| 35 |
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* |
| 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). |
| 39 |
< |
* [4] Vardeman & Gezelter, in progress (2009). |
| 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 |
|
*/ |
| 42 |
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|
| 43 |
|
#include <iostream> |
| 58 |
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calcRef(); |
| 59 |
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} |
| 60 |
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|
| 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 |
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|
| 64 |
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Vector3d newCoor; |
| 65 |
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Vector3d curRefCoor; |
| 67 |
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|
| 68 |
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if(mol->getNIntegrableObjects() != nIntegrableObjects){ |
| 69 |
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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 |
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painCave.isFatal = 1; |
| 74 |
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simError(); |
| 75 |
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} |
| 76 |
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|
| 77 |
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Molecule::IntegrableObjectIterator ii; |
| 78 |
< |
StuntDouble* integrableObject; |
| 78 |
> |
StuntDouble* sd; |
| 79 |
|
int i; |
| 80 |
< |
for (integrableObject = mol->beginIntegrableObject(ii), i = 0; integrableObject != NULL; |
| 81 |
< |
integrableObject = mol->nextIntegrableObject(ii), ++i) { |
| 80 |
> |
for (sd = mol->beginIntegrableObject(ii), i = 0; sd != NULL; |
| 81 |
> |
sd = mol->nextIntegrableObject(ii), ++i) { |
| 82 |
|
|
| 83 |
|
newCoor = rotMat * refCoords[i]; |
| 84 |
|
newCoor += offset; |
| 85 |
|
|
| 86 |
< |
integrableObject->setPos(newCoor); |
| 87 |
< |
integrableObject->setVel(V3Zero); |
| 86 |
> |
sd->setPos(newCoor); |
| 87 |
> |
sd->setVel(V3Zero); |
| 88 |
|
|
| 89 |
< |
if(integrableObject->isDirectional()){ |
| 90 |
< |
integrableObject->setA(rotMat * integrableObject->getA()); |
| 91 |
< |
integrableObject->setJ(V3Zero); |
| 89 |
> |
if(sd->isDirectional()){ |
| 90 |
> |
sd->setA(rotMat * sd->getA()); |
| 91 |
> |
sd->setJ(V3Zero); |
| 92 |
|
} |
| 93 |
|
} |
| 94 |
|
} |
| 96 |
|
void MoLocator::calcRef( void ){ |
| 97 |
|
AtomStamp* currAtomStamp; |
| 98 |
|
RigidBodyStamp* rbStamp; |
| 99 |
< |
int nAtoms; |
| 99 |
> |
unsigned int nAtoms; |
| 100 |
|
int nRigidBodies; |
| 101 |
|
std::vector<RealType> mass; |
| 102 |
|
Vector3d coor; |
| 109 |
|
nAtoms= myStamp->getNAtoms(); |
| 110 |
|
nRigidBodies = myStamp->getNRigidBodies(); |
| 111 |
|
|
| 112 |
< |
for(size_t i=0; i<nAtoms; i++){ |
| 112 |
> |
for(unsigned int i = 0; i < nAtoms; i++){ |
| 113 |
|
|
| 114 |
|
currAtomStamp = myStamp->getAtomStamp(i); |
| 115 |
|
|
| 116 |
|
if( !currAtomStamp->havePosition() ){ |
| 117 |
|
sprintf( painCave.errMsg, |
| 118 |
< |
"MoLocator error.\n" |
| 119 |
< |
" Component %s, atom %s does not have a position specified.\n" |
| 120 |
< |
" This means MoLocator cannot initalize it's position.\n", |
| 118 |
> |
"MoLocator::calcRef error.\n" |
| 119 |
> |
"\tComponent %s, atom %s does not have a position specified.\n" |
| 120 |
> |
"\tThis means MoLocator cannot initalize it's position.\n", |
| 121 |
|
myStamp->getName().c_str(), |
| 122 |
|
currAtomStamp->getType().c_str()); |
| 123 |
|
|
| 180 |
|
|
| 181 |
|
refMolCom /= molMass; |
| 182 |
|
|
| 183 |
< |
//move the reference center of mass to (0,0,0) and adjust the reference coordinate |
| 184 |
< |
//of the integrabel objects |
| 183 |
> |
//move the reference center of mass to (0,0,0) and adjust the |
| 184 |
> |
//reference coordinate of the integrabel objects |
| 185 |
|
for(int i = 0; i < nIntegrableObjects; i++) |
| 186 |
|
refCoords[i] -= refMolCom; |
| 187 |
|
} |
| 188 |
|
|
| 189 |
< |
RealType getAtomMass(const std::string& at, ForceField* myFF) { |
| 189 |
> |
RealType MoLocator::getAtomMass(const std::string& at, ForceField* myFF) { |
| 190 |
|
RealType mass; |
| 191 |
|
AtomType* atomType= myFF->getAtomType(at); |
| 192 |
|
if (atomType != NULL) { |
| 198 |
|
return mass; |
| 199 |
|
} |
| 200 |
|
|
| 201 |
< |
RealType getMolMass(MoleculeStamp *molStamp, ForceField *myFF) { |
| 202 |
< |
int nAtoms; |
| 201 |
> |
RealType MoLocator::getMolMass(MoleculeStamp *molStamp, ForceField *myFF) { |
| 202 |
> |
unsigned int nAtoms; |
| 203 |
|
RealType totMass = 0; |
| 204 |
|
nAtoms = molStamp->getNAtoms(); |
| 205 |
|
|
| 206 |
< |
for(size_t i = 0; i < nAtoms; i++) { |
| 206 |
> |
for(unsigned int i = 0; i < nAtoms; i++) { |
| 207 |
|
AtomStamp *currAtomStamp = molStamp->getAtomStamp(i); |
| 208 |
|
totMass += getAtomMass(currAtomStamp->getType(), myFF); |
| 209 |
|
} |
| 210 |
|
return totMass; |
| 211 |
|
} |
| 212 |
< |
RotMat3x3d latVec2RotMat(const Vector3d& lv){ |
| 212 |
> |
|
| 213 |
> |
RotMat3x3d MoLocator::latVec2RotMat(const Vector3d& lv){ |
| 214 |
|
|
| 215 |
|
RealType theta =acos(lv[2]); |
| 216 |
|
RealType phi = atan2(lv[1], lv[0]); |
| 217 |
|
RealType psi = 0; |
| 218 |
|
|
| 219 |
< |
return RotMat3x3d(phi, theta, psi); |
| 216 |
< |
|
| 219 |
> |
return RotMat3x3d(phi, theta, psi); |
| 220 |
|
} |
| 221 |
|
} |
| 222 |
|
|
