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void setup() {
  // CTC, OC0A toggle on compare match, prescale 1/8
  TCCR0A = _BV(COM0A0)|_BV(WGM01);
  TCCR0B = _BV(CS01);

  // toggle every 35.5 μs at 16 MHz and 1/8 prescale
  OCR0A = 70;

  // phase and frequency correct PWM, TOP is OCR1A, OC1C clear on compare match and set at BOTTOM, no prescale
  TCCR1A = _BV(COM1C1)|_BV(WGM10);
  TCCR1B = _BV(WGM13)|_BV(CS10);

  // period of 2 ms at 16 MHz and no prescale
  OCR1A = 16000;

  // on-time of 1 ms at 16 MHz and no prescale
  OCR1C = 8000;

  // no interrupts from the timers
  TIMSK0 = 0;
  TIMSK1 = 0;

  // only output a 1 when both timers are outputting a 1
  PORTB &= ~_BV(PORTB7);

  // halt the timers and reset the prescaler
  GTCCR |= _BV(TSM);
  GTCCR |= _BV(PSRSYNC);

  // reset both timers
  TCNT0 = 0;
  TCNT1 = 0;

  // enable output
  DDRB |= _BV(DDB7);

  // let the timers run
  GTCCR &= ~_BV(TSM);
}

void loop() {
  // Just adjust the frequencies and duty cycle as required here.
  // Everything is handled by the hardware and takes effect immediately upon writing to the register.
  // OCR1A: the desired period of the slower signal, in 8ths of microseconds. Can be up to 65535.
  // OCR1C: the desired on-time of the slower signal, in 8ths of microseconds. Can be up to 65535.
  // OCR0A: 1 less than the desired period of the faster signal, in microseconds. Can be up to 255.
  // The on-time of the faster signal is always half of the period.
  // If necessary, you can trade precision for more range for any of the above values by adjusting the prescaler.
}

void setup() {
  // CTC, OC0A toggle on compare match, prescale 1/8
  TCCR0A = _BV(COM0A0)|_BV(WGM01);
  TCCR0B = _BV(CS01);

  // toggle every 35.5 μs at 16 MHz and 1/8 prescale
  OCR0A = 70;

  // phase and frequency correct PWM, TOP is OCR1A, OC1C clear going up and set going down, no prescale
  TCCR1A = _BV(COM1C1)|_BV(WGM10);
  TCCR1B = _BV(WGM13)|_BV(CS10);

  // period of 2 ms at 16 MHz and no prescale
  OCR1A = 16000;

  // on-time of 1 ms at 16 MHz and no prescale
  OCR1C = 8000;

  // no interrupts from the timers
  TIMSK0 = 0;
  TIMSK1 = 0;

  // only output a 1 when both timers are outputting a 1
  PORTB &= ~_BV(PORTB7);

  // halt the timers and reset the prescaler
  GTCCR |= _BV(TSM);
  GTCCR |= _BV(PSRSYNC);

  // reset both timers
  TCNT0 = 0;
  TCNT1 = 0;

  // enable output
  DDRB |= _BV(DDB7);

  // let the timers run
  GTCCR &= ~_BV(TSM);
}

void loop() {
  // Just adjust the frequencies and duty cycle as required here.
  // Everything is handled by the hardware and takes effect immediately upon writing to the register.
  // OCR1A: the desired period of the slower signal, in 8ths of microseconds. Can be up to 65535.
  // OCR1C: the desired on-time of the slower signal, in 8ths of microseconds. Can be up to 65535.
  // OCR0A: 1 less than the desired period of the faster signal, in microseconds. Can be up to 255.
  // The on-time of the faster signal is always half of the period.
  // If necessary, you can trade precision for more range for any of the above values by adjusting the prescaler.
}

void setup() {
  // CTC, OC0A toggle on compare match, prescale 1/8
  TCCR0A = _BV(COM0A0)|_BV(WGM01);
  TCCR0B = _BV(CS01);

  // toggle every 35.5 μs at 16 MHz and 1/8 prescale
  OCR0A = 70;

