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The recommended setup for running AutoTune uses a 3 position Flight Mode Switch.  With this, you can take off and fly Attitude mode with default PIDs, run AutoTune with default PIDs and fly Attitude mode with new PIDs, all without using the GCS:
Pos#1 - Attitude mode using bank 1
Pos#2 - AutoTune using bank 1 with SystemIdentSettings.DestinationPidBank set to 2 (that is the default)
Pos#3 - Attitude mode using bank 2 (bank 2 is where the tuned PIDs are written by default)
PID bank 1 should have default PIDs or something that is at least known to fly without oscillations.
This setup can all be done at home, and everything else can be done at the flying field, without using the GCS. 

With this FMS (Flight Mode Switch) setup, you always have Pos#1 to fall back on.  Use Pos#1 to recover from any bad situation or to start over and run AutoTune again.

Remove anything that is expensive or fragile (e.g. cameras and antennas, but understand that transmitters must remain unpowered any time they don't have an antenna attached) from the multicopter if this is your first experience with AutoTune on this multicopter.

 Arm and take off in Pos#1 which is Attitude mode with default (or other known-good) PIDs.  These PIDs must not oscillate for the tuning to work.  Switch to Pos#2 which is AutoTune mode which is also configured to use default (or other known-good) PIDs.  After a few seconds the copter begins to shake.  Fly it smoothly.  Don't let the copter touch anything (such as the ground) while tuning is running.  60 seconds after that, the shaking stops and the tuning is complete.  The PIDs have already been written to the destination PID bank, but are only stored in RAM memory at this point.  The standard procedure is to land and disarm which writes the PIDs to permanent storage.  The PIDs will be written to permanent settings if you disarm before powering off.  The PIDs will be discarded if the copter is powered off without disarming it.

That covers the basics of AutoTune.  Many people will be satisfied with using and knowing only what has already been described.  Enhanced functionality, further tweaks, and safety issues are discussed below.

Further Information follows:
Any time after tuning is complete, you can switch to Pos#3 which is Attitude mode using the tuned PIDs to test them.  Use caution!  It's recommended that when tuning completes you land and disarm, but if you were to switch to Pos#3, even without landing, you would be flying the new PIDs.  If you have time and access to a GCS at this point and understand what reasonable PID values look like, you could examine the new PIDs before you fly them.

To test fly your new PIDs, switch to Pos#3 (Attitude with tuned PIDs), arm, and cautiously take off.  Beginners beware: a slow increase in motor power for takeoff is not recommended as it causes PID windup.  It is best to start with motors off and immediately jump up the smallest amount you can to barely get off the ground and stay off.  You can learn the correct amount of throttle by starting with small blips and giving bigger and bigger blips until you learn how much throttle it takes to take off.  Before you take off, mentally prepare yourself to immediately apply zero throttle if something doesn't feel right.  A fall from 3 feet / 1 meter generally causes little or no damage.

You can simply retune by running AutoTune again if you want to.  The use of Attitude mode when testing the new PIDs is recommended (but not required), even for experts.  AutoTune mode itself is a modified form of Attitude mode and it doesn't matter what other modes you have as far as the tune is concerned.

In the worst case scenario where you don't have your FMS set up as recommended, oscillation may cause it to climb, and the only way to get down is to cut power for short periods and let if fall.  Automatic leveling in that case is very desirable.  This isn't an issue if you have the FMS set up as recommended.  In that case, just switch to Pos#1.

Tricopters are a special issue.  They may or may not tune correctly.  An assumption is made that the control delay is the same for roll pitch and yaw.  This is not true for tricopters which use a servo for yaw, but use motor thrust for roll / pitch An alternate FMS setup for a 2 position FMS removes the ability to fly with default PIDs once you have run AutoTune:
Pos#1 - Attitude mode using bank 2 (bank 2 is where the tuned PIDs are written by default)
Pos#2 - AutoTune using bank 1 with SystemIdentSettings.DestinationPidBank set to 2 (that is the default)
PID bank 1 should have default PIDs or something that is at least known to fly without oscillations.
PID bank 2 start out with the same PIDs as bank 1, but the PIDs will be changed by AutoTune.

It is possible to arm in Pos#1, then switch to Pos#2 and immediately take off before the AutoTune shaking starts, if your tuned PIDs don't work and you want to retune.

Remove anything that is expensive or fragile (e.g. cameras and antennas, but understand that transmitters must remain unpowered any time they don't have an antenna attached) from the multicopter if this is your first experience with AutoTune on this multicopter.  Be aware though, that you eventually need to tune in "flight trim".  Things like cameras and FPV gear that even moderately affect the total weight of the copter should be mounted to get a good tune.

