Li 8100

Using the LI-8100A
Soil Gas Flux System

& the LI-8150 Multiplexer
with support for

Using the LI-8100A Soil Gas Flux System
and the LI-8150 Multiplexer
LI-COR Biosciences
4647 Superior Street
Lincoln, Nebraska 68504
Phone: +1-402-467-3576
Toll free: 800-447-3576 (U.S. and Canada)
envsales@licor.com
Regional Offices
LI-COR Biosciences GmbH

Siemensstraße 25A
61352 Bad Homburg
Germany
Phone: +49 (0) 6172 17 17 771
envsales-gmbh@licor.com
LI-COR Biosciences UK Ltd.

St. John’s Innovation Centre
Cowley Road
Cambridge
CB4 0WS
United Kingdom
Phone: +44 (0) 1223 422102
envsales-UK@licor.com
LI-COR Distributor Network:

www.licor.com/env/distributors
NOTICE
The information contained in this document is subject to change without notice. LI-COR MAKES NO WARRANTY OF
ANY KIND WITH REGARD TO THIS MATERIAL, INCLUDING, BUT NOT LIMITED TO THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. LI-COR shall not be liable for
errors contained herein or for incidental or consequential damages in connection with the furnishing, performance, or
use of this material.
This document contains proprietary information, which is protected by copyright. All rights are reserved. No part of this
document may be photocopied, reproduced, or translated to another language without prior written consent of LI-COR,
Inc.
Printing History
Printing History: 1st Printing May, 2010
Major Revision: August, 2015
Build Date: 01/2020
© Copyright 2010-2015, LI-COR, Inc.
Publication Number: 984-11123
New editions of this manual will incorporate all material since the previous editions. Update packages may be used
between editions, which new information to be merged into the manual by the user. The printing date indicates the edi-
tion. The printing date changes when a new edition is printed. Minor corrections and updates, which are incorporated at
reprint, do not cause the date to change.
The LI-8100A is covered by U.S. Patent #7,509,836; 7,568,374; 7,748,253; 7,856,899, China Patent #ZL200580042074.0 and
other foreign equivalents.
Microsoft® and Windows® are registered trademarks of Microsoft Corporation. Eurofast® is a registered trademark of
Turck Inc. CompactFlash® is a registered trademark of SanDisk Corporation in the United States. Apple®, the Apple
logo, iPod®, iPad, and iPod Touch® are registered trademarks of Apple Inc. App Store is a service mark of Apple Inc.
Google Play is a trademark of Google Inc. Ascarite II is a registered trademark of the Arthur H. Thomas Company. Drier-
ite is a registered trademark of the W. A. Hammond Drierite Company, Ltd. All other trademarks or registered trade-
marks are the property of their respective owners.
ii
Notes on Safety
This LI-COR product has been designed to be safe when operated in the manner described in this manual. The safety of
this product cannot be assured if the product is used in any other way than is specified in this manual. The product is
intended to be used by qualified personnel. Read this entire manual before using the product.
Equipment markings:
The product is marked with this symbol when it is necessary for you to refer to the manual or
accompanying documents in order to protect against injury or damage to the product.
The product is marked with this symbol when a hazardous voltage may be present.
The product is marked with this symbol if a Chassis Ground connection is required.
The product is marked with this symbol to indicate that a direct current (DC) power supply is
required.
WARNING Warnings must be followed carefully to avoid bodily injury.
CAUTION Cautions must be observed to avoid damage to your equipment.
Manual markings:
Warning Warnings must be followed carefully to avoid bodily injury.

Caution Cautions must be observed to avoid damage to your equipment.
Note Notes contain important information and useful tips on the operation of your equipment.
NOTE: This equipment has been tested and found to comply with the limits for a Class A digital device, pursuant to Part
15 of the FCC Rules. These limits are designed to provide reasonable protection against harmful interference when the
equipment is operated in a commercial environment. This equipment generates, uses, and can radiate radio frequency
energy and, if not installed and used in accordance with the instruction manual, may cause harmful interference to radio
communications. Operation of this equipment in a residential area is likely to cause harmful interference in which case
the user will be required to correct the interference at his own expense.
CE Marking:
This product is a CE-marked product. For conformity information, contact LI-COR Support at envsupport@licor.com.
Outside of the U.S., contact your local sales office or distributor.
iii
LI-8100A
LI-8100A Automated Soil Gas Flux System
Part Name Toxic and Hazardous Substances or Elements
(Pb) (Hg) (Cd) (Cr(VI)) (PBB) (PBDE)
X O O O O O
PCBs)
Electro- X O X O O O
mechanical Parts)
X O O O O O
Optics)
X O O O O X
Cables and Wires)
X O O O O O
(Metal Parts)
O O O O O O
(Plastic Parts)
SJ/T 11364
O= GB/T 26572
(indicates that the content of the toxic and hazardous substance in all the Homogeneous
Materials of the part is below the concentration limit requirement as described in GB/T 26572).
X= GB/T 26572
(indicates that the content of the toxic and hazardous substance in at least one Homogeneous
Material of the part exceeds the concentration limit requirement as described in GB/T 26572).
Doc. #53-15988-A
June 22, 2016
page 1 of 1
iv
Contents
Section 1. Getting started

What is the LI-8100A? 1-1
Useful software 1-1
The LI-8100A PC Software 1-1
The LI-8100App 1-1
SoilFluxPro Software 1-2
What's what 1-2
Analyzer control unit 1-2
Auxiliary sensor interface 1-3
RS-232 serial cable 1-3
Ethernet cable 1-3
Ethernet card 1-3
Wireless router 1-4
CompactFlash® memory card 1-4
Shoulder strap kit 1-4
Calibration sheet 1-4
Spare parts kit 1-5
Optional accessories 1-5
Chambers 1-9
10 cm survey chamber 1-9
Long-term chambers 1-12
The measurement cycle 1-13
Terminology 1-13
Theory of operation 1-19
Measuring carbon dioxide flux from soils 1-19
Deriving the flux equation: the model 1-20
Measuring net carbon exchange 1-28
Section 2. Initial setup

