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Thank you for selecting the Atomic LS Truck EFI System! MSD’s Atomic EFI systems are designed
with two major goals; to simplify installation of EFI and deliver better overall performance from your
engine. Simplicity is achieved through wired-less technology to ease installation plus the Atomic is
simple to program with no PC required! Performance is delivered through advanced control of the
fuel and ignition, just as you’d expect from MSD.
4 - Fuel Rail Brackets
8 - Injector Retainer Clips
8 - Short Spacers, Black (PN 2957)
8 - Long Spacers, Black (PN 2958)
4 - 6mm x 16mm HEX Head Bolts
8 - 6mm x 12mm Bolts
4 - 6/32” Socket Head Cap Screws
8 - 8/32” Socket Head Cap Screws
8 - M6 x 90mm Intake Bolts (PN 2957)
8 - M6 x 100mm Intake Bolts (PN 2958)
8 - #12 Washers
2 - 90º - 6AN Fittings
1 - 18” High Pressure Fuel Hose
2 - Fuel Rail End Caps
Parts Required, Not Included:
Fuel System: Fuel Pump, Fuel Filter,
Injectors, Injector O-Rings,
Regulator, and Fuel Line.
Thread sealer for intake bolts.
Not legal for use on pollution controlled vehicles: The MSD Atomic EFI system is not CARB
approved for use on emission controlled vehicles.
modifications must be carried out by a qualified automotive technician. Installation of fuel system
parts requires handling of gasoline. Ensure that work is performed in a well ventilated area with an
approved fire extinguisher nearby. Extinguish all open flames, prohibit smoking and eliminate all
sources of ignition in the area of the vehicle before beginning the installation. When working with
fuel systems, eye goggles and other safety apparel should be worn to protect against debris and
sprayed gasoline. The finished work must be thoroughly checked to ensure there are no fuel leaks.
Installation of this product requires detailed knowledge of automotive systems
and repair procedures. Installation of fuel system parts and any fuel tank
Page 2
2 INSTALLATION INSTRUCTIONS
FGH
DLPHI
DLPHI
CAPABILITIES
The Atomic LS Truck kit is designed to fit the original equipment (OE) 3-bolt and 4-bolt throttle body
truck intakes. The Atomic LS Truck is a self integrated Fuel and Ignition controller for GEN-III and
GEN-IV motors that requires no programming with a PC. The interface is controlled through a supplied
hand held controller. The ECU only needs basic configuration information. Once the engine warms
up to operating temperature, the ECU tunes itself using a basic configuration to ensure the best
performance and throttle response for your engine. The atomic will adjust timing and fuel curves on
the fly which in turn produces the smoothest idle, best fuel economy, and superior wide open throttle
performance at all times. This also means that weather and altitude changes aren’t a problem with this
system. The Atomic LS Truck kit supports the factory Variable Valve Timing (VVT) configuration as well.
The Atomic LS Truck kit uses all OE sensors with the exception of the wideband O2 sensor. The
Atomic LS Truck system only supports a cable driven throttle body at this time.
Note: The 4-bolt electronic control throttle body will have to be converted to a cable drive throttle
body like the MSD PN 2940.
COMPONENTS
Power Module: The Power Module of the Atomic LS is the communication
hub of the system and provides the high current fuel pump circuit
and other input/outputs for optional features. The unit has two
ports for the MSD CAN system as well as a wiring harness. There
are connections for the WB02, the Handheld Monitor as well as
Rail Power and CAN communication to the integrated fuel rails.
Handheld Programmer: The Atomic LS Truck kit is a self-tuning fuel and
ignition control system. The system only needs the basic engine
configuration information to build a fuel table for the engine. The
Handheld Programmer is used to enter all the engine parameters
into the ECU, and uses the MSD CAN to communicate with the
ECU. Once the engine has been started and warmed up to operating
temperature, the ECU will monitor the sensors. The ECU will then adjust
the fuel tables and ignition in order to maintain a properly running engine.
Fuel Rails/ECU: The Fuel Rails/ECU is combination of the electronics that drive
an ECU and a fuel rail assembly built into one unit. All of the engine sensor
connectors (except for the wideband O2 which connects to the Power
Module directly) are found on the fuel rails. The fuel rails are equipped
with -6AN fittings, but will accept -8AN fittings (the internal rail orifice is
the same diameter as the -8AN).
PREPARING THE INTAKE MANIFOLD FOR
INSTALLATION OF THE ATOMIC LS FUEL RAILS
The intake manifold must be modified in order to install the Atomic
LS fuel rails. Removal of the intake manifold for modification and
installation of the fuel rails is recommended but not required. If
care is taken while the intake is removed from the motor, the intake
gaskets can be reused.
of the centering bushing used to align the intake on eight of the
ten intake bolts/bushings (Figure 2). Take care not to damage
the centering bushings as they will be reused with the new intake
bolts.
Note: If the manifold is modified on the motor, plug the injector
bosses to prevent debris falling into the motor.
Figure 1a
FUEL RAIL INSTALLATION (3 AND 4-BOLT
THROTTLE BODY INTAKE MANIFOLD)
1. Preassemble the rail brackets with the spacers and centering
bushing. Coat the ends of the bolts with thread sealant.
2. The angled end of the bracket is always facing to the left when
installed correctly on either side of the engine (Figure 3).
NOTE: The spacers for the 4-bolt intakes are slightly longer
1ST PASS: 42 IN LB - 44 IN LB
2ND PASS: 87 IN LB - 89 IN L2
Figure 4 Intake Manifold Torque Specifications.
3. One of the fuel rails is shorter than the
other. The shorter rail is installed on
the driver side of the engine (Figure
5).
