Neighbor tables

Solvent properties, transition state trajectory, future research issues, 232-233 Space inversion symmetry (P) ab initio calculations, 253—259 barium fluroide molecules, 256-259 ytterbium molecule, 254—256 electric dipole moment search, 241-242 nonconservation, 239—241 Spatial neighbor tables, Monte Carlo heat flow simulation, 68—70... 

TABLE 4 8. Nearest-Neighbor Table for the Three Nearest Neighbors for KNN Example... 

TABLE 4.10. Nearest-Neighbor Table for the Prediction of the Four Unknowns ... 

Table 4.15 fists the nearest-neighbor table and goodness values for the unknown samples-... 

Nearest-neighbor table (table of K nearest neighbors for all samples)... 

Goodness Value The goodness values for the three unknowns are listed in the last column of Table 4.15. Consist nt with the nearest-neighbor table, unknowns 1 and 2 have a goodness val e less than 8, and so are considered reliable classifications. Unknown 3 has a goodness value greater than 8, further indicating a problem with the classification. 

TABLE 4.15. Nearest-Neighbor Table and Goodness Values of Three Unknown Samples... 

The ny value of a particular molecular fragment is assigned according to the hybridization state of the fragment s immediate neighbors. Table 1.3 summarizes the five types of adjacent atom hybridization used. (See also Figurel.3). 

As we have seen on the CRAY the ability to gather data together is essential. Memory speed must be commensurate with floating point speed. When nearest neighbor tables are used fast scatter operations are also needed. The two essential random memory operations needed are ... 

Brown, Clarke, Okuda, and Yamazaki also adopted a domain decomposition parallelization strategy on the Fujitsu API 000 machine. " They describe an algorithm that is a development of a spatial decomposition technique due to Liem and co-workers but incorporated decomposition of three-dimensional space in all three dimensions with linked-cell and neighbor table techniques for enhanced efficiency. Communications between processors were minimized without incurring the penalties associated with redundant force calculation. 

The two summations are dimensionless properties of the lattice structure, and accurate values can be obtained by summing over the first few sets of nearest neighbors (Table 21.3). The resulting total energy for the fee lattice is... 

Each atom in the original crystalline supercell is numbered, its coordinates are listed in a coordinate table and its four covalently bonded neighbors are listed in a neighbor table. Two neighboring atoms are then selected at random, corresponding to atoms 2 and 5 in the example of Fig. 1. Then neighboring atoms, illustrated by atoms 1 and 6 in Fig. 1, are... 

If a pair of trial bond switches is accepted, the coordinate table and the neighbor table are updated. 

Because we are interested in systems with rather short-range interactions with a well-defined cut-off, it is inefficient to examine all of the pairs of particles ij at each time-step to determine which ones have a nonzero force between them. An alternative is to divide the simulation cell into smaller cells of size r< -t- r, where is a small skin of order 0.3-0.5ct. Now one simply has to check pairs within neighboring cells to determine which pairs ij have a nonzero force. The extra skin allows one to create a list of neighbors, which only has to be updated every 10-20 time steps. Combining the link cell with a Verlet neighbor table is the most efficient method for doing any off-lattice simulation with short-range interactions. To obtain... 

ACD = Available Chemicals Directory CAS = Chemical Abstracts Service CSD = Cambridge Structural Database DEC = dynamically expanding context FA = factor analysis LVQ = learning vector quantization MDS = multidimensional scaling NNT = nearest-neighbor table PCA = principal component analysis QSAR = quantitative structure-activity relationships SOM = self-organized map. 

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