The Atomic Pi has 6 GPIO pins available to users, and additional lines connected to the BNO055 sensor. Here's a overview of them.

Addressing

In order to use GPIO pins from Linux, it's important to understand how they are addressed in various situations.

Each GPIO has a global number in the integer GPIO namespace used with the legacy GPIO interface (e.g. through sysfs). This is considered a legacy interface but there are currently no plans to remove it. However, in addition to that, recent Linux kernels expose GPIO chips, which are basically named sets of GPIOs of the same hardware origin with a single base number; GPIOs are numbered sequentially within a chip, but the global GPIO namespace itself needn't be contiguous.

Pin description

Generally available pins:

Schematic name	GPIO chip id	Chip pin number	Global pin number	Connected devices
ISH_GPIO_0	gpiochip3	21	335
ISH_GPIO_1	gpiochip3	18	332	LED Green (active low)
ISH_GPIO_2	gpiochip3	24	338	LED Yellow (active low)
ISH_GPIO_3	gpiochip3	15	329
ISH_GPIO_4	gpiochip3	22	336
ISH_GPIO_7	gpiochip3	16	330

These signals are available on the Atomic Pi's 26-pin connector. If you have the Enchilada breakout board, the signals are available as on it as well. Connector pin numbers are as follows:

Schematic name	26-pin connector number	Enchilada connector number
ISH_GPIO_0	24	9
ISH_GPIO_1	25	10
ISH_GPIO_2	26	11
ISH_GPIO_3	18	3
ISH_GPIO_4	19	4
ISH_GPIO_7	20	5

"Volume control button" pins (available on the "VOLUME"/"VOL" connectors, can be used as regular GPIO pins):

Schematic name	GPIO chip id	Chip pin number	Global pin number	Description
GPIO_DFX_2	gpiochip1	7	348	Volume up pin
GPIO_DFX_4	gpiochip1	5	346	Volume down pin

Other pins (not on the 26-pin connector or the Enchilada connector):

Schematic name	GPIO chip id	Chip pin number	Global pin number	Connected devices
I2C2_3P3_SDA	gpiochip0	62	476	BNO055 I2C SDA
I2C2_3P3_SCL	gpiochip0	66	480	BNO055 I2C SCL
AU_MIC_SEL	gpiochip1	0	341	XMOS Audio microphone loopback selector
XMOS_RESET	gpiochip1	8	349	XMOS Audio reset (active low)
BN_INT	gpiochip1	17	358	BNO055-generated interrupt (active low)
BN_RESET	gpiochip1	25	366	BNO055 reset (active low)

The XMOS_RESET line is controlled by a system service, atomicpi-hold-xmos, to bring up the XMOS Audio device.

The AU_MIC_SEL line must be configured to logical 0 to record audio from microphone, or to logical 1 for loopback (recording audio being played back).

Using the interrupt and reset lines is not strictly required for BNO055 operation. Additional devices may be connected to its I2C bus but that would require soldering.

Note that the system core contains other GPIO pins, some connected to internal circuits. Reading the datasheet is strongly recommended before attempting to configure them!

Using GPIOs from the shell

GPIO pin constants can be pulled in by including /usr/lib/atomicpi.sh:

. /usr/lib/atomicpi.sh

The traditional sysfs way of manipulating GPIOs from the command line is documented at:

https://www.kernel.org/doc/Documentation/gpio/sysfs.txt

It is listed as deprecated but there are no plans to remove it.

. /usr/lib/atomicpi.sh
echo $ATOMICPI_ISH_GPIO_1 >/sys/class/gpio/export
echo $ATOMICPI_ISH_GPIO_2 >/sys/class/gpio/export
echo low >/sys/class/gpio/$ATOMICPI_ISH_GPIO_1/direction
while true; do
    echo low > /sys/class/gpio/$ATOMICPI_ISH_GPIO_2/direction
    sleep 1
    echo high > /sys/class/gpio/$ATOMICPI_ISH_GPIO_2/direction
    sleep 1
done
echo $ATOMICPI_ISH_GPIO_2 >/sys/class/gpio/unexport
echo $ATOMICPI_ISH_GPIO_1 >/sys/class/gpio/unexport

Constants storing global GPIO indices are prefixed by ATOMICPI_.