4. Lubricate the o-rings on the injectors with
some motor oil or silicone lubricant.
Install the clips onto the injector before
they are pushed into the fuel rail bung.
The injector clip will automatically secure
the injector to the rail.
5. Push the fuel injectors into the bung
without forcing them on. The injectors
should slide in easily (Figure 6).
6. Plug the fuel injector pigtails into the fuel
rail connections (Figure 7).
7. Connect the fuel injector pigtails into the injectors. The
long wires connect to the injectors on each end of the
fuel rail. The short wires connect to two inner injectors
(Figure 8).
8. Plug the FPS (fuel pressure sensor) connector into the
fuel pressure sensor under the fuel rail (Figure 9).
9. Connect the CAN cable from one rail to the other
(Figure 10).
10. Connect the heavy red Rail Power wire together
between the two rails (Figure 11).
11.Repeat steps 3-6 for the passenger side fuel rail
assembly.
NOTE: The Driver Side Rail is SHORTER
than the Passenger Side Raile.
12. Place the spacer/bushing/rail bracket assemblies onto the intake
manifold.
13. Use the torque sequence on page 4, Figure 4 to torque the
manifold bolts down correctly. Bolts #9 and #10 will use the stock
length bolts/bushings.
14. Check the rail brackets with a straight edge (Figure 12).
15. Install the rails onto the manifold. Use the supplied 6mm bolts to
secure the rails to the rail brackets. Torque to 85 in lb – 87 in. lb.
(Figure 13).
16. STOP. Visually inspect and ensure all the injectors are sitting evenly
and the injector o-rings are not pinched or visible. Failure to install the injectors correctly can result in fuel leaks and engine fire.
17. Begin routing the sensor harnesses and plugging them into the
appropriate sensors.
18.
Line the end of the fuel rail cover up with the edge of the black
mold on the rear of the fuel rail (Figure 14). Slide the cover towards
the rear of the engine to engage the locking tabs on the fuel rail.
(Figure 15).
19. Secure the rail covers onto the fuel rail with the
supplied 8/32 socket head cap screws (Figure 15).
20. Install the fuel rail end cap onto the cover and secure
it with the supplied 6/32 socket head cap screws.
FUEL RAIL COVER INSTALLATION
Figure 15 Fuel Rail Cover.
OVERVIEW
Follow these steps to install both covers. To remove the covers reverse the steps.
END CAP
6/32
SCREWS
1. Line the end of the fuel rail cover up with the edge of the black mold on the rear of the fuel rail (Figure 14).
2. Slide the cover towards the rear of the engine to engage the locking tabs on the fuel rail.
3. Install the 8/32 screws that secure the covers to the fuel rails.
4. Install the end caps and secure with the 6/32 screws.
SLIDE TOWARD REAR TO ENGAGE.
FRONTREAR
COVER - TOP VIEW
END CAP
6/32
SCREWS
8/32 SCREWS ON BACK OF COVER
LOCKING TABS
EDGE OF
BLACK MOLD
FUEL RAIL/ECU WIRING
The Atomic LS Truck kit has several adapter harnesses in order for the kit to install with all the different
variations of the truck motors. These adapter harnesses plug into the connectors found on the rails
themselves. The IAC and TPS connectors are on both rails to accommodate the different throttle
body configurations.
Air Conditioning kick up (AC): When 12v is applied to this wire, the ECU will kick up the IAC count and
Fan #1 to compensate for the engine load change created by the air conditioning compressor.
Alternator: The kit is supplied with a harness that has two alternator connectors on one end. This is
done to accommodate the two different alternator ends used by GM. Identify which connector
is needed, and cut the other connector off. Use the heatshrink caps provided in the parts bag
to seal the wire end.
Cam Sensor: The kit supports both the 1x and 4x cam sensors. The easiest way to identify the cam
sensor on a stock engine would be by locating the sensor on the motor. The 4x sensor is
mounted on the timing chain cover. The 1x sensor is located on the back of the motor.
Controller area network (CAN): The kit utilizes a CAN communication for wiring between the fuel
rails, Power module and Handheld Monitor.
Crank sensor: The kit supports both the 24x and the 58x crankshaft
trigger wheels. The easiest way to identify which crank trigger
wheel is in the motor, remove the starter, crank sensor (behind
the sensor), and look into the motor to identify the crank
trigger wheel (Figure 16).
Engine Coolant Temperature (ECT) sensor: The engine coolant
temperature is monitored by the ECU for fuel and ignition
adjustments in closed loop operation.
Fuel Pressure (FP) Sensor: The kit includes a fuel pressure sensor
which is already installed on the driver side fuel rail.
Idle Air Control (IAC) Sensor: The kit has a connector on each
rail to accommodate different intake styles. The sensor only
plugs into the driverside IAC connector.
Ignition Coils: The kit has a factory connector that will connect to
the factory coil bracket harness on each valve cover (not
Figure 16 Crank Shaft
Reluctors.
supplied with the kit). There is an extra ground wire with each
coil bracket connector that should be grounded to the back
of each cylinder head.
Injectors: The kit supports following injector part numbers -
Delphi connector (Figure 17) :
GM:17113553 AC Delco:17113553
GM:17113698 AC Delco:17113698
EV6 connector (Figure 18):
GM:12574927 AC Delco:217-1563
GM:12613411 AC Delco:217-3411
GM:12250681 AC Delco:217-1621
The kit does NOT support the following
flex fuel injector-
GM:12580426 AC Delco:217-1626
Figure 17 Delphi
Connector.
Figure 18 EV6
Connector.
