Changes to improve embeding of TS geometry

The conversion of the estimate into a TS geometry is
not perfect. Error is introduced, especially with the
X-H distance. This reduces that error, but does not
eliminate it.

Further improvement could involve the minimum distances.
The minimum distance of the X-H atoms from others are not
modified much, and are a possible source of the problem.
Remove input and log file printing

Gaussian input and log files were printed to
bash, but this created very large output files
when a list of reactions were run. The printing is
also unnecessary since we keep the log files.
Alter the distance range setting to 0.02

We previously used distance limits of 0.1 Angstroms
when setting the estimated distance limits of the
TS geometry. This introduced error into the geometry
when embedding. By reducing this first to 0.05, then
to 0.02, and also increasing the spring constant when
optimizing with UFF, the error between the estimated made
and what is embedded has been significantly reduced.

This could be better optimized. This change works well if
the estimates are really good, but if they are not the algo
should allow for some variability in the geometry estimate
(reduce the spring constant, go back to 0.1 diff).