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Welcome to the Wales group software wiki!

This wiki will contain the documentation for all the software we maintain in the group, along with worked examples and useful tips. We're currently in the process of migrating from an old website so please bear with us while we hammer out the problems and set things up. --Csw34 22:57, 20 July 2010 (UTC)

Software

All of our software is freely available open source under the GPL. However, there are cases when we interface to commercial codes such as AMBER and CHARMM. These files are absent from the source tarball. If you do have a license, please contact Professor Wales for access to a full version. We work on three separate

• GMIN: A program for finding global minima and calculating thermodynamic properties from basin-sampling.

GMIN employs the basin-hopping algorithm described by Wales and Doye (J. Phys. Chem. A, 101, 5111, 1997) to locate global minima on a potential energy surface. Many potentials are included. The latest version also includes an implementation of basin-sampling as described in T.V. Bogdan, D.J. Wales and F. Calvo (J. Chem. Phys., 124, 044102, 2006).

• OPTIM: A program for optimizing geometries and calculating reaction pathways

The geometry optimization scheme in OPTIM is based on eigenvector-following and was originally built from the optimizer in the ACES package written By Prof. John F. Stanton. OPTIM has analytic first and second derivatives coded for dozens of empirical potentials, and can also treat systems involving periodic boundary conditions and solve general optimization problems such as least squares fits.

• PATHSAMPLE: A driver for OPTIM to create stationary point databases using discrete path sampling and perform kinetic analysis

Scripts

We have developed many scripts within the group to use in conjunction with our software:

Scripts here...

Contact details

If you have something to add to this wiki, or would like to contribute code, please get in touch with Professor Wales.