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So it is like the Pagan Romans calling Christians "atheists"?
I think they would actually refer to them as 'heretics'. That would be more applicable.
Unlikely - I don't think classical Latin had the word heretic. 'Haeresis' (heresy) meant only a school of thought. The word heresy attained it's modern meaning only in Christian writings; and even this modern meaning isn't really one which makes sense from the point of view of pagan Romans looking at Christians. Heretics tend to be people doing your religion wrong - it's used for heterodox interpretations of Christian dogma. A Catholic might have called a Protestant a heretic, but not a Buddhist. The Buddhist would be an unbeliever, or a pagan, or an infidel.
Atheist, on the other hand, was used in classical Latin, but it did not have the modern sense of not believing in a god or gods. A better translation in modern English might be 'ungodly'. It was used not to refer to a person's belief, but rather their actions - atheists were those who did not participate in the expected religious rites of the community. And LNA is right - early Christians were indeed condemned for atheism due to their refusal to take part in (pagan) religious rites.