Diamond Systems Atlas User manual

ATLAS Single Board Computer
PCI/104-Express SBC with Intel N2800 Cedar Trail CPU
Revision
Date
Comments
Rev A.00
1/17/2014
Initial Release
Copyright 2014
FOR TECHNICAL SUPPORT Diamond Systems Corporation
PLEASE CONTACT: 555 Ellis Street
Mountain View, CA 94043 USA
[e-mail] Tel [phone]
Fax [phone]
www.diamondsystems.com

Atlas User Manual Rev A.00 www.diamondsystems.com Page 2
CONTENTS
Important Safe-Handling Information.....................................................................................................................4
1. Introduction.......................................................................................................................................................5
1.1 Atlas SBC Features.......................................................................................................................................6
1.2 Thermal Considerations ................................................................................................................................7
2. Functional Overview.........................................................................................................................................8
2.1 Block Diagram ...............................................................................................................................................8
2.2 Atlas Dimensions...........................................................................................................................................9
2.3 Connector and Jumper Locations............................................................................................................... 10
2.3.1 Connector Summary.......................................................................................................................... 11
2.3.2 Configuration Jumper Summary........................................................................................................ 11
3. Getting Started............................................................................................................................................... 12
3.1 Introducing the Atlas Development Kit ....................................................................................................... 12
3.1.1 Atlas Cable Kit ................................................................................................................................... 13
3.2 System Setup ............................................................................................................................................. 14
3.2.1 Keyboard and Mouse......................................................................................................................... 14
3.2.2 mSATA Flashdisk Socket .................................................................................................................. 14
3.2.3 Mass Storage Devices....................................................................................................................... 14
3.2.4 Connecting Power.............................................................................................................................. 14
3.2.5 Display ............................................................................................................................................... 14
3.2.6 Installing Atlas in an Enclosure (optional).......................................................................................... 14
3.3 Booting the System .................................................................................................................................... 15
3.3.1 BIOS Setup........................................................................................................................................ 15
3.3.2 Operating System Drivers.................................................................................................................. 15
4. Interface Connector Details.......................................................................................................................... 16
4.1 External Battery (BAT)................................................................................................................................ 16
4.2 SATA (SATA).............................................................................................................................................. 16
4.3 Ethernet (LAN)............................................................................................................................................ 17
4.4 Serial Ports (COM12, COM34 & COM56).................................................................................................. 17
4.5 USB 1-2 (USB12) ....................................................................................................................................... 18
4.6 USB 3-4 (USB34) ....................................................................................................................................... 18
4.7 Utility Signals (Utility).................................................................................................................................. 19
4.8 LCD Backlight (LCD Backlight)................................................................................................................... 19
4.9 LCD Panel (LVDS Interface) (LCD)............................................................................................................ 20
4.10 PCI-104....................................................................................................................................................... 20
4.11 PCIe/104 Connector................................................................................................................................... 21
4.12 Power Input (Power Input).......................................................................................................................... 21
4.13 GPIO (GPIO) .............................................................................................................................................. 22
4.14 PCIe MiniCard / mSATA............................................................................................................................. 22
4.15 Audio (Audio).............................................................................................................................................. 23
4.16 VGA (VGA)................................................................................................................................................. 23
5. Configuration Jumper Details ...................................................................................................................... 24
5.1 PCI-104 Voltage (JP1)................................................................................................................................ 24
5.2 CMOS RAM Reset (JP2)............................................................................................................................ 24
5.3 RS-422/485 Termination Resistors (JP4)................................................................................................... 25
5.4 LCD Backlight Power Select –INV VSEL (JP5)......................................................................................... 25
5.5 LCD Panel Power Select –LVDS VSEL (JP6)........................................................................................... 25
6. BIOS ................................................................................................................................................................ 26
6.1 Entering the BIOS....................................................................................................................................... 26
6.2 Viewing and Modifying the BIOS Settings.................................................................................................. 26
6.3 Restoring Default BIOS Settings................................................................................................................ 27
6.4 Setup Utility Settings .................................................................................................................................. 27
6.4.1 Main Menu ......................................................................................................................................... 27
6.4.2 Advanced Menu................................................................................................................................. 28
6.4.3 Security Menu.................................................................................................................................... 33
6.4.4 Power Menu....................................................................................................................................... 33
6.4.5 Boot Menu.......................................................................................................................................... 34
6.4.6 Exit Menu........................................................................................................................................... 34
7. Watchdog Timer............................................................................................................................................. 35
8. Flashdisk Modules......................................................................................................................................... 35
8.1 Overview..................................................................................................................................................... 35

