By default, the FluxEngine client assumes you have a PC 80 track double sided high density drive, either 3.5" or 5.25", as these are the most common. This may not be the case, and you need to tell the FluxEngine client what kind of drive you have.
Forty-track drives have the same geometry as eighty-track drives, but have a head that is twice as big, so halving the number of tracks on the disk. Examples of forty track drives include the Commodore 1541, IBM 360kB, or the Brother 120kB format (which uses a rare 3.5" single-sided forty-track drive).
When a forty-track disk is inserted into an eighty-track drive, then each head position will only see half of each track. For reading this isn't a problem --- FluxEngine will actually read both halves and combine the results --- but writing is more problematic. Traditionally, if you wanted to write a forty-track disk in an eighty-track drive, you had to use a brand new disk; the drive would write to one half of the track, leaving the other half blank. If both halves contained data, then the wider head on a forty track drive would pick both up, producing a garbled result. This led to a very confusing situation where forty-track disks written on an eighty-track drive would read and write fine on an eight-track drive but wouldn't work at all on a forty-track drive.
FluxEngine is capable of both reading and writing forty-track formats on an eighty-track drive. It avoids the situation described above by writing one half of the track and then magnetically erasing the other half. This does produce a weaker signal on the disk, but in my testing the disks work just fine in forty-track drives.
If you actually have a forty track drive, you need to tell FluxEngine. This is
done by adding the special profile 40track_drive:
fluxengine write ibm --360 40track_drive -i image.img -d drive:0
It should then Just Work. This is supported by both FluxEngine and Greaseweazle hardware.
Obviously you can't write an eighty-track format using a forty-track drive!
The Apple II had special drives which supported microstepping: when commanded to move the head, then instead of moving in single-track steps as is done in most other drives, the Apple II drive would move in quarter-track steps. This allowed much less precise head alignment, as small errors could be corrected in software. (The Brother word processor drives were similar.) The bus interface is different from normal PC drives.
The FluxEngine client supports these with the apple2_drive profile:
fluxengine write apple2 apple2_drive -i image.img -d drive:0
This is supported only by Greaseweazle hardware.
PC drives have a standard interface which doesn't really have a name but is commonly referred to as 'the PC 34-pin interface'. There are a few other interfaces, most notably the Shugart standard. This is also 34 pin and is very similar to the PC interface but isn't quite electrically compatible. It supports up to four drives on a bus, unlike the PC interface's two drives, but the drives must be jumpered to configure them. This was mostly used by older 3.5" drives, such as those on the Atari ST. the How It Works page for the pinout.
The FluxEngine client supports these with the shugart_drive profile:
fluxengine write atarist720 shugart_drive -i image.img -d drive:0
(If you have a 40-track Shugart drive, use both shugart_drive and
40track_drive.)
This is supported only by Greaseweazle hardware.