¿Cómo configurar Atmel SAM D20 para la fuente de reloj interna de 48MHz?

La secuencia correcta para ejecutar un Atmel SAM D20 a 48MHz, sin oscilador externo y solo usando el DFLL48M y el OSC8M se muestra en el ejemplo de código a continuación.

void initializeSystemFor48MHz()
{
    // Change the timing of the NVM access 
    NVMCTRL->CTRLB.bit.RWS = NVMCTRL_CTRLB_RWS_HALF_Val; // 1 wait state for operating at 2.7-3.3V at 48MHz.

    // Enable the bus clock for the clock system.
    PM->APBAMASK.bit.GCLK_ = true;

    // Initialise the DFLL to run in closed-loop mode at 48MHz
    // 1. Make a software reset of the clock system.
    GCLK->CTRL.bit.SWRST = true;
    while (GCLK->CTRL.bit.SWRST && GCLK->STATUS.bit.SYNCBUSY) {};
    // 2. Make sure the OCM8M keeps running.
    SYSCTRL->OSC8M.bit.ONDEMAND = 0;
    // 3. Set the division factor to 64, which reduces the 1MHz source to 15.625kHz
    GCLK->GENDIV.reg =
        GCLK_GENDIV_ID(3) | // Select generator 3
        GCLK_GENDIV_DIV(64); // Set the division factor to 64
    // 4. Create generic clock generator 3 for the 15KHz signal of the DFLL
    GCLK->GENCTRL.reg =
        GCLK_GENCTRL_ID(3) | // Select generator 3
        GCLK_GENCTRL_SRC_OSC8M | // Select source OSC8M
        GCLK_GENCTRL_GENEN; // Enable this generic clock generator
    while (GCLK->STATUS.bit.SYNCBUSY) {}; // Wait for synchronization
    // 5. Configure DFLL with the
    GCLK->CLKCTRL.reg =
        GCLK_CLKCTRL_ID_DFLL48M | // Target is DFLL48M
        GCLK_CLKCTRL_GEN(3) | // Select generator 3 as source.
        GCLK_CLKCTRL_CLKEN; // Enable the DFLL48M
    while (GCLK->STATUS.bit.SYNCBUSY) {}; // Wait for synchronization
    // 6. Workaround to be able to configure the DFLL.
    SYSCTRL->DFLLCTRL.bit.ONDEMAND = false;
    while (!SYSCTRL->PCLKSR.bit.DFLLRDY) {}; // Wait for synchronization.
    // 7. Change the multiplication factor. 
    SYSCTRL->DFLLMUL.bit.MUL = 3072; // 48MHz / (1MHz / 64)
    SYSCTRL->DFLLMUL.bit.CSTEP = 1; // Coarse step = 1
    SYSCTRL->DFLLMUL.bit.FSTEP = 1; // Fine step = 1
    while (!SYSCTRL->PCLKSR.bit.DFLLRDY) {}; // Wait for synchronization.
    // 8. Start closed-loop mode
    SYSCTRL->DFLLCTRL.reg |=
        SYSCTRL_DFLLCTRL_MODE | // 1 = Closed loop mode.
        SYSCTRL_DFLLCTRL_QLDIS; // 1 = Disable quick lock.
    while (!SYSCTRL->PCLKSR.bit.DFLLRDY) {}; // Wait for synchronization.
    // 9. Clear the lock flags.
    SYSCTRL->INTFLAG.bit.DFLLLCKC = 1;
    SYSCTRL->INTFLAG.bit.DFLLLCKF = 1;
    SYSCTRL->INTFLAG.bit.DFLLRDY = 1;
    // 10. Enable the DFLL
    SYSCTRL->DFLLCTRL.bit.ENABLE = true;
    while (!SYSCTRL->PCLKSR.bit.DFLLRDY) {}; // Wait for synchronization.
    // 11. Wait for the fine and coarse locks.
    while (!SYSCTRL->INTFLAG.bit.DFLLLCKC && !SYSCTRL->INTFLAG.bit.DFLLLCKF) {};
    // 12. Wait until the DFLL is ready.
    while (!SYSCTRL->INTFLAG.bit.DFLLRDY) {};  

