Version 1.4.7 features enhanced hydrogen saturation procedure, Ubuntu 14.04, and structure optimization

With v1.4.7 a better hydrogen saturation procedure was implemented.

So far, we dealt with each bond to be saturated one after the other and could handle up to bond degree of three. The problem with the old code was that placement of saturation hydrogen was independent of that for another bond. This could result in hydrogens being placed on top of each other or at least very close. This occurred for example with the SLES molecule when the sulfur bonds were saturated due to its high valency.

Now, we calculate optimal places for saturation globally per molecule prior to the fragmentation procedure. After fragments have been determined and cut bonds need to be saturated, the required positions of the hydrogen are looked up from a table created by this prior calculation. This ensures that hydrogen placed by the saturation of two different bonds are optimally far away from each other.

Note that hydrogen saturation is a perturbation of the underlying Fock matrix (in the case a Hartree-Fock solver is used). Hence, resulting energies are affected and will now be slightly different.

There is a new make target extracheck that runs when mpqc (​http://www.mpqc.org/) is installed and can found in the path: It compares resulting values for some molecules against stored ones. There, relative differences (for bond order of 3) of up to 1e-5 are admissable!

Furthermore, the version now compiles on Ubuntu 14.04 systems. Some changes were necessary due to new boost and gcc versions.

Last but not least a simple Structural Optimization procedure based on the fragmentation has been implemented. This is so far just using calculated forces and some fixed stepwidth dampening scheme to look for the minimum. Enhancements are coming up but will take some more time.