You can use TIOA1 as well, but you will have to modify the sketch. TIOA1 is output by Timer Counter 0 Channel 1, and the pin is PA2:
/******************************************************************************/
/*** 1MHz/ 50% Duty cycle PWM thru TIOA1 ***/
/******************************************************************************/
void setup() {
/************* Timer Counter 0 Channel 0 to generate PWM pulses thru TIOA0 ************/
PMC->PMC_PCER0 |= PMC_PCER0_PID28; // Timer Counter 0 channel 1 IS TC0, TC1 power ON, page 38
PIOA->PIO_PDR |= PIO_PDR_P2;
PIOA->PIO_ABSR &= ~PIO_PA2A_TIOA1; // PA2 is driven by the TC, peripheral type A, page 858
TC0->TC_CHANNEL[1].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 TIOA1 on RA compare match
| TC_CMR_ACPC_SET; // Set TIOA1 on RC compare match
TC0->TC_CHANNEL[1].TC_RC = 42; //<********************* Frequency = (Mck/2)/TC_RC = 1 MHz
TC0->TC_CHANNEL[1].TC_RA = 21; //<******************** Duty cycle = (TC_RA/TC_RC) * 100 = 50 %
TC0->TC_CHANNEL[1].TC_CCR = TC_CCR_SWTRG | TC_CCR_CLKEN; // Software trigger TC0 counter and enable
}
void loop() {
}