First Things First 2-1
Get connected 2-3
Connecting over serial or USB 2-3
Connecting directly over Ethernet 2-4
Connecting over a local area network 2-5
Connecting to a computer over wireless 2-6
Connecting with iOS version 8.4.1 and older 2-8
Connecting with the TP-Link Wireless Router 2-10
Exploring the analyzer control unit 2-13
v
Batteries 2-13
Indicator panel 2-13
The measurement flow path 2-14
PC adapter cards 2-15
About data records and storage options 2-16
Wireless card 2-17
Air filters 2-17
Using soil collars 2-17
Tips for installing and using soil collars 2-18
Insertion depth 2-18
Measuring the chamber offset 2-18
More details on the survey chambers 2-21
The bellows flow path 2-23
Connecting a survey chamber 2-24
More details on the long-term chambers 2-25
Connecting a long-term chamber 2-26
Leveling the chamber 2-28
Changing the long-term chamber open position 2-28
Tips for using the 8100-104C clear chamber 2-30
Shading effects 2-30
Measuring photosynthetically active radiation 2-30
Section 3. Making single-chamber measurements

An indoor tutorial 3-1
An outdoor tutorial 3-3
Survey measurements checklist 3-5
Automatic restart function 3-6
Using the auxiliary sensor interface 3-8
Auxiliary sensor interface terminals 3-9
Connecting auxiliary sensors 3-11
Connecting the Omega soil temperature probe 3-13
Connecting the GS1 soil moisture probe 3-14
Connecting the EC-5 soil moisture probe 3-15
Connecting the 8100-203 soil temperature probe 3-16
Connecting the Delta-T ThetaProbe 3-17
Placing soil temperature and moisture probes 3-18
Tips for success 3-19
Section 4. Overview of the LI-8150 multiplexer

What's what 4-1
Cable and tube assembly 4-1
Power cable 4-2
Spare parts kit 4-2
vi
AC to DC power supply 4-2
Cable and tube extension 4-2
Soil moisture probes 4-3
Soil temperature thermistor 4-3
How it works 4-4
Using the AC to DC power supply 4-6
LI-8100A and LI-8150 cable connections 4-10
Section 5. Using the multiplexer

Do this first 5-1
Multiplexed measurement tutorial 5-1
Long-term measurements checklist 5-8
Connecting the GS1 soil moisture probe 5-10
Connecting the 8150-203 soil temperature probe 5-12
Connecting the LI-190R Quantum Sensor 5-14
Connecting other sensors 5-18
The leak test 5-19
Section 6. Transferring data from the LI-8100A

Transfer data over a serial, USB, or network connection 6-1
Transfer data from the CompactFlash card 6-2
About data files 6-3
Header variables 6-5
Raw records and summary records 6-7
System variables 6-9
Footer variables 6-10
Section 7. Calibrating the LI-8100A

Carbon dioxide and water vapor gas standards 7-2
Zero gases 7-2
Carbon dioxide span gases 7-3
Water vapor span gases 7-3
Setting the zeros 7-4
Setting the span: Carbon dioxide 7-6
Setting the span: Water vapor 7-7
Two point span 7-8
vii
Section 8. Troubleshooting
System will not power on or powers on incompletely 8-1
Connection and communication problems 8-2
Cannot connect to the instrument over wireless 8-2
Cannot connect to the instrument over Ethernet 8-3
Cannot connect over RS-232 serial or USB 8-3
LI-8100A will not recognize the multiplexer 8-4
Chamber issues 8-4
Long-term chamber will not close or open 8-4
Survey chamber will not close or open, or does so very slowly 8-4
Measurements stop immediately after starting 8-5
Data and measurement issues 8-5
Unexpected drift, shift in data values, or lack of responsiveness 8-5
Noisy data 8-5
High initial carbon dioxide concentrations 8-6
Low flow rate 8-7
Unreasonable RH readings 8-7
Unreasonable chamber temperature readings 8-7
Still having trouble? 8-7
Section 9. Maintenance
Analyzer control unit maintenance 9-1
Updating the instrument software 9-1
Replacing the air filters 9-3
Cleaning the optical bench 9-4
Fuses 9-10
6400-03 batteries 9-13
10 cm survey chamber maintenance 9-15
Replacing the gaskets 9-15
Replacing the bellows on the 10 cm chamber 9-18
Foam seal gasket 9-21
Soil collar gasket 9-22
Chamber gasket 9-22
Long-term chamber maintenance 9-28
Replacing the collar gasket 9-28
Replacing the tubing and cable assembly 9-28
Replacing the thermistor assembly 9-32
Replacing the shaft seal assembly 9-33
Changing the clear and opaque chamber bowls 9-36
Multiplexer maintenance 9-39
Multiplexer fuses 9-39
viii
Tubing 9-40
Air filters 9-40
Solenoid valves 9-41
Section 10. Customizations and other applications

Trace gas flux measurements 10-1
Flask measurements 10-1
Profile measurements 10-2
Trace gas sampling kit 10-2
Chamber control kit 10-2
The GPS accessory 10-2
XML communication 10-3
Logging data to a computer 10-4
Making soil collars 10-4
Appendix A. Specifications
Appendix B. Software compatibility table
Appendix C. Pin assignments
Appendix D. References
Appendix E. Warranty
Appendix F. Index
ix
x
Section 1.
Getting started
What is the LI-8100A?

The LI-8100A is an automated system for measuring soil CO2 flux. It can be used
to survey a study site with one portable chamber or deployed for long-term meas-
urements with one chamber. It can also support up to 16 chambers with the mul-
tiplexer. For gases other than CO2 , you can add another trace gas analyzer to the LI-
8100A system and compute flux of the other gases.
The LI-8100A is configured from a computer running the Windows® operating sys-
tem, but with the optional wireless communication card you can configure and
operate the LI-8100A from older iPhone®, iPod touch®, iPad® (iOS version 8.4.1
and older). With the TP-LINK battery-powered router you can use any iOS device
and most Android devices.
Useful software
The following software applications are available for the LI-8100A.
The LI-8100A PC Software

The PC software provides all the functionality of the app and more—including
charts and data transfer capabilities—through computer running the Windows oper-
ating system. With this software, you can connect using Ethernet, RS-232, or wire-
lessly if the LI-8100A is equipped with a wireless communication card.
The LI-8100App
The LI-8100APP is the simplest way to use the LI-8100A. Download the
LI-8100APP on the Apple® App Store or Google Play™.
Using the LI-8100A 1-1

