This part is the adapter used in front of the real ATmega328P running our Arduino software.
In the Uno R3 case, this adapter is an ATmega16U2 (16 KB) with specialized firmwares to be able to interact with the ATmega328P.
ATmega328P (UART) ↔ ATmega16U2 (USB) ↔ our computer, and this chip also facilitates flashing new programs onto the ATmega328P.

You can find information about ATmega328P on the Arduino Uno R3: Arduino Uno R3 - ATmega328P

You can find original firmwares in:

The firmware files are organized as follows:

For convenience, they are merged in: Arduino-COMBINED-dfu-usbserial-atmega16u2-Uno-Rev3.hex
Both are inspired by LUFA (Projects/USBtoSerial & Bootloaders/DFU)

The DFU firmware is inside Arduino-COMBINED-dfu-usbserial-atmega16u2-Uno-Rev3.hex
You can extract the original DFU firmware part with: srec_cat -output Arduino-dfu-atmega16u2-Uno-Rev3.hex -intel Arduino-COMBINED-dfu-usbserial-atmega16u2-Uno-Rev3.hex -intel -exclude 0x0000 0x3000
The DFU firmware alone is now located in the Arduino-dfu-atmega16u2-Uno-Rev3.hex file.

With default fuses values, the memory map for Intel HEX files is:

Start End Size Section Contents
0x000000 0x003fff 16 KB Flash (see below) User program + Bootloader
0x000000 0x002fff 12 KB Flash (Program) User program code
0x003000 0x003fff 4 KB Flash (Bootloader) Bootloader code
0x810000 0x8101ff 512 bytes EEPROM User data
0x820000 0x820002 3 bytes Fuses Low, High, and Extended fuse bits
0x830000 0x830000 1 byte Lock Bits Protection flags

You can see other values in the datasheet:

  • ATmega16U2 uses an addressing mode in words (16 bits), not bytes (8 bits): so bootloader start at 0x1800 in words… but also 0x3000 in bytes
  • EEPROM is not really @ 0x810000, as fuses or lock, but programmer softwares are using different addresses to not mix different memory areas.

Technically, an ATmega8U2 (8 KB) would have been enough: 4 KB of program code + 4 KB of bootloader code.

Building firmwares

You can build a fixed DFU firmware, and a new version of USBtoSerial thank to:

sudo apt update
sudo apt upgrade --assume-yes
sudo apt install build-essential avr-libc binutils-avr gcc-avr srecord git

git clone https://github.com/abcminiuser/lufa.git
cd lufa
git apply --whitespace=nowarn --verbose ../lufa_usbtoserial_dfu.patch
make --directory=Bootloaders/DFU
make --directory=Projects/USBtoSerial
srec_info Projects/USBtoSerial/USBtoSerial.hex -intel Bootloaders/DFU/BootloaderDFU.hex -intel

You now need an external programmer (not flip1) in order to replace bootloader (DFU), see below.

Programming

Tested with flip1 (with limitations), avrispmkII & pickit4_isp

flip1 (dfu)

Notes

The DFU mode is available by making contact between GND (6) and RESET (5) pins (then release) on the ATmega16U2 ISP connector (top right). Then flashing is available by USB - no hardware programmer needed.

      -------
 GND | 6.↔.5 | RESET
MOSI | 4. .3 | CLK
 VCC | 2. .1 | MISO
      -------

Do not use the Arduino header or the Arduino ISP connector (bottom of the board)

In DFU mode, only flash & eeprom memories are available (and the bootloader part is not writable).

Original Arduino DFU firmware is incorrect, returning an incorrect device signature to the programmer:

  • KO - avrdude - checking device signature ;
    • OK - …when ignoring bad signature with -F parameter ;
  • OK - dfu-programmer - not checking device signature ;
  • OK - Atmel Flip - not checking device signature ;
  • KO - Microchip studio - checking device signature.
> avrdude -v -c flip1 -p ATmega16U2
[...]
AVR device initialized and ready to accept instructions
Device signature = 94 00 00
Error: expected signature for ATmega16U2 is 1E 94 89
  - double check chip or use -F to carry on regardless
[...]

