The Atlas is a floating translucent diamond which plays a large part in the story of No Man's Sky. It is stated by Sean Murray in IGN's 18 Minute Gameplay video that Atlas is a central computer system where all data is stored. Not much is known about the Atlas, which is part of the larger Atlas Discovery Network.
The Atlas is a mysterious object which features in the advertisements and logo for No Man's Sky. The developers have described it as challenging "Explorers attempting the journey to centre of the Galaxy." Despite this seemingly aggressive description, the name itself suggests it can be used as some sort of star map or travel catalyst, though specifics and descriptions have yet to be released.
The Portals are mysterious structures throughout the universe. If walked through, you are sent to another planet much closer to the center of the galaxy, with more resources and dangers, but to get back to your ship you have to go back through the portal or you will probably never find it again.