    // Switch the main clock speed.
    // 1. Set the divisor of generic clock 0 to 0
    GCLK->GENDIV.reg =
        GCLK_GENDIV_ID(0) | // Select generator 0
        GCLK_GENDIV_DIV(0);
    while (GCLK->STATUS.bit.SYNCBUSY) {}; // Wait for synchronization       
    // 2. Switch generic clock 0 to the DFLL
    GCLK->GENCTRL.reg =
        GCLK_GENCTRL_ID(0) | // Select generator 0
        GCLK_GENCTRL_SRC_DFLL48M | // Select source DFLL
        GCLK_GENCTRL_IDC | // Set improved duty cycle 50/50
        GCLK_GENCTRL_GENEN; // Enable this generic clock generator
    while (GCLK->STATUS.bit.SYNCBUSY) {}; // Wait for synchronization
}

Este es el código C ++ para Atmel Studio. Solo requiere la inclusión de "sam.h" y nada más.

Aquí está el código de inicio del entorno de desarrollo Arduino para Arduino Zero, que se basa en el SAMD21G18. Debería ser lo suficientemente similar

/**
 * \brief SystemInit() configures the needed clocks and according Flash Read Wait States.
 * At reset:
 * - OSC8M clock source is enabled with a divider by 8 (1MHz).
 * - Generic Clock Generator 0 (GCLKMAIN) is using OSC8M as source.
 * We need to:
 * 1) Enable XOSC32K clock (External on-board 32.768Hz oscillator), will be used as DFLL48M reference.
 * 2) Put XOSC32K as source of Generic Clock Generator 1
 * 3) Put Generic Clock Generator 1 as source for Generic Clock Multiplexer 0 (DFLL48M reference)
 * 4) Enable DFLL48M clock
 * 5) Switch Generic Clock Generator 0 to DFLL48M. CPU will run at 48MHz.
 * 6) Modify PRESCaler value of OSCM to have 8MHz
 * 7) Put OSC8M as source for Generic Clock Generator 3
 */
// Constants for Clock generators
#define GENERIC_CLOCK_GENERATOR_MAIN      (0u)
#define GENERIC_CLOCK_GENERATOR_XOSC32K   (1u)
#define GENERIC_CLOCK_GENERATOR_OSCULP32K (2u) /* Initialized at reset for WDT */
#define GENERIC_CLOCK_GENERATOR_OSC8M     (3u)
// Constants for Clock multiplexers
#define GENERIC_CLOCK_MULTIPLEXER_DFLL48M (0u)

void SystemInit( void )
{
  /* Set 1 Flash Wait State for 48MHz, cf tables 20.9 and 35.27 in SAMD21 Datasheet */
  NVMCTRL->CTRLB.bit.RWS = NVMCTRL_CTRLB_RWS_HALF_Val ;

  /* Turn on the digital interface clock */
  PM->APBAMASK.reg |= PM_APBAMASK_GCLK ;

  /* ----------------------------------------------------------------------------------------------
   * 1) Enable XOSC32K clock (External on-board 32.768Hz oscillator)
   */
  SYSCTRL->XOSC32K.reg = SYSCTRL_XOSC32K_STARTUP( 0x6u ) | /* cf table 15.10 of product datasheet in chapter 15.8.6 */
                         SYSCTRL_XOSC32K_XTALEN | SYSCTRL_XOSC32K_EN32K ;
  SYSCTRL->XOSC32K.bit.ENABLE = 1 ; /* separate call, as described in chapter 15.6.3 */

  while ( (SYSCTRL->PCLKSR.reg & SYSCTRL_PCLKSR_XOSC32KRDY) == 0 )
  {
    /* Wait for oscillator stabilization */
  }

  /* Software reset the module to ensure it is re-initialized correctly */
  /* Note: Due to synchronization, there is a delay from writing CTRL.SWRST until the reset is complete.
   * CTRL.SWRST and STATUS.SYNCBUSY will both be cleared when the reset is complete, as described in chapter 13.8.1
   */
  GCLK->CTRL.reg = GCLK_CTRL_SWRST ;

  while ( (GCLK->CTRL.reg & GCLK_CTRL_SWRST) && (GCLK->STATUS.reg & GCLK_STATUS_SYNCBUSY) )
  {
    /* Wait for reset to complete */
  }