Intake Air Temperature (IAT) sensor: The sensor is supplied in the parts bag. It is recommended
to install the sensor in the intake air track before the throttle body. A ¾” hole is required
for the sensor.
Map sensor: The kit supports the original equipment (OE) Delphi and Bosch sensors. A harness
is supplied for each sensor.
Oil Pressure (Oil) sensor: The kit utilizes the factory oil pressure sensor. There are different style
sensors, but the connector is the same between these sensors.
Power: The heavy gauge wire supplies 12v to both fuel rails from the power module.
Throttle Position (TPS) Sensor: The kit has a connector on each rail for the TPS sensor. This is
done for ease of installation and only the driver side connector is used. The kit only supports
a cable driven throttle body at this time and includes an adapter harness for the TPS sensor
used on a cable driven throttle body.
Wide Band O2 Sensor: A wide band O2 sensor is supplied with the kit. The O2 sensor is used by
the ECU to monitor air/fuel ratios (AFR) in the exhaust gases. Adjustments are made by
the ECU in closed loop to maintain (AFR).
Variable Valve Timing (VVT): The kit supports the VVT system. Plugs into VVT Connector on the
front of the timing chain cover in VVT capable engines.
The Power Module of the Atomic EFI system handles high
current circuits such as the fuel pump and WBO2. The unit has
two ports for the MSD CAN system as well as a wiring harness.
The CAN ports will provide communication between the Power
Module, the passenger side fuel/ECU rail and the Handheld
Monitor. It is important to select a proper mounting location
for the Power Module. The unit can be mounted in the interior
or the engine compartment as long as it is away from direct
heat sources. It is not recommended to mount the unit in an
enclosed area, such as the glove box. When a suitable location
is found, make sure all wires reach their connections. Also
be sure that the CAN port can be accessed for use with the
Handheld Monitor. Use the
Power Module as a template
and mark the location of the
holes. Use a size #20 drill
bit to prepare a hole for the
supplied self tapping screws.
CONTROLLER
Assemble the sleeves in the
power module (Figure 20).
LS
Figure 20 Mounting Hardware.
®
MONITOR
CONNECTOR
ONLY
POWER MODULE
WIRING (Figure 21)
Not all of the wires from
the Power Module need to
be connected for proper
operation of the Atomic LS
Truck kit. Some of the wires
such as the nitrous input or
electric fan controls, only
need to be connected if their
functions are being used.
In the chart labeled Power
Module Wiring, wires marked
“REQ” must be connected
for the system to operate
while those marked “OPT”
are optional depending on
FUEL PUMP
GROUND
BATTERY 1*
BATTERY 2*
the features needed. For the
initial installation and start
up, it is recommended to
connect only the required
* BATTERY 1 AND 2
MUST BOTH BE
CONNECTED
wires.
NOTE: The Power Module
uses two heavy gauge (Red)
wires that connect to the
battery. Both leads must be
connected in order for the
Power Module and Atomic LS Truck kit to operate correctly.
ORANGE
BLACK
HEAVY RED
HEAVY RED
Figure 21 Power Module Wiring Diagram.
CAN
ONLY
RED SLED POWER
RED FAN 1
DARK BLUE LAUNCH
BROWN/WHITE NITROUS
BROWN SPEED REF (-)
LT BLUE SPEED (+)
GRAY TACH
RED SW 12V
ORANGE FAN 2
LT GREEN MIL GROUND
Battery 1, Must be connected to Positive (+) Battery terminal.
Ground, Connect to solid, clean engine ground.
Pump, Connect to Fuel Pump Positive terminal.
Battery 2, Must be connected to Positive (+) Battery terminal.
Fan 1, Supplies ground to activate Fan 1
2 Step Connect to switched 12V to activate.
Nitrous, When supplied with 12 volts, timing will be retarded and the
air/fuel ratio will be corrected to the target nitrous setting.
Speed Ref. (-)
Speed Signal (+)
Tach, Supplies 12V square wave signal
Switched 12V, Connect to ignition switch
Fan 2, Supplies ground to activate Fan 2 at desired temperature.
Supplies power to the Fuel Rail
IP
VM
H-
WBO2
H+
IA
UN
MIL Ground
This wire functions as a Malfunction Indicator
Lamp (MIL). This wire will provide a ground
in the event of a diagnostic code.
FUEL SYSTEM REQUIREMENTS
The Atomic LS fuel injection system requires a high pressure fuel pump system. The fuel system is not
supplied due to the large variety of applications incorporating the LS engine platform. Depending on
the engine combination, the Atomic LS requires a minimum of 58-62 psi continuous to operate. When
selecting a pump, regulator and lines, be sure each component is designed to perform at high pressure.
MSD offers fuel pumps, fuel hose and accessories to complete the installation. The following guidelines
are intended to help set up a fuel system for the Atomic LS. The Atomic is capable of operating with a
return or returnless style system.
that can result in fuel pump cavitation or poor engine performance. For this reason MSD does not
recommend the use of a hard line for the fuel system in PWM mode.
NOTE: IF RUNNING A RETURNLESS
FUEL SYSTEM, THE PUMP MUST
BE MOUNTED IN THE TANK.
MSD ADJUSTABLE
REGULATOR
FUEL
FILTER
FUEL TANK
FUEL
PUMP
IT IS RECOMMENDED TO MOUNT
THE FUEL PUMP IN THE TANK
WHENEVER POSSIBLE. IF IT MUST
BE MOUNTED EXTERNALLY
THE PUMP WITHIN 2-FEET OF THE
FUEL TANK SENDING UNIT.
Figure 22 Fuel Line Routing.
