_Problem_

The LED does not blink as expected when programmed by the Arduino IDE. Only programming with Atmel Studio 6/7 works. Best guess, modified Arduino bootloader and sketch startup code are required to accommodate the lack of a discrete timing crystal. Reconfiguration of USB clocking source may also prove necessary. This explanation is consitent with all observed behavior, including the SODAQ bootloader functionality, as well as subsequent lack of sketch functionality.

Schematic provided as ATSAMD21J18_Minimal_Schematic.pdf. Atmel Studio example "LED_TOGGLE1/Debug/LED_TOGGLE1.hex" works, uploaded by SAM-ICE. Arduino example "sketch/Release/sketch.elf" should, but does not, work, regardless of upload method.

Arduino has substantial community-written libraries, and is an open-source solution. If we can make this particular chip, ATSAMD21J18, work with the Arduino IDE, functionality beyond Arduino Mega will be available as a single $6 chip. Notable functionality includes 48MHz clock, 32bit math, 256kB ROM, extensively reconfigurable SERCOM interfaces, fast analog IO, onboard clocks, and minimal PCB requirements.


_Development_

https://github.com/mirage335/ArduinoCore-samd

arduino/ArduinoCore-samd#157


_Debugging Procedure_

1) Created working LED toggle firmware in Atmel Studio 6, based on "port_pin_toggle_output_level(LED_0_PIN);".
2) Installed SAM-BA bootloader from Atmel, device became visible to 'lsusb' command under Linix/UNIX.
3) Uploaded essentially empty Arduino sketch successfully.
4) Carefully worked out and understood Arduino/ARM/SAM pin mapping and port manipulation functions.
5) Configured an example sketch to blink LED connected to PB07.
6) Successfully uploaded. No effect.
7) Successively added println statements, attempted to toggle other LEDs. No result.
8) Uploaded Arduino Zero bootloader. Not visible to 'lsusb'.
9) Compared Autonomo bootloader to offical Arduino Zero bootloader. No difference. Uploaded anyway. Not visible to 'lsusb'.
10) Uploaded Atmel SAM-BA bootloader, copied resultant fuse settings. Uploaded Autonomo bootloader. Set fuse settings copied down earlier, noticed some differences. Still not visible to 'lsusb'. Cannot upload Arduino code.
11) Uploaded Arduino blink sketch ".hex" file directly through Atmel Studio. Still, no LEDs light up.
12) Restored original Atmel Studio 6 LED blink code. Now, that does not work either!
13) Frustration. Uploaded Atmel SAM-BA bootloader. At least shows up through 'lsusb'.
14) After repeatedly switching firmwares, checking fuses, and finally loading an old precompiled '*.hex" file from the Atmel Studio file project, original LED blink works again.
15) Uploaded Atmel SAM-BA bootloader. Then rebuilt and executed original LED blink project, still using SAM-ICE. Still works.
16) Built and uploaded LED blink Arduino Zero sketch with Atmel Studio 7, through "Native USB Port", having uploaded SAM-BA bootloader. Connected to serial port. No data or debugging information.
17) Stripped out pin toggle code from sketch, leaving just Serial/SerialUSB statements. Still, no data received.

18) Uploaded Arduino Zero bootloader to an "Arduino M0" board. Uploaded sketch with "Arduino.cc" IDE. Still, no data received.
19) Essentially restored "Arduino M0" firmware. Uploaded sketch with "Arduino.org" IDE. Still, no data received. Sketch itself now considered highly suspect.
20) After adding obvious "Serial.begin", Arduino M0 sketch works exactly as expected, with port manipulation.
21) With same modification, success is achieved by uploaded Arduino Zero bootloader to an "Arduino M0" board, then uploading sketch with "Arduino.cc" IDE. Blinking LED and serial data are working normally.

22) Returned to original hardware.
23) Uploaded Arduino Zero bootloader. Non-functional, no USB presence.
24) Uploaded Atmel SAM-BA bootloaders.
25) Uploaded corrected sketch through Arduino IDE integrated under Atmel Studio 7, through USB, just like an Arduino Zero. Still, no data received.

26) Compiled Arduino Zero bootloader for ATSMD21J18A target, uploaded, debugged, with Atmel Studio 7. Again, does not present a USB interface, although the debugger shows code is running.

