Passes file prefix from phonons to geom_opt by default, so the file names for structures written consistent unless overwritten
Adds option to save generated structures (and initial, potentially optimized structure) when running eos in a single file
Prevents writing via geom_opt, as the same structures can be saved more safely within eos
If we also tried to save the optimization trajectory, this would still be overwritten by each structure in turn, but at that point I think it's probably better to recommend dealing with them as separate steps
Resolves #187 & #188
phononstogeom_optby default, so the file names for structures written consistent unless overwritteneosin a single filegeom_opt, as the same structures can be saved more safely withineos