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 |
|
|
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; |