27) Once again, tried uploading the sketch code through SAM-ICE programmer, without any results. This is strange, considering such an approach usually worked well with the AVR based ATMega32U4.
28) Uploaded working sketch directly to "Arduino M0" through SAM-ICE programmer, using Arduino IDE integrated into Atmel Studio 7. Failure and loss of USB presence contradicts success on the forums.
29) Reaffirmed operation of "Arduino M0" through Arduino Zero IDE and bootloader through Atmel Studio 7 integration. Notably, power cycling or reset button press was occasionally necessary to start the sketch.
30) Reaffirmed directly uploading sketch hex file with SAM-ICE to "Arduino M0" does not work.

31) Reaffirmed directly uploading sketch to original ATSAMD21J hardware does not work.

32) Uploaded SODAQ bootloader, USB presence detected as Arduino SA device, as normal for Arduino Zero bootloader.
33) Uploaded sketch directly from Arduino IDE through SODAQ bootloader. Lost USB presence, non-functional.
34) Retried same procdure using SODAQ Autonomo board definition. Same result.

35) Clock mechanism is apparently discovered to be set by both bootloader and sketch, as documented at https://forum.arduino.cc/index.php?topic=331052.0 . Correctly configuring the clock in both cases is now a high priority.

36) Bootloader from SODAQ found to use OSC8M, as shown at https://github.com/SodaqMoja/SodaqCore-samd/blob/autonomo/bootloaders/zero/main.c#L58 . This explains why that bootloader works, then fails upon loading an Arduino sketch, which even for the SODAQ boards, is configured to rely on an external 32kHz crystal.

37) Replaced references to XOSC32K with OSC32K, and removed XTALEN bit, in Arduino Zero bootloader board_init.c . Subsequently crashes during either Serial or USB init .
38) Attempted to run modified Arduino Zero bootloader code on real "Arduino M0". Same result.
39) Attempted to modify board_init.c to pass clock to an output pin for diagnosis. Unsuccessful pin muxing code placed in repository.

_Sketch_


#define PORT_GROUP PORTB
#define PORT_NUMBER 7

volatile uint32_t *setPin = &PORT->Group[PORT_GROUP].OUTSET.reg;  // Ptr to PortA Data Output Value Set register
volatile uint32_t *clrPin = &PORT->Group[PORT_GROUP].OUTCLR.reg;  // Ptr to PortA Data Output Value Clear register
volatile uint32_t *dirPin = &PORT->Group[PORT_GROUP].DIRSET.reg;  // Ptr to PortA Data Direction Set register

const uint32_t  PinMASK = (1ul << PORT_NUMBER);   // Generate bit mask, binary one PORT_NUMBER places to the left

// the setup function runs once when you press reset or power the board
void setup()
{
  Serial.begin(115200);
  
  // initialize digital pin as an output.
  *dirPin = PinMASK;
}

// the loop function runs over and over again forever
void loop()
{
  *setPin = PinMASK;        // turn the LED on (HIGH is the voltage level)
  delay(250);              // wait for a second
  *clrPin = PinMASK;        // turn the LED off by making the voltage LOW
  delay(250);              // wait for a second
  SerialUSB.println("cycle");
  Serial.println("cycle");
}


_PIN_

Pin numbers are enumerated by an array in local code.
~/.arduino15/packages/arduino/hardware/samd/1.6.4/variants/arduino_zero

Position in the g_APinDescription array is the pin number. For example, for the Arduino Zero, the first entry is pin 0, and corresponds to PA11 as described in the Atmel datasheet.
//{ PORTA, 11, PIO_SERCOM, (PIN_ATTR_DIGITAL), No_ADC_Channel, NOT_ON_PWM, NOT_ON_TIMER, EXTERNAL_INT_11 }, // RX: SERCOM0/PAD[3]
References for the arduino pinout confirm this first pin, index 0, is indeed used as an RX pin, and indeed connected to chip pin labeled PA11.