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8.2 Models and Capacities ............................................................................................................................... 35
8.3 Features...................................................................................................................................................... 36
8.4 Installation................................................................................................................................................... 36
9. Power Supply ................................................................................................................................................. 36
10. Battery Backup............................................................................................................................................... 36
11. Thermal Pad ................................................................................................................................................... 37
12. Specifications................................................................................................................................................. 38
1.1 Operating System Support......................................................................................................................... 38
1.2 Mechanical, Electrical, Environmental........................................................................................................ 38
All trademarks are the property of their respective owners.

Atlas User Manual Rev A.00 www.diamondsystems.com Page 4
IMPORTANT SAFE-HANDLING INFORMATION
WARNING: ESD-Sensitive Electronic Equipment!
Observe ESD-safe handling procedures when working with this product.
Always use this product in a properly grounded work area and wear
appropriate ESD-preventive clothing and/or accessories.
Always store this product in ESD-protective packaging when not in use.
Safe Handling Precautions
Atlas contains numerous I/O connectors that connect to sensitive electronic components. This creates many
opportunities for accidental damage during handling, installation and connection to other equipment. The list here
describes common causes of failure found on boards returned to Diamond Systems for repair. This information is
provided as a source of advice to help you prevent damaging your Diamond (or any vendor’s) embedded
computer boards.
ESD damage –This type of damage is almost impossible to detect, because there is no visual sign of failure or
damage. The symptom is that the board simply stops working, because some component becomes defective.
Usually the failure can be identified and the chip can be replaced.
To prevent ESD damage, always follow proper ESD-prevention practices when handling computer boards.
Damage during handling or storage –On some boards we have noticed physical damage from mishandling. A
common observation is that a screwdriver slipped while installing the board, causing a gouge in the PCB surface
and cutting signal traces or damaging components.
Another common observation is damaged board corners, indicating the board was dropped. This may or may not
cause damage to the circuitry, depending on what is near the corner. Most of our boards are designed with at
least 25 mils clearance between the board edge and any component pad, and ground / power planes are at least
20 mils from the edge to avoid possible shorting from this type of damage. However these design rules are not
sufficient to prevent damage in all situations.
A third cause of failure is when a metal screwdriver tip slips, or a screw drops onto the board while it is powered
on, causing a short between a power pin and a signal pin on a component. This can cause overvoltage / power
supply problems described below. To avoid this type of failure, only perform assembly operations when the
system is powered off.
Sometimes boards are stored in racks with slots that grip the edge of the board. This is a common practice for
board manufacturers. However our boards are generally very dense, and if the board has components very close
to the board edge, they can be damaged or even knocked off the board when the board tilts back in the rack.
Diamond recommends that all our boards be stored only in individual ESD-safe packaging. If multiple boards are
stored together, they should be contained in bins with dividers between boards. Do not pile boards on top of each
other or cram too many boards into a small location. This can cause damage to connector pins or fragile
components.
Power supply wired backwards –Our power supplies and boards are not designed to withstand a reverse
power supply connection. This will destroy each IC that is connected to the power supply. In this case the board
will most likely will be unrepairable and must be replaced. A chip destroyed by reverse power or by excessive
power will often have a visible hole on the top or show some deformation on the top surface due to vaporization
inside the package. Check twice before applying power!
Bent connector pins –This type of problem is often only a cosmetic issue and is easily fixed by bending the pins
back to their proper shape one at a time with needle-nose pliers. This situation can occur when pulling a ribbon
cable off of a pin header. Note: If the pins are bent too severely, bending them back can cause them to weaken
unacceptably or even break, and the connector must be replaced.