IN-TANK PUMPS
The MSD Atomic Fuel Pump (not supplied) can be used in the tank however it would require a sock,
or filter element on the pickup side of the pump. It is important to note that the wiring used to run the
pump will need to meet requirements to be submersed in fuel. When wiring an in-tank pump, it is
recommended to use a wire that conforms to SAE specifications J1128 and J378. This wiring features
a Thermoplastic insulated wiring with polyvinyl chloride insulation for protection against gasoline,
oil, and more. In addition, different fuel line will be required internally if the pump is to be mounted
in the tank. Fuel line that meets SAE 30R10 specifications MUST be used. Failure to do so will cause
severe damage to your engine and/or fuel system.
WARNING: Improper installation or use of fuel system components can cause severe damage your
engine and/or fuel system that will not be covered by the manufacturer’s warranty.
Atomic Fuel Pump, PN 2925: This pump features 3/8” inlet and outlet. The pump will support
approximately 525 hp and is approved for in-tank use (no wiring or in-tank mounting hardware/
pickup element are supplied).
Fuel Pump Kit, PN 2920: This Kit is supplied with MSD’s PWM Fuel Pump, a pre and post-filter, 15-ft
of 3/8 fuel injection line and mounting hardware.
Fuel System Return Kit, PN 2922: If you plan on running a return line with your Atomic LS, this kit
provides another 15-ft of 3/8” injection line, an MSD Regulator and two push-lock fittings.
High Horsepower Fuel Kit, PN 2921: This pump will support the power demands of engines up to
650 horsepower. The pump features 3/8” inlet and outlet. The pump will support approximately
650 hp and is approved for in-tank use (no wiring or in-tank mounting hardware/sock are
supplied).
FUEL INLET FITTINGS AND CROSS-OVER LINE
LS engines require a cross-over fuel line to
route the fuel from one bank to the other. This is
typically done at the front of the engine (Figure
23). Due to the variety of intake manifolds and
accessories a cross-over line must be made for
each application.
Figure 23 Installing Fuel Hose to the Push-Lock Fittings.
Page 12
12 INSTALLATION INSTRUCTIONS
MSD supplies a length of fuel hose and two 90° -6AN
fittings to prepare a fuel crossover line. The fittings utilize
Push-Lock technology and are designed exclusively for
use with the supplied hose. These fittings do not use
clamps, however it is imperative to follow the installation
instructions.
Proper installation begins with a clean, square cut of
the hose. A hose cutting tool or new razor blade are
recommended. When installing the hose it is important
that the hose is pushed on all the way to the thin beauty
ring (Figure 24). This means the hose should fully overlap
the inboard barb. Too little of engagement, as well as overengagement, will result in a compromised connection
that is prone to failure.
1. Determine the length of hose needed. Mark the hose
and cut it using a hose cutter or new razor blade.
There should be minimal disturbance of the outer
jacket, braids and inner liner. The cut plane should
be perpendicular to the hose axis. (Figure 25).
2. Before installing the hose to the fitting, it is important
to anchor the fitting. Proper installation cannot be
achieved by holding the hose and fitting in your hands.
For best results, the hose should be installed with
minimal twisting or pausing.
3. Apply a light coat of oil to the barbs on the fitting and
inside the hose. Use care not to get oil on the outside
of the hose as it will be impossible to get a firm grip
on the hose.
4. With the fitting anchored securely, push the hose over
the barbs. The hose is properly installed when it is flush
with the thin edge of the beauty ring (Figure 26). At
this point, the hose end should have rolled over the
inboard barb.
WARNING: MSD’s Push-Lock fittings are designed
for use with the MSD fuel hose only. Do
not use the MSD fuel hose with other
fittings. Do not use MSD Push-Lock
fittings with other fuel hose. Compatibility
issues may cause fuel leaks. Fuel Inlet
Fittings and Cross-Over Line: LS engines
require a cross-over fuel line to route the
fuel from one bank to the other. This is
typically done at the front of the engine.
Due to the variety of intake manifolds
and accessories a cross-over line must
be made for each application.
The supplied MSD Push-Lock AN
fittings are designed only for use with
the supplied fuel hose (Aeroquip AQP
FC598). We do not recommend mixing
Push-Lock style fittings and hoses from
different manufacturers. Doing so may
result in fuel leaks and expose other
dangerous incompatibilities.
Figure 24 Installing Fuel Hose to the Push-Lock Fittings.
CORRECT CLEAN,
SQUARE CUT
INCORRECT
JAGGED, ROUGH
CUT RESULTS IN
A COMPROMISED
CONNECTION
Figure 25 Severing the Hose Properly.
Properly Installed Push-Lock Fitting
END OF HOSE IS FLUSH
WITH THE THIN EDGE
OF THE BEAUTY RING.
Improperly Installed Push-Lock Fitting
EXCESSIVE GAP TO
BEAUTY RING RESULTS
IN A COMPROMISED
CONNECTION.
The MSD Atomic EFI system requires a single Wide
Band Oxygen Sensor (WBO2) for operation. MSD
02 SENSOR
suggests that the bung for this sensor be installed
prior to starting any other part of the conversion
process. By having the WBO2 in place first, there is a
reduced chance of the vehicle being immobilized for
an extended time. The bung for the WBO2 provided
AT LEAST
10°
by MSD has a plug included so that the vehicle can
be driven between the time of exhaust modification
and installing the rest of the Atomic system, if needed.
The WBO2 can be installed in either exhaust bank.
EXHAUST
COLLECTOR
Figure 27 WBO2 Sensor Location.
The sensor connects to the Power Module, so install
the sensor on the bank closest to where you plan to
mount the Module. The bung should be installed by a qualified exhaust technician and pressure tested.