  /* ----------------------------------------------------------------------------------------------
   * 2) Put XOSC32K as source of Generic Clock Generator 1
   */
  GCLK->GENDIV.reg = GCLK_GENDIV_ID( GENERIC_CLOCK_GENERATOR_XOSC32K ) ; // Generic Clock Generator 1

  while ( GCLK->STATUS.reg & GCLK_STATUS_SYNCBUSY )
  {
    /* Wait for synchronization */
  }

  /* Write Generic Clock Generator 1 configuration */
  GCLK->GENCTRL.reg = GCLK_GENCTRL_ID( GENERIC_CLOCK_GENERATOR_XOSC32K ) | // Generic Clock Generator 1
                      GCLK_GENCTRL_SRC_XOSC32K | // Selected source is External 32KHz Oscillator
//                      GCLK_GENCTRL_OE | // Output clock to a pin for tests
                      GCLK_GENCTRL_GENEN ;

  while ( GCLK->STATUS.reg & GCLK_STATUS_SYNCBUSY )
  {
    /* Wait for synchronization */
  }

  /* ----------------------------------------------------------------------------------------------
   * 3) Put Generic Clock Generator 1 as source for Generic Clock Multiplexer 0 (DFLL48M reference)
   */
  GCLK->CLKCTRL.reg = GCLK_CLKCTRL_ID( GENERIC_CLOCK_MULTIPLEXER_DFLL48M ) | // Generic Clock Multiplexer 0
                      GCLK_CLKCTRL_GEN_GCLK1 | // Generic Clock Generator 1 is source
                      GCLK_CLKCTRL_CLKEN ;

  while ( GCLK->STATUS.reg & GCLK_STATUS_SYNCBUSY )
  {
    /* Wait for synchronization */
  }

  /* ----------------------------------------------------------------------------------------------
   * 4) Enable DFLL48M clock
   */

  /* DFLL Configuration in Closed Loop mode, cf product datasheet chapter 15.6.7.1 - Closed-Loop Operation */

  /* Remove the OnDemand mode, Bug http://avr32.icgroup.norway.atmel.com/bugzilla/show_bug.cgi?id=9905 */
  SYSCTRL->DFLLCTRL.bit.ONDEMAND = 0 ;

  while ( (SYSCTRL->PCLKSR.reg & SYSCTRL_PCLKSR_DFLLRDY) == 0 )
  {
    /* Wait for synchronization */
  }

  SYSCTRL->DFLLMUL.reg = SYSCTRL_DFLLMUL_CSTEP( 31 ) | // Coarse step is 31, half of the max value
                         SYSCTRL_DFLLMUL_FSTEP( 511 ) | // Fine step is 511, half of the max value
                         SYSCTRL_DFLLMUL_MUL( (VARIANT_MCK/VARIANT_MAINOSC) ) ; // External 32KHz is the reference

  while ( (SYSCTRL->PCLKSR.reg & SYSCTRL_PCLKSR_DFLLRDY) == 0 )
  {
    /* Wait for synchronization */
  }

  /* Write full configuration to DFLL control register */
  SYSCTRL->DFLLCTRL.reg |= SYSCTRL_DFLLCTRL_MODE | /* Enable the closed loop mode */
                           SYSCTRL_DFLLCTRL_WAITLOCK |
                           SYSCTRL_DFLLCTRL_QLDIS ; /* Disable Quick lock */

  while ( (SYSCTRL->PCLKSR.reg & SYSCTRL_PCLKSR_DFLLRDY) == 0 )
  {
    /* Wait for synchronization */
  }

  /* Enable the DFLL */
  SYSCTRL->DFLLCTRL.reg |= SYSCTRL_DFLLCTRL_ENABLE ;

  while ( (SYSCTRL->PCLKSR.reg & SYSCTRL_PCLKSR_DFLLLCKC) == 0 ||
          (SYSCTRL->PCLKSR.reg & SYSCTRL_PCLKSR_DFLLLCKF) == 0 )
  {
    /* Wait for locks flags */
  }

  while ( (SYSCTRL->PCLKSR.reg & SYSCTRL_PCLKSR_DFLLRDY) == 0 )
  {
    /* Wait for synchronization */
  }

