A 'Fear Simulation' is a simulation that the Dauntless use to help you know and overcome your fears.
This simulation in 1 or 2 years before the factions were disbanded happens at the end of Dauntless initiation, before it was the first thing the Dauntless initiates did after they got to the compound as seen in The Transfer: A Divergent Story.
Before entering the fear landscape, participants are injected with a serum that will bring their fears to the surface of their brains. During Dauntless initiation, the Dauntless leaders and usually the initiates trainer are watching the initiates fears and taking count of how many they have. For each fear, their heartbeat is measured and the landscape will not change until your heartbeat and breathing slows to a normal pace. Or the initiate can choose to face their fear. This is what Tris chooses to do instead of killing her family in her final simulation.
Fear simulations are like the regular simulations the Dauntless initiates must take in stage two of initiation. But everyone, not just Divergents, know that it is not real. However, Divergent people can manipulate the simulations in their minds to make their results quicker and their fears easier to deal with.
Most people have about 10-15 fears. However, the record for least number of fears ”in recent years” is 4, which is the result Tobias Eaton got on his fear landscape. This is how Tobias got the nickname "Four".
Tris originally had 7 fears, but later had 6 which included: To be devoured by crows - symbolic of powerlessness. Drowning in a tank of water - symbolic for weakness and inability to escape. Men reaching for her in her Abnegation room - symbolic, scared of death. Kill family or be killed by Jeanine - symbolic for watching family die and being responsible for it. Intercourse/Intimacy with Tobias/Four - symbolic for the fear that Tobias/Four only wants her for her body (no longer a fear).
Those fear landscapes? They're straight up symbol factories, like dream journals and cheesy poetry. Everything means something else.
But not all of these fears are symbolic in the way we usually think about symbols. When Four shows that his fear landscape includes his father, we don't say "what could his father be a symbol of?" No, in that case, we know that Four's fear landscape is pretty straightforward: his dad is there because Four is still afraid of his dad's abuse; Four is afraid of claustrophobic spaces because he used to be put in a closet as punishment. Those are some pretty literal interpretations.
By contrast, Tris's fears are a little less literal and a little more symbolic. She's afraid of being attacked by birds in a field, but she doesn't have a bird-phobia (unless she's seen Hitchcock's The Birds one too many times). As Tris notes when she's going through her fear landscape, the bird fear "isn't about the birds. It's about control" ; the drowning in the box fear "is not about the water; it is about my inability to escape the tank" . For each of her fears, Tris gives us the breakdown of what each symbolizes. This is probably the most intense therapy session Tris will ever go through. And like a good therapy session, we learn more about who Tris is by seeing what her fears are and what symbols they come in.
For example, there are lots of ways that a lack of control could appear to Tris, but it appears to her as a dangerous flock of crows. Why crows? This is just a theory, but it might have to do with the fact that Tris symbolizes her family as birds (ravens) when she gets her first tattoo. And maybe the fact that it's a flock of crows (instead of just one big crow) has to do with her feelings about crowds, which she doesn't seem to love: the Abnegation all blend together, but crowds of Dauntless aren't always a great time, unless they're working together as a community, like when she goes zip lining.