I believe my advisor doesn't think I am smart. How should I deal with this?
It sounds like you are interpreting your advisor's comments about how your work is going as an indication that your advisor doesn't think you're smart or capable.

However, that's not necessarily what it means at all. It's only human for an advisor to express some occasional disappointment about how the work is going. (Every advisor thinks the work should be going faster!!! It's practically in the advisor rulebook.) 

And some people (unfortunately) express criticism more often than they express praise. This could just be your advisor's style.

It's not necessarily an indication of what your advisor thinks about you as a student and researcher.

So in answer to your question of "How to deal with this?":

Instead of inferring what your advisor thinks of your abilities from his comments about your work, ask him directly what he thinks of your abilities!

Ask your advisor: "How am I doing, in general? What areas do I need to improve in? What strengths do I have that I can play up?"

This is your chance to find out what your advisor sees in you, get some constructive criticism about your research skills in general (not about your current project). It's also a chance for you to tell your advisor how you think you're doing, and correct any misperceptions he may have about how hard you are working or how long the work should take.