| 94 |
|
RigidBodyStamp* rbStamp; |
| 95 |
|
int nAtoms; |
| 96 |
|
int nRigidBodies; |
| 97 |
< |
std::vector<double> mass; |
| 97 |
> |
std::vector<RealType> mass; |
| 98 |
|
Vector3d coor; |
| 99 |
|
Vector3d refMolCom; |
| 100 |
|
int nAtomsInRb; |
| 101 |
< |
double totMassInRb; |
| 102 |
< |
double currAtomMass; |
| 103 |
< |
double molMass; |
| 101 |
> |
RealType totMassInRb; |
| 102 |
> |
RealType currAtomMass; |
| 103 |
> |
RealType molMass; |
| 104 |
|
|
| 105 |
|
nAtoms= myStamp->getNAtoms(); |
| 106 |
|
nRigidBodies = myStamp->getNRigidBodies(); |
| 107 |
|
|
| 108 |
|
for(size_t i=0; i<nAtoms; i++){ |
| 109 |
|
|
| 110 |
< |
currAtomStamp = myStamp->getAtom(i); |
| 110 |
> |
currAtomStamp = myStamp->getAtomStamp(i); |
| 111 |
|
|
| 112 |
|
if( !currAtomStamp->havePosition() ){ |
| 113 |
|
sprintf( painCave.errMsg, |
| 114 |
|
"MoLocator error.\n" |
| 115 |
|
" Component %s, atom %s does not have a position specified.\n" |
| 116 |
|
" This means MoLocator cannot initalize it's position.\n", |
| 117 |
< |
myStamp->getID(), |
| 118 |
< |
currAtomStamp->getType() ); |
| 117 |
> |
myStamp->getName().c_str(), |
| 118 |
> |
currAtomStamp->getType().c_str()); |
| 119 |
|
|
| 120 |
|
painCave.isFatal = 1; |
| 121 |
|
simError(); |
| 138 |
|
|
| 139 |
|
for(int i = 0; i < nRigidBodies; i++){ |
| 140 |
|
|
| 141 |
< |
rbStamp = myStamp->getRigidBody(i); |
| 141 |
> |
rbStamp = myStamp->getRigidBodyStamp(i); |
| 142 |
|
nAtomsInRb = rbStamp->getNMembers(); |
| 143 |
|
|
| 144 |
|
coor.x() = 0.0; |
| 148 |
|
|
| 149 |
|
for(int j = 0; j < nAtomsInRb; j++){ |
| 150 |
|
|
| 151 |
< |
currAtomStamp = myStamp->getAtom(rbStamp->getMember(j)); |
| 151 |
> |
currAtomStamp = myStamp->getAtomStamp(rbStamp->getMemberAt(j)); |
| 152 |
|
currAtomMass = getAtomMass(currAtomStamp->getType(), myFF); |
| 153 |
|
totMassInRb += currAtomMass; |
| 154 |
|
|
| 182 |
|
refCoords[i] -= refMolCom; |
| 183 |
|
} |
| 184 |
|
|
| 185 |
< |
double getAtomMass(const std::string& at, ForceField* myFF) { |
| 186 |
< |
double mass; |
| 185 |
> |
RealType getAtomMass(const std::string& at, ForceField* myFF) { |
| 186 |
> |
RealType mass; |
| 187 |
|
AtomType* atomType= myFF->getAtomType(at); |
| 188 |
|
if (atomType != NULL) { |
| 189 |
|
mass = atomType->getMass(); |
| 194 |
|
return mass; |
| 195 |
|
} |
| 196 |
|
|
| 197 |
< |
double getMolMass(MoleculeStamp *molStamp, ForceField *myFF) { |
| 197 |
> |
RealType getMolMass(MoleculeStamp *molStamp, ForceField *myFF) { |
| 198 |
|
int nAtoms; |
| 199 |
< |
double totMass = 0; |
| 199 |
> |
RealType totMass = 0; |
| 200 |
|
nAtoms = molStamp->getNAtoms(); |
| 201 |
|
|
| 202 |
|
for(size_t i = 0; i < nAtoms; i++) { |
| 203 |
< |
AtomStamp *currAtomStamp = molStamp->getAtom(i); |
| 203 |
> |
AtomStamp *currAtomStamp = molStamp->getAtomStamp(i); |
| 204 |
|
totMass += getAtomMass(currAtomStamp->getType(), myFF); |
| 205 |
|
} |
| 206 |
|
return totMass; |
| 207 |
|
} |
| 208 |
|
RotMat3x3d latVec2RotMat(const Vector3d& lv){ |
| 209 |
|
|
| 210 |
< |
double theta =acos(lv[2]); |
| 211 |
< |
double phi = atan2(lv[1], lv[0]); |
| 212 |
< |
double psi = 0; |
| 210 |
> |
RealType theta =acos(lv[2]); |
| 211 |
> |
RealType phi = atan2(lv[1], lv[0]); |
| 212 |
> |
RealType psi = 0; |
| 213 |
|
|
| 214 |
|
return RotMat3x3d(phi, theta, psi); |
| 215 |
|
|
