| 35 |
|
* |
| 36 |
|
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
|
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
< |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 39 |
|
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
|
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 58 |
|
calcRef(); |
| 59 |
|
} |
| 60 |
|
|
| 61 |
< |
void MoLocator::placeMol( const Vector3d& offset, const Vector3d& ort, Molecule* mol){ |
| 61 |
> |
void MoLocator::placeMol( const Vector3d& offset, const Vector3d& ort, |
| 62 |
> |
Molecule* mol) { |
| 63 |
|
|
| 64 |
|
Vector3d newCoor; |
| 65 |
|
Vector3d curRefCoor; |
| 67 |
|
|
| 68 |
|
if(mol->getNIntegrableObjects() != nIntegrableObjects){ |
| 69 |
|
sprintf( painCave.errMsg, |
| 70 |
< |
"MoLocator error.\n" |
| 71 |
< |
" The number of integrable objects of MoleculeStamp is not the same as that of Molecule\n"); |
| 70 |
> |
"MoLocator::placeMol error.\n" |
| 71 |
> |
"\tThe number of integrable objects of MoleculeStamp is not\n" |
| 72 |
> |
"\tthe same as that of Molecule\n"); |
| 73 |
|
painCave.isFatal = 1; |
| 74 |
|
simError(); |
| 75 |
|
} |
| 96 |
|
void MoLocator::calcRef( void ){ |
| 97 |
|
AtomStamp* currAtomStamp; |
| 98 |
|
RigidBodyStamp* rbStamp; |
| 97 |
– |
unsigned int nAtoms; |
| 98 |
– |
int nRigidBodies; |
| 99 |
|
std::vector<RealType> mass; |
| 100 |
|
Vector3d coor; |
| 101 |
|
Vector3d refMolCom; |
| 102 |
– |
int nAtomsInRb; |
| 102 |
|
RealType totMassInRb; |
| 103 |
|
RealType currAtomMass; |
| 104 |
|
RealType molMass; |
| 105 |
|
|
| 106 |
< |
nAtoms= myStamp->getNAtoms(); |
| 107 |
< |
nRigidBodies = myStamp->getNRigidBodies(); |
| 106 |
> |
std::size_t nAtoms= myStamp->getNAtoms(); |
| 107 |
> |
std::size_t nRigidBodies = myStamp->getNRigidBodies(); |
| 108 |
|
|
| 109 |
< |
for(unsigned int i = 0; i < nAtoms; i++){ |
| 109 |
> |
for(std::size_t i = 0; i < nAtoms; i++){ |
| 110 |
|
|
| 111 |
|
currAtomStamp = myStamp->getAtomStamp(i); |
| 112 |
|
|
| 113 |
|
if( !currAtomStamp->havePosition() ){ |
| 114 |
|
sprintf( painCave.errMsg, |
| 115 |
< |
"MoLocator error.\n" |
| 116 |
< |
" Component %s, atom %s does not have a position specified.\n" |
| 117 |
< |
" This means MoLocator cannot initalize it's position.\n", |
| 115 |
> |
"MoLocator::calcRef error.\n" |
| 116 |
> |
"\tComponent %s, atom %s does not have a position specified.\n" |
| 117 |
> |
"\tThis means MoLocator cannot initalize it's position.\n", |
| 118 |
|
myStamp->getName().c_str(), |
| 119 |
|
currAtomStamp->getType().c_str()); |
| 120 |
|
|
| 137 |
|
} |
| 138 |
|
} |
| 139 |
|
|
| 140 |
< |
for(int i = 0; i < nRigidBodies; i++){ |
| 140 |
> |
for(std::size_t i = 0; i < nRigidBodies; i++){ |
| 141 |
|
|
| 142 |
|
rbStamp = myStamp->getRigidBodyStamp(i); |
| 143 |
< |
nAtomsInRb = rbStamp->getNMembers(); |
| 143 |
> |
