93 lines
3.1 KiB
Python
93 lines
3.1 KiB
Python
# ----------------------------------------------------------------------
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# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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# http://lammps.sandia.gov, Sandia National Laboratories
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# Steve Plimpton, sjplimp@sandia.gov
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#
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# Copyright (2003) Sandia Corporation. Under the terms of Contract
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# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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# certain rights in this software. This software is distributed under
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# the GNU General Public License.
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#
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# See the README file in the top-level LAMMPS directory.
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# -------------------------------------------------------------------------
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################################################################################
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# LAMMPS data structures
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# Written by Richard Berger <richard.berger@temple.edu>
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################################################################################
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class NeighList:
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"""This is a wrapper class that exposes the contents of a neighbor list.
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It can be used like a regular Python list. Each element is a tuple of:
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* the atom local index
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* its number of neighbors
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* and a pointer to an c_int array containing local atom indices of its
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neighbors
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Internally it uses the lower-level LAMMPS C-library interface.
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:param lmp: reference to instance of :py:class:`lammps`
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:type lmp: lammps
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:param idx: neighbor list index
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:type idx: int
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"""
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def __init__(self, lmp, idx):
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self.lmp = lmp
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self.idx = idx
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def __str__(self):
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return "Neighbor List ({} atoms)".format(self.size)
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def __repr__(self):
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return self.__str__()
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@property
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def size(self):
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"""
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:return: number of elements in neighbor list
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"""
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return self.lmp.get_neighlist_size(self.idx)
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def get(self, element):
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"""
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Access a specific neighbor list entry. "element" must be a number from 0 to the size-1 of the list
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:return: tuple with atom local index, number of neighbors and ctypes pointer to neighbor's local atom indices
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:rtype: (int, int, ctypes.POINTER(c_int))
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"""
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iatom, numneigh, neighbors = self.lmp.get_neighlist_element_neighbors(self.idx, element)
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return iatom, numneigh, neighbors
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# the methods below implement the iterator interface, so NeighList can be used like a regular Python list
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def __getitem__(self, element):
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return self.get(element)
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def __len__(self):
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return self.size
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def __iter__(self):
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inum = self.size
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for ii in range(inum):
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yield self.get(ii)
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def find(self, iatom):
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"""
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Find the neighbor list for a specific (local) atom iatom.
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If there is no list for iatom, (-1, None) is returned.
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:return: tuple with number of neighbors and ctypes pointer to neighbor's local atom indices
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:rtype: (int, ctypes.POINTER(c_int))
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"""
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inum = self.size
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for ii in range(inum):
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idx, numneigh, neighbors = self.get(ii)
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if idx == iatom:
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return numneigh, neighbors
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return -1, None
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