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md2011-03-note_Part_3

md2011-03-note_Part_3 - V N L I For generating the neighbor...

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Unformatted text preview: V N L I For generating the neighbor list, we need to define a new distance r m > r cut , and include in the list of each atom i all those atoms j for which r ij 6 r m . I The list hast to be updated every N m steps so that the skin distance r m- r cut > N m h v max i Δ t , (8) where h v max i is the time average for that atom which has the highest velocity. I A more efficient way is to monitor the total displacement of each atom d M after each update of the neighbor list, and update when d M becomes too large. Notes I Practical implementation of the Verlet list is to use a row-vector of integers: N nbr i is the number of neighbors for atom i , and j 1 . . . j N nbr i are the indices of those neighbors. N is the total number of atoms. I This is probably the easiest efficient way of constructing a neighbor list. I However, it’s not the most efficient one for a large number of particles....
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md2011-03-note_Part_3 - V N L I For generating the neighbor...

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