Proper installation of the oxygen sensor is critical to the performance of the Atomic EFI. Improper
installation could lead to engine damage.
1. Locate the ideal spot to install the WBO2.
a. This location should be 2-4 inches after the exhaust collector. The sensor must be more than
18 inches forward of the exhaust tip. For applications where short or open headers are used,
install the WBO2 in the primary tube of the rear cylinder at least 8 inches away from the exhaust
port. The Atomic will not work on “Zoomie” style headers.
b. The WBO2 sensor should be at least 10˚ above horizontal to allow condensation runoff.
Without this angle the sensor is significantly more likely to sustain water damage (Figure 27).
c. Never place a WBO2 on the outside of a bend.
d. The WBO2 must be mounted in the exhaust prior to any catalytic converter, if applicable.
2. Drill a 7/8” hole in the exhaust where the WBO2 will go.
3. Weld in the supplied bung. Ensure the weld goes completely around the bung and is air tight.
4. Insert supplied plug in bung. Never run the vehicle with a WBO2 installed but not plugged in to
the harness and powered up; it will damage the sensor.
5. When completing the Atomic EFI installation, remove the plug and insert the WBO2 for use. MSD
suggests using a small amount of anti-seize on the threads.
Note: The Atomic EFI is extremely sensitive to air leaks in the exhaust system. Any air leak between
the engine and the WBO2 will cause the Atomic to have false readings, which can lead to poor
engine performance, misfires, and an inability to properly auto-tune. Extended running of the
Atomic EFI with an exhaust leak can result in detonation and severe engine damage. Improper
installation of the oxygen sensor, and any damage that may result from such an installation,
is not covered by the manufacturer’s warranty.
WARNING: DO NOT ATTEMPT TO START THE ENGINE. Before turning the ignition key to the
ON position, confirm all fuel line connections are tight and all electrical connections
are correct. After confirming all electrical connections and fuel lines, turn the ignition
key to the ON position. Check every hose and fitting connection for any signs of fuel
leaks. The Handheld screen should illuminate and display the Main Menu.
PROGRAMMING
The Handheld Monitor plugs into the Power Module via the CAN connection. It can be removed once
the initial setup is complete, or can remain connected for use of features such as the dash or digital
gauge displays. The Handheld Monitor features a joystick to scroll through the settings. Scroll up
and down to the setting and push the joy stick to the right to select the options. When the selection
is made, either push in, or go back (push to the left) to save/confirm settings changes.
MAIN MENU
Six selections will come up the Monitor under the Main Menu.
If this is the first time powering up the Atomic LS, select Initial
Setup (Figure 28).
Atomic LS Dash: This selection allows you to view a variety
of engine functions in real time when the engine is
running. Refer to page 21 for a complete description
of each parameter in the Atomic Dash.
Atomic LS Gauges: This setting puts five important values
in gauge form to ease viewing the data. This includes
engine rpm, oil pressure, engine coolant temperature,
speed (when connected), battery voltage, and air/fuel
ratio.
Initial Setup: These are values that are required to start the
engine.
Advanced Setup: Optional settings for features and optimized
drivability settings.
Diagnostics: This screen will help you troubleshoot and
identify potential issues.
Display Setup: Provides adjustments for the appearance of
the monitor screen. See page 20 for more information.
Scroll down to Initial Setup and push the joystick to the right.
The following parameters must be programmed.
Engine Type: This value determines the engine platform (Figure
29). There are over 26 engine combinations to select
from. This setting is important as once an engine type
is programmed, other settings will default to the OEM
components that were supplied on that engine.For
example, if LQ4 is selected, the coil, injector and MAP
sensor will automatically set to the OEM components.
Engine Size: Once the engine type has been selected, the
stock cubic inches will automatically be set. If the engine
has been modified with a different stroke or bore, select
and input the size. The range is from 100-800 cubic
inches (Figure 29).
Camshaft Type: There are three cam selections to choose;
Street/Stock, Mild and Performance. Note that if the
lobe separation angle (LSA) is less than 108°, it is
recommended to input the next larger cam. Cams with
over 250° are not recommended for use with the Atomic
LS system (Figure 29).
Handheld Main Menu
Engine Type
CAM
DURATION AT .050"
Street Stock Less than 210°
Mild 211° - 230°
Performance 231° - 250°
Coils: Once the engine type is selected, the OEM coil pack
will be automatically loaded in the default calibration
file. If a different coil or an MSD LS Coil pack is used,
change the setting to the correct coil type (Figure 29).
Note: There is a setting in Display Setup labeled User Mode.
When User Mode is changed from Basic to Advanced,
the coil selection menu will open up to all the coil
combinations preprogrammed into the Atomic LS
system.
Fuel Injector: Once the engine type is selected above, the
OEM style injector will be automatically loaded in the
default calibration file. If a different injector is used,
change the setting to the correct injector. Most LS
based injectors have the part number stamped on
them (Figure 30).
Note: There is a setting in Display Setup labeled User
Mode. When User Mode is changed from Basic
to Advanced, the fuel injector selection menu
Fuel Injector Type
will open up to all the fuel injector combinations
preprogrammed into the Atomic LS system.
This setting will also unlock a setting called
User Defined. User Defined allows the injector
flow rate to manually be entered by selecting
Set Calibration (Figure 30).
MAP Sensor: Once the engine type is selected above, the
OEM MAP Sensor will be automatically selected.
(Figure 30).
Fuel Injector
Note: There is a setting in Display Setup labeled User
Mode. When User Mode is changed from Basic
to Advanced, the MAP sensor selection menu
will open up to all the MAP Sensor combinations
preprogrammed into the Atomic LS system.