Atlas User Manual Rev A.00 www.diamondsystems.com Page 5
1. INTRODUCTION
Atlas is a high performance, highly integrated small form factor single board computer in the PCI/104-Express
form-factor. Atlas incorporates a wealth of standard PC-style I/O plus on-board digital I/O. Atlas provides
PCIe/104 I/O expansion by means of a new miniature, cost-effective expansion connector that supports most
PCIe/104 I/O modules. A PCIe MiniCard socket is available for additional add-on I/O. An integrated, bottom-
mounted heatspreader dissipates heat efficiently to the system enclosure. This configuration leaves the SBC’s top
side free for easy access to memory, on-board I/O, and expansion sockets.
Key feature highlights include:
Compact, low-power, high-performance, stackable SBC
1.86GHz Intel N2800 CPU
2GB or 4GB soldered 64-bit DDR3 SDRAM
Comprehensive set of I/O interfaces:
- 4 USB 2.0 ports
- 4 RS-232/422/485 and 2 RS-232 serial ports
- 1 Gigabit Ethernet port
- 1 SATA port
- 18-bit LVDS LCD with dual independent displays
- VGA CRT
- ALC892 Codec based High Definition Audio with Stereo Line-Out, Stereo Line-In and Microphone
- USB keyboard and mouse support
- 8 programmable general purpose I/O lines
- Programmable watchdog timer
PCIe MiniCard socket auto-selects for either PCIe MiniCard module or mSATA flashdisk module
PC/104-Plus form factor (4.55” x 3.775”) with wings
Stackable I/O expansion flexibility
- PCI-104
- PCIe/104
-40°C to +75°C operating temperature
Atlas Models
Processor Type
Processor Clock
On-board RAM
ATLN2800-4G
Intel Atom N2800 CPU
1.86GHz
4GB DDR3 DRAM
ALTN2800-2G
Intel Atom N2800 CPU
1.86GHz
2GB DDR3 DRAM

Atlas User Manual Rev A.00 www.diamondsystems.com Page 6
1.1 Atlas SBC Features
Atlas is a compact, rugged, single board computer that features the Intel Atom N2800 Cedar Trail processor in the
PC/104-Plus form factor.
Functions
Intel Atom N2800 processor clocked at 1.86GHz
Cooling: Fanless design incorporates heatspreader and conduction cooling to the enclosure
Memory: 2GB or 4GB DDR3 memory soldered on board
Display options:
The video circuit consists of Intel’s GMA500 controller integrated into the processor. This circuit offers
dual independent simultaneous display support with both VGA and LVDS outputs. The video controller
shares main memory for its frame buffer.
- 18-bit LVDS flat panel interface supports dual independent displays; 1366 x 768 maximum resolution
- LVDS backlight power: +5V or +12V jumper selectable
- VGA CRT; 1280 x 1024 maximum resolution
4 USB 2.0 ports on headers
6 serial ports; Ports 1-4 supports TX, RX, RTS and CTS with RS-232/422/485 capability and Ports 5 & 6
support TX, RX, RTX and CTS RS-232 only
Networking: One Intel 82574IT based Gigabit Ethernet port on pin header, with on-board magnetics
Mass storage:
- One SATA port
- mSATA flashdisk mounting location supporting up to 64GB
Keyboard/Mouse: support for USB
Realtek ALC892 Codec based High Definition Audio with Stereo Line-Out, Stereo Line-In and
Microphone.
8 general purpose I/O lines
Programmable watchdog timer
Expansion socket: PCIe MiniCard full size auto-selects for either PCIe MiniCard module or mSATA
flashdisk module
Stackable I/O expansion buses: PCI-104 and PCIe/104
Input power: 5VDC ±5%
Power consumption: 7.53W idle
Operating temperature: -40°C to +75°C (-40°F to +167°F)
PC/104-Plus form factor with wings: mm x mm (4.550” x 3.775”)
Weight: 7.6oz (215.5 grams) with heatspreader
RoHS: Compliant