Note: The Android app is only compatible with devices that use 32-bit archi-
tecture (ARMv7 or earlier). It will not run on devices that use 64-bit architecture.
l For older devices, you can use the Cisco wireless communication card. See Con-
necting with iOS version 8.4.1 and older on page 2-8.
l For newer iOS devices, Android devices, or Windows PCs, you can use a battery-
powered router. See Connecting with the TP-Link Wireless Router on page 2-10.
SoilFluxPro Software
SoilFluxPro™ software (formerly FV8100) is a free PC- and Mac-compatible applic-
ation for analyzing data from the LI-8100A. In SoilFluxPro, you can recompute
data sets, graph data, analyze results, and create .kml files for mapping geor-
eferenced measurements. SoilFluxPro is an essential part of the LI-8100A system.
Get it from http://www.licor.com/soilfluxpro.
What's what
If you have just taken delivery of your LI-8100A check the packing list to verify that
you received everything ordered, including the following items:
Analyzer control unit

The analyzer control unit houses the system elec-
tronics and infrared gas analyzer. The interior of the
control unit contains the indicator panel, brackets for
the optional rechargeable battery, and an access panel
that provides access to the memory card, wireless card,
filters, and other components.
1-2 Using the LI-8100A

Auxiliary sensor interface

The auxiliary sensor interface (part num-
ber 8100-663) is to connect up to 8 ancil-
lary sensors to the LI-8100A system
without a multiplexer. It also provides
connections for an external power supply.
Typically you'll connect soil moisture
probes or temperature probes to the inter-
face, but you can log analog data from
nearly any sensor. See Using the auxiliary
sensor interface on page 3-8.
RS-232 serial cable

The RS-232 serial cable (part number 392-10587) is a 2-meter cable with a round
connector on one end that connects to the RS-232 serial port on the left side of the
analyzer control unit. The other end of the cable has a 9-pin female DB- 9 con-
nector for attaching to your computer.
Most modern computers don't have an RS-232 serial port, so you'll need to use the
serial-to-USB adapter (part number 6400-27) to make this connection. LI-COR
provides a serial-to-USB adapter that is compatible with our instruments. Not all
serial-to-USB adapters will work, however. The adapter must have the FTDI chipset
to be compatible.
Ethernet cable
The Ethernet cable (part number 392-09436) is a 2-meter cable with a round con-
nector on one end that connects to the Ethernet port on the left side of the analyzer
control unit. The other end of the cable has an RJ45 (Ethernet) connector for
attaching to your computer or to a network wall socket.
Ethernet card
The Ethernet card (part number 6400-26) is installed in the LI-8100A prior to deliv-
ery. It fits into one of the two internal PCMCIA (PC) card slots under the analyzer
control unit access panel. The card has an RJ45 junction that connects to an
internal Ethernet cable.
Auxiliary sensor interface 1-3

Wireless router
A TP-LINK TL-MR3040 wireless router (part number 590-16299) may be included
in the spares kit. The wireless router is required if you want to connect with the LI-
8100A using an iOS device (running iOS 9.0 and newer) or Android OS devices.
See Connecting with the TP-Link Wireless Router on page 2-10 for details.
CompactFlash® memory card

NOTE: Type II CompactFlash cards are slightly thicker than Type I cards; as a res-
ult, the adapter sleeve is also thicker, and may be more difficult to remove from
the LI-8100A Analyzer Control Unit case when inserted in tandem with a wire-
less card.
The CompactFlash memory card (part

number 8100-554) and adapter sleeve are
installed in the LI-8100A prior to deliv-
ery. It is a Type I industrial grade card
rated for high temperature use. Other
commercially available cards are com-
patible with the LI-8100A. However, we
cannot guarantee their stability under
high temperatures. Type II Com-
pactFlash cards can also be used with the
LI-8100A, with the appropriate adapter
sleeve.
Shoulder strap kit

The shoulder strap (part number 604-10643) can be attached to the analyzer con-
trol unit. Clip the strap ends to the rings that are attached to the analyzer control
unit on either side of the handle.
Calibration sheet
This calibration sheet is a copy of the calibration information entered into the LI-
8100A at the factory. Keep it in a safe place for future reference. LI-COR also
retains copies of calibration information for your soil CO2 flux system.

Spare parts kit

This box contains replacement parts for your LI-8100A. As you become familiar
with the system you will learn which items to keep close at hand and which items
to store away. Additional spares kits are packaged with the soil chambers. An
optional bellows kit (part number 8100-623) is also available from LI-COR that can
be used to replace damaged bellows on either the 10 cm or 20 cm Survey Cham-
bers.
The spares kits include these commonly used items:
Description Qty. LI-COR Part No.

Analyzer Control Unit Spares Kit 1 9981-032
O-rings 20 192-02597
Bev-a-line Tubing 10' 222-01824
Balston Disposable Air Filters 2 300-01961
Quick Connect Straight Union 1 300-03123
Quick Connect Right Angle 2 300-03125
Quick Connect Plug 2 300-07124
Quick Connect Coupling 1 300-07125
Quick Connect Union “Y” 2 300-03367
Quick Connect Port Plug 1 9981-118
3 Amp Fuse 1 439-04215
Auxiliary Sensor Interface Spares Kit 1 9981-028
Strain Relief 5 198-07221
EPDM Plugs 10 610-08324
Santoprene 1’ 222-08325
3 Amp Fuse 1 439-04215
Optical Bench Kit 1 9981-029
Wrapped Point Cleaning Swabs 5 610-05314
Sock Tip Swab 5 610-05315
Bev-a-line Tubing 1' 222-01824
O-rings 4 192-00226
Optional accessories
Optional accessories may be included with your system. If not, they are available
form LI-COR or your distributor.
Spare parts kit 1-5

6400-03 Rechargeable battery

The 6400-03 rechargeable batteries are 12
volt lead acid batteries. Batteries are
charged prior to shipping, but may dis-
charge during shipping and storage. It is
a good idea to test your batteries to make
sure they are charged.
The 6400-03 batteries require the LI-6020
Battery Charger for recharging. One
6400-03 battery provides approximately 3-
4 hours of battery life at 25 °C, depend-
ing on pump usage or wireless card
usage.
NOTE: There are 2 battery connectors in the case. You can attach a second, fully
charged battery before removing the discharged battery to provide uninterrupted
operation.
LI-6020 Battery charger

The LI-6020 can charge up to four 6400-03 batteries at a time. It is compatible with
115 and 230 VAC main power.
Soil temperature probes

