There are four major parts to Remote Agent on DS1 that are all separate programs.
Executive: This is the top-level program that takes a plan and tells the system what to do. A plan is a list of instructions like "Turn on the camera. Thrust with the third attitude-controlling thruster for 2.5 seconds. Take a picture."
Mission Manager: The mission manager keeps track of mission objectives like how much fuel it needs to have in reserve at each time in the mission, or scientific objectives.
Planner/Scheduler: This program is given the goals of the mission. It generates a plan that fits those goals. Then the executive carries it out.
Mode ID and Reconfiguration system: (MIR for short. This is not to be confused with the Russian space station, Mir.) MIR watches the health of the spacecraft, which means it knows which parts of the craft are still working and which ones have broken. It can tell the executive which parts work. If the executive needs to use a part that has broken down, it can suggest work-arounds and reconfigurations that would serve nearly the same purpose.
In normal operation, the Executive reaches a point where it needs a new plan. It asks the Planner for a new one. The Planner takes input from the Mission Manager and MIR and comes up with a new plan. The Executive takes the plan, and then if things go wrong, it can ask MIR for a way to work around whatever isn't working. If neither the Executive or MIR can come up with a solution, the executive asks for a new plan.
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When is Remote Agent on?
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What is artificial intelligence?
What happens to a ship when its remote agent "dies?"
Is Remote Agent like the robots in science fiction movies?
What is a remote agent?
How are satellites with no remote agent controlled?
Why don't we just send astronauts on deep space trips?
What are the distinguishing characteristics of agents as opposed to a normal program?
How does PS work?
How does the Smart Executive work?
How does the Mode Identification and Recovery system work?