| 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, 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 |
|
|
| 43 |
|
#include "selection/SelectionManager.hpp" |
| 43 |
– |
#include "primitives/Molecule.hpp" |
| 44 |
|
#include "brains/SimInfo.hpp" |
| 45 |
< |
namespace oopse { |
| 45 |
> |
namespace OpenMD { |
| 46 |
|
SelectionManager::SelectionManager(SimInfo* info) : info_(info){ |
| 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 |
< |
int nStuntDoubles = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies(); |
| 55 |
< |
|
| 56 |
< |
bsSelection_.resize(nStuntDoubles); |
| 57 |
< |
stuntdoubles_.resize(nStuntDoubles); |
| 54 |
> |
stuntdoubles_.resize(nObjects_[STUNTDOUBLE]); |
| 55 |
> |
bonds_.resize(nObjects_[BOND]); |
| 56 |
> |
bends_.resize(nObjects_[BEND]); |
| 57 |
> |
torsions_.resize(nObjects_[TORSION]); |
| 58 |
> |
inversions_.resize(nObjects_[INVERSION]); |
| 59 |
> |
molecules_.resize(nObjects_[MOLECULE]); |
| 60 |
|
|
| 61 |
|
SimInfo::MoleculeIterator mi; |
| 54 |
– |
Molecule* mol; |
| 62 |
|
Molecule::AtomIterator ai; |
| 56 |
– |
Atom* atom; |
| 63 |
|
Molecule::RigidBodyIterator rbIter; |
| 64 |
< |
RigidBody* rb; |
| 64 |
> |
Molecule::BondIterator bondIter; |
| 65 |
> |
Molecule::BendIterator bendIter; |
| 66 |
> |
Molecule::TorsionIterator torsionIter; |
| 67 |
> |
Molecule::InversionIterator inversionIter; |
| 68 |
|
|
| 69 |
< |
|
| 70 |
< |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 69 |
> |
Molecule* mol; |
| 70 |
> |
Atom* atom; |
| 71 |
> |
RigidBody* rb; |
| 72 |
> |
Bond* bond; |
| 73 |
> |
Bend* bend; |
| 74 |
> |
Torsion* torsion; |
| 75 |
> |
Inversion* inversion; |
| 76 |
|
|
| 77 |
< |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 77 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 78 |
> |
mol = info_->nextMolecule(mi)) { |
| 79 |
> |
molecules_[mol->getGlobalIndex()] = mol; |
| 80 |
> |
|
| 81 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; |
| 82 |
> |
atom = mol->nextAtom(ai)) { |
| 83 |
|
stuntdoubles_[atom->getGlobalIndex()] = atom; |
| 84 |
< |
} |
| 85 |
< |
|
| 86 |
< |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 84 |
> |
} |
| 85 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 86 |
> |
rb = mol->nextRigidBody(rbIter)) { |
| 87 |
|
stuntdoubles_[rb->getGlobalIndex()] = rb; |
| 88 |
< |
} |
| 89 |
< |
|
| 90 |
< |
} |
| 91 |
< |
|
| 88 |
> |
} |
| 89 |
> |
for (bond = mol->beginBond(bondIter); bond != NULL; |
| 90 |
> |
bond = mol->nextBond(bondIter)) { |
| 91 |
> |
bonds_[bond->getGlobalIndex()] = bond; |
| 92 |
> |
} |
| 93 |
> |
for (bend = mol->beginBend(bendIter); bend != NULL; |
| 94 |
> |
bend = mol->nextBend(bendIter)) { |
| 95 |
> |
bends_[bend->getGlobalIndex()] = bend; |
| 96 |
> |
} |
| 97 |
> |
for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; |
| 98 |
> |
torsion = mol->nextTorsion(torsionIter)) { |
| 99 |
> |
torsions_[torsion->getGlobalIndex()] = torsion; |
| 100 |
> |
} |
| 101 |
> |
for (inversion = mol->beginInversion(inversionIter); inversion != NULL; |
| 102 |
> |
inversion = mol->nextInversion(inversionIter)) { |
| 103 |
> |
inversions_[inversion->getGlobalIndex()] = inversion; |
| 104 |
> |
} |
| 105 |
> |
} |
| 106 |
|
} |
| 107 |
|
|
| 75 |
– |
|
| 108 |
|