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LED Indicators
Atlas provides a set of LED indicators for various features as follows. All LEDS are located near their respective
function.
Power input: Green LED when +5VDC is applied
Power on: Green LED when SBC is powered on
Ethernet: Green / yellow / orange; link, activity, and speed
Programmable LED: Blue, connected to a GPIO line on the SCH3116 super I/O chip; this LED is off
during power-up and is turned on in the BIOS to indicate a successful system
BIOS startup.
PCIe MiniCard socket: 3 LEDs to support WWAN, WPAN, WLAN signals from the connector
Operating System Support
Windows Embedded Standard 7
Windows Embedded CE
Linux 2.6.xx
1.2 Thermal Considerations
All models of Atlas are specified for a -40oC to +75oC operating range, the temperature being measured at the
outside surface of the heatspreader. Diamond Systems provides a heatspreader attached to the Atlas single
board computer as a conductive cooled thermal layer. However, this heatspreader by itself does not constitute
the complete thermal solution necessary for any specific implementation, but provides a common interface
between the single board computer and the customer’s implementation-specific thermal solution.
The outside surface of the Atlas heatspreader must be kept at a temperature not to exceed +75oC. If your
environment causes the temperature on the outside surface of the heatspreader to exceed this temperature, you
are responsible for removing the additional heat from the system through either an additional passive thermal
solution or fan solution.

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2. FUNCTIONAL OVERVIEW
2.1 Block Diagram
Figure 2 shows Atlas’functional blocks.
Figure 2: Atlas SBC Functional Block Diagram

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2.2 Atlas Dimensions
Figure 3 shows the overall dimensions of the Atlas SBC.Atlas conforms to PC/104 specifications for the 4
corners and 4 mounting holes as well as component height limits on the top and bottom sides. Wings, or
extensions on the left and right sides, provide additional room for I/O connectors. The wings extend 0.5” past the
standard PC/104 board edges as shown in the drawing below.
.
Figure 3: Atlas Dimensions, inches

Atlas User Manual Rev A.00 www.diamondsystems.com Page 10
2.3 Connector and Jumper Locations
Figure 4 illustrates the position of interface connectors, bus connectors, and jumper blocks located on the Atlas
SBC, which features PCI-104 and PCIe/104 stackable I/O.
Figure 4: Atlas SBC Connector Locations
COM56
COM34
COM12
SATA
USB12
USB34
PCIe/104
GPIO
Power
Input
LCD
(on underside of board)
PCI-104
LCD
Backlight
Audio
Utility
VGA
PCIe MiniCard
/ mSATA
LAN
External
Battery
JP1
JP2
JP4
JP5
JP6

