Trouble with setting the PWM frequency for Arduino Due
There are a few things to do. I've used this successfully in the past with older projects. 

As a side note one can very easily change PWM settings on pins with the esp32, a single line of code being ledcSetup(PWM_Channel_Number, Frequency, resolution) without ever having to actually dive into modifying variant.h

To Quote Kerry D. Wong:


  If you take a look at the function PWMC_ConfigureClocks in pwmc.c, you will see that the highest PWM frequency can be accommodated as the function input is 42 MHz, this is because inside the function it calls FindClockConfiguration which in turn ensures that the frequency parameter passed in is less than the MCK frequency. Thus for integer dividers, the highest frequency we can pass in is 42 MHz (with divider 2).
  
  To achieve the highest output frequency, we can use a one bit PWM which essentially just outputs a square wave with a duty cycle of one. We can then set the prescaler to 2 to obtain an 84 MHz waveform.


#include &lt;Arduino.h&gt;

uint32_t pwmPin = 8;
uint32_t maxDutyCount = 2;
uint32_t clkAFreq = 42000000ul;
uint32_t pwmFreq = 42000000ul; 

void setup() {
  pmc_enable_periph_clk(PWM_INTERFACE_ID);
  PWMC_ConfigureClocks(clkAFreq, 0, VARIANT_MCK);

  PIO_Configure(
    g_APinDescription[pwmPin].pPort,
    g_APinDescription[pwmPin].ulPinType,
    g_APinDescription[pwmPin].ulPin,
    g_APinDescription[pwmPin].ulPinConfiguration);

  uint32_t channel = g_APinDescription[pwmPin].ulPWMChannel;
  PWMC_ConfigureChannel(PWM_INTERFACE, channel , pwmFreq, 0, 0);
  PWMC_SetPeriod(PWM_INTERFACE, channel, maxDutyCount);
  PWMC_EnableChannel(PWM_INTERFACE, channel);
  PWMC_SetDutyCycle(PWM_INTERFACE, channel, 1);

  pmc_mck_set_prescaler(2);
}

void loop() 
{



  Note that VARIANT_MCK is defined in /arduino-1.5.7/hardware/arduino/sam/variants/arduino_due_x/variant.h as 84000000. PWM_INTERFACE_ID and PWM_INTERFACE are defined in variant.h as ID_PWM and PWM which in turn are defined in /arduino-1.5.7/hardware/arduino/sam/system/CMSIS/Device/ATMEL/sam3xa/include/sam3x8e.h.
  
  So as the conclusion, the highest stable frequency we can generate using an Arduino Due is 84 MHz. The pictures below show the captured waveforms under different frequencies. For the 21 MHz waveform, pwmFreq is set to 21000000, no prescaler is used. For the 42 Mhz waveform, pwmFreq is set to 420000 with no prescaler. The 84 MHz waveform is generated with set to 42000000 and the prescaler set to 2.


Hope this helps.