Arm and take off in Pos#1 which is Attitude mode with default (or other known-good) PIDs.  These PIDs must not oscillate for the tuning to work.  Switch to Pos#2 which is AutoTune mode which is also configured to use default (or other known-good) PIDs.  After a few seconds the copter begins to shake.  Fly it smoothly.  Don't let the copter touch anything (such as the ground) while tuning is running.  60 seconds after that, the shaking stops and the tuning is complete.  The PIDs have already been written to the destination PID bank, but are only stored in RAM memory at this point.  The standard procedure is to land and disarm which writes the PIDs to permanent storage.  The PIDs will be written to permanent settings if you disarm before powering off.  The PIDs will be discarded if the copter is powered off without disarming it.

Switch to Pos#3 (Pos#1 for the 2 position FMS) which now holds the tuned PIDs.  Cautiously take off, and be ready to immediately cut power to zero if there is any problem.  You are now flying tuned PIDs.  If for some reason you want to run AutoTune again, just switch to Pos#2 as before.

That covers the basics of AutoTune.  If you don't want to use additional AutoTune features, you can remove AutoTune from your FMS at this point.  Enhanced functionality, further tweaks, and safety issues are discussed below.

Further Information follows:
Any time after tuning is complete, you can switch to Pos#3 which is Attitude mode using the tuned PIDs to test them.  Use caution!  It's recommended that when tuning completes you land and disarm, but if you were to switch to Pos#3, even without landing, you would be flying the new PIDs.  If you have time and access to a GCS at this point and understand what reasonable PID values look like, you could examine the new PIDs before you fly them.

To test fly your new PIDs, switch to Pos#3 (Attitude with tuned PIDs), arm, and cautiously take off.  Beginners beware: a slow increase in motor power for takeoff is not recommended as it causes PID windup.  It is best to start with motors off and immediately jump up the smallest amount you can to barely get off the ground and stay off.  You can learn the correct amount of throttle by starting with small blips and giving bigger and bigger blips until you learn how much throttle it takes to take off.  Before you take off, mentally prepare yourself to immediately apply zero throttle if something doesn't feel right.  A fall from 3 feet / 1 meter generally causes little or no damage.

You can simply retune by running AutoTune again if you want to.  The use of Attitude mode when testing the new PIDs is recommended (but not required), even for experts.  AutoTune mode itself is a modified form of Attitude mode and it doesn't matter what other modes you have as far as the tune is concerned.

In the worst case scenario where you don't have your FMS set up as recommended, oscillation may cause it to climb, and the only way to get down is to cut power for short periods and let if fall.  Automatic leveling in that case is very desirable.  This isn't an issue if you have the FMS set up as recommended.  In that case, just switch to Pos#1.

Tricopters are a special issue.  They may or may not tune correctly.  An assumption is made that the control delay is the same for roll pitch and yaw.  This is not true for tricopters which use a servo for yaw, but use motor thrust for roll / pitch.

If you intend to fly this copter both with and without a significant payload attached (like a camera) or with different batteries (weight, cell count) then ideally you would tune each case separately and store them in different PID banks.  Probably the easiest way to handle the simple case of with/without a camera is to tune with the camera, copy bank2 to bank3, retune without the camera and leave that in bank 2.  Then remove AutoTune from your FMS and add flight modes that include both bank 2 (without camera) and bank 3 (with camera).  Note that the lighter total weight has smaller PIDs.  Smaller PIDs will work when carrying an extra load that wasn't there when tuning (it is a bit mushy), but if you use the larger PIDs that come from tuning with a camera mounted when the camera is not mounted, you may get some minor oscillations.

It won't arm:
 It won't arm if you
- try to arm it in AutoTune mode
-
have put SystemIdent stabilization on Thrust on any FMS switch position
- use GPS Assist with AutoTune
- enable it on a vehicle that is not a multicopter

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Using SmoothQuick semi-permanently:
It isn't necessary to manually enable the AutoTune module because it will be enabled each time the FC boots with AutoTune in the FMS.

If you do enable the AutoTune module manually then it will always be running, even if there is no AutoTune flight mode or SystemIdent stabilization mode in your FMS.  In that case your SmoothQuick Accessory knob (or FMS 3x toggle) is always active to change the PIDs in the destination PID bank (default 2) and you can adjust PIDs from smooth to quick any time you need it.

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SystemIdent stabilization mode:
AutoTune is a flight mode that can directly go on the FMS.  SystemIdent is a stabilization mode that can be put in a Stabilized1-6 flight mode.  There is no reason to use SystemIdent stabilization mode.  What you will get is a mode that acts a lot like the shaking part of AutoTune, but the shakes may be bigger or smaller.  SystemIdent stabilization mode has been hidden in the GCS GUI.  It can only be enabled with settings on the System tab.

Field descriptions:
System.SystemIdentSettings are stored permanently but do not show up in logs.  DataObjects.SystemIdentState shows up in logs but is not stored permanently.  Read the source if you need to know more of the technical aspects of their fields. 

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