Atlas User Manual Rev A.00 www.diamondsystems.com Page 11
2.3.1 Connector Summary
The following table summarizes the functions of Atlas’s interface, utility, and power connectors. Signal functions
relating to all of Atlas’s interface connectors are discussed in greater detail in Section 4 of this document.
Diamond offers an optional Atlas Cable Kit (number C-ATLN-KIT), which provides mating cable assemblies for
most of Atlas’ I/O interface connectors.
Connector Function
Silkscreen Label
External Battery
BAT
SATA
SATA
Gigabit Ethernet
LAN
Serial Ports 1 & 2
COM12
Serial Ports 3 & 4
COM34
Serial Ports 5 & 6
COM56
USB Ports
USB12 & USB34
Utility Signals
Utility
LCD Backlight
LCD Backlight
LCD (LVDS) Panel
LCD
PCIe/104
PCIe/104
PCI-104
PCI-104
Power Input
Power Input
GPIO
GPIO
PCIe MiniCard / mSATA
PCIe MiniCard
Audio
Audio
VGA
VGA
2.3.2 Configuration Jumper Summary
The Atlas SBC contains jumper blocks for configuring the following features. The board also contains locations for
installation of 0-ohm resistors in place of all valid jumper positions for a rugged configuration. The 0-ohm resistors
are oriented and labeled in a way that provides easy understanding of their use and easy interpretation of their
settings.
Atlas’configuration jumpers are listed below. Refer to Section 5 of this document for details regarding the
configuration of these jumper groups.
Jumper Group Function
Jumper Block
Array Size
PCI voltage (default: +5V)
JP1
1 X 3
CMOS RAM Reset (default: no clear)
JP2
1 X 3
Serial Port 1 RS-422/485 mode differential termination
resistor: Enable or Disable (default: Disable)
JP4
1 X 8
LCD backlight power: 5V or 12V (default: 5V)
(+12V provided through the input power connector)
JP5
1 X 3
LCD panel supply voltage: 3.3V or 5V (default: 3.3V)
JP6
1 X 3
-

Atlas User Manual Rev A.00 www.diamondsystems.com Page 12
Important Safe-Handling Information
WARNING: ESD-Sensitive Electronic Equipment!
Observe ESD-safe handling procedures when working
with this product.
Always use this product in a properly grounded work area
and wear appropriate ESD-preventive clothing and/or
accessories.
Always store this product in ESD-protective packaging
when not in use.
Please refer to page 4 of this manual (“Important Safe-Handling Information”) for further
details.
3. GETTING STARTED
First-time Atlas SBC users normally receive the product as part of Diamond’s Atlas Development Kit, which
provides everything needed to ensure rapid application development. This section of the Atlas User Manual
covers basic hardware setup, power connection, system boot-up, and initial software configuration. After Atlas is
up and running, refer to the later sections of this manual for the detailed hardware and software reference
information needed to adapt the product to specific applications.
3.1 Introducing the Atlas Development Kit
The Atlas Development Kit provides everything required for Atlas-based rapid application development. The table
on the next page lists the boards, cables, and other items included. Each kit contains an Atlas SBC and mSATA
flashdisk pre-loaded with a bootable operating system image, either Linux (LNX) or Windows Embedded
Standard 7 (WE7).
Item
Diamond P/N
Description
1
ATLN2800-2G
Atlas SBC with 2GB DDR3 SDRAM on-board
2
88916xx
16GB mSATA flashdisk with bootable OS pre-loaded
3
C-ALTN-KIT
Atlas Cable Kit
4
PS-5V-04
5V AC Power Adapter
5
6981xxx
Power cable from PS-5V-04 to Atlas
5
7461611
Atlas Quick Start Guide (not shown)
6
6710010
Software and Documentation CD
7
DOC-PKG
Diamond Systems Document Package (not shown)

Atlas User Manual Rev A.00 www.diamondsystems.com Page 13
3.1.1 Atlas Cable Kit
The Atlas Cable Kit (number C-ATLN-KIT) provides convenient access to most of Atlas’s I/O features. The kit’s
cable assemblies are shown in the photo below, and identified in the table that follows.
Item
Qty
Description
Diamond P/N
Connects to…
1
1
Power input cable
6981074
Power Input
2
3
Dual serial cable
6981075
COM12, COM34
& COM56
3
1
HD Audio cable
6981076
Audio
4
1
Digital I/O cable
6981077
GPIO
5
1
Utility cable
6981078
Utility
6
1
Gigabit Ethernet cable to RJ45
6981080
LAN
7
2
Dual USB cable
6981082
USB12 & USB34
8
1
VGA cable
6981084
VGA
Note: On each interface cable, the end of the cable connector that has a red wire going to it
should be oriented toward the end of the board connector that is labeled “pin 1” (typically the pin
with a square pad on the PCB).

