The Giants have an agreement in place with left-hander Javier Lopez for three years and $13 million pending a physical, sources confirmed on Thursday. Lopez, 36, was coming off a two-year, $8.5 million deal. He gets an ever so slight bump ($4.33 million from $4.25 million) in salary. It’s the third year that mattered most to him, since his first choice was to remain with the Giants. No word yet on if Lopez will receive any kind of no-trade protection as part of the deal. That’s likely what the two sides are resolving now.