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Emergency stop. l.15 \AtBeginDocument {\bibliographystyle{unsrturl}}^^M *** (cannot \read from terminal in nonstop modes) Here is how much of TeX's memory you used: 2273 strings out of 493089 29979 string characters out of 6134842 79010 words of memory out of 5000000 5776 multiletter control sequences out of 15000+600000 6199 words of font info for 17 fonts, out of 8000000 for 9000 1141 hyphenation exceptions out of 8191 35i,0n,26p,238b,80s stack positions out of 5000i,500n,10000p,200000b,80000s ! ==> Fatal error occurred, no output PDF file produced!