DFU firmware problem was fixed in 2013/2015 in the LUFA project ( https://github.com/abcminiuser/lufa ).
Bonus: TX/RX leds are now flashing to show we’re in DFU mode :)

Windows user: Atmel DFU driver can be found in Microchip Studio or FLIP, but is available here for convenience: atmel_usb_dfu_driver.zip (it’s only a libusb wrapper)

Before flashing

Make backup before any write operation: avrdude -c flip1 -p ATmega16U2 -F -U flash:r:backup_flash.hex:i
You can restore the flash by: avrdude -c flip1 -p ATmega16U2 -F -U flash:w:backup_flash.hex:i

Flash

As bootloader part is not writable in DFU mode, you can only flash the firmware part usbserial inside the chip (by forcing using -F parameter when using original bootloader):

> avrdude -v -c flip1 -p ATmega16U2 -F -U flash:w:Arduino-usbserial-atmega16u2-Uno-Rev3.hex:i
[...]
AVR device initialized and ready to accept instructions
Device signature = 94 00 00
Warning: expected signature for ATmega16U2 is 1E 94 89
Auto-erasing chip as flash memory needs programming (-U flash:w:...)
specify the -D option to disable this feature
Erased chip
Reading 4034 bytes for flash from input file Arduino-usbserial-atmega16u2-Uno-Rev3.hex
in 1 section [0, 0xfc1]: 32 pages and 62 pad bytes
Writing 4034 bytes to flash
Writing | ################################################## | 100% 0.31 s
Reading | ################################################## | 100% 0.04 s
4034 bytes of flash verified
[...]

When using fixed bootloader:

> avrdude -v -c flip1 -p ATmega16U2 -U flash:w:USBtoSerial.hex:i
[...]
AVR device initialized and ready to accept instructions
Device signature = 1E 94 89 (ATmega16U2)
Auto-erasing chip as flash memory needs programming (-U flash:w:...)
specify the -D option to disable this feature
Erased chip
Reading 3968 bytes for flash from input file USBtoSerial.hex
in 1 section [0, 0xf7f]: 31 pages and 0 pad bytes
Writing 3968 bytes to flash
Writing | ################################################## | 100% 0.31 s
Reading | ################################################## | 100% 0.05 s
3968 bytes of flash verified
[...]

pickit4_isp or avrispmkII

Notes

When using a hardware programmer, connect it to the ATmega16U2 ISP connector (located at the top right)

      -----
 GND |6. .5| RESET
MOSI |4. .3| CLK
 VCC |2. .1| MISO
      -----

When using a programmer, you can interact with fuses, lock, eeprom, and bootloader part of flash

When using pickit4, you may need to switch mode to avr: avrdude -c pickit4_isp -p ATmega16U2 -x mode=avr (-x mode=pic to switch back)

Original fuses

Fuse Name Value
LOW 0xef
HIGH 0xd9
EXTENDED 0xf4
LOCK 0xcf
  • Bootloader 2048 words (4 KB when in bytes), @ 0x1800 (0x3000 when in bytes)
  • LPM and SPM prohibited in Boot Section

You can check them with:

  • version < 8.0: avrdude -c pickit4_isp -p ATmega16U2 -U lfuse:r:-:h -U hfuse:r:-:h -U efuse:r:-:h -U lock:r:-:h
  • version >= 8.0: avrdude -c pickit4_isp -p ATmega16U2 -U lfuse,hfuse,efuse,lock:r:-:h

Check connection

> avrdude -c pickit4_isp -p ATmega16U2 -v
[...]
Using port            : usb
Using programmer      : pickit4_isp
AVR part              : ATmega16U2
Programming modes     : SPM, ISP, HVPP, debugWIRE
Programmer type       : JTAG3_ISP
Description           : MPLAB(R) PICkit 4 in ISP mode
ICE HW version        : 6
ICE FW version        : 1.15 (rel. 20)
Serial number         : BUR222474515
Vtarget               : 0.0 V
SCK period            : 8.0 us
Vtarget               : 5.01 V

AVR device initialized and ready to accept instructions
Device signature = 1E 94 89 (ATmega16U2)
[...]

