Hey Irem,
1. There is no optimization other than what the compiler provides for JIT code.
2. Yes you need to define the entire potential including type differences in the single function body.
3. The box updater is not for NPT simulations. In MC use the hoomd.hpmc.update.BoxMC to run NPT or the hoomd.md.methods.NPT in MD for the NPT ensemble.
Best,
Brandon
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