This setting will also unlock a setting called
User Defined. User Defined allows the Slope
and offset to manually be entered by selecting
Set Calibration.
Injector Lbs/Hr
Fuel Pump Type: There are three selections for the fuel pump
system. Select the system in use with the Atomic LS
Truck system (Figure 30).
•Pulse Width Modulated: This selection is used
only when running a returnless fuel system with NO
regulator.
•Non-PWM with Regulator: This selection is used
when running a return style system with a regulator.
•PWM with Regulator: This selection is used when
running a return style system with a regulator. It will
run the pump at 50% duty cycle at idle producing
quieter pump operation and will increase the duty
cycle to 100% as the throttle and injector load
increase.
Note: It is recommended to use Non-PWM with a regulator
when setting fuel pressure as the PWM setting may
decrease fuel pressure slightly at idle.
Idle RPM Target: Select the rpm that the engine should idle
at. The rpm range is adjustable in 25 rpm increments
(Figure 31).
Note: Running too high of an idle speed in an automatic
transmission equipped vehicle with a stock torque
converter can cause idle issues in gear.
Rev Limit: The rev limiter can be set as a fuel cut-off or ignition
cut-off limiter. The default setting is as a fuel cut-off
limiter set at 6500 RPM. The programming range for
both rev-limiters is 3000 RPM-10,000 RPM (Figure 31).
Idle RPM Target
The ignition cut should only be used on race vehicles
with a very free flowing exhaust. DO NOT use with
catalytic converters or severe damage may result!
Variable Cam Timing: The Atomic LS truck system supports
the factory Variable Cam Timing. The default setting
is set at Disable. Change the setting to Enable for use
with a factory VVT engine (Figure 31).
Once all of the settings in the Initial Setup menu are selected,
the Atomic has enough information to start and run the engine.
It is recommended to scroll through the advanced settings to
program selections that may be useful after the initial start up
(such as the cooling fan activation temperatures).
ADVANCED SETUP
The Advanced Setup features are optional as the Initial Setup
menu provides the Atomic EFI with the values needed to run
the engine. Features in the Advanced Menu are designed to
deliver additional features and advanced tuning functions to
further enhance the drivability and overall performance of the
engine.
Fans: This setting sets the temperatures to activate two electric
fans. Each circuit will be activated by supplying ground
through the Red (Pin A) and Orange (Pin H) wires of
the GT-Series 16 pin harness from the Power Module. A
relay is required for both circuits since those wires are a
low current ground. The fans will activate at the desired
temperature and will remain on until the temperature
falls below 10° of the setting. Settings are 100°-300°F
(Figure 31).
A/F Targets: The Atomic LS provides an option to set an air/fuel
target for Idle, Part Throttle, Wide Open (WOT), Nitrous
and Boost. The Atomic will use its self-learning technology
to adjust the fuel delivery to meet the target air/fuel ratio.
The values are adjusted in 0.1 increments and range from
rich at 10:1 to dead lean at 16:1. The ideal air/fuel ratio for
cruising is called stoichiometric and is commonly referred
as a 14.7:1 air/fuel ratio.
Boost: The Atomic will switch to the commanded boost
Ignition Timing: The Atomic provides a base timing table for each
engine application. You can also modify these settings at
idle (closed throttle), part throttle, wide open throttle (WOT),
nitrous, and boost. Each setting is adjustable +/-10°. Note
that the values programmed are set for stock engines using
91 octane fuel. For lower octane fuels it is recommended
to retard the timing 5° as a starting point. Timing can be
retarded up to 20° in 0.1° increments. Note that in order
Igniton Timing
to alter the timing for nitrous use, the Nitrous Selection in
the Advanced menu MUST be programmed to ENABLE.
When the nitrous is activated by supplying 12 volts to the
Brown/White (Pin C) wire the timing will retard (Figure 32).
TPS Enrichment: To assist in throttle transitions the Atomic EFI
has a feature to increase fuel delivery by a prescribed
percentage any time there is an increase in throttle
position. If needed, make small changes in no more than
5% increments without further testing. Most engines will
find 25% sufficient. Most applications will accept 15%-35%
TPS Enrichment
enrichment. Adjustable from 0-100% in 1% increments
(Figure 32).
MAP Enrichment: To assist in manifold pressure transitions the
Atomic EFI offers a MAP enrichment feature. This function
adds fuel based on MAP transitions while moving the
throttle. Large cam vehicles with low vacuum generally
required a slightly smaller number while stock/small
camshaft vehicles with a high vacuum may require more.
If needed make small changes of no more than 5%
increments without further testing, 25% is sufficient for
MAP Enrichment Setting
most engines but between 15-35% is normal. Typically,
the higher the vacuum the higher the percentage needed.
Adjustable from 0-100% in 1% increments (Figure 32).
2-Step: This setting will rev-limit the engine at the programmed
RPM when the Blue wire is activated with 12V. The 2-Step
setting is used in drag racing applications to help launch
the car at a consistant RPM. The blue wire is normally
connected to a clutch switch or a brake switch. The default
setting is 10,000 RPM and can be adjusted from 1000
RPM to 7500 RPM in 25 RPM increments (Figure 32). The
ignition cut should only be used on race vehicles with a
very free flowing exhaust. DO NOT use with catalytic
Nitrous: This setting enables the nitrous timing retard in the
Ignition timing and the nitrous AFR in AF Target setting.
The default setting is DISABLED (Figure 33).