Before flashing

Make backup before any write operation: avrdude -c pickit4_isp -p ATmega16U2 -U flash:r:backup_flash.hex:i
You can restore the flash by: avrdude -c pickit4_isp -p ATmega16U2 -e -U flash:w:backup_flash.hex:i

The -e will erase the eeprom too (if previous fuses values were wrong, it may be not erased, feel free to check with: avrdude -c pickit4_isp -p ATmega16U2 -U eeprom:r:-:h before trying again)

Flash original firmware

even if the original DFU firmware part isn’t perfect, it’s enough to have something working

avrdude -c pickit4_isp -p ATmega16U2 -e -U flash:w:Arduino-COMBINED-dfu-usbserial-atmega16u2-Uno-Rev3.hex:i -U lfuse:w:0xef:m -U hfuse:w:0xd9:m -U efuse:w:0xf4:m -U lock:w:0xcf:m

or with all combined (avrdude version >= 8.0):

avrdude -c pickit4_isp -p ATmega16U2 -e -U flash,lfuse,hfuse,efuse,lock:w:Arduino-COMBINED-dfu-usbserial-atmega16u2-Uno-Rev3_fuses_lock.hex:i

You can produce this combined file with fuses & lock with:

srec_cat -output Arduino-COMBINED-dfu-usbserial-atmega16u2-Uno-Rev3_fuses_lock.hex -intel ^
  Arduino-COMBINED-dfu-usbserial-atmega16u2-Uno-Rev3.hex -intel ^
  -generate 0x820000 0x820003 -repeat_data 0xef 0xd9 0xf4 ^
  -generate 0x830000 0x830001 -constant 0xcf

You can add -generate 0x810000 0x810200 -constant 0xff ^ before the first -generate if you really want the EEPROM data (normally erased when programming)

Flash fixed firmware

Files: USBtoSerial.hex & BootloaderDFU.hex

avrdude -c pickit4_isp -p ATmega16U2 -e -U flash:w:USBtoSerial.hex:i -U flash:w:BootloaderDFU.hex:i -U lfuse:w:0xef:m -U hfuse:w:0xd9:m -U efuse:w:0xf4:m -U lock:w:0xcf:m

or with all combined (avrdude version >= 8.0):

File: usbserial-bootloaderdfu_fuses_lock.hex

avrdude -c pickit4_isp -p ATmega16U2 -e -U flash,lfuse,hfuse,efuse,lock:w:usbserial-bootloaderdfu_fuses_lock.hex:i

You can produce this combined file with fuses & lock with:

srec_cat -output usbserial-bootloaderdfu_fuses_lock.hex -intel ^
  USBtoSerial.hex -intel ^
  BootloaderDFU.hex -intel ^
  -generate 0x820000 0x820003 -repeat_data 0xef 0xd9 0xf4 ^
  -generate 0x830000 0x830001 -constant 0xcf

You can add -generate 0x810000 0x810200 -constant 0xff ^ before the first -generate if you really want the EEPROM data (normally erased when programming)

Atmel original DFU

if you don’t want to use the LUFA one…

I don’t have any untouched ATmega16U2 (aka not related to Arduino), so I’m unable to dump (if any?) original bootloader from it.
It seems you can find older/other ones in: https://ww1.microchip.com/downloads/aemDocuments/documents/OTH/ProductDocuments/SoftwareLibraries/Firmware/megaUSB_DFU_Bootloaders.zip

Unfortunately, no ATmega16U2 inside, but a at90usb162-bl-usb-1_0_5.hex for a AT90USB162.
As the ATmega16U2 is an optimized version of the AT90USB162, we can use this bootloader as-is with various programmer software (including avrdude by forcing).

For convenience, I patched (PID & Product) it to create a new atmega16u2-bl-usb-1_0_5.hex, the result is:

> avrdude -c flip1 -p ATmega16U2 -v
[...]
Using port            : usb
Using programmer      : flip1
AVR part              : ATmega16U2
Programming modes     : SPM, ISP, HVPP, debugWIRE
Programmer type       : flip1
Description           : FLIP bootloader using USB DFU v1 (doc7618)
    USB Vendor          : ATMEL (0x03EB)
    USB Product         : ATmega16U2 DFU (0x2FEF)
    USB Release         : 0.0.0
    USB Serial No       : 1.0.5
    USB max packet size : 32

AVR device initialized and ready to accept instructions
Device signature = 1E 94 89 (ATmega16U2)

References

ATmega / Microchip

Arduino

SRecord

LUFA

Programmers

Hardware

Software