I have attached a script that seems to work well (with ATK 2016.2). Have decreased the number of k-points along C to 3, and tightened the SCF convergence criteria to get accurate forces. Yes, the Si-Be bond lengths increase, but do no look unreasonable.
Tips:
- You may also want to try the more accurate (and slower) SG15 pseudopoentials with 100 Ha cutoff energy.
- Your system is periodic along C, but 50 k-points is far too many (as long as this is not an electrode for a device configuration).
- 20 electronic bands for the DiagonalizationSolver may help speed up things.