Additionally, several utilities allow GPIO control using the more modern interface (and chip id + pin index addressing):

Constants storing "<chip id> <pin index>" are prefixed by ATOMICPICHIP_. Due to shell expansion rules, ${ATOMICPICHIP_ISH_GPIO_0} (without quotes) will expand to two arguments, the chip id and the pin index, which is what most of the following utilities expect.

List all GPIO chips, print their labels and number of GPIO lines:

gpiodetect

Find a GPIO line by name (the output of this command can be used as input for gpioget/gpioset):

gpiofind <name>

Print information about all lines of the specified GPIO chip(s) (or all chips if none are specified):

gpioinfo <gpiochip1> ...

Read line value(s) from a GPIO chip:

gpioget [-l] <chip name/number> <offset 1> <offset 2> ...

Options:
  -l, --active-low:     set the line active state to low

Set GPIO line values of a GPIO chip:

 gpioset [OPTIONS] <chip name/number> <offset1>=<value1> <offset2>=<value2> ...

 Options:
   -l, --active-low:     set the line active state to low
   -m, --mode=[exit|wait|time|signal] (defaults to 'exit'):
                 tell the program what to do after setting values
   -s, --sec=SEC:        specify the number of seconds to wait (only valid for --mode=time)
   -u, --usec=USEC:      specify the number of microseconds to wait (only valid for --mode=time)
   -b, --background:     after setting values: detach from the controlling terminal

 Modes:
   exit:         set values and exit immediately
   wait:         set values and wait for user to press ENTER
   time:         set values and sleep for a specified amount of time
   signal:       set values and wait for SIGINT or SIGTERM

Wait for events on GPIO lines:

gpiomon [OPTIONS] <chip name/number> <offset 1> <offset 2> ...

Options:
  -l, --active-low:     set the line active state to low
  -n, --num-events=NUM: exit after processing NUM events
  -s, --silent:         don't print event info
  -r, --rising-edge:    only process rising edge events
  -f, --falling-edge:   only process falling edge events
  -F, --format=FMT      specify custom output format

Format specifiers:
  %o:  GPIO line offset
  %e:  event type (0 - falling edge, 1 rising edge)
  %s:  seconds part of the event timestamp
  %n:  nanoseconds part of the event timestamp

See /usr/lib/atomicpi.sh for details.

Using GPIOs from Node.JS

var atomicpi = require("atomicpi");
var GPIO = require("sysfs-gpio");
console.log("Control by signal ID");
GPIO.export(atomicpi.signals.ISH_GPIO_0.global_idx, (pin) => {
   pin.out();
   pin.high();
});
console.log("Control with signal ID lookup on Enchilada connector first");
GPIO.export(atomicpi.signals[atomicpi.connectors.enchilada.leds.green].global_idx, (pin) => {
   pin.out();
   pin.low();
});
process.stdin.resume();

atomicpi.signals contains a mapping from the signal name (e.g. "ISH_GPIO_0") to {chip,chip_idx,global_idx}. You will need global_idx most of the time as sysfs-gpio uses the legacy sysfs interface.

See /usr/lib/node/atomicpi.js and sysfs-gpio documentation for details.

Using GPIOs from Python

import atomicpi
import gpio as GPIO
# Control by signal ID
GPIO_0=atomicpi.signals.ISH_GPIO_0.global_idx
GPIO.setup(GPIO_0, GPIO.OUT)
GPIO.output(GPIO_0, True)
# Control with signal ID lookup on Enchilada connector first
GREEN_LED=atomicpi.signals[atomicpi.connectors.enchilada.leds.green].global_idx
GPIO.setup(GREEN_LED, GPIO.OUT)
GPIO.output(GREEN_LED, False)
GPIO.cleanup(GPIO_0)
GPIO.cleanup(GREEN_LED)

atomicpi.signals contains a mapping from the signal name (e.g. "ISH_GPIO_0") to {chip,chip_idx,global_idx}. You will need global_idx most of the time as gpio uses the legacy sysfs interface.

The gpio library largely mimics the Raspberry Pi RPIO library.

See /usr/lib/python/dist-packages/atomicpi.py and gpio documentation for details.