Square wave function programming on Arduino Due

My understanding is, you want a blocksignal with a period of about 200 ms and a duty cycle of 50%?

You can program a timer which generates an interrupt each 100ms. In the interrupt handler you can then toggle the output pin.

This code makes a 15kHz blockwave with 50% dutycycle. Credits to ard_newbie who posted it as an answer to my question couple of months ago.
Change the prescaler, RA and RC register to get the needed values

/**************************************************************************************/
/*       PWM pulses on TIOA0 (arduino pin 2) Frequency = 15 KHz, Duty cycle = 50%     */
/*       Interruptions on TIOA0 rising and falling edges                              */               
/**************************************************************************************/

void setup() {

  /*************  Timer Counter 0 Channel 0 to generate PWM pulses thru TIOA0  ************/
  PMC->PMC_PCER0 |= PMC_PCER0_PID27;       // TC0 power ON - Timer Counter 0 channel 0 IS TC0
 
  PIOB->PIO_PDR |= PIO_PDR_P25;           // PB25 is no more driven by the GPIO
  PIOB->PIO_ABSR |= PIO_PB25B_TIOA0;

  TC0->TC_CHANNEL[0].TC_CMR = TC_CMR_TCCLKS_TIMER_CLOCK1  // MCK/2, clk on rising edge
                              | TC_CMR_WAVE               // Waveform mode
                              | TC_CMR_WAVSEL_UP_RC        // UP mode with automatic trigger on RC Compare
                              | TC_CMR_ACPA_CLEAR          // Clear TIOA0 on RA compare match
                              | TC_CMR_ACPC_SET;           // Set TIOA0 on RC compare match


  TC0->TC_CHANNEL[0].TC_RC = 2800;  //<*********************  Frequency = (Mck/2)/TC_RC  Hz = 15 KHz
  TC0->TC_CHANNEL[0].TC_RA = 1400;  //<********************   Duty cycle = (TC_RA/TC_RC) * 100  %  = 80 %

  TC0->TC_CHANNEL[0].TC_IER = TC_IER_CPCS       // Interrupt on RC compare match
                              | TC_IER_CPAS;    // Interrupt on RA compare match
                             
  NVIC_EnableIRQ(TC0_IRQn);                     // Interrupt enable
                           
  TC0->TC_CHANNEL[0].TC_CCR = TC_CCR_SWTRG | TC_CCR_CLKEN; // Software trigger TC0 counter and enable
}
void TC0_Handler()
{
 uint32_t status;
 status = TC0->TC_CHANNEL[0].TC_SR;  // Read and clear TC0 status register

 if(status & TC_SR_CPAS) {
  // Toggle pin 1
 }
 else  // if(status & TC_SR_CPCS)
  {
  // Toggle pin 2
 }
}
void loop() {
 
}