| 6 |
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* 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 |
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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). |
| 41 |
|
*/ |
| 42 |
|
#include "selection/IndexFinder.hpp" |
| 43 |
|
#include "primitives/Molecule.hpp" |
| 44 |
< |
namespace oopse { |
| 44 |
> |
namespace OpenMD { |
| 45 |
|
|
| 45 |
– |
|
| 46 |
– |
|
| 46 |
|
IndexFinder::IndexFinder(SimInfo* info) : info_(info){ |
| 47 |
< |
nStuntDoubles_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies(); |
| 48 |
< |
bitSets_.resize(info_->getNGlobalMolecules()); |
| 47 |
> |
nObjects_.push_back(info_->getNGlobalAtoms()+info_->getNGlobalRigidBodies()); |
| 48 |
> |
nObjects_.push_back(info_->getNGlobalBonds()); |
| 49 |
> |
nObjects_.push_back(info_->getNGlobalBends()); |
| 50 |
> |
nObjects_.push_back(info_->getNGlobalTorsions()); |
| 51 |
> |
nObjects_.push_back(info_->getNGlobalInversions()); |
| 52 |
> |
nObjects_.push_back(info_->getNGlobalMolecules()); |
| 53 |
> |
|
| 54 |
> |
selectionSets_.resize(info_->getNGlobalMolecules()); |
| 55 |
|
init(); |
| 56 |
|
} |
| 57 |
|
|
| 53 |
– |
|
| 58 |
|
void IndexFinder::init() { |
| 59 |
|
|
| 60 |
|
SimInfo::MoleculeIterator mi; |
| 57 |
– |
Molecule* mol; |
| 61 |
|
Molecule::AtomIterator ai; |
| 59 |
– |
Atom* atom; |
| 62 |
|
Molecule::RigidBodyIterator rbIter; |
| 63 |
+ |
Molecule::BondIterator bondIter; |
| 64 |
+ |
Molecule::BendIterator bendIter; |
| 65 |
+ |
Molecule::TorsionIterator torsionIter; |
| 66 |
+ |
Molecule::InversionIterator inversionIter; |
| 67 |
+ |
|
| 68 |
+ |
Molecule* mol; |
| 69 |
+ |
Atom* atom; |
| 70 |
|
RigidBody* rb; |
| 71 |
+ |
Bond* bond; |
| 72 |
+ |
Bend* bend; |
| 73 |
+ |
Torsion* torsion; |
| 74 |
+ |
Inversion* inversion; |
| 75 |
|
|
| 76 |
< |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 76 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 77 |
> |
mol = info_->nextMolecule(mi)) { |
| 78 |
|
|
| 79 |
< |
OOPSEBitSet bs(nStuntDoubles_); |
| 79 |
> |
SelectionSet ss(nObjects_); |
| 80 |
> |
ss.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex()); |
| 81 |
> |
|
| 82 |
|
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 83 |
< |
bs.setBitOn(atom->getGlobalIndex()); |
| 83 |
> |
ss.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex()); |
| 84 |
|
} |
| 85 |
< |
|
| 86 |
< |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 87 |
< |
bs.setBitOn(rb->getGlobalIndex()); |
| 85 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 86 |
> |
rb = mol->nextRigidBody(rbIter)) { |
| 87 |
> |
ss.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex()); |
| 88 |
|
} |
| 89 |
+ |
for (bond = mol->beginBond(bondIter); bond != NULL; |
| 90 |
+ |
bond = mol->nextBond(bondIter)) { |
| 91 |
+ |
ss.bitsets_[BOND].setBitOn(bond->getGlobalIndex()); |
| 92 |
+ |
} |
| 93 |
+ |
for (bend = mol->beginBend(bendIter); bend != NULL; |
| 94 |
+ |
bend = mol->nextBend(bendIter)) { |
| 95 |
+ |
ss.bitsets_[BEND].setBitOn(bend->getGlobalIndex()); |
| 96 |
+ |
} |
| 97 |
+ |
for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; |
| 98 |
+ |
torsion = mol->nextTorsion(torsionIter)) { |
| 99 |
+ |
ss.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex()); |
| 100 |
+ |
} |
| 101 |
+ |
for (inversion = mol->beginInversion(inversionIter); inversion != NULL; |
| 102 |
+ |
inversion = mol->nextInversion(inversionIter)) { |
| 103 |
+ |
ss.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex()); |
| 104 |
+ |
} |
| 105 |
|
|
| 106 |
< |
bitSets_[mol->getGlobalIndex()] = bs; |
| 107 |
< |
} |
| 76 |
< |
|
| 106 |
> |
selectionSets_[mol->getGlobalIndex()] = ss; |
| 107 |
> |
} |
| 108 |
|
} |
| 109 |
|
|
| 110 |
< |
OOPSEBitSet IndexFinder::find(int molIndex){ |
| 111 |
< |
return bitSets_[molIndex]; |
| 110 |
> |
SelectionSet IndexFinder::find(int molIndex){ |
| 111 |
> |
return selectionSets_[molIndex]; |
| 112 |
|
} |
| 113 |
|
|
| 114 |
< |
OOPSEBitSet IndexFinder::find(int begMolIndex, int endMolIndex){ |
| 115 |
< |
OOPSEBitSet bs(nStuntDoubles_); |
| 114 |
> |
SelectionSet IndexFinder::find(int begMolIndex, int endMolIndex){ |
| 115 |
> |
SelectionSet ss(nObjects_); |
| 116 |
|
|
| 117 |
|
for (int i = begMolIndex; i < endMolIndex; ++i) { |
| 118 |
< |
bs |= bitSets_[i]; |
| 119 |
< |
} |
| 120 |
< |
|
| 90 |
< |
return bs; |
| 118 |
> |
ss |= selectionSets_[i]; |
| 119 |
> |
} |
| 120 |
> |
return ss; |
| 121 |
|
} |
| 92 |
– |
|
| 93 |
– |
|
| 122 |
|
} |
| 123 |
|
|
