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#include <utility> |
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#include <vector> |
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|
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< |
#include "brains/Exclude.hpp" |
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> |
#include "brains/PairList.hpp" |
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#include "io/Globals.hpp" |
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#include "math/Vector3.hpp" |
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#include "math/SquareMatrix3.hpp" |
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#include "utils/LocalIndexManager.hpp" |
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|
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//another nonsense macro declaration |
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< |
#define __C |
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> |
#define __OOPSE_C |
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#include "brains/fSimulation.h" |
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|
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namespace oopse{ |
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return i != molecules_.end() ? i->second : NULL; |
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} |
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|
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+ |
int getGlobalMolMembership(int id){ |
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+ |
return globalMolMembership_[id]; |
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+ |
} |
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+ |
|
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RealType getRcut() { |
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return rcut_; |
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} |
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* @see #SimCreator::setGlobalIndex |
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*/ |
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void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) { |
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< |
assert(globalGroupMembership.size() == nGlobalAtoms_); |
| 377 |
> |
assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_)); |
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globalGroupMembership_ = globalGroupMembership; |
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} |
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|
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* @see #SimCreator::setGlobalIndex |
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*/ |
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void setGlobalMolMembership(const std::vector<int>& globalMolMembership) { |
| 386 |
< |
assert(globalMolMembership.size() == nGlobalAtoms_); |
| 386 |
> |
assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_)); |
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globalMolMembership_ = globalMolMembership; |
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} |
| 389 |
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|
| 441 |
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GenericData* getPropertyByName(const std::string& propName); |
| 442 |
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|
| 443 |
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/** |
| 444 |
< |
* add all exclude pairs of a molecule into exclude list. |
| 444 |
> |
* add all special interaction pairs (including excluded |
| 445 |
> |
* interactions) in a molecule into the appropriate lists. |
| 446 |
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*/ |
| 447 |
< |
void addExcludePairs(Molecule* mol); |
| 447 |
> |
void addInteractionPairs(Molecule* mol); |
| 448 |
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|
| 449 |
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/** |
| 450 |
< |
* remove all exclude pairs which belong to a molecule from exclude list |
| 450 |
> |
* remove all special interaction pairs which belong to a molecule |
| 451 |
> |
* from the appropriate lists. |
| 452 |
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*/ |
| 453 |
+ |
void removeInteractionPairs(Molecule* mol); |
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|
| 448 |
– |
void removeExcludePairs(Molecule* mol); |
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|
| 450 |
– |
|
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/** Returns the unique atom types of local processor in an array */ |
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std::set<AtomType*> getUniqueAtomTypes(); |
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|
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int nConstraints_; /**< number of constraints in local processors */ |
| 544 |
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|
| 545 |
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simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/ |
| 546 |
< |
Exclude exclude_; |
| 546 |
> |
PairList excludedInteractions_; |
| 547 |
> |
PairList oneTwoInteractions_; |
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> |
PairList oneThreeInteractions_; |
| 549 |
> |
PairList oneFourInteractions_; |
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PropertyMap properties_; /**< Generic Property */ |
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SnapshotManager* sman_; /**< SnapshotManager */ |
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|