StuntDouble* SelectionManager::beginSelected(int& i) { |
| 109 |
< |
i = bsSelection_.firstOnBit(); |
| 109 |
> |
i = ss_.bitsets_[STUNTDOUBLE].firstOnBit(); |
| 110 |
|
return i == -1 ? NULL : stuntdoubles_[i]; |
| 111 |
|
} |
| 112 |
+ |
|
| 113 |
|
StuntDouble* SelectionManager::nextSelected(int& i) { |
| 114 |
< |
i = bsSelection_.nextOnBit(i); |
| 114 |
> |
i = ss_.bitsets_[STUNTDOUBLE].nextOnBit(i); |
| 115 |
|
return i == -1 ? NULL : stuntdoubles_[i]; |
| 116 |
|
} |
| 117 |
|
|
| 118 |
|
StuntDouble* SelectionManager::beginUnselected(int& i){ |
| 119 |
< |
i = bsSelection_.firstOffBit(); |
| 119 |
> |
i = ss_.bitsets_[STUNTDOUBLE].firstOffBit(); |
| 120 |
|
return i == -1 ? NULL : stuntdoubles_[i]; |
| 121 |
|
} |
| 122 |
+ |
|
| 123 |
|
StuntDouble* SelectionManager::nextUnSelected(int& i) { |
| 124 |
< |
i = bsSelection_.nextOffBit(i); |
| 124 |
> |
i = ss_.bitsets_[STUNTDOUBLE].nextOffBit(i); |
| 125 |
|
return i == -1 ? NULL : stuntdoubles_[i]; |
| 126 |
|
} |
| 127 |
|
|
| 128 |
+ |
Bond* SelectionManager::beginSelectedBond(int& i) { |
| 129 |
+ |
i = ss_.bitsets_[BOND].firstOnBit(); |
| 130 |
+ |
return i == -1 ? NULL : bonds_[i]; |
| 131 |
+ |
} |
| 132 |
|
|
| 133 |
< |
SelectionManager operator| (const SelectionManager& sman1, const SelectionManager& sman2) { |
| 133 |
> |
Bond* SelectionManager::nextSelectedBond(int& i) { |
| 134 |
> |
i = ss_.bitsets_[BOND].nextOnBit(i); |
| 135 |
> |
return i == -1 ? NULL : bonds_[i]; |
| 136 |
> |
} |
| 137 |
> |
|
| 138 |
> |
Bond* SelectionManager::beginUnselectedBond(int& i){ |
| 139 |
> |
i = ss_.bitsets_[BOND].firstOffBit(); |
| 140 |
> |
return i == -1 ? NULL : bonds_[i]; |
| 141 |
> |
} |
| 142 |
> |
|
| 143 |
> |
Bond* SelectionManager::nextUnSelectedBond(int& i) { |
| 144 |
> |
i = ss_.bitsets_[BOND].nextOffBit(i); |
| 145 |
> |
return i == -1 ? NULL : bonds_[i]; |
| 146 |
> |
} |
| 147 |
> |
|
| 148 |
> |
Bend* SelectionManager::beginSelectedBend(int& i) { |
| 149 |
> |
i = ss_.bitsets_[BEND].firstOnBit(); |
| 150 |
> |
return i == -1 ? NULL : bends_[i]; |
| 151 |
> |
} |
| 152 |
> |
|
| 153 |
> |
Bend* SelectionManager::nextSelectedBend(int& i) { |
| 154 |
> |
i = ss_.bitsets_[BEND].nextOnBit(i); |
| 155 |
> |
return i == -1 ? NULL : bends_[i]; |
| 156 |
> |
} |
| 157 |
> |
|
| 158 |
> |
Bend* SelectionManager::beginUnselectedBend(int& i){ |
| 159 |
> |
i = ss_.bitsets_[BEND].firstOffBit(); |
| 160 |
> |
return i == -1 ? NULL : bends_[i]; |
| 161 |
> |
} |
| 162 |
> |
|
| 163 |
> |
Bend* SelectionManager::nextUnSelectedBend(int& i) { |
| 164 |
> |
i = ss_.bitsets_[BEND].nextOffBit(i); |
| 165 |
> |
return i == -1 ? NULL : bends_[i]; |
| 166 |
> |
} |
| 167 |
> |
|
| 168 |
> |
Torsion* SelectionManager::beginSelectedTorsion(int& i) { |
| 169 |
> |
i = ss_.bitsets_[TORSION].firstOnBit(); |
| 170 |
> |
return i == -1 ? NULL : torsions_[i]; |
| 171 |
> |
} |
| 172 |
> |
|
| 173 |
> |
Torsion* SelectionManager::nextSelectedTorsion(int& i) { |
| 174 |
> |
i = ss_.bitsets_[TORSION].nextOnBit(i); |
| 175 |
> |
return i == -1 ? NULL : torsions_[i]; |
| 176 |
> |
} |
| 177 |
> |
|
| 178 |
> |
Torsion* SelectionManager::beginUnselectedTorsion(int& i){ |
| 179 |
> |
i = ss_.bitsets_[TORSION].firstOffBit(); |
| 180 |
> |
return i == -1 ? NULL : torsions_[i]; |
| 181 |
> |
} |
| 182 |
> |
|
| 183 |
