The vnl and nc files are not generated simultaneously with the starting of job. The generation of vnl file depends on the position of ".addToSample()" in your script file. For the generation of nc file, it will occur when the self-consistent calculation starts.
Currently, no support for the ATK2.0 version. The method of geometry optimization implemented in ATK2.0 has been clearly indicated, i.e., the conjugate gradient method.