std::size_t nAtomsInRb = rbStamp->getNMembers(); |
| 144 |
|
|
| 145 |
|
coor.x() = 0.0; |
| 146 |
|
coor.y() = 0.0; |
| 147 |
|
coor.z() = 0.0; |
| 148 |
|
totMassInRb = 0.0; |
| 149 |
|
|
| 150 |
< |
for(int j = 0; j < nAtomsInRb; j++){ |
| 150 |
> |
for(std::size_t j = 0; j < nAtomsInRb; j++){ |
| 151 |
|
|
| 152 |
|
currAtomStamp = myStamp->getAtomStamp(rbStamp->getMemberAt(j)); |
| 153 |
|
currAtomMass = getAtomMass(currAtomStamp->getType(), myFF); |
| 170 |
|
refMolCom.y() = 0; |
| 171 |
|
refMolCom.z() = 0; |
| 172 |
|
|
| 173 |
< |
for(int i = 0; i < nIntegrableObjects; i++){ |
| 173 |
> |
for(std::size_t i = 0; i < nIntegrableObjects; i++){ |
| 174 |
|
refMolCom += refCoords[i] * mass[i]; |
| 175 |
|
molMass += mass[i]; |
| 176 |
|
} |
| 177 |
|
|
| 178 |
|
refMolCom /= molMass; |
| 179 |
|
|
| 180 |
< |
//move the reference center of mass to (0,0,0) and adjust the reference coordinate |
| 181 |
< |
//of the integrabel objects |
| 182 |
< |
for(int i = 0; i < nIntegrableObjects; i++) |
| 180 |
> |
//move the reference center of mass to (0,0,0) and adjust the |
| 181 |
> |
//reference coordinate of the integrabel objects |
| 182 |
> |
for(std::size_t i = 0; i < nIntegrableObjects; i++) |
| 183 |
|
refCoords[i] -= refMolCom; |
| 184 |
|
} |
| 185 |
|
|
| 186 |
< |
RealType getAtomMass(const std::string& at, ForceField* myFF) { |
| 186 |
> |
RealType MoLocator::getAtomMass(const std::string& at, ForceField* myFF) { |
| 187 |
|
RealType mass; |
| 188 |
|
AtomType* atomType= myFF->getAtomType(at); |
| 189 |
|
if (atomType != NULL) { |
| 190 |
< |
mass = atomType->getMass(); |
| 190 |
> |
mass = atomType->getMass(); |
| 191 |
|
} else { |
| 192 |
|
mass = 0.0; |
| 193 |
|
std::cerr << "Can not find AtomType: " << at << std::endl; |
| 195 |
|
return mass; |
| 196 |
|
} |
| 197 |
|
|
| 198 |
< |
RealType getMolMass(MoleculeStamp *molStamp, ForceField *myFF) { |
| 198 |
> |
RealType MoLocator::getMolMass(MoleculeStamp *molStamp, ForceField *myFF) { |
| 199 |
|
unsigned int nAtoms; |
| 200 |
|
RealType totMass = 0; |
| 201 |
|
nAtoms = molStamp->getNAtoms(); |
| 202 |
|
|
| 203 |
< |
for(unsigned int i = 0; i < nAtoms; i++) { |
| 203 |
> |
for(std::size_t i = 0; i < nAtoms; i++) { |
| 204 |
|
AtomStamp *currAtomStamp = molStamp->getAtomStamp(i); |
| 205 |
|
totMass += getAtomMass(currAtomStamp->getType(), myFF); |
| 206 |
|
} |
| 207 |
|
return totMass; |
| 208 |
|
} |
| 209 |
< |
RotMat3x3d latVec2RotMat(const Vector3d& lv){ |
| 209 |
> |
|
| 210 |
> |
RotMat3x3d MoLocator::latVec2RotMat(const Vector3d& lv){ |
| 211 |
|
|
| 212 |
|
RealType theta =acos(lv[2]); |
| 213 |
|
RealType phi = atan2(lv[1], lv[0]); |
| 214 |
|
RealType psi = 0; |
| 215 |
|
|
| 216 |
< |
return RotMat3x3d(phi, theta, psi); |
| 217 |
< |
|
| 216 |
> |
return RotMat3x3d(phi, theta, psi); |
| 217 |
|
} |
| 218 |
|
} |
| 219 |
|
|
