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As mentioned in the DRCSim User Guide, Stand mode is the hub to all the behavioral modes, I've added a diagram to clarify this point. So to recover from a fall, you must first go back to User mode, then to Stand mode. Below is an example path to recovery:

  1. Put the robot under PID control, (i.e. set k_effort[0:28] to 255 for all joints), then
  2. Get the robot back on to its feet with your own controller. Drive Atlas into PID controlled Stand pose (for example, see VRCPlugin::SetPIDStand() for approximate target joint positions taken from a snapshot of joint states while standing).
  3. Once the robot stabilizes, you can then switch to BDI STAND mode mode and set all k_effort[0:28] to 0 simultaneously (for example, see SetBDIStand() for reference).