The Omega Soil Temperature Probe (6000-09TC) is a 2-wire thermocouple sensor
that can be wired to the auxiliary sensor interface for survey measurements.
l See Connecting the Omega soil temperature probe on page 3-13 to connect to the
auxiliary sensor interface.
The 8100-203 and 8150-203 soil temperature probe has a 2-wire adapter cable for
connection to the auxiliary sensor interface. Alternatively, the connector can be
removed for installation into a long-term chamber when using the multiplexer.
l The 8100-203 is a bare wire thermistor used for single-chamber long term meas-
urements. It connects to the auxiliary sensor interface (see Connecting the 8100-
203 soil temperature probe on page 3-16).

l The 8150-203 thermistor probe has a plug for direct connection to the 8100-
104/C Long Term Chambers when used with the multiplexer (see Connecting
the 8150-203 soil temperature probe on page 5-12).
Soil moisture probes

The GS1 Soil Moisture Sensor (Decagon Devices, Inc., Pullman, WA) is a dielectric
sensor that measures volumetric water content of the soil.
l The 8100-205 probe has a 3-wire connector for connection to the auxiliary
sensor interface on the LI-8100A (see Connecting the GS1 soil moisture probe on
page 3-14).
l The 8150-205 probe has a plug for direct connections to the 8100-104/C Long
Term chambers when used with the multiplexer (see Connecting the GS1 soil
moisture probe on page 5-10).
The ECH2O Model EC-5 soil moisture probe (Decagon Devices, Inc., Pullman,
WA) is a dielectric sensor that measures volumetric water content of the soil.
l The 8100-202 probe has a 3-wire connector for connection to the auxiliary
sensor interface on the LI-8100A (see Connecting the EC-5 soil moisture probe on
page 3-15).
l The 8150-202 probe has a plug for direct connection to the 8100-104/C Long
Term chambers when used with the multiplexer (see Connecting the EC-5 soil
moisture probe on page 5-11).
The Delta-T ThetaProbe is a more durable sensor that provides a more precise meas-
urement of volumetric water content.
l The 8100-204 probe has bare wire leads, and is for use with the auxiliary sensor
interface (see Connecting the Delta-T ThetaProbe on page 3-17).
l The 8150-204 probe has a connector pre-installed for direct connection to the
8100-104/C long-term chambers when used with the multiplexer (see Con-
necting the Delta-T ThetaProbe on page 5-13).
8100-104 and 8100-104C conversion kits

The 8100-104 long-term chamber’s opaque “bowl” can be swapped out with the
clear bowl used on the 8100-104C long-term chamber (using part number 8100-

910), and vice versa (using part number 8100-911). Each kit includes the replace-
ment chamber bowl and all mounting hardware required.
Wireless communications package1

The wireless communications package (part number 8100-565) includes 8100-570
Apple iPod Touch (32 GB), serial cable (part number 392-10587), USB-to-RS232
adapter (part number 6400-27), wireless card (part number 8100-552), and iPod
Micro Case (part number 8100-571).
GPS mapping kit

The mapping kit (part number 8100-405) is an accessory for use with the LI-8100A
Automated Soil CO2 Flux System when making survey measurements with the
8100-102 or 8100-103 chamber or for continuous measurements. The mapping kit
adds geographical data (latitude, longitude, speed, and direction) to observations of
soil CO2 flux or CO2 concentration. The mapping kit can be used with the survey
chambers to map soil CO2 flux data across the area of interest, or it can be used in
a continuous measurement mode (without a chamber) to map CO2 concentrations
across a transect.
The mapping kit includes a GPS receiver (part number 9981-185), mounting
bracket (part number 9981-211), 12-pin Eurofast splitter cable (part number 392-
12388), and spare parts kit (part number 9981-186) with intake tube and con-
nectors. See The GPS accessory on page 10-2 for details.
1May not be available in all areas.

Chambers
Depending on the system you ordered, you may have one or more of the following
chambers.
10 cm survey chamber
The 10 cm survey chamber (8100-102) includes the chamber, spares kit (part num-
ber 8100-621), replacement gasket kit (part number 8100- 622), and the 6000-09TC
soil temperature probe.
Spares kit
Table 1-1. The 10 cm chamber spares kit components.
10 cm Survey Chamber Spares Kit 1 8100-621
Cable Ties 10 218-08499
Bev-a-line Tubing (11'; 3.35 m) 1 222-01824
Thumb Nut 4 165-00140
10 cm Soil Collars 6 6581-157
Gasket kit
Table 1-2. The 10 cm chamber gasket kit components.
10 cm Survey Chamber Gasket Kit 1 8100-622
Foam Seal Gaskets 20 6560-229
Soil Collar Gaskets 2 6581-065
Chamber Flange Gaskets 2 6581-066
Manifold Gaskets 2 6581-057
Chamber Gasket Trim (2.2'; 0.67 m) 1 226-07390
Loctite Adhesive 1 208-05786
10-32 x 1/2" screws 4 122-00014
4-40 x 3/8" screws 18 122-01578
8-32 x 1/2" screws 4 122-04328
Chambers 1-9
Bellows kit
The bellows kit is an optional accessory that can be purchased individually.
Table 1-3. The bellows kit components.

LI-8100A Bellows Kit (optional) 1 8100-623
Silicone Lubricant 1 210-01958-1
10-32 x 1/2" screws with o-ring 4 138-07470
Manifold Gasket 1 6581-057
Bellows, 3" I.D. x 4.25" O.D. 1 254-7219
20 cm survey chamber
The 20 cm survey chamber (8100-103) includes the chamber, spares kit (part num-
ber 8100-631), replacement gasket kit (part number 8100- 632), and the 6000-09TC
soil temperature probe.
Spares kit
Table 1-4. The 20 cm survey chamber spares kit components.
8100-103 Survey Chamber Spares Kit 1 8100-631
Cable Ties 10 218-08499
Bev-a-line Tubing (11'; 3.35 m) 1 222-01824
Thumb Nut 4 165-00140

Gasket kit
Table 1-5. The 20 cm survey chamber gasket kit components.
20 cm Survey Chamber Gasket Kit 1 8100-632
Cap Nuts 4 163-02618
Foam Seal Gaskets 20 6581-107
Manifold Gaskets 2 6581-057
Soil Collar Gaskets 4 6581-108
Chamber Gasket Trim (6'; 1.8 m) 1 224-07606
10-32 x 1/2" screws 4 122-00014
4-40 x 3/4" screws 2 158-07847
Flat washer, #10 4 167-00154
Bellows kit
The bellows kit is an optional accessory that can be purchased individually.
Table 1-6. The bellows kit components.

