On August 6, 1964, Pope Paul VI issued the encyclical Ecclesiam Suam. It is fascinating to read the document with 49 years of hindsight now to put it into perspective. You can read the whole encyclical here:
http://www.vatican.va/holy_father/paul_vi/encyclicals/documents/hf_p-vi_enc_06081964_ecclesiam_en.html
It is worth the time to read it in its entirety, but I would especially recommend paragraphs 99 and 100 where it speaks to atheism as a growing evil. We are still facing many of the same challenges today.
On this Feast of the Transfiguration of Our Lord Jesus Christ may we each be blessed abundantly through the overflowing grace of Almighty God!