3.6. Determine sel

All descriptors require to set sel, which means the expected maximum number of type-i neighbors of an atom. DeePMD-kit will allocate memory according to sel.

sel should not be too large or too small. If sel is too large, the computing will become much slower and cost more memory. If sel is not enough, the energy will be not conserved, making the accuracy of the model worse.

To determine a proper sel, one can calculate the neighbor stat of the training data before training:

dp neighbor-stat -s data -r 6.0 -t O H

where data is the directory of data, 6.0 is the cutoff radius, and O and H is the type map. The program will give the max_nbor_size. For example, max_nbor_size of the water example is [38, 72], meaning an atom may have 38 O neighbors and 72 H neighbors in the training data.

The sel should be set to a higher value than that of the training data, considering there may be some extreme geometries during MD simulations. As a result, we set to [46, 92] in the water example.