Research software

The following codes are the result of research carried out in collaboration with Dr. Francisco Pereira from Centro de Informática e Sistemas da Universidade de Coimbra (CISUC).

EA_MOL

Evolutionary algorithm for the global minimum search of molecular clusters. It has been applied for various molecular clusters: water (up to n=20), benzene (up to n=30), and benzene cation (up to n=20). Published in J. Phys. Chem. A 115, 2130-2138 (2011); paper available from the journal or from the authors upon request.

SAICS

Superimposing algorithm for the identification of chiral structures. The method uses a probability driven approach, which involves the application of the Hungarian algorithm to several randomly generated orientations of one of the comparing structures, followed by reorientation to tune for the best superposition. Basically, the identification of enantiomers is achieved by applying such scheme, a second time, to the mirror-image of one of the comparing structures. See the original paper for details. Download the most recent version (v1.3) of SAICS on the top right of this page.

GAFit

This package may be applied to a wide range of fitting problems (download the manual on the top right of this page), though it has been especially designed to reduce the hard (and tedious) work involved in the development of potential energy surfaces of complex systems. The least-squares fitting procedure uses a genetic algorithm and it is interfaced with CHARMM and MOPAC programs in order to facilitate force-field parameterizations and tune specific reaction parameters (SRP) for semiempirical Hamiltonians. In addition, it contains several programs to help the user in the preparation of the input files. This software is a collaborative work with Dr. Francisco Pereira and the group of Dr. Emilio Martínez-Núñez and Dr. Saulo Vázquez from the University of Santiago de Compostela. Download the most recent version (v2024a) of GAFit and the related publication.

Didactic tools

Traj2d

Fortran code that implements the classical trajectory method to study A+BC type reactions in 2D. Published in Quim. Nova 26, 769-778 (2003); paper available from the journal (text in portuguese).

Wavecalc

Internet toolkit to solve the Schrödinger equation for various unidimensional potential models, i.e, potential box, double-well, harmonic oscillator, Lennard-Jones, Morse and extended-Rydberg potentials. Published in J. Chem. Educ. 85, 591 (2008); paper and other documentation are available from the journal or from the authors upon request.