_PORT_

Read/write pin code, including digitalWrite(), is defined in local code.
~/.arduino15/packages/arduino/hardware/samd/1.6.4/cores/arduino

For writing a digital pin, the digitalWrite() function ultimately relys on one line to actually set the pin high.
//PORT->Group[g_APinDescription[ulPin].ulPort].OUTSET.reg = (1ul << g_APinDescription[ulPin].ulPin) ;

From here, some basic substitutions are illuminating.
PORT->Group[g_APinDescription[ulPin].ulPort].OUTSET.reg = (1ul << g_APinDescription[ulPin].ulPin) ;
PORT->Group[g_APinDescription[0].ulPort].OUTSET.reg = (1ul << g_APinDescription[ulPin].ulPin) ;
PORT->Group[PORTA].OUTSET.reg = (1ul << g_APinDescription[ulPin].ulPin) ;

PORT->Group[PORTA].OUTSET.reg = (1ul << g_APinDescription[ulPin].ulPin) ;
PORT->Group[PORTA].OUTSET.reg = (1ul << g_APinDescription[0].ulPin) ;
PORT->Group[PORTA].OUTSET.reg = (1ul << 11) ;	//Assuming the second ulPin refers to hardware port/pin designator PA11.

These substitutions are confirmed by a post on arduino forums - https://forum.arduino.cc/index.php?topic=334073.0 .

//volatile uint32_t *setPin = &PORT->Group[g_APinDescription[PIN].ulPort].OUTSET.reg;
//const uint32_t  PinMASK = (1ul << g_APinDescription[PIN].ulPin);
//*setPin = PinMASK;

//volatile uint32_t *setPin = &PORT->Group[PORTA].OUTSET.reg;
//const uint32_t  PinMASK = (1ul << 11);
//*setPin = PinMASK;


See Atmel datasheet, and arduino forums - https://forum.arduino.cc/index.php?topic=334073.0 .

-Example-

//From https://forum.arduino.cc/index.php?topic=334073.0 .

#include <Arduino.h>

#define PIN 10

#ifdef _VARIANT_ARDUINO_ZERO_
volatile uint32_t *setPin = &PORT->Group[g_APinDescription[PIN].ulPort].OUTSET.reg;
volatile uint32_t *clrPin = &PORT->Group[g_APinDescription[PIN].ulPort].OUTCLR.reg;

const uint32_t  PinMASK = (1ul << g_APinDescription[PIN].ulPin);
#endif

void setup() {
  pinMode(PIN, OUTPUT);
}

void loop() {
  while(1) {
#ifdef _VARIANT_ARDUINO_ZERO_
  *setPin = PinMASK;
  *clrPin = PinMASK;
#else
    digitalWrite(PIN, HIGH);
    digitalWrite(PIN, LOW);
#endif
  }
}

-Example-
#define PORT_NUMBER 17    // Digital pin 13 is port pin PA17

volatile uint32_t *setPin = &PORT->Group[PORTA].OUTSET.reg;  // Ptr to PortA Data Output Value Set register
volatile uint32_t *clrPin = &PORT->Group[PORTA].OUTCLR.reg;  // Ptr to PortA Data Output Value Clear register
volatile uint32_t *dirPin = &PORT->Group[PORTA].DIRSET.reg;  // Ptr to PortA Data Direction Set register

const uint32_t  PinMASK = (1ul << PORT_NUMBER);   // Generate bit mask, binary one 17 places to the left

// the setup function runs once when you press reset or power the board
void setup()
{
  // initialize digital pin 13 (PA17) as an output.
  *dirPin = PinMASK;
}

// the loop function runs over and over again forever
void loop()
{
  *setPin = PinMASK;        // turn the LED on (HIGH is the voltage level)
  delay(1000);              // wait for a second
  *clrPin = PinMASK;        // turn the LED off by making the voltage LOW
  delay(1000);              // wait for a second
}

_SERCOM_
//SPIClass SPI1 (&sercom1, 12, 13, 11, SPI_PAD_0_SCK_1, SERCOM_RX_PAD_3);

As documented by https://learn.adafruit.com/using-atsamd21-sercom-to-add-more-spi-i2c-serial-ports/creating-a-new-spi .

_Reset_
Double-tap on a reset pin immediately after startup may be necessary to re-enter bootloader in case of bad code locking up the MCU.

_Bootloader_
As described by the Femtoduino USB GitHub readme, after the relevant bootloader hex file has been extracted, it can be flashed through the following GUI sequence.
Atmel Studio 6 --> Tools --> Device Programmer --> Memories

Assert "Erase Flash before programming" and "Verify Flash after programming" before clicking "Program".

The "SAM-BA Bootloader for SAM D21", "Application Note", also mentions this process, along with a file AT07175.zip, containing the necessary HEX files. This package is available under a different name, from the Atmel website, under the SAMD21J18 documents list.

This procedure ultimately proved successful.

