SearchFill: A stochastic optimization code for detecting atomic vacancies in crystalline and non-crystalline systems Original Research Article

We present an implementation of a stochastic optimization algorithm applied to location of atomic vacancies. Our method labels an empty point in space as a vacancy site, if the total spatial overlap of a “virtual sphere”, centered around the point, with the surrounding atoms (and other vacancies) falls below a tolerance parameter. A Metropolis-like algorithm displaces the vacancies randomly, using an “overlap temperature” parameter to allow for acceptance of moves into regions with higher overlap, thus avoiding local minima. Once the algorithm has targeted a point with low overlap, the overlap temperature is decreased, and the method works as a steepest descent optimization.