GAFita computational tool kit for parameterizations of potential energy surfaces

Roberto Rodríguez Fernández

The potential energy surface (PES) of a molecular system governs many of its chemical properties, and particularly, the dynamics, that is, the spatial evolution of nuclei with time Most of the chemical dynamics simulations performed nowadays involve integration of the classical equations of motion, calculating the forces on atoms at each step either directly by electronic structure calculations –direct dynamics– or from analytical PES. Even for small-size systems, the use of an analytical surface may be a convenient choice. However, to our knowledge, there is not a general code that allows users to parametrize analytical surfaces in a relatively easy way. The aim of the present work was to write a suite of programs to assist users in developing them. GAFit was initially developed to facilitate fittings of intermolecular potentials and reparametrizations of semiempirical Hamiltonians using a genetic algorithm. However, it can be easily adjusted for other purposes in which fittings of a series of parameters are needed. The functionality of the package was extended separating the core itself from the fitting targets. Users can choose, upon their programming skills, from introducing their custom potentials directly into code, use an easy pre-coded potential template to do so, or for those with no programming knowledge at all, that can use an analytical expression or the most used potentials coded just ready to use. A complete set of tools were added to the package to facilitate the creation and configuration of input files. In addition, an external interface was developed to interact with external programs. Using this interface the tools needed to use GAFit to parametrize the MOPAC program were developed. A further MOPAC enhanced interface permits running parallel copies of MOPAC to speed up calculations and face up some problems encountered during the first stage development.


Supervised by:
Emilio Martinez Nuñez and Saulo A. Vázquez Rodríguez

Defence University:
University of Santiago de Compostela

Year of Defence:

Ricardo Mosquera Castro (Chair), Antonio Fernández Ramos (Secretary), Enrique Manuel Cabaleiro Lago (Committee member), Jorge Manuel Campos Marques (Committee member) and Jose Manuel Hermida Ramon (Committee member)