Calibrate Speed: If there is speed output on the transmission,
a reference signal can be delivered to the Atomic
LS. On manual transmission equipped vehicles, the
Calibrate Speed option improves drivability when
transitioning from high RPM conditions to an idle
(such as comming off of a hill / between moving and
coming to a complete stop). The Power Module has
Advanced Setup
a Brown (Pin D) wire and a Light Blue (Pin E) wire.
These wires connect to a magnetic pickup monitoring
driveshaft speed with a collar mounted on a yoke. To
program the calibration, drive to 40mph on an open
road to maintain speed. Once at 40mph, select YES
on the handheld. This will calibrate the speed input.
This option will also enable a speedometer reading in
the handheld Atomic LS Dash (Figure 33).
Note: Use of a minimum four magnet collar is
recommended with this option.
Enable or Disable Nitrous
Racepak Dash: This setting allows the Atomic LS Truck kit to
interface with a Racepak dash such an IQ3. Disable is
the default setting. Racepak offers an optional V-net
sensor to connect their dash to the MSD Can-Bus
connector (Figure 33).
ensure the crank sensor is providing an RPM signal.
HANDHELD DISPLAY OPTIONS
Display Setup: The display Setup controls the look of the
handheld unit and the Firmware version. The Atomic
LS can be reset to factory default in this section as well
(Figure 34).
LCD Contrast: Adjust the contrast on the LCD screen if it is
hard to see the display. Contrast is adjusted using the
joystick to go up or down in five percentage increments.
Backlight Level: The brightness of the screen is determined
by this setting. The Backlight Level may need to be
adjusted depending on outside light levels. Brightness
is adjusted using the joystick to go up or down in five
percentage increments (Figure 34).
Display Units: The Atomic can display items in either English (cubic inches, Fahrenheit) or Metric
(liters, Celsius). Set Atomic Defaults: Use this feature to reset the Atomic EFI. Selecting “YES”
on this screen will take all setting, including fuel maps, back to the factory defaults. This can
be done when installing the Atomic on a different engine, or for troubleshooting reasons
(Figure 34).
User Mode: This setting can be changed from Basic to Advanced. When the User Mode setting is
changed to Advance the fuel injector selection menu, coil selection menu, and the MAP sensor
menu will open up to all the combinations preprogrammed into the Atomic LS system. The
fuel injector flow rate and MAP sensor Slope and Offset can be manually entered by selecting
user defined in the selection menu (Figure 34).
Set Atomic Defaults: This setting resets all the programming parameters to the default settings out
of the box (Figure 34).
Firmware Versions: The Atomic Firmware version can be found in this section (Figure 34).
The Atomic LS Dash is a live display when the engine is running.
This is a brief description of each parameter in the Atomic LS Dash.
ATOMIC LS DASH:
Tach Displays engine RPM.
Speed Displays Speed if speed if speed sensor is equipped and calibrated.
ECT Displays coolant temperature.
IAT Displays intake air temperature.
TPS Displays throttle position sensor percentage.
BARO Displays barometric pressure
MAP Displays manifold absolute pressure
FUEL PRESS Displays fuel pressure.
OIL PRESS Displays oil pressure.
BAT VOLTS Displays battery voltage.
A/F RATIO Displays air/fuel ratio.
INJ DUTY Displays injector duty cycle.
IGN TIMING Displays ignition timing.
IAC POS Displays idle air control motor position.
THROTTLE Displays throttle condition closed/part/WOT (Wide Open Throttle)
CLOSED LOOP Displays closed loop on or off.
LEARNING Displays Atomic LS learning on or off.
FAN 1 Displays Fan 1 on or off.
FAN 2 Displays Fan 2 on or off.
DECEL FUEL Displays if decel fuel is active
IDLE COND Displays if engine is in an idle condition
FLOOD CLEAR Displays if throttle is in a flood clear condition (no fuel will go in)
REV LIMIT Displays if the rev limiter is active
TWO STEP Displays if the two step is active.
NITROUS Displays if the nitrous is active.
The following chart gives the most likely solution(s) to each
possible error.
Figure 35
CLEARING HISTORY ERRORS
CODE NAME
TPS
MAP
IAT
ECT
BATT
INJ DC
FUEL
PRESSURE
WBO2
WHAT IT MEANS
There is no reading for the Throttle Position Sensor.
There is no reading for the Manifold Absolute Pressure Sensor.
There is no reading for the Inlet Air Temperature Sensor. The ECU will default
to 275°F when shorted or -40°F when
open.
There is no reading for the Engine Coolant Temperature Sensor. The ECU will
default to 275°F when shorted or -40°F
when open.
The Atomic is receiving the wrong voltage. The unit is measuring either less
than 9 volts or greater than 16 volts.
Excessive Injector Duty Cycle
There is no reading for the Fuel Pressure
Sensor.
A. "NOT CONNECTED" indicates that no
sensor is detected.
B. "ERROR" indicates that the sensor
has failed.
PROBABLE CORRECTION(S)
The sensor may be at fault. Check wiring and/or replace sensor.
The sensor maybe at fault. Check wiring and/or replace sensor.
Faulty sensor; loose or no connection. Check wiring and/or replace sensor.
Faulty sensor; loose or no connection. Check wiring and/or replace sensor.
Check the battery connection from the Power Module to the
battery. Ensure that the battery and alternator are working correctly.
If you are running a returnless fuel system, your engine's needs
may exceed the Atomic's maximum capabilities. If you are running a return system check to see that you are maintaining the
recommended fuel pressure. If you have adequate fuel pressure the engine's needs may exceed the Atomic's system capabilities.
Faulty sensor; loose or no connection. Check wiring and/or replace sensor.