  // phase and frequency correct PWM, TOP is OCR1A, OC1C clear on compare match and set at BOTTOM, no prescale
  TCCR1A = _BV(COM1C1)|_BV(WGM10);
  TCCR1B = _BV(WGM13)|_BV(CS10);

  // period of 2 ms at 16 MHz and no prescale
  OCR1A = 31999;

  // on-time of 1 ms at 16 MHz and no prescale
  OCR1C = 15999;

  // no interrupts from the timers
  TIMSK0 = 0;
  TIMSK1 = 0;

  // only output a 1 when both timers are outputting a 1
  PORTB &= ~_BV(PORTB7);

  // halt the timers and reset the prescaler
  GTCCR |= _BV(TSM);
  GTCCR |= _BV(PSRSYNC);

  // reset both timers
  TCNT0 = 0;
  TCNT1 = 0;

  // enable output
  DDRB |= _BV(DDB7);

  // let the timers run
  GTCCR &= ~_BV(TSM);
}

void loop() {
  // Just adjust the frequencies and duty cycle as required here.
  // Everything is handled by the hardware and takes effect immediately upon writing to the register.
  // OCR1A: 1 less than the desired period of the slower signal, in 16ths of microseconds. Can be up to 65535.
  // OCR1C: 1 less than the desired on-time of the slower signal, in 16ths of microseconds. Can be up to 65535.
  // OCR0A: 1 less than the desired period of the faster signal, in microseconds. Can be up to 255.
  // The on-time of the faster signal is always half of the period.
  // If necessary, you can trade precision for more range for any of the above values by adjusting the prescaler.
}

void setup() {
  // CTC, OC0A toggle on compare match, prescale 1/8
  TCCR0A = _BV(COM0A0)|_BV(WGM01);
  TCCR0B = _BV(CS01);

  // toggle every 35.5 μs at 16 MHz and 1/8 prescale
  OCR0A = 70;

  // phase and frequency correct PWM, TOP is OCR1A, OC1C clear on compare match and set at BOTTOM, no prescale
  TCCR1A = _BV(COM1C1)|_BV(WGM10);
  TCCR1B = _BV(WGM13)|_BV(CS10);

  // period of 2 ms at 16 MHz and no prescale
  OCR1A = 16000;

  // on-time of 1 ms at 16 MHz and no prescale
  OCR1C = 8000;

  // no interrupts from the timers
  TIMSK0 = 0;
  TIMSK1 = 0;

  // only output a 1 when both timers are outputting a 1
  PORTB &= ~_BV(PORTB7);

  // halt the timers and reset the prescaler
  GTCCR |= _BV(TSM);
  GTCCR |= _BV(PSRSYNC);

  // reset both timers
  TCNT0 = 0;
  TCNT1 = 0;

  // enable output
  DDRB |= _BV(DDB7);

  // let the timers run
  GTCCR &= ~_BV(TSM);
}

void loop() {
  // Just adjust the frequencies and duty cycle as required here.
  // Everything is handled by the hardware and takes effect immediately upon writing to the register.
  // OCR1A: the desired period of the slower signal, in 8ths of microseconds. Can be up to 65535.
  // OCR1C: the desired on-time of the slower signal, in 8ths of microseconds. Can be up to 65535.
  // OCR0A: 1 less than the desired period of the faster signal, in microseconds. Can be up to 255.
  // The on-time of the faster signal is always half of the period.
  // If necessary, you can trade precision for more range for any of the above values by adjusting the prescaler.
}

void setup() {
  // CTC, OC0A toggle on compare match, prescale 1/64
  TCCR0A = _BV(COM0A0)|_BV(WGM01);
  TCCR0B = _BV(CS01)|_BV(CS00);

  // 1ms at 16 MHz and 1/64 prescale
  OCR0A = 249;

  // fast PWM, TOP is OCR1A, OC1C clear on compare match and set at BOTTOM, no prescale
  TCCR1A = _BV(COM1C1)|_BV(WGM11)|_BV(WGM10);
  TCCR1B = _BV(WGM13)|_BV(WGM12)|_BV(CS10);

  // 71.4375μs at 16 MHz and no prescale
  OCR1A = 1142;

