pele.utils.neighbor_list#
classes to build and maintain neighborlists
- class pele.utils.neighbor_list.NeighborListSubsetBuild[source]
-
class NeighborListSubsetBuild(basepot):The same as NeighborListSubset except only do the building.
This class will build the neighbor lists, but can’t check whether they need to be rebuilt. This is meant to be used in situations where multiple neighbor lists are being maintained and we don’t want to do repetative checks for whether the lists should be rebuilt
It has the added benefit that no copy of coords is saved, so it takes up less memory.
- Parameters:
- natoms
number of atoms
- rcut
the cutoff distance for the potential
- rskin
the skin distance. atoms are listed as neighbors if they are closer then rlist = rcut + rskin. A larger rskin will have more interaction pairs, but will need to be updated less frequently
- Alist
The list of atoms that are interacting
- Blistthe list of atoms that are interacting with Alist
if Blist is None or Blist is Alist then the atoms in Alist will be assumed to be interacting with each other. Duplicate interactions will be avoided.
- boxl
if not None, then the system is in a periodic box of size boxl
- class pele.utils.neighbor_list.NeighborListPotentialBuild[source]
-
class NeighborListPotentialBuild(basepot):a potential wrapper for a neighbor list, but only rebuild when told to
- Parameters:
- neighborList
the neighbor list object
- pot
the potential object
- NeighborListPotentialBuild.buildList()[source]
-
def buildList(self, coords):instruct the neighbor list object to rebuild it’s list
- class pele.utils.neighbor_list.NeighborListPotentialMulti[source]
-
class NeighborListPotentialMulti(basepot):A wrapper for multiple NeighborListPotentialBuild
This will wrap multiple instances of NeighborListPotentialBuild. This class will the check the coords and control when the neighbor lists are rebuilt.
- Parameters:
- potentials
a list of neighbor list potential objects. Each potential must have attribute
potential.buildList(coords)
- natoms
number of atoms
- rcut
the cutoff distance for the potential
- rskin
the skin distance. atoms are listed as neighbors if they are closer then rlist = rcut + rskin. A larger rskin will have more interaction pairs, but will need to be updated less frequently
- boxl
if not None, then the system is in a periodic box of size boxl