A. Check to see that the sensor is securely plugged into the
system. Inspect wiring if it is plugged into the system.
B. The sensor will need to be replaced.
Note that 'warming up' is normal during start-up for the first 20
seconds.
FP CAV
MAP SELECT
BARO
This code will set if there is an issue with
Fuel Pump Cavitation (similar to vapor
lock). It can only set when running a
returnless fuel system. This may occur
when the commanded fuel pressure
(from the ECU) is different than the fuel
pressure (at the sending unit).
ECU compares the MAP reading with
the Baro reading on key up. If these are
different by more than 5kPa, the code
is activated.
The Baro sensor voltage is out of range,
and the ECU has defaulted to the last
known good Baro value.
Check the fuel system and etermine that it meets the requirements
to run a returnless (PWM) system. Check the filters, the sock in
the tank, and inspect the lines for any kinks or pinches that
would affect the fuel flow and pressure of the system. If the code
continues, the fuel system may need to be converted to an in-tank
fuel pump and/or regulated (return) fuel system.
Double check your MAP selection and make sure that you
selected the correct P/N of sensor. It could also mean a problem
with the Baro or MAP sensor itself (see above codes).
Turn the ignition off. Wait 10 seconds, and turn the ignition
back on. If the code remains, call customer service. Unless the
vehicle has been through a large change in altitude since the
last ignition on/off cycle (towed somewhere), everything will
function normally.
If a flood condition occurs, turn the key on then press the accelerator to wide-open throttle. This tells
the ECU to turn off the injectors. Crank the engine to clear the flood condition until the engine starts
(release the throttle).
Note: The TPS is self calibrating so the key must be in the ON position prior to pressing the accelerator.
INSTRUCTIONS FOR UPDATING THE ATOMIC EFI
In order to update the Atomic EFI you will first need to download the updated files from AtomicEFI.com.
(Right click and choose "Save Target As" if it doesnt download automatically)
UPDATED: 05-31-13 Version numbers below.
ALL THREE UPDATES MUST BE DONE SIMULTANEOUSLY
1. The update will reset all settings in the Atomic EFI.
a. Be sure that you make note of all settings in the Initial and Advanced Set-ups prior to performing
the update.
2. Download the update files from AtomicEFI.com
a. Be sure they are saved in a place that you will find them (the desktop is often the best place to
save them).
b. DO NOT rename the files, the Atomic EFI will only recognize files with the names assigned by
MSD.
3. Transfer the files to the Micro-SD Card that came with the Atomic.
You will need an SD Card reader for this – if you do already not have a reader, they can be found at
most electronics stores for less than $10.
a. Open the Micro-SD card’s window on your computer.
b. Drag and drop the MSD files into the folder.
c. The files must remain in the main folder do NOT put them in a sub-folder.
4. Move the Micro-SD card to the Atomic EFI’s Handheld
5. Ensure the Handheld is plugged in to the Power Module
6. Turn the vehicle’s ignition switch to Key-On
a. Do not start the engine
7. At this time the Atomic will automatically update the Handheld.
a. This process will take approximately 30 seconds, do not remove power.
8. When the handheld update is complete you will be prompted to update the Atomic ECU as well.
a. Use the Handheld joystick see “YES” by pushing the joystick up.
b. Push the joystick in to accept.
9. At this time the Atomic ECU will be updated.
a. This process will take approximately 30 seconds.
b. The beginning of this process will display “Erasing” – this is normal, do not remove power.
c. The handheld’s screen will notify you when the update is complete.
10. Use the handheld’s joystick to go back (left) to the main menu.
11. Input all previous settings for the Initial and Advanced setups.
12. Enjoy your updated Atomic EFI.
You can check to see that the Atomic update is successful by looking at the version numbers on the
Handheld. To do so go to:
In case of malfunction, this MSD component will be repaired free of charge according to the terms of the warranty.
When returning MSD components for warranty service, Proof of Purchase must be supplied for verification. After
the warranty period has expired, repair service is based on a minimum and maximum fee.
All returns must have a Return Material Authorization (RMA) number issued to them before
being returned. To obtain an RMA number please contact MSD Customer Service at 1 (888) MSD-7859 or visit
our website at www.msdperformance.com/rma to automatically obtain a number and shipping information.
When returning the unit for repair, leave all wires at the length in which you have them installed. Be sure to include
a detailed account of any problems experienced, and what components and accessories are installed on the vehicle.
The repaired unit will be returned as soon as possible using Ground shipping methods (ground shipping is covered
by warranty). For more information, call MSD at (915) 855-7123. MSD technicians are available from 7:00 a.m. to
5:00 p.m. Monday - Friday (mountain time).
Limited Warranty
M
SD warrants this product to be free from defects in material and workmanship under its intended normal use*,
when properly installed and purchased from an authorized MSD dealer, for a period of one year from the date of
the original purchase. This warranty is void for any products purchased through auction websites. If found to be
defective as mentioned above, it will be repaired or replaced at the option of MSD. Any item that is covered under
this warranty will be returned free of charge using Ground shipping methods.
This shall constitute the sole remedy of the purchaser and the sole liability of MSD. To the extent permitted by
law, the foregoing is exclusive and in lieu of all other warranties or representation whether expressed or implied,
including any implied warranty of merchantability or fitness. In no event shall MSD or its suppliers be liable for special
or consequential damages.
*Intended normal use means that this item is being used as was originally intended and for the original application
as sold by MSD. Any modifications to this item or if it is used on an application other than what MSD markets the
product, the warranty will be void. It is the sole responsibility of the customer to determine that this item will work for
the application they are intending. MSD will accept no liability for custom applications.