A class that implements neighbor lists from two lists or a single list of atoms.
More...
#include <NeighborList.h>
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| | NeighborList (const std::vector< PLMD::AtomNumber > &list0, const std::vector< PLMD::AtomNumber > &list1, const bool &do_pair, const bool &do_pbc, const PLMD::Pbc &pbc, const double &distance=1.0e+30, const unsigned &stride=0) |
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| | NeighborList (const std::vector< PLMD::AtomNumber > &list0, const bool &do_pbc, const PLMD::Pbc &pbc, const double &distance=1.0e+30, const unsigned &stride=0) |
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| std::vector< PLMD::AtomNumber > & | getFullAtomList () |
| | Return the list of all atoms. These are needed to rebuild the neighbor list. More...
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| std::vector< PLMD::AtomNumber > & | getReducedAtomList () |
| | Update the indexes in the neighbor list to match the ordering in the new positions array and return the new list of atoms that must be requested to the main code. More...
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| void | update (const std::vector< PLMD::Vector > &positions) |
| | Update the neighbor list and prepare the new list of atoms that will be requested to the main code. More...
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| unsigned | getStride () const |
| | Get the update stride of the neighbor list. More...
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| unsigned | getLastUpdate () const |
| | Get the last step in which the neighbor list was updated. More...
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| void | setLastUpdate (unsigned step) |
| | Set the step of the last update. More...
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| unsigned | size () const |
| | Get the size of the neighbor list. More...
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| std::pair< unsigned, unsigned > | getClosePair (unsigned i) const |
| | Get the i-th pair of the neighbor list. More...
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| std::vector< unsigned > | getNeighbors (unsigned i) |
| | Get the list of neighbors of the i-th atom. More...
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| | ~NeighborList () |
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| void | initialize () |
| | Initialize the neighbor list with all possible pairs. More...
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| std::pair< unsigned, unsigned > | getIndexPair (unsigned i) |
| | Return the pair of indexes in the positions array of the two atoms forming the i-th pair among all possible pairs. More...
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| void | setRequestList () |
| | Extract the list of atoms from the current list of close pairs. More...
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A class that implements neighbor lists from two lists or a single list of atoms.
Definition at line 36 of file NeighborList.h.
| PLMD::NeighborList::NeighborList |
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const std::vector< PLMD::AtomNumber > & |
list0, |
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const std::vector< PLMD::AtomNumber > & |
list1, |
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const bool & |
do_pair, |
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const bool & |
do_pbc, |
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const PLMD::Pbc & |
pbc, |
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const double & |
distance = 1.0e+30, |
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const unsigned & |
stride = 0 |
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| PLMD::NeighborList::NeighborList |
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const std::vector< PLMD::AtomNumber > & |
list0, |
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const bool & |
do_pbc, |
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const PLMD::Pbc & |
pbc, |
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const double & |
distance = 1.0e+30, |
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const unsigned & |
stride = 0 |
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| PLMD::NeighborList::~NeighborList |
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| pair< unsigned, unsigned > PLMD::NeighborList::getClosePair |
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unsigned |
i | ) |
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| vector< AtomNumber > & PLMD::NeighborList::getFullAtomList |
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Return the list of all atoms. These are needed to rebuild the neighbor list.
Definition at line 75 of file NeighborList.cpp.
| pair< unsigned, unsigned > PLMD::NeighborList::getIndexPair |
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unsigned |
i | ) |
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private |
Return the pair of indexes in the positions array of the two atoms forming the i-th pair among all possible pairs.
Definition at line 79 of file NeighborList.cpp.
| unsigned PLMD::NeighborList::getLastUpdate |
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const |
Get the last step in which the neighbor list was updated.
Definition at line 144 of file NeighborList.cpp.
| vector< unsigned > PLMD::NeighborList::getNeighbors |
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unsigned |
i | ) |
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| vector< AtomNumber > & PLMD::NeighborList::getReducedAtomList |
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Update the indexes in the neighbor list to match the ordering in the new positions array and return the new list of atoms that must be requested to the main code.
Definition at line 125 of file NeighborList.cpp.
| unsigned PLMD::NeighborList::getStride |
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const |
| void PLMD::NeighborList::initialize |
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Initialize the neighbor list with all possible pairs.
Definition at line 68 of file NeighborList.cpp.
| void PLMD::NeighborList::setLastUpdate |
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unsigned |
step | ) |
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| void PLMD::NeighborList::setRequestList |
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Extract the list of atoms from the current list of close pairs.
Definition at line 115 of file NeighborList.cpp.
| unsigned PLMD::NeighborList::size |
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const |
| void PLMD::NeighborList::update |
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const std::vector< PLMD::Vector > & |
positions | ) |
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Update the neighbor list and prepare the new list of atoms that will be requested to the main code.
Definition at line 94 of file NeighborList.cpp.
| double PLMD::NeighborList::distance_ |
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| bool PLMD::NeighborList::do_pair_ |
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| bool PLMD::NeighborList::do_pbc_ |
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| unsigned PLMD::NeighborList::lastupdate_ |
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| unsigned PLMD::NeighborList::nallpairs_ |
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| std::vector<std::pair<unsigned,unsigned> > PLMD::NeighborList::neighbors_ |
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| unsigned PLMD::NeighborList::nlist0_ |
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| unsigned PLMD::NeighborList::nlist1_ |
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| bool PLMD::NeighborList::reduced |
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| unsigned PLMD::NeighborList::stride_ |
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| bool PLMD::NeighborList::twolists_ |
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private |
The documentation for this class was generated from the following files:
1.8.8