Options apply to all files converted in one run. For instance, if the mode 'list' is used, options will apply to all files in the list. Identically, if the modes 'difference' or 'ddplot' are used, then the options will also be applied to all files.
Options can be called in any order in the command-line (i.e. before or after the input file or the formats to output). However when an option is invoked, it must be followed by its parameters in the correct order.
When several options are called in the command-line, they are applied to the system in the order of their appearence in the command-line (including if you call the same option several times). For instance if you call "pikashu initial.xyz final.xsf -expand 2 2 6 -cut above 3 z
" it will first expand the system and then cut it; while if you call "pikashu initial.xyz final.xsf -cut above 3 z -expand 2 2 6
" the system will first be cut and then expanded.
Note that the maximum number of options that can be called in one command-line is 20, which should be more than enough in most cases. If you find it is not enough, then simply apply your transformations by running pikashu
several times, or edit the source code of the program (this variable is set in comv.f90
).