| 6 |
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* redistribute this software in source and binary code form, provided |
| 7 |
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* that the following conditions are met: |
| 8 |
|
* |
| 9 |
< |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* publication of scientific results based in part on use of the |
| 11 |
< |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
< |
* the article in which the program was described (Matthew |
| 13 |
< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
< |
* |
| 18 |
< |
* 2. Redistributions of source code must retain the above copyright |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
|
* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
|
* distribution. |
| 28 |
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* arising out of the use of or inability to use software, even if the |
| 29 |
|
* University of Notre Dame has been advised of the possibility of |
| 30 |
|
* such damages. |
| 31 |
+ |
* |
| 32 |
+ |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
+ |
* research, please cite the appropriate papers when you publish your |
| 34 |
+ |
* work. Good starting points are: |
| 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, 234107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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|
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#include <iostream> |
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#include "utils/MoLocator.hpp" |
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#include "types/AtomType.hpp" |
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|
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< |
namespace oopse { |
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> |
namespace OpenMD { |
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MoLocator::MoLocator( MoleculeStamp* theStamp, ForceField* theFF){ |
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|
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myStamp = theStamp; |
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calcRef(); |
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} |
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|
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< |
void MoLocator::placeMol( const Vector3d& offset, const Vector3d& ort, Molecule* mol){ |
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> |
void MoLocator::placeMol( const Vector3d& offset, const Vector3d& ort, |
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> |
Molecule* mol) { |
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> |
|
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Vector3d newCoor; |
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Vector3d curRefCoor; |
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RotMat3x3d rotMat = latVec2RotMat(ort); |
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|
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if(mol->getNIntegrableObjects() != nIntegrableObjects){ |
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sprintf( painCave.errMsg, |
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"MoLocator error.\n" |
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" The number of integrable objects of MoleculeStamp is not the same as that of Molecule\n"); |
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> |
"MoLocator::placeMol error.\n" |
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> |
"\tThe number of integrable objects of MoleculeStamp is not\n" |
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> |
"\tthe same as that of Molecule\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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Molecule::IntegrableObjectIterator ii; |
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< |
StuntDouble* integrableObject; |
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> |
StuntDouble* sd; |
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int i; |
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< |
for (integrableObject = mol->beginIntegrableObject(ii), i = 0; integrableObject != NULL; |
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< |
integrableObject = mol->nextIntegrableObject(ii), ++i) { |
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> |
for (sd = mol->beginIntegrableObject(ii), i = 0; sd != NULL; |
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> |
sd = mol->nextIntegrableObject(ii), ++i) { |
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|
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newCoor = rotMat * refCoords[i]; |
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newCoor += offset; |
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+ |
|
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+ |
sd->setPos(newCoor); |
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+ |
sd->setVel(V3Zero); |
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|
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< |
integrableObject->setPos( newCoor); |
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< |
integrableObject->setVel(V3Zero); |
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< |
|
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< |
if(integrableObject->isDirectional()){ |
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< |
integrableObject->setA(rotMat * integrableObject->getA()); |
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< |
integrableObject->setJ(V3Zero); |
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> |
if(sd->isDirectional()){ |
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> |
sd->setA(rotMat * sd->getA()); |
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> |
sd->setJ(V3Zero); |
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} |
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} |
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} |
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void MoLocator::calcRef( void ){ |
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AtomStamp* currAtomStamp; |
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RigidBodyStamp* rbStamp; |
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< |
int nAtoms; |
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< |
int nRigidBodies; |
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< |
std::vector<double> mass; |
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> |
std::vector<RealType> mass; |
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Vector3d coor; |
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Vector3d refMolCom; |
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< |