  /* ----------------------------------------------------------------------------------------------
   * 5) Switch Generic Clock Generator 0 to DFLL48M. CPU will run at 48MHz.
   */
  GCLK->GENDIV.reg = GCLK_GENDIV_ID( GENERIC_CLOCK_GENERATOR_MAIN ) ; // Generic Clock Generator 0

  while ( GCLK->STATUS.reg & GCLK_STATUS_SYNCBUSY )
  {
    /* Wait for synchronization */
  }

  /* Write Generic Clock Generator 0 configuration */
  GCLK->GENCTRL.reg = GCLK_GENCTRL_ID( GENERIC_CLOCK_GENERATOR_MAIN ) | // Generic Clock Generator 0
                      GCLK_GENCTRL_SRC_DFLL48M | // Selected source is DFLL 48MHz
//                      GCLK_GENCTRL_OE | // Output clock to a pin for tests
                      GCLK_GENCTRL_IDC | // Set 50/50 duty cycle
                      GCLK_GENCTRL_GENEN ;

  while ( GCLK->STATUS.reg & GCLK_STATUS_SYNCBUSY )
  {
    /* Wait for synchronization */
  }

  /* ----------------------------------------------------------------------------------------------
   * 6) Modify PRESCaler value of OSC8M to have 8MHz
   */
  SYSCTRL->OSC8M.bit.PRESC = SYSCTRL_OSC8M_PRESC_1_Val ;
  SYSCTRL->OSC8M.bit.ONDEMAND = 0 ;

  /* ----------------------------------------------------------------------------------------------
   * 7) Put OSC8M as source for Generic Clock Generator 3
   */
  GCLK->GENDIV.reg = GCLK_GENDIV_ID( GENERIC_CLOCK_GENERATOR_OSC8M ) ; // Generic Clock Generator 3

  /* Write Generic Clock Generator 3 configuration */
  GCLK->GENCTRL.reg = GCLK_GENCTRL_ID( GENERIC_CLOCK_GENERATOR_OSC8M ) | // Generic Clock Generator 3
                      GCLK_GENCTRL_SRC_OSC8M | // Selected source is RC OSC 8MHz (already enabled at reset)
//                      GCLK_GENCTRL_OE | // Output clock to a pin for tests
                      GCLK_GENCTRL_GENEN ;

  while ( GCLK->STATUS.reg & GCLK_STATUS_SYNCBUSY )
  {
    /* Wait for synchronization */
  }

  /*
   * Now that all system clocks are configured, we can set CPU and APBx BUS clocks.
   * There values are normally the one present after Reset.
   */
  PM->CPUSEL.reg  = PM_CPUSEL_CPUDIV_DIV1 ;
  PM->APBASEL.reg = PM_APBASEL_APBADIV_DIV1_Val ;
  PM->APBBSEL.reg = PM_APBBSEL_APBBDIV_DIV1_Val ;
  PM->APBCSEL.reg = PM_APBCSEL_APBCDIV_DIV1_Val ;

  SystemCoreClock=VARIANT_MCK ;

  /* ----------------------------------------------------------------------------------------------
   * 8) Load ADC factory calibration values
   */

  // ADC Bias Calibration
  uint32_t bias = (*((uint32_t *) ADC_FUSES_BIASCAL_ADDR) & ADC_FUSES_BIASCAL_Msk) >> ADC_FUSES_BIASCAL_Pos;

  // ADC Linearity bits 4:0
  uint32_t linearity = (*((uint32_t *) ADC_FUSES_LINEARITY_0_ADDR) & ADC_FUSES_LINEARITY_0_Msk) >> ADC_FUSES_LINEARITY_0_Pos;

  // ADC Linearity bits 7:5
  linearity |= ((*((uint32_t *) ADC_FUSES_LINEARITY_1_ADDR) & ADC_FUSES_LINEARITY_1_Msk) >> ADC_FUSES_LINEARITY_1_Pos) << 5;

  ADC->CALIB.reg = ADC_CALIB_BIAS_CAL(bias) | ADC_CALIB_LINEARITY_CAL(linearity);

  /*
   * 9) Disable automatic NVM write operations
   */
  NVMCTRL->CTRLB.bit.MANW = 1;
}

Hice que ATSAMD10 funcione con un reloj de 48Mhz, con el código de inicio de Atmel, configurando el estado de espera de NVM en 1 en la configuración de la CPU. Configuración en 0 (predeterminado) se detiene la CPU.