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Caution! Be sure the PS-5V-04 AC power adapter is disconnected from
its AC power source prior to performing the following step.
3.2 System Setup
This section outlines a simple process for preparing Atlas for first-time operation using the Atlas Development Kit.
Additional details regarding Atlas’s interface functions and connections may be found in Section 4 of this
document.
3.2.1 Keyboard and Mouse
Atlas supports operation using a USB-based keyboard and mouse devices. Plug the USB keyboard connector
and USB mouse cable into the Atlas Cable Kit cable number 6981082 and the end of the cable into connector
USB12 on the Atlas SBC.
3.2.2 mSATA Flashdisk Socket
Atlas provides a location for on-board installation of an optional mSATA flashdisk in the connector PCIe MiniCard
/ mSATA socket. Plug the mSATA flashdisk module in the Development Kit into this socket on Atlas. Remove the
screws from the mounting stand-offs before installing the flashdisk. Secure the flashdisk to Atlas with the screws
once the flashdisk is installed.
3.2.3 Mass Storage Devices
If desired, connect SATA hard drives to Atlas by connecting a SATA cable to the SATA connector and then to the
SATA drive. Atlas can operate with a combination of SATA and CD-ROM drives, and can boot from either of
them.
3.2.4 Connecting Power
Connect cable 6981074 to the PS-5V-04 AC power adapter or an ATX power supply. Connect the other end of
the 6981074 cable to the Power Input connector on the Atlas SBC.
3.2.5 Display
Atlas provides interfaces for both LVDS flat panel displays and VGA output. Connect the VGA cable, 6981084,
between the VGA connector and a VGA-compatible display.
3.2.6 Installing Atlas in an Enclosure (optional)
Install the Atlas single board computer in an enclosure that has an appropriate mounting-hole pattern (2.8”
square).
Atlas’ heatspreader has four #6-32 threaded holes on 2.8” centers for mounting. Select four #6-32 threaded
screws of the proper length and head type to work with your enclosure. Allow a minimum of 0.25” and maximum
of 0.40” screw length for insertion into Atlas’s heatspreader. The total screw length will depend on the thickness
of your enclosure wall.

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3.3 Booting the System
Power-up the VGA video monitor. Then plug the PS-5V-04 AC power adapter to an AC outlet. Atlas should begin
its boot-up sequence immediately, as evidenced by BIOS messages on the connected VGA display. You can run
the BIOS Setup utility and proceed to install an operating system on the boot drive just as you would on a normal
desktop PC.
3.3.1 BIOS Setup
Atlas’s BIOS provides a wide range of configuration options. When you power up Atlas for the first time, you
should immediately enter the BIOS “Setup” utility in order to adjust BIOS settings to match your system’s
peripheral devices and other requirements, and to configure various other hardware and software parameters.
Options configurable via Setup typically include:
Number and type of mass storage devices
Boot device priority
Video display type and resolution
IDA, SATA, serial, and parallel interface modes and protocols
PCI and PnP configuration
Power management setup
Automatic power-up after LAN connection, RTC alarm, power resumption, etc.
System monitoring and security functions
3.3.2 Operating System Drivers
Atlas will boot and run the operating system from the mSATA flashdisk. Atlas should now be fully operational.
If you desire to run a different operating system, depending on the operating system to be installed, it may be
necessary to install software drivers for on-board interface controllers. Drivers for Windows Embedded Standard
7, Windows Embedded CE, and Linux 2.6, if required, are included on the Software and Documentation CD that
is included in the Atlas Development Kit.

