the reason why sometimes g03 and g09 are giving different energies is they use different initial guesses by default. Otherwise a slightly difference (e.g. 0.00001 au) in results is just due to the numerical roundoff errors.
Most times, even different guesses will still lead to them same result. If not, then one needs to be extremely careful; it is necessary to check the electronic state and configuration rather than compare the energies only.
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+1/98
很多常见体系应该是一直的，新版本就是补Bug+增加新方法。一个公司不会随便就大量改源代码的。