LI-8100A Bellows Kit (optional) 1 8100-623
Silicone Lubricant 1 210-01958-1
10-32 x 1/2" screws with o-ring 4 138-07470
Manifold Gasket 1 6581-057
Bellows, 3" I.D. x 4.25" O.D. 1 254-7219

Long-term chambers
The 8100-104 and 8100-104C long-term chamber include the chamber, spares kit
(part number 8100-613), and a replacement gasket kit (part number 8100-612).
Chamber spares kit

Table 1-7. The long-term chamber spares kit components.
8100-104/C Long-Term Chamber Spares Kit 1 8100-613
Cable Ties 9 218-08499
Urethane Tubing (6'; 1.8 m) 1 222-00303
Thumb Nut 4 165-00140
Bumpers 4 191-08069
Cap Plugs 5 620-08297
Gasket kit
Table 1-8. The long-term chamber gasket kit components.
8100-104/C Long-Term Chamber Gasket Kit 1 8100-612
Collar Gasket 2 6581-060
Chamber Gasket Trim (6'; 1.8 m) 1 224-07606
6-32 x 3/8" screws 4 122-00009
4-40 x 3/8" screws 18 122-01578

The measurement cycle

The measurement cycle begins with an optional pre-purge period with the chamber
open, after which the chamber closes. Upon closing, the dead band starts and the
instrument begins logging data. When the observation is finished the post-purge
begins. Then the cycle repeats as configured.
CO2 Concentration
(µmol/mol)
Measurement (2 observations)
Observation #1 Observation #2
Chamber Chamber Observation Chamber Chamber Observation

Opens Closes Length Opens Closes Length
Pre-purge Dead Data Post- Pre-purge Dead Data

(optional) Band Logged purge (optional) Band Logged
Time
Figure 1-1. A typical measurement cycle.
Terminology
This section addresses terminology of the measurement and software. The com-
puter software and mobile apps use the same terminology where possible but slight
differences may occur from time to time.
Chamber
Under the configuration menu, select the chamber connected to the port. Select
Custom to enter information about a user-constructed chamber, or select a chamber
from the list.
Chamber offset
The chamber offset is used to compute volume of the system. See Measuring the
chamber offset on page 2-18 for details.
The measurement cycle 1-13

Dead band
The dead band is the time period that starts when the chamber closes completely,
and continues until steady mixing is established and the measurement begins. The
dead band requirement changes depending upon the chamber geometry, system
flow rate, collar, and site characteristics. A dead band between 10 and 30 seconds
generally provides adequate mixing, but the actual time can (and should) be optim-
ized in post processing in SoilFluxPro.
Destination
Data collected by the LI-8100A is stored to the instrument's internal memory or to
an optional CompactFlash card. You can log to one or the other, but not both at
the same time. Data stored to the internal memory can be transferred to a Com-
pactFlash card or to the PC at any time, but not when a file is open.
Extension tube volume

The volume of the tube between the chamber multiplexer. You will not enter a
tube volume when using a single chamber because the volume is included with
chamber volume.
l For a long-term single-chamber measurements, connect the chamber to the ana-

lyzer control unit with the 2-meter tube (part number 8100-704). If, for some
reason, you use the 15-meter tube (part number 8150-705) in this con-
figuration, you need to use a long dead band and pre-purge, and recompute the
data in SoilFluxPro after updating the system volume to include the long tube.
l For long-term multiplexed measurements, use the 15-meter tube and enter 237
cm 3 for the volume.
l For a custom tube, compute the volume and enter it. To compute volume of
Bev-a-line IV, use the internal diameter of 1/8" (0.3175 cm) and the total
length—including the AIR IN and AIR OUT tubes. The examples below are for
the 15-meter tube.
1-1
1-2
For simplicity you can multiply the total tube length (meters) by 7.91. Be sure the
length includes the AIR IN and AIR OUT tubes.

1-3
General purpose input

The general purpose input is for any device that outputs a 0 to 5 V signal.
Measurement file
In the interface, enter a file name and optional comments. The comments appear
in the header information. Files can be created in the standard data file format,
where the entire data set is placed in a single file, as defined by the measurement
configuration. Large files can be split into smaller files, in increments of 1 day or 1
week. Files split by the day are appended with a date, beginning at 12:00 a.m. each
day; files split by the week are appended with a date, beginning at a period 7 days
after the first measurement is taken.
Click the Append data to an existing file button to add new measurement data at
the end of the currently defined file.
Measurement start
Enter a start time. You can start the measurement immediately or choose to begin
the measurement at a specified date and time.
Observation count
For survey measurements, you can make repeated observations under the same set
of parameters by setting the observation count to reflect the number of times to
repeat the observation.
Observation length
The observation length is the time period from the instant the chamber is closed
until just before it begins to open again, and includes the specified Dead Band
period. At moderate to low CO2 fluxes an observation length of 90 to 120 seconds
is usually adequate.
Note that the LI-8100A starts logging data when the chamber is actuated and starts
to close. Raw, or Type 1 records are recorded throughout the entire observation
period. The elapsed time (labeled ETime in the data output) does not increment,
however, until the chamber is closed. While the chamber is closing, ETime will
Terminology 1-15
register a count up to 0 from seconds until 0 (in older versions of software it

simply registered -1).
Optional data fields

Variables that can be logged at your discretion. They include: Hour, Day of Year,
Relative Humidity, Case Temperature, Input Voltage, H2 O Absorption, CO2 Absorp-
tion, Raw IRGA Outputs, V1, V2, V3, V4, Thermocouple 1, Thermocouple 2, Ther-
mocouple 3, Thermocouple 4, and GPS variables.
Post-purge
The post-purge is the amount of time during which air continues to flow through
the chamber as it begins to open, after the measurement is complete. This is import-
ant in certain cases where environmental factors may influence the amount of CO2
or moisture that is present in the gas sampling lines. For example, in hot, moist
conditions, you may want to increase the post-purge to ensure that the gas
sampling lines are purged of moisture that may condense in the lines, before the
next measurement using that chamber is started. In most cases, a post-purge of
about 45 seconds is adequate.
NOTE: The post-purge function accommodates the use of the LI-8150 Mul-
tiplexer, where it is important to purge the gas sampling lines before making the
next measurement with that chamber. Because the post-purge starts after the
measurement is complete, it has slightly different implications for use in single-
chamber mode. As shown in Figure 1-1 on page 1-13, after the first measurement
is complete, the Post-purge starts, followed by the pre-purge; thus, the post-purge
and pre-purge become additive. In most single-chamber applications, the com-
bination of the two delays is unnecessary. Before the first measurement starts, the
chamber will not close until the pre-purge has finished; again, in most cases this
delay is unnecessary, particularly when moving the chamber from collar to col-
lar. For these reasons, you may want to use the post-purge instead of the pre-
purge; in other words, set the pre-purge to zero, and set the post-purge to 20-30
seconds, or more, depending on the conditions.
Pre-purge
In multiplexed configurations while chambers are open, or between measurements
in survey configurations, CO2 may accumulate in the open chamber. The pre-

