I think I'm getting somewhere with this... try this:
volatile boolean l;
void TC0_Handler()
{
long dummy=REG_TC0_SR0; // vital - reading this clears some flag
// otherwise you get infinite interrupts
l= !l;
}
void setup(){
pinMode(13,OUTPUT);
pinMode(2,OUTPUT); // port B pin 25
analogWrite(2,255); // sets up some other registers I haven't worked out yet
REG_PIOB_PDR = 1<<25; // disable PIO, enable peripheral
REG_PIOB_ABSR= 1<<25; // select peripheral B
REG_TC0_WPMR=0x54494D00; // enable write to registers
REG_TC0_CMR0=0b00000000000010011100010000000000; // set channel mode register (see datasheet)
REG_TC0_RC0=100000000; // counter period
REG_TC0_RA0=30000000; // PWM value
REG_TC0_CCR0=0b101; // start counter
REG_TC0_IER0=0b00010000; // enable interrupt on counter=rc
REG_TC0_IDR0=0b11101111; // disable other interrupts
NVIC_EnableIRQ(TC0_IRQn); // enable TC0 interrupts
}
void loop(){
digitalWrite(13,l);
}
The timer controls the output of pin 2 and the interrupt toggles a flag which is output on pin 13.