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4. INTERFACE CONNECTOR DETAILS
This section describes the functions associated with the Atlas SBC, bus expansion, utility, I/O interfaces, and
power connectors in greater detail. Section 3.1.1 contains a list of ready-to-use interface cables included in
Diamond’s Atlas Cable Kit.
4.1 External Battery (BAT)
Atlas has provision for an external battery connection via connector BAT, a two-pin connector.
A connector and jumper are provided to disable the on-board battery and enable use of an external battery
instead. The external battery voltage requirement is 3.3V +/-10%. The jumper also clears the CMOS RAM when it
is removed and no external battery is connected.
1
Ground
2
Battery+
Connector type: HIROSE, DF13-2P-1.25DSA(50)
4.2 SATA (SATA)
The SATA connector is an industry-standard right-angle connector. It is mounted flush with the edge of the board
so as to plug the SATA cable to an external hard drive.
1
Ground
2
Transmit+
3
Transmit-
4
Ground
5
Receive-
6
Receive+
7
Ground
Connector type: SAMTEC

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4.3 Ethernet (LAN)
This connector provides access to the board's Gigabit Ethernet port.
NC
1
2
Key
DA+
3
4
DA-
DB+
5
6
DB-
DC+
7
8
DC-
DD+
9
10
DD-
Connector type: 2x5 2mm pitch vertical pin header with 4.0mm min high posts and gold flash plating
4.4 Serial Ports (COM12, COM34 & COM56)
Atlas provides six serial ports of which Ports 1-4 support RS-232/422/485 multiprotocol with the TX, RX, RTS and
CTS signals. Ports 5 and 6 support RS-232 with the TX, RX, RTS and CTS signals as shown in the pinouts
below. In RS-232 mode ports 1-4 offer 4 wires plus ground (TX, RX, RTS, CTS, GND) and operate at speeds up
to 115.2kbps. Console redirection can be set up in the BIOS for Port 1. TX/RX 121ohm line termination resistors
are jumper-selectable for Ports 1-4 in RS-422/485 mode.
The serial ports are provided on 2x5 pin headers with 2 ports per header labeled as COM12, COM34, and
COM56. The pin definition depends on the serial protocol selected. The pinouts below describe each protocol.
RS-232 RS-422 RS-485
TX1
1
2
RTS1
TX1+
1
2
TX1-
TX1/RX1+
1
2
TX1/RX1-
RX1
3
4
CTS1
RX1+
3
4
RX1-
NC
3
4
NC
GND
5
6
GND
GND
5
6
GND
GND
5
6
GND
TX2
7
8
RTS2
TX2+
7
8
TX2-
TX2/RX2+
7
8
TX2/RX2-
RX2
9
10
CTS2
RX2+
9
10
RX2-
NC
9
10
NC
TX3
1
2
RTS3
TX3+
1
2
TX3-
TX3/RX3+
1
2
TX3/RX3-
RX3
3
4
CTS3
RX3+
3
4
RX3-
NC
3
4
NC
GND
5
6
GND
GND
5
6
GND
GND
5
6
GND
TX4
7
8
RTS4
TX4+
7
8
TX4-
TX4/RX4+
7
8
TX4/RX4-
RX4
9
10
CTS4
RX4+
9
10
RX4-
NC
9
10
NC
TX5
1
2
RTS5
RX5
3
4
CTS5
GND
5
6
GND
TX6
7
8
RTS6
RX6
9
10
CTS6
Connector type:2x5 2mm pitch vertical pin headers with 4.0mm min high posts and gold flash plating

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4.5 USB 1-2 (USB12)
This connector provides access to two of the board's four USB 2.0 ports, USB1 and USB2. The shield pin is tied
to system ground.
NC (Key)
1
2
Shield
USB2 GND
3
4
USB1 GND
USB2 Data+
5
6
USB1 Data+
USB2 Data-
7
8
USB1 Data-
USB2 Pwr
9
10
USB1 Pwr
Connector type: 2x5 2mm pitch vertical pin headers with 4.0mm min high posts and gold flash plating
4.6 USB 3-4 (USB34)
This connector provides access to two of the board's four USB 2.0 ports, USB3 and USB4. The shield pin is tied
to system ground.
NC (Key)
1
2
Shield
USB4 GND
3
4
USB3 GND
USB4 Data+
5
6
USB3 Data+
USB4 Data-
7
8
USB3 Data-
USB4 Pwr
9
10
USB3 Pwr
Connector type: 2x5 2mm pitch vertical pin headers with 4.0mm min high posts and gold flash plating

