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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:

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).

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