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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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< |
* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
< |
* |
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* 2. Redistributions of source code must retain the above copyright |
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> |
* 1. Redistributions of source code must retain the above copyright |
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|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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> |
* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
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* distribution. |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
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+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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|
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#ifndef PRIMITIVES_CUTOFFGROUP_HPP |
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#include "primitives/Atom.hpp" |
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#include "math/Vector3.hpp" |
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|
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namespace oopse { |
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namespace OpenMD { |
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class CutoffGroup { |
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public: |
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+ |
|
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CutoffGroup() : snapshotMan_(NULL), globalIndex(-1), localIndex_(-1) { |
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|
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< |
CutoffGroup() { |
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> |
storage_ = &Snapshot::cgData; |
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haveTotalMass = false; |
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totalMass = 0.0; |
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} |
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|
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/** |
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* Sets the Snapshot Manager of this cutoffGroup |
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*/ |
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void setSnapshotManager(SnapshotManager* sman) { |
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snapshotMan_ = sman; |
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} |
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|
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+ |
|
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void addAtom(Atom *atom) { |
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cutoffAtomList.push_back(atom); |
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} |
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|
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> |
|
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Atom *beginAtom(std::vector<Atom *>::iterator & i) { |
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i = cutoffAtomList.begin(); |
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return i != cutoffAtomList.end() ? *i : NULL; |
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} |
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< |
|
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> |
|
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Atom *nextAtom(std::vector<Atom *>::iterator & i) { |
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i++; |
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return i != cutoffAtomList.end() ? *i : NULL; |
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std::vector<Atom*> getAtoms() { return cutoffAtomList; } |
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RealType getMass() { |
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std::vector<Atom *>::iterator i; |
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Atom * atom; |
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RealType mass; |
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|
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> |
|
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|
if (!haveTotalMass) { |
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totalMass = 0; |
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< |
|
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for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) { |
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mass = atom->getMass(); |
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> |
|
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> |
for(Atom* atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) { |
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> |
RealType mass = atom->getMass(); |
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totalMass += mass; |
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} |
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< |
|
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> |
|
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haveTotalMass = true; |
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} |
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< |
|
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> |
|
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return totalMass; |
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} |
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< |
|
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< |
void getCOM(Vector3d & com) { |
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> |
|
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> |
void updateCOM() { |
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std::vector<Atom *>::iterator i; |
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Atom * atom; |
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– |
Vector3d pos; |
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– |
RealType mass; |
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|
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< |
com[0] = 0; |
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com[1] = 0; |
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com[2] = 0; |
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> |
DataStorage& data = snapshotMan_->getCurrentSnapshot()->*storage_; |
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> |
int storageLayout = data.getStorageLayout(); |
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> |
|
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|
totalMass = getMass(); |
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< |
|
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> |
|
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|
if (cutoffAtomList.size() == 1) { |
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< |
com = beginAtom(i)->getPos(); |
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> |
data.position[localIndex_] = beginAtom(i)->getPos(); |
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|
} else { |
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+ |
data.position[localIndex_] = V3Zero; |
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for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) { |
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< |
mass = atom->getMass(); |
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< |
pos = atom->getPos(); |
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< |
com += pos * mass; |
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< |
} |
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> |
data.position[localIndex_] += atom->getMass() * atom->getPos(); |
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> |
} |
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> |
data.position[localIndex_] /= totalMass; |
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> |
} |
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|
|
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< |
com /= totalMass; |
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> |
if (storageLayout & DataStorage::dslVelocity) { |
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> |
if (cutoffAtomList.size() == 1) { |
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> |
data.velocity[localIndex_] = beginAtom(i)->getVel(); |
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> |
} else { |
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> |
data.velocity[localIndex_] = V3Zero; |
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> |
for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) { |
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> |
data.velocity[localIndex_] += atom->getMass() * atom->getVel(); |
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> |
} |
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> |
data.velocity[localIndex_] /= totalMass; |
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> |
} |
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} |
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|
} |
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|
|
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+ |
|
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+ |
Vector3d getPos() { |
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+ |
return ((snapshotMan_->getCurrentSnapshot())->*storage_).position[localIndex_]; |
| 136 |
+ |
} |
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+ |
Vector3d getVel() { |
| 138 |
+ |
return ((snapshotMan_->getCurrentSnapshot())->*storage_).velocity[localIndex_]; |
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+ |
} |
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+ |
|
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|
int getNumAtom() { |
| 142 |
|
return cutoffAtomList.size(); |
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|
} |
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< |
|
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> |
|
| 145 |
|
int getGlobalIndex() { |
| 146 |
|
return globalIndex; |
| 147 |
|
} |
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< |
|
| 148 |
> |
|
| 149 |
|
void setGlobalIndex(int id) { |
| 150 |
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this->globalIndex = id; |
| 151 |
|
} |
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|
|
| 153 |
< |
private: |
| 153 |
> |
/** |
| 154 |
> |
* Returns the local index of this cutoffGroup |
| 155 |
> |
* @return the local index of this cutoffGroup |
| 156 |
> |
*/ |
| 157 |
> |
int getLocalIndex() { |
| 158 |
> |
return localIndex_; |
| 159 |
> |
} |
| 160 |
|
|
| 161 |
+ |
/** |
| 162 |
+ |
* Sets the local index of this cutoffGroup |
| 163 |
+ |
* @param index new index to be set |
| 164 |
+ |
*/ |
| 165 |
+ |
void setLocalIndex(int index) { |
| 166 |
+ |
localIndex_ = index; |
| 167 |
+ |
} |
| 168 |
+ |
|
| 169 |
+ |
private: |
| 170 |
+ |
|
| 171 |
|
std::vector<Atom *>cutoffAtomList; |
| 172 |
|
bool haveTotalMass; |
| 173 |
|
RealType totalMass; |
| 174 |
< |
int globalIndex; |
| 134 |
< |
}; |
| 174 |
> |
int globalIndex; |
| 175 |
|
|
| 176 |
< |
} //end namespace oopse |
| 176 |
> |
int localIndex_; |
| 177 |
> |
DataStoragePointer storage_; |
| 178 |
> |
SnapshotManager* snapshotMan_; |
| 179 |
|
|
| 180 |
+ |
}; |
| 181 |
+ |
} //end namespace OpenMD |
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|
#endif //PRIMITIVES_CUTOFFGROUP_HPP |