Autonomo is apparently a SAMD21J18 based Arduino Zero clone, with Arduino support. Apparently, it ships with an identical bootloader to the actual Arduino Zero, despite using a slightly different chip. Strangely though, unlike the official Atmel SAM-BA bootloader, neither this nor the Arduino Zero bootloader result in any USB functionality as seen by 'lsusb', virtual serial port, or attempted sketch upload. Setting fuses to those set along with Atmel SAM-BA bootloader programming did not bring USB functionality online with Arduino/Autonomo bootloader.

_Connectivity_
SAM-BA bootloader explictly states PA25/PA24 must be connected to USB D+/D-. Sparkfun breakout for similar chip also meets this specification. Arduino zero schematic for another similar chip also meets this specification.

_Clock_
Some SAMD21 breakoutboards seem to include a dedicated crystal oscillator. Since the SAMD21J18 includes a "high-accuracy" RTC clock internally, this is not desired.

_Factory_
As stated in the "SAM-BA Bootloader for SAM D21", "Application Note", these chips are NOT factory programmed with the SAM-BA bootloader.

_Datasheet_
ATSAMD21J18/ATSAMD21G18 - https://cdn.sparkfun.com/datasheets/Dev/Arduino/Boards/Atmel-42181-SAM-D21_Datasheet.pdf

_Comparable_
SparkFun SAMD21 Breakout - https://github.com/sparkfun/SAMD21_Dev_Breakout
SparkFun SAMD21 Breakout Design/Firmware - https://github.com/sparkfun/SAMD21_Dev_Breakout

Arduino Zero - https://www.arduino.cc/en/Main/ArduinoBoardZero
Arduino Zero Cores/Bootloaders - https://github.com/arduino/ArduinoCore-samd

Atmel SAMD21J18 SAM-BA Bootloader - http://www.atmel.com/images/Atmel-42366-SAM-BA-Bootloader-for-SAM-D21_ApplicationNote_AT07175.zip

SAMD21J YouTube Video - https://www.youtube.com/watch?v=HE9Wrq-Gvrc
SAMD21J Forum Topic - https://forum.arduino.cc/index.php?topic=359757.0

SODAQ - https://github.com/SodaqMoja/SodaqCore-samd/tree/autonomo/bootloaders/zero

_Reference_
https://hackaday.io/project/6276-arduino-zero-sam-d20d21-breakout-board
https://www.sparkfun.com/products/13672
https://github.com/sparkfun/SAMD21_Dev_Breakout/tree/master/Firmware
https://github.com/femtoduino/femto-usb

https://github.com/arduino/ArduinoCore-samd/tree/master/bootloaders/zero
https://github.com/arduino/ArduinoCore-samd

arduino/ArduinoCore-samd#7

https://forum.arduino.cc/index.php?topic=382407.0

https://hackaday.io/project/7996-mini-sam

https://hackaday.io/project/6062-jack

https://learn.adafruit.com/using-atsamd21-sercom-to-add-more-spi-i2c-serial-ports/muxing-it-up

https://learn.adafruit.com/using-atsamd21-sercom-to-add-more-spi-i2c-serial-ports/creating-a-new-spi

https://github.com/arduino/ArduinoCore-samd

https://github.com/OpenROV/openrov-arduino-cores

http://forum.arduino.cc/index.php?topic=129868.15

https://hackaday.io/project/7576-sam-dev

https://forum.arduino.cc/index.php?topic=334073.0

https://cdn-learn.adafruit.com/assets/assets/000/030/929/medium800/adafruit_products_2995_pinout_v1_0.png?1457306311

http://forum.sodaq.com/t/use-arduino-ide-1-6-6-for-autonomo/25
http://downloads.sodaq.net/package_sodaq_index.json

https://www.youtube.com/watch?v=HE9Wrq-Gvrc

http://forum.arduino.cc/index.php?topic=413400.0


https://forum.arduino.cc/index.php?topic=331052.0

http://community.atmel.com/forum/samd21-example-general-clock-output-gclkio
http://community.atmel.com/comment/1856736#comment-1856736


https://github.com/RIOT-OS/RIOT/commit/164721657dd74d355427418d85d47abfdd8b9637

http://atmel.force.com/support/articles/en_US/FAQ/How-to-configure-DFLL48M-oscillator-as-main-clock-in-ASF-project-for-SAMR21-SAMD21-SAMD20-SAMD10-SAMD11

http://forum.arduino.cc/index.php?topic=342697.5;imode