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#include <utility> |
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#include <vector> |
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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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//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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namespace oopse{ |
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i = molecules_.find(index); |
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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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RealType getRcut() { |
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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_); |
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> |
assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_)); |
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globalGroupMembership_ = globalGroupMembership; |
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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) { |
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< |
assert(globalMolMembership.size() == nGlobalAtoms_); |
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> |
assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_)); |
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globalMolMembership_ = globalMolMembership; |
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} |
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GenericData* getPropertyByName(const std::string& propName); |
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/** |
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< |
* add all exclude pairs of a molecule into exclude list. |
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> |
* add all special interaction pairs (including excluded |
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* interactions) in a molecule into the appropriate lists. |
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*/ |
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< |
void addExcludePairs(Molecule* mol); |
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> |
void addInteractionPairs(Molecule* mol); |
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/** |
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< |
* remove all exclude pairs which belong to a molecule from exclude list |
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> |
* remove all special interaction pairs which belong to a molecule |
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> |
* from the appropriate lists. |
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*/ |
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+ |
void removeInteractionPairs(Molecule* mol); |
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– |
void removeExcludePairs(Molecule* mol); |
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– |
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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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std::vector<int> globalGroupMembership_; |
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/** |
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< |
* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the |
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* the size of globalMolMembership_ is nGlobalAtoms. Its index is global index of an atom, and the |
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* corresponding content is the global index of molecule this atom belong to. |
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* It is filled by SimCreator once and only once, since it is never changed during the simulation. |
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*/ |
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int nConstraints_; /**< number of constraints in local processors */ |
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simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/ |
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< |
Exclude exclude_; |
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> |
PairList excludedInteractions_; |
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> |
PairList oneTwoInteractions_; |
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> |
PairList oneThreeInteractions_; |
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> |
PairList oneFourInteractions_; |
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PropertyMap properties_; /**< Generic Property */ |
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SnapshotManager* sman_; /**< SnapshotManager */ |
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RealType rsw_; /**< radius of switching function*/ |
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RealType rlist_; /**< neighbor list radius */ |
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< |
bool ljsp_; /**< use shifted potential for LJ*/ |
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< |
bool ljsf_; /**< use shifted force for LJ*/ |
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> |
int ljsp_; /**< use shifted potential for LJ*/ |
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> |
int ljsf_; /**< use shifted force for LJ*/ |
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bool fortranInitialized_; /**< flag indicate whether fortran side |
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is initialized */ |
