The Timer Counter blocks of Arduino Due's AT91SAM3X8E

The AT91SAM3X8E embedds nine general-purpose 32-bit timers/counters. They are organized in three blocks (TC0, TC1, TC2) each containing three channels (0, 1, 2). Each block and channel has input lines for their clock and input/output lines which can be used in different ways, such as PWM pins etc.

Resources

Information on the Timer Counter and its I/O signals pins can be found here:

• Section 37 Timer Counter (TC) in the Atmel SAM3X Datasheet
  You find this chapter on the pages 869 through 920. It explains in detail how to operate the counter in different modes and has nice diagrams that show you how the clock input works and how to set up interrupts based on counter values etc.
• Arduino Due's SAM3X Pin Mapping and the
• Arduino Due pinout diagram.

The Timer Counter Signals / Pins

Many of the I/O lines of the Timer Counter are directly accessible on pin headers of the Arduino Due board. This section helps you to find out which of them are and which are not.

In order to actually connect those signals (TCLKx, TIOAx and TIOBx) to the pins on the Arduino Due, you must tell the Parallel I/O Controllers (PIOA, PIOB, PIOC or PIOD) to set up their mux (multiplexer) accordingly.
A useful resource to find out how to set the PIOs is Arduino's const array of PinDescriptions and the definition of PinDescription, the data type of its entries.

Overview of the I/O lines of the Timer Counter

Here is a table of the Timer Counter channels and their TCLKx (external clock input), TIOAx (I/O Line A) and TIOBx (I/O Line B) signals:

Instance	TC	Channel	External Clock Input	I/O Line A	I/O Line B
T0	TC0	0	TCLK0	TIOA0	TIOB0
T1	TC0	1	TCLK1	TIOA1	TIOB1
T2	TC0	2	TCLK2	TIOA2	TIOB2
T3	TC1	0	TCLK3	TIOA3	TIOB3
T4	TC1	1	TCLK4	TIOA4	TIOB4
T5	TC1	2	TCLK5	TIOA5	TIOB5
T6	TC2	0	TCLK6	TIOA6	TIOB6
T7	TC2	1	TCLK7	TIOA7	TIOB7
T8	TC2	2	TCLK8	TIOA8	TIOB8

TCLKx

Here is how the external clock inputs are routed to pins on the Arduino Due board:

Clock Input	Port Pin of µC	Pin on Arduino Due Board
TCLK0	PB 26	Digital Pin 22
TCLK1	PA 4	Analog In 5
TCLK2	PA 7	Digital Pin 31
TCLK3	PA 22	Analog In 3
TCLK4	PA 23	Analog In 2
TCLK5	PB 16	DAC1
TCLK6	PC 27	/
TCLK7	PC 30	LED "RX"
TCLK8	PD 9	Digital Pin 30

TIOAx

Here is how the I/O Lines A are routed to pins on the Arduino Due board:

I/O Line A	Port Pin of µC	Pin on Arduino Due Board
TIOA0	PB 25	Digital Pin 2
TIOA1	PA 2	Analog In 7
TIOA2	PA 5	/
TIOA3	PE 9	/
TIOA4	PE 11	/
TIOA5	PE 13	/
TIOA6	PC 25	Digital Pin 5
TIOA7	PC 28	Digital Pin 3
TIOA8	PD 7	Digital Pin 11

TIOBx

Here is how the I/O Lines B are routed to pins on the Arduino Due board:

I/O Line B	Port Pin of µC	Pin on Arduino Due Board
TIOB0	PB 27	Digital Pin 13 / Amber LED "L"
TIOB1	PA 3	Analog In 6
TIOB2	PA 6	Analog In 4
TIOB3	PE 10	/
TIOB4	PE 12	/
TIOB5	PE 14	/
TIOB6	PC 26	Digital Pin 4 (also connected to PA29)
TIOB7	PC 29	Digital Pin 10 (also connected to PA28)
TIOB8	PD 8	Digital Pin 12

TC Clock Source Selection

The clock of the counters can be set very flexibly to internal or external signals. To use the channel as a timer, it makes sense to connect its clock input to an internal timer clock. Here are the options:

Name	Definition
TIMER_CLOCK1	MCK / 2
TIMER_CLOCK2	MCK / 8
TIMER_CLOCK3	MCK / 32
TIMER_CLOCK4	MCK / 128
TIMER_CLOCK5	SLCK

Where MCK is the master clock (84 MHz for the Arduino Due) and SLCK is the slow clock (which can be clocked at 32.768 kHz by Y2 on the Arduino Due).