> |
Torsion* SelectionManager::nextUnSelectedTorsion(int& i) { |
| 184 |
> |
i = ss_.bitsets_[TORSION].nextOffBit(i); |
| 185 |
> |
return i == -1 ? NULL : torsions_[i]; |
| 186 |
> |
} |
| 187 |
> |
|
| 188 |
> |
Inversion* SelectionManager::beginSelectedInversion(int& i) { |
| 189 |
> |
i = ss_.bitsets_[INVERSION].firstOnBit(); |
| 190 |
> |
return i == -1 ? NULL : inversions_[i]; |
| 191 |
> |
} |
| 192 |
> |
|
| 193 |
> |
Inversion* SelectionManager::nextSelectedInversion(int& i) { |
| 194 |
> |
i = ss_.bitsets_[INVERSION].nextOnBit(i); |
| 195 |
> |
return i == -1 ? NULL : inversions_[i]; |
| 196 |
> |
} |
| 197 |
> |
|
| 198 |
> |
Inversion* SelectionManager::beginUnselectedInversion(int& i){ |
| 199 |
> |
i = ss_.bitsets_[INVERSION].firstOffBit(); |
| 200 |
> |
return i == -1 ? NULL : inversions_[i]; |
| 201 |
> |
} |
| 202 |
> |
|
| 203 |
> |
Inversion* SelectionManager::nextUnSelectedInversion(int& i) { |
| 204 |
> |
i = ss_.bitsets_[INVERSION].nextOffBit(i); |
| 205 |
> |
return i == -1 ? NULL : inversions_[i]; |
| 206 |
> |
} |
| 207 |
> |
|
| 208 |
> |
Molecule* SelectionManager::beginSelectedMolecule(int& i) { |
| 209 |
> |
i = ss_.bitsets_[MOLECULE].firstOnBit(); |
| 210 |
> |
return i == -1 ? NULL : molecules_[i]; |
| 211 |
> |
} |
| 212 |
> |
|
| 213 |
> |
Molecule* SelectionManager::nextSelectedMolecule(int& i) { |
| 214 |
> |
i = ss_.bitsets_[MOLECULE].nextOnBit(i); |
| 215 |
> |
return i == -1 ? NULL : molecules_[i]; |
| 216 |
> |
} |
| 217 |
> |
|
| 218 |
> |
Molecule* SelectionManager::beginUnselectedMolecule(int& i){ |
| 219 |
> |
i = ss_.bitsets_[MOLECULE].firstOffBit(); |
| 220 |
> |
return i == -1 ? NULL : molecules_[i]; |
| 221 |
> |
} |
| 222 |
> |
|
| 223 |
> |
Molecule* SelectionManager::nextUnSelectedMolecule(int& i) { |
| 224 |
> |
i = ss_.bitsets_[MOLECULE].nextOffBit(i); |
| 225 |
> |
return i == -1 ? NULL : molecules_[i]; |
| 226 |
> |
} |
| 227 |
> |
|
| 228 |
> |
SelectionManager operator| (const SelectionManager& sman1, |
| 229 |
> |
const SelectionManager& sman2) { |
| 230 |
|
SelectionManager result(sman1); |
| 231 |
|
result |= sman2; |
| 232 |
|
return result; |
| 233 |
|
} |
| 234 |
< |
SelectionManager operator& (const SelectionManager& sman1, const SelectionManager& sman2) { |
| 234 |
> |
|
| 235 |
> |
SelectionManager operator& (const SelectionManager& sman1, |
| 236 |
> |
const SelectionManager& sman2) { |
| 237 |
|
SelectionManager result(sman1); |
| 238 |
|
result &= sman2; |
| 239 |
|
return result; |
| 104 |
– |
|
| 240 |
|
} |
| 241 |
< |
SelectionManager operator^ (const SelectionManager& sman1, const SelectionManager& sman2) { |
| 241 |
> |
|
| 242 |
> |
SelectionManager operator^ (const SelectionManager& sman1, |
| 243 |
> |
const SelectionManager& sman2) { |
| 244 |
|
SelectionManager result(sman1); |
| 245 |
|
result ^= sman2; |
| 246 |
|
return result; |
| 110 |
– |
|
| 247 |
|
} |
| 248 |
< |
SelectionManager operator-(const SelectionManager& sman1, const SelectionManager& sman2){ |
| 248 |
> |
|
| 249 |
> |
SelectionManager operator-(const SelectionManager& sman1, |
| 250 |
> |
const SelectionManager& sman2){ |
| 251 |
|
SelectionManager result(sman1); |
| 252 |
|
result -= sman2; |
| 253 |
|
return result; |
| 116 |
– |
|
| 254 |
|
} |
| 255 |
|
|
| 256 |
|
} |
