| 6 |
|
* redistribute this software in source and binary code form, provided |
| 7 |
|
* 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 |
|
* 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, 24107 (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 |
|
|
| 43 |
|
#include <iostream> |
| 49 |
|
#include "utils/MoLocator.hpp" |
| 50 |
|
#include "types/AtomType.hpp" |
| 51 |
|
|
| 52 |
< |
namespace oopse { |
| 52 |
> |
namespace OpenMD { |
| 53 |
|
MoLocator::MoLocator( MoleculeStamp* theStamp, ForceField* theFF){ |
| 54 |
|
|
| 55 |
|
myStamp = theStamp; |
| 59 |
|
} |
| 60 |
|
|
| 61 |
|
void MoLocator::placeMol( const Vector3d& offset, const Vector3d& ort, Molecule* mol){ |
| 62 |
+ |
|
| 63 |
|
Vector3d newCoor; |
| 64 |
|
Vector3d curRefCoor; |
| 65 |
|
RotMat3x3d rotMat = latVec2RotMat(ort); |
| 73 |
|
} |
| 74 |
|
|
| 75 |
|
Molecule::IntegrableObjectIterator ii; |
| 76 |
< |
StuntDouble* integrableObject; |
| 76 |
> |
StuntDouble* sd; |
| 77 |
|
int i; |
| 78 |
< |
for (integrableObject = mol->beginIntegrableObject(ii), i = 0; integrableObject != NULL; |
| 79 |
< |
integrableObject = mol->nextIntegrableObject(ii), ++i) { |
| 78 |
> |
for (sd = mol->beginIntegrableObject(ii), i = 0; sd != NULL; |
| 79 |
> |
sd = mol->nextIntegrableObject(ii), ++i) { |
| 80 |
|
|
| 81 |
|
newCoor = rotMat * refCoords[i]; |
| 82 |
|
newCoor += offset; |
| 83 |
+ |
|
| 84 |
+ |
sd->setPos(newCoor); |
| 85 |
+ |
sd->setVel(V3Zero); |
| 86 |
|
|
| 87 |
< |
integrableObject->setPos( newCoor); |
| 88 |
< |
integrableObject->setVel(V3Zero); |
| 89 |
< |
|
| 85 |
< |
if(integrableObject->isDirectional()){ |
| 86 |
< |
integrableObject->setA(rotMat * integrableObject->getA()); |
| 87 |
< |
integrableObject->setJ(V3Zero); |
| 87 |
> |
if(sd->isDirectional()){ |
| 88 |
> |
sd->setA(rotMat * sd->getA()); |
| 89 |
> |
sd->setJ(V3Zero); |
| 90 |
|
} |
| 91 |
|
} |
| 92 |
|
} |
| 94 |
|
void MoLocator::calcRef( void ){ |
| 95 |
|
AtomStamp* currAtomStamp; |
| 96 |
|
RigidBodyStamp* rbStamp; |
| 97 |
< |
int nAtoms; |
| 97 |
> |
unsigned int nAtoms; |
| 98 |
|
int nRigidBodies; |
| 99 |
|
std::vector<RealType> mass; |
| 100 |
|
Vector3d coor; |
| 107 |
|
nAtoms= myStamp->getNAtoms(); |
| 108 |
|
nRigidBodies = myStamp->getNRigidBodies(); |
| 109 |
|
|
| 110 |
< |
for(size_t i=0; i<nAtoms; i++){ |
| 110 |
> |
for(unsigned int i = 0; i < nAtoms; i++){ |
| 111 |
|
|
| 112 |
|
currAtomStamp = myStamp->getAtomStamp(i); |
| 113 |
|
|
| 197 |
|
} |
| 198 |
|
|
| 199 |
|
RealType getMolMass(MoleculeStamp *molStamp, ForceField *myFF) { |
| 200 |
< |
int nAtoms; |
| 200 |
> |
unsigned int nAtoms; |
| 201 |
|
RealType totMass = 0; |
| 202 |
|
nAtoms = molStamp->getNAtoms(); |
| 203 |
|
|
| 204 |
< |
for(size_t i = 0; i < nAtoms; i++) { |
| 204 |
> |
for(unsigned int i = 0; i < nAtoms; i++) { |
| 205 |
|
AtomStamp *currAtomStamp = molStamp->getAtomStamp(i); |
| 206 |
|
totMass += getAtomMass(currAtomStamp->getType(), myFF); |
| 207 |
|
} |