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4.7 Utility Signals (Utility)
This connector provides utility signals and LED indicator signals for Atlas as follows.
Gnd
1
2
Reset-
Gnd
3
4
PWRBTN-
NC
5
6
NC
+5V
7
8
Speaker
+3.3V
9
10
Power On LED
+3.3V
11
12
LAN Activity LED
+3.3V
13
14
LAN Link 100 LED
+3.3V
15
16
Lan Link 1000 LED
Speaker PC speaker. Connect a speaker between this pin and +5V.
Power LED Referenced to +3.3V. Does not require any external series resistor. Connect LED
directly between this pin and +3.3V pin.
LAN Link 100 Illuminated for 100Mbps Ethernet operation
LAN Link 1000 Illuminated for 1000Mbps Ethernet operation
LAN Activity Illuminated during any Ethernet activity
Reset- Connection between this pin and ground will generate a system reset condition. It is
intended for use with a momentary switch.
PWRBTN- A momentary connection between this pin and ground will power-up/power-down the
board.
Connector type: 2x8 2mm pitch vertical pin header with 4.0mm min high posts and gold flash plating
4.8 LCD Backlight (LCD Backlight)
This connector provides the backlight power and control for the optional LCD panel.
Note: If needed, +12V must be provided on the input power connector.
1
Power +5V/+12V, jumper selectable (default +5V), fused
2
Power +5V/+12V, jumper selectable (default +5V), fused
3
Ground
4
Ground
5
Enable (GPIO output), 0 = off, open circuit = on
6
Brightness, 0-5VDC variable; 0V = max, 5V = min
The brightness control for the LCD backlight has a weak pull-down resistor to ensure maximum brightness when it
is not connected externally. Brightness may be controlled by a GPIO pin on the CPU or embedded microcontroller
or by pin 6 on this connector. A jumper selects the source of the brightness signal to this pin.
Connector type:Molex 53261-0671 or equivalent
Mating connector: Socket: Molex 51021-0600 or equivalent
Terminals: Molex 50058 / 50079 series or equivalent

Atlas User Manual Rev A.00 www.diamondsystems.com Page 20
4.9 LCD Panel (LVDS Interface) (LCD)
This connector is mounted on the top side of Atlas. It provides connection to an LVDS LCD display. The LCD
panel power is jumper selectable for 3.3V (default) or 5V.
LVDS_DATA3+
1
2
LVDS_DATA3-
SCAN_DIRECTION
3
4
LVDS_MAP
GND
5
6
LVDS_CLK+
LVDS_CLK-
7
8
GND
LVDS_DATA2+
9
10
LVDS_DATA2-
GND
11
12
LVDS_DATA1+
LVDS_DATA1-
13
14
GND
LVDS_DATA0+
15
16
LVDS_DATA0-
GND
17
18
GND
VCC_LCD, fused
19
20
VCC_LCD, fused
Connector type: Hirose part number DF14-20P-1.25H(20) or equivalent
Cable-mount socket: Hirose part number DF14-20S-1.25C or equivalent
4.10 PCI-104
The PCI-104 (PCI) bus connector is provided on the top side to enable the mounting of additional I/O boards. The
PCI connector is non-stack through (top side only) and is located in the standard PCI-104 location. Its pinout is
as defined in the PC/104-Plus specification available on www.pc104.org. The VIO pins are jumper-selected and
are protected with a polyswitch resettable fuse.