entry way from outdoor atrium

Since the credit language refers to "public entry points" I would assume that an internal courtyard would not be subject to the requirements.

I would recommend caution here since the intent of the credit is reduce/prevent the amount of particulate matter that is tracked into a building's interior on the occupants' shoes. If your open-air courtyard features landscaping, soil, gravel or any other type of material that could be carried into the building on a regular basis, I'd say that it would be important to have entryway mats at those building entrances. The key point here is that people are entering the building interior at these locations. "Public entry point" simply means that the entryway is not a private entrance used by a single individual or family; if these courtyards are accessible to any of your building occupants, they would be considered public entry points.