int nAtomsInRb; |
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< |
double totMassInRb; |
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< |
double currAtomMass; |
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< |
double molMass; |
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> |
RealType totMassInRb; |
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> |
RealType currAtomMass; |
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> |
RealType molMass; |
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|
|
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< |
nAtoms= myStamp->getNAtoms(); |
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< |
nRigidBodies = myStamp->getNRigidBodies(); |
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> |
std::size_t nAtoms= myStamp->getNAtoms(); |
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> |
std::size_t nRigidBodies = myStamp->getNRigidBodies(); |
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|
|
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< |
for(size_t i=0; i<nAtoms; i++){ |
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> |
for(std::size_t i = 0; i < nAtoms; i++){ |
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|
|
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currAtomStamp = myStamp->getAtomStamp(i); |
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|
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if( !currAtomStamp->havePosition() ){ |
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sprintf( painCave.errMsg, |
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< |
"MoLocator error.\n" |
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< |
" Component %s, atom %s does not have a position specified.\n" |
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< |
" This means MoLocator cannot initalize it's position.\n", |
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> |
"MoLocator::calcRef error.\n" |
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> |
"\tComponent %s, atom %s does not have a position specified.\n" |
| 117 |
> |
"\tThis means MoLocator cannot initalize it's position.\n", |
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myStamp->getName().c_str(), |
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currAtomStamp->getType().c_str()); |
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|
|
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|
} |
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|
} |
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|
|
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< |
for(int i = 0; i < nRigidBodies; i++){ |
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> |
for(std::size_t i = 0; i < nRigidBodies; i++){ |
| 141 |
|
|
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|
rbStamp = myStamp->getRigidBodyStamp(i); |
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< |
nAtomsInRb = rbStamp->getNMembers(); |
| 143 |
> |
std::size_t nAtomsInRb = rbStamp->getNMembers(); |
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|
|
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|
coor.x() = 0.0; |
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|
coor.y() = 0.0; |
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|
coor.z() = 0.0; |
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|
totMassInRb = 0.0; |
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|
|
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< |
for(int j = 0; j < nAtomsInRb; j++){ |
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> |
for(std::size_t j = 0; j < nAtomsInRb; j++){ |
| 151 |
|
|
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|
currAtomStamp = myStamp->getAtomStamp(rbStamp->getMemberAt(j)); |
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currAtomMass = getAtomMass(currAtomStamp->getType(), myFF); |
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|
refMolCom.y() = 0; |
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refMolCom.z() = 0; |
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|
|
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< |
for(int i = 0; i < nIntegrableObjects; i++){ |
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> |
for(std::size_t i = 0; i < nIntegrableObjects; i++){ |
| 174 |
|
refMolCom += refCoords[i] * mass[i]; |
| 175 |
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molMass += mass[i]; |
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} |
| 177 |
|
|
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refMolCom /= molMass; |
| 179 |
|
|
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< |
//move the reference center of mass to (0,0,0) and adjust the reference coordinate |
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< |
//of the integrabel objects |
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< |
for(int i = 0; i < nIntegrableObjects; i++) |
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> |
//move the reference center of mass to (0,0,0) and adjust the |
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> |
//reference coordinate of the integrabel objects |
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> |
for(std::size_t i = 0; i < nIntegrableObjects; i++) |
| 183 |
|
refCoords[i] -= refMolCom; |
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|
} |
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|
|
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< |
double getAtomMass(const std::string& at, ForceField* myFF) { |
| 187 |
< |
double mass; |
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> |
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(); |
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|
} else { |
| 192 |
|
mass = 0.0; |
| 193 |
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std::cerr << "Can not find AtomType: " << at << std::endl; |
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|
return mass; |
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|
} |
| 197 |
|
|
| 198 |
< |
double getMolMass(MoleculeStamp *molStamp, ForceField *myFF) { |
| 199 |
< |
int nAtoms; |
| 200 |
< |
double totMass = 0; |
| 198 |
> |
RealType MoLocator::getMolMass(MoleculeStamp *molStamp, ForceField *myFF) { |
| 199 |
> |
unsigned int nAtoms; |
| 200 |
> |
RealType totMass = 0; |
| 201 |
|
nAtoms = molStamp->getNAtoms(); |
| 202 |
|
|
| 203 |
< |
for(size_t 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 |
< |
double theta =acos(lv[2]); |
| 213 |
< |
double phi = atan2(lv[1], lv[0]); |
| 214 |
< |
double psi = 0; |
| 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); |
| 215 |
< |
|
| 216 |
> |
return RotMat3x3d(phi, theta, psi); |
| 217 |
|
} |
| 218 |
|
} |
| 219 |
|
|
