Our optimization algorithm is designed to be used in automated frameworks without the need for manual intervention. However, the complexity of optimization in a basis of internal coordinates frequently frustrates attempts at automation. For example, when a bending angle of a molecule becomes linear or nearly linear during the course of optimization, displacement of the bending angle coordinate becomes ill-defined. To solve this problem, it is necessary to redefine the internal coordinate system to replace the linear bending angle with a different coordinate. Occasionally, this may require the addition of fictional "dummy atoms" that act as scaffolding off of which the replacement coordinate can be defined. The process of adding dummy atoms and dealing with the additional degrees of freedom they bring to the optimization problem poses a difficulty for automation efforts.