purge turns on the flow pump when the chamber is open. This mixes air in the
chamber in order to bring conditions in the chamber closer to ambient.
When an observation is complete, the chamber will automatically rise off of the
soil collar. If the observation count is set to 2 or more, the pre-purge sets the time
during which the chamber is open. Under very still conditions it may take 2
minutes or more for the chamber air to return to ambient conditions. Under windy
conditions the chamber CO2 concentration may return to ambient levels in as little
as 20 or 30 seconds. Note, too, that the pre-purge begins as soon as the chamber
starts to open. Therefore, it is possible to set a delay time that is too short for the
chamber to fully open before it begins closing again. Chambers typically take about
15 seconds to close.
Presets
Once you have defined a measurement protocol it can be stored and reused from
the preset menu.
Repeat Sequence
Repeat measurement allows you to repeat the defined protocol at a regular interval.
This function is particularly useful when making long term, unattended meas-
urements.
For example, you could specify a 90 second observation length, 45 second dead
band, observation delay of 2 minutes, and observation count of 3. This protocol
could then be repeated every hour for 240 hours (10 days). The resulting data set
would include 240 measurements, with each measurement consisting of three 90-
second observations on the chosen port. The maximum number of repeats is
12000.
Soil area
The surface area of soil in the chamber.
l For the 10 cm soil collar it is 80.1 cm 2 .

l For the 20 cm soil collar it is 317.8 cm 2 .
l For home-made soil collars, compute surface area and enter it.
Terminology 1-17
Soil moisture probe

For a soil moisture probe, such as the Decagon EC-5 or Delta-T ThetaProbe soil
moisture probes.
Stop observation if RH reaches…

This setting will protect equipment from condensation under high humidity con-
ditions. Enable the setting and enter a relative humidity (RH) value of 80 to 90% if
humidity is a concern at the measurement site. The observation will abort if the
measured relative humidity in the chamber exceeds this value at any time during
the observation. If the observation is aborted, a message is logged in the log file,
and the measurement will continue at the next observation.
NOTE: If this is set to 0% RH, you probably will not collect any data because
each measurement will abort any time the RH value is greater than 0% (and RH
will always be greater than 0%). Therefore, we recommend disabling this setting
unless you are working in a very humid environment.
Temp. source
Under the configuration menu, this setting specifies the temperature source for
flux calculations.
Total system volume

The computed volume of the system.
Treatment label
The treatment label is embedded as a separate column in the resulting data records.
It is in the measurement header, viewable as a column in the summary view of
SoilFluxPro software.
Turn off flow pump(s) between measurements

You can elect to turn off the flow pump between repeated measurements to con-
serve battery life and extend the life of the pump by enabling the check box.

Theory of operation
Carbon dioxide in the soil is produced by respiration from plant roots and microor-
ganisms surrounding the roots, and from heterotrophic microorganisms that meta-
bolize plant litter and soil organic matter. In some soils, CO2 is also generated by
the action of rainwater on calcareous substrates. Temperature and moisture are
important drivers of these processes.
Carbon dioxide moves from the sites of production to the atmosphere primarily by
diffusion through air-filled pores and cracks in the soil, but it can also be driven by
local changes in pressure due to wind or volumetric displacement by rain. The air-
filled porosity of the soil varies with soil type and moisture content, so these char-
acteristics can have a significant effect on CO2 movement in the soil.
Measuring carbon dioxide flux from soils

The LI-8100A uses the rate of increase of CO2 in a measurement chamber to estim-
ate the rate at which CO2 diffuses into free air outside the chamber. For such an
estimate to be valid, conditions must be similar inside and outside the chamber.
These conditions include the concentration gradient driving diffusion, barometric
pressure, temperature, and moisture of the soil.
The CO2 gradient between the soil surface layer and air are not exactly the same
inside and outside the chamber, because there is an increase in CO2 mole fraction
inside the chamber. The diffusion rate is estimated and corrected for this using an
analytical technique that takes into account the effects of increasing chamber CO2
concentration on the diffusion gradient. This makes it possible to estimate the ini-
tial rate of CO2 increase that occurred immediately after the chamber closed.
It is also important to consider the effect of the presence of the chamber on CO2
gradients within the soil. Detailed diffusion model studies have shown that cham-
bers can alter gas concentration gradients in the soil, leading to errors in CO2 flux
estimates (Healy, et al., 1996). We generally recommend limiting measurement
times to 90 to 180 seconds in order to keep chamber CO2 concentration changes as
small as possible, and minimize this effect.
Soil CO2 flux varies substantially in both space and time. The LI-8100A can be
used to sample both types of variability. The survey chamber allows rapid meas-
urements to be made at many sites and the long-term chamber supports automated,
Theory of operation 1-19

sequential measurements at a single site over time. Both chambers have carefully
designed pressure vents to prevent pressure gradients and wind incursion from out-
side the chamber. Both chambers close automatically, minimizing mechanical dis-
turbances during the measurement. The long-term chamber moves away from the
soil measurement area when a measurement is not in progress. For example, if a 2-
minute measurement is made once every 30 minutes, the soil will be fully exposed
to sun, wind and precipitation more than 93% of the time. This is an important
consideration to ensure that the moisture and temperature of the soil within the
measurement collar are similar to the surrounding soil.
Deriving the flux equation: the model

ca
k
cc wc v
u
Soil Chamber
sfc sfw
cs
Figure 1-2. A chamber of volume v (m3 ) and surface area s (m2 ) sitting over the soil,
which has CO2 efflux rate fc (mol m-2 s-1 ) and water evaporation flux rate fw (mol m-2
s-1 ).
At constant pressure, the total rate at which water evaporates into the chamber sfw
(mol s-1 ) is balanced by a small flow rate of air out of the chamber u (mol s-1 ). The
CO2 mole fraction of the air outside the chamber is ca, inside the chamber is cc,
and in the soil is cs, all in mol mol-1 . The chamber air water vapor mole fraction is
wc (mol mol-1 ). The rate constant k (s-1 ) characterizes leaks (if any) due to diffusion
of CO2 between the soil chamber and outside air. The chamber volume v includes
the volume of the pump and measurement loop.
The mass balance equations for CO2 , water vapor, and air take the form
storage = flux in - flux out 1-4
We neglect the effects of leaks for now, but we will consider them later.

