8/9/2019 Neighbor Map

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8/9/2019 Neighbor Map

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Consider atom number 91. The red circle defines the distance up to which possible

interacting neighbors are to be taken into account. The radius of this circle is close

but somewhat larger than rcut. Now, for the atom 91 we just produce the list of the

atoms that are within this circle and this list is the map of interacting neighbors. The

atoms belonging to this group are listed above and in calculation only those atoms

will be included when evaluating the interactions of the atom 91 with the rest of theatoms in the block.

When you have the block of atoms prepared and all atoms are numbered you generate

the neighbor list by creating the following two arrays:

NEIGHBORS N,K) and NOFNEIGHBORS N)

N=1, , 400

K=1, , Kmax, where Kmax is the maximum number of neighbors

expected.

You can create the above arrays as follows:

For each atom j (j = 1 400) find all its neighbors at a distance in

which interaction may occur. Lets say atom j has m such

neighbors. Store atom numbers of these m neighbors in

NEIGHBORS(j,1), NEIGHBORS(j,2), NEIGHBORS(j,3), ,

NEIGHBORS(j,m). Also store the value m in

NOFNEIGHBORS(j) . These two arrays represent the map or list

of neighbors.

8/9/2019 Neighbor Map

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Very first time you have to try for all the atoms in the block if they

are neighbors of the atom j. But, when the list of neighbors has

been established you will only consider interaction of the atom j

with those atoms that are in its neighbor map. This will save an

enormous amount of time compared with testing all possible

interactions all the time.