |
|
|
| 196 |
< |
mass = myAtoms[i]->getMass(); |
| 196 |
> |
mass = myIntegrableObjects[i]->getMass(); |
| 197 |
|
mtot += mass; |
| 198 |
|
|
| 199 |
< |
myAtoms[i]->getPos( aPos ); |
| 199 |
> |
myIntegrableObjects[i]->getPos( aPos ); |
| 200 |
|
|
| 201 |
|
for( j = 0; j < 3; j++) |
| 202 |
|
COM[j] += aPos[j] * mass; |
| 220 |
|
|
| 221 |
|
mtot = 0.0; |
| 222 |
|
|
| 223 |
< |
for (i=0; i < nAtoms; i++) { |
| 224 |
< |
if (myAtoms[i] != NULL) { |
| 223 |
> |
for (i=0; i < myIntegrableObjects.size(); i++) { |
| 224 |
> |
if (myIntegrableObjects[i] != NULL) { |
| 225 |
|
|
| 226 |
< |
mass = myAtoms[i]->getMass(); |
| 226 |
> |
mass = myIntegrableObjects[i]->getMass(); |
| 227 |
|
mtot += mass; |
| 228 |
|
|
| 229 |
< |
myAtoms[i]->getVel(aVel); |
| 229 |
> |
myIntegrableObjects[i]->getVel(aVel); |
| 230 |
|
|
| 231 |
|
for (j=0; j<3; j++) |
| 232 |
|
COMvel[j] += aVel[j]*mass; |
| 243 |
|
|
| 244 |
|
double Molecule::getTotalMass() |
| 245 |
|
{ |
| 246 |
< |
int natoms; |
| 238 |
< |
Atom** atoms; |
| 246 |
> |
|
| 247 |
|
double totalMass; |
| 248 |
|
|
| 241 |
– |
natoms = getNAtoms(); |
| 242 |
– |
atoms = getMyAtoms(); |
| 249 |
|
totalMass = 0; |
| 250 |
< |
for(int i =0; i < natoms; i++){ |
| 251 |
< |
totalMass += atoms[i]->getMass(); |
| 250 |
> |
for(int i =0; i < myIntegrableObjects.size(); i++){ |
| 251 |
> |
totalMass += myIntegrableObjects[i]->getMass(); |
| 252 |
|
} |
| 253 |
|
|
| 254 |
|
return totalMass; |