CO2 mass balance

1-5
H2O mass balance
1-6
Air mass balance

1-7
is the number density of CO2 in the chamber, is the number density of

water vapor in the chamber, and is the total number density of air in the cham-
ber (all in mol m -3 ); , where is the number density of dry air
in the chamber.
The number density of air is given by the ideal gas law, , where R
is the gas constant (8.314 Pa m3 K-1 mol-1 ),
and TK is the absolute temperature (K).
From equation 1-7, with ρ and TK constant, and sfw >> sfc,
1-8
Combining equations 1-6 and 1-8, and noting that , we find
1-9
Combining equations 1-5, 1-8 and 1-9 gives

1-10
Equation 1-10 has the same form as that used in the LI-6400 Portable Pho-
tosynthesis System for soil respiration; however, it can be simplified by defining
, which is the chamber CO2 mole fraction corrected for water
vapor dilution. This is called Cdry (ppm) in the LI-8100A data output.
Differentiating we find,
1-11

Substituting this into equation 1-10 gives

1-12
Equation 1-12 has an important advantage over equation 1-10 because it is not
necessary to estimate the rate of increase in water vapor mole fraction. In most
measurements, the water vapor mole fraction increases in a highly non-linear fash-
ion, and the rate is estimated with a linear function. Thus, in effect, equation 1-10
forces us to use average values for and . But with equation 1-12, the dilu-
tion correction is made point-by-point, and estimates of the initial values at time
zero are used to estimate fc at the instant the chamber closed. This is both easier
and more accurate than the procedure required to implement equation 1-10.
In order to use equation 1-12 the initial values must be known for ρ and TK (to
compute ρ c), as well as the initial values for wc and . After the chamber
closes, the LI-8100A performs a linear regression with time on the first 10 values of
each measured variable. The initial values of ρ , TK and wc are obtained from the
time zero intercepts of these regressions; however, finding the initial value for
requires a little more work.
To do this, fc is defined in terms of the CO2 mole fraction gradient across the soil-
to-chamber interface and a transfer coefficient, to obtain
1-13
where cs is the CO2 mole fraction in the soil surface layer communicating with the
chamber (mol mol-1 ), g is conductance to CO2 (m s-1 ), and ρ c is the density of air
(mol m -3 ). The soil and chamber must be isothermal for equation 1-13 to hold.
Combining equation 1-13 with equation 1-12, considering all variables except cc' to
be constant, and rearranging, gives
1-14
where . When wc = ws , cs', gives the dilution-corrected CO2

mole fraction in the soil layer communicating with the chamber. We do not expect
wc to equal ws exactly, but most of the time they will differ by less than 0.02 mol
mol-1 or so, which introduces only a small uncertainty in cs'. If cs' is taken as a con-
stant, then equation 1-14 can be integrated to give

1-15
where A = sg v-1 is a rate constant (s-1 ) and cc'(0) is the initial value of the dilution-
corrected CO2 mole fraction when the chamber closes. The rate of change in cc'(t)
at any time can be computed from the derivative of equation 1-15.
1-16
Calculating the flux from measured data

In the LI-8100A, equations 1-12, 1-14 and 1-15 are implemented in a form that
presents the variables in more familiar and intuitive units. Equation 1-12 is com-
puted as
1-17
where Fc is the soil CO2 efflux rate (μmol m -2 s-1 ), V is volume (cm 3 ), P0 is the ini-
tial pressure (kPa), W0 is the initial water vapor mole fraction (mmol mol-1 ), S is
soil surface area (cm 2 ), T0 is initial air temperature (°C), and is the initial rate
of change in water-corrected CO2 mole fraction (μmol mol-1 ).

Examine Figure 1-3 on the next page to see C'(t) vs t data that were obtained from a
soil CO2 flux measurement with two observations. The data are marked to show
when the chamber closed and when it opened.

600
Observation Length
Observation Delay
550
Chamber Chamber Chamber
closed opens closed
Chamber
Cdry (ppm)
Dead Band begins to

500 close
Observation #1
Observation #2
450
Cdry initial value
t0
400
0 50 100 150 200 250 300 350 400
Time (s)
Figure 1-3. Soil CO2 flux data were collected on bare soil in a tropical greenhouse near Lin-
coln, NE in February 2004. Two observations are shown. About 60% of the data from the
first observation has been removed for clarity. For both observations, the observation length
was 120 seconds, dead band was 30 seconds, and pre-purge was 120 seconds. The chamber
begins to close at the end of the pre-purge and the first data point used in the analysis is
collected after the chamber touches down; the difference represents the time required for the
chamber to close. Observation #1: t0 =7.3s, C0 ' = 434 ppm, Cx' = 1016 ppm, flux = 6.4
μmol m-2 s-1 ; observation #2: t0 = 2.0s, C0 ' = 425 ppm, Cx' = 1145 ppm, flux = 6.0 μmol
m-2 s-1 .
The dead band is the time until steady chamber mixing is established, and typically
lasts 10s to 30s. After mixing is stable, the data are fit with an empirical equation
that has a form similar to equation 1-15:
1-18
where C'(t) is the instantaneous water-corrected chamber CO2 mole fraction, C0 ' is
the value of C'(t) when the chamber closed, and Cx' is a parameter that defines the
asymptote, all in μmol CO2 per mol dry air (µmol mol-1 ); a is a parameter that
defines the curvature of the fit (s-1 ).