  // 35.6875μs at 16 MHz and no prescale
  OCR1C = 570;

  // no interrupts from the timers
  TIMSK0 = 0;
  TIMSK1 = 0;

  // only output a 1 when both timers are outputting a 1
  PORTB &= ~_BV(PORTB7);

  // halt the timers and reset the prescaler
  GTCCR |= _BV(TSM);
  GTCCR |= _BV(PSRSYNC);

  // reset both timers
  TCNT0 = 0;
  TCNT1 = 0;

  // enable output
  DDRB |= _BV(DDB7);

  // let the timers run
  GTCCR &= ~_BV(TSM);
}

void loop() {
  // We don't have to do anything here! Hooray!
}

With that sketch, pin 13 on the MEGA will have the desired waveform. There's two big advantages to this method. First, it doesn't require any CPU resources at all (no loops or interrupts) once it's set up, so you can do whatever else you want to do in loop without thinking about it, or nothing at all if this is all this Arduino is responsible for. Second, it's as accurate as it's possible to get with a 16 MHz oscillator (the 500 Hz component is perfect, and the 14 kHz component is approximately 13998 Hz with a duty cycle of 49.956 %). The one disadvantage, though, is that millis and everything else in the Arduino library that uses timers internally won't work quite right, since we're using the same hardware timers that they depend on.

EDIT: I just noticed that you need to be able to change the duty cycle of the 500 Hz component. To do this, you'd have to switch timers 0 and 1, since you can't have both arbitrary frequency and duty cycle on timer 0 in this configuration. I'll update this code tomorrow to show how that's done.

void setup() {
  // CTC, OC0A toggle on compare match, prescale 1/8
  TCCR0A = _BV(COM0A0)|_BV(WGM01);
  TCCR0B = _BV(CS01);

  // toggle every 35.5 μs at 16 MHz and 1/8 prescale
  OCR0A = 70;

  // phase and frequency correct PWM, TOP is OCR1A, OC1C clear on compare match and set at BOTTOM, no prescale
  TCCR1A = _BV(COM1C1)|_BV(WGM10);
  TCCR1B = _BV(WGM13)|_BV(CS10);

  // period of 2 ms at 16 MHz and no prescale
  OCR1A = 31999;

  // on-time of 1 ms at 16 MHz and no prescale
  OCR1C = 15999;

  // no interrupts from the timers
  TIMSK0 = 0;
  TIMSK1 = 0;

  // only output a 1 when both timers are outputting a 1
  PORTB &= ~_BV(PORTB7);

  // halt the timers and reset the prescaler
  GTCCR |= _BV(TSM);
  GTCCR |= _BV(PSRSYNC);

  // reset both timers
  TCNT0 = 0;
  TCNT1 = 0;

  // enable output
  DDRB |= _BV(DDB7);

  // let the timers run
  GTCCR &= ~_BV(TSM);
}

void loop() {
  // Just adjust the frequencies and duty cycle as required here.
  // Everything is handled by the hardware and takes effect immediately upon writing to the register.
  // OCR1A: 1 less than the desired period of the slower signal, in 16ths of microseconds. Can be up to 65535.
  // OCR1C: 1 less than the desired on-time of the slower signal, in 16ths of microseconds. Can be up to 65535.
  // OCR0A: 1 less than the desired period of the faster signal, in microseconds. Can be up to 255.
  // The on-time of the faster signal is always half of the period.
  // If necessary, you can trade precision for more range for any of the above values by adjusting the prescaler.
}

With that sketch, pin 13 on the Mega will have the desired waveform. There's two big advantages to this method. First, it doesn't require any CPU resources at all (no loops or interrupts) once it's set up, so you can dedicate all of loop to reading the potentiometer and adjusting the duty cycle without worrying about glitches in the output. Second, being entirely hardware controlled means its output will be accurate and perfectly consistent (the 500 Hz component is perfect, and the 14 kHz component is approximately 14085 Hz). The one disadvantage, though, is that millis and everything else in the Arduino library that uses timers internally won't work quite right, since we're using the same hardware timers that they depend on.