The initial value of C'(t), called C0 ' in equation 1-18, is computed from the inter-
cept of a linear regression of the first 10 points after the chamber closes. This is
used as a parameter in the non-linear regression that fits equation 1-17 to the C'(t)
vs t data between the end of the Dead Band and the end of the observation. This
regression yields values for the parameters Cx', a and t0 . t = t0 represents the time
when C'(t) in equation 1-18 equals its initial value when the chamber closes, or C'
(t0 ) = C0 '. The delay between the instant the chamber closed and t0 gives the time
required to establish steady mixing. CO2 offsets or time delays can occur when the
chamber closes, and these events can cause t0 to be positive or negative in value.
All the initial values needed to obtain the soil CO2 efflux rate, Fc, in equation 1-17
can now be computed. The initial values P0 , T0 and W0 are all obtained from the
intercepts of linear regressions of the first 10 measurements of P, T and W after the
chamber closes. The rate of change of dilution-corrected chamber CO2 mole frac-
tion can be computed at any time from
1-19
When t = t0 ,
1-20
Equation 1-20 gives an estimate of the rate of change in C' at the instant the cham-
ber closed. This value must be estimated mathematically. It cannot be measured dir-
ectly at any time during the measurement because imperfect mixing prevents an
accurate estimate early in the measurement cycle, and later in the cycle, the increas-
ing chamber CO2 concentration continuously reduces the gradient between soil
and chamber. This suppresses the rate, as can be seen from equation 1-19 and also
in Figure 1-3 on the previous page.
Relationship between the model and the empirical equation

The diffusion model provides an equation with a form that allows correction for
the effect of changing gradients on the rate, which in turn, makes it possible to
estimate the initial rate. It is worthwhile to distinguish between the model function
given in equation 1-15 and the empirical function in equation 1-18. As just
described, the units are different in the two expressions; but more important, for
the parameters cs and A in equation 1-15 to have their defined meaning, the
assumptions underlying the derivation must be true. By contrast, equations 1-18

through 1-20 are treated as empirical functions and are used only to estimate the
CO2 rate of change, dC'/dt. The parameters Cx', a and t0 do not depend upon a spe-
cific theoretical interpretation, and may or may not provide reliable estimates of soil
parameters.
Correcting for initial CO2 concentrations that differ between measurements

Different measurements may begin at different CO2 concentrations, which intro-
duces variation into the data, because the flux rate changes with chamber CO2 con-
centration. Correcting the measurements to a common target CO2 concentration
may reduce such variation. For a given curve fit, the CO2 rate of change can be
computed at any CO2 concentration according to
1-21
This calculation is supported in the SoilFluxPro software, which is included with

the LI-8100A.
Evaluation of other methods for computing soil CO2 efflux

Other approaches have been used for computing CO2 flux in transient meas-
urements. One commonly used method is to fit a linear function to what is some-
times referred to as "the linear portion" of the curve. Unfortunately, there is no
linear portion, as can be seen from careful inspection of Figure 1-3 on page 1-24.
The slope is meaningless in the initial phase before steady mixing is established,
and after steady mixing is established, the extent of the non-linearity depends upon
the soil surface-to-chamber volume ratio and the flux rate. During this time, CO2 vs
time curves are always concave in a downward direction, meaning that linear
regression over this portion of the data set will give an underestimate of the rate of
change. In every case we have tested so far, the average rate measured by linear
regression is less than the initial rate measured by non-linear regression. Never-
theless, linear regression is a robust numerical approach and the mean values for
the CO2 efflux rate reported by the LI-8100A in Type 3 records are computed by
this method. We recommend you use these only for comparison to the initial val-
ues, which are obtained by fitting equation 1-18 to the data using a non-linear
regression method.
Another approach that has been used to estimate the initial rate is to fit a poly-
nomial to the CO2 concentration vs time data. This approach is theoretically sound

inasmuch as a power series can be generated from a Taylor series approximation to

equation 1-18. Usually, the data are fit with a quadratic equation. We tested this
approach and found that while it can be justified on theoretical grounds, it does
not work very well in practice. The shape of even a second order polynomial is sens-
itive to small perturbations in the data. This makes initial rate calculations subject
to much larger variations than when the same data are analyzed by nonlinear
regression using equation 1-18.
Effects of high chamber CO2 concentrations

Finally, we consider the importance of choosing appropriate observation times and
pre-purge times. We do not have experience on all soil types, and cannot give abso-
lute recommendations for the best observation length in all situations.
Nevertheless, our experience so far suggests that 60s to 120s will often work well.
This prevents large build-ups in chamber CO2 concentration at typical change rates
such as 0.5 ppm s-1 . We have found that optimal dead band length can vary from
about 10s to 60s, with 30s being a good value to use as a first estimate.
Dead bands and observation times can be adjusted after the fact, using SoilFluxPro
software (formerly FV8100). This program provides curve fit analysis tools that can
be used to find the optimal dead band lengths and observation lengths. Therefore, it
is not critical to choose the right dead band and observation length in the field; as
long as the observation lengths are long enough, they can be optimized later, if
necessary.
Long observations can have the effect of capping the soil and causing the CO2 con-
centration to build up in the soil under the chamber. This phenomenon can be
observed by performing a sequence of observations in which the chamber con-
centration is allowed to increase several hundred ppm during each observation.
When the pre-purge is set to be just long enough to allow the chamber atmosphere
to come back to the ambient CO2 concentration, the initial rates in sequential
observations can often be observed to increase as the soil CO2 concentration
increases. This is expected according to equation 1-20, dCc'/dt = a(Cx' - Cambient'), if
it is assumed that Cx' = Csoil'. Thus, long observation lengths may perturb the very
process we wish to measure.
Another effect of high chamber CO2 concentrations is to promote leaks between
the chamber and atmosphere. Leaks can be ignored when the gradient between the
chamber atmosphere and ambient atmosphere are small. But when the gradient is

not small, leaks cannot be neglected and it can be shown that the parameters in
equation 1-15 are altered to become
1-22
where k and ca' are the leak rate time constant and water-corrected ambient CO2
concentration, respectively, and the expression for cx' replaces cs' in equation 1-15.
Thus, when chamber CO2 concentrations are high, the rate constant and asymptote
will reflect leaks from the system. Variables that are stored in data files are
described in Table 6-4 on page 6-9.
Measuring net carbon exchange

At the ecosystem level, carbon (CO2 ) is fixed through photosynthetic carbon meta-
bolism, and then fixed carbon is used for growth and development of plants. Some
of the fixed carbon will be lost through respiration. Inside a clear chamber, net car-
bon exchange (NCE) is defined as the carbon exchange between an ecosystem and
the atmosphere, which is the photosynthesis uptake minus the total respiration,
including above ground respiration and soil respiration. It is a key variable for
understanding the carbon balance of an ecosystem. NCE can be readily measured
with the eddy covariance method over a large uniform field or with the chamber-
based method for short and small canopies. If no plants are present inside the clear
chamber, then the measured NCE is the soil respiration.
LAI v
Ci
C c, wc
gl
s gs
Cs
Figure 1-4. Diagram showing a chamber volume of v (m3 ) and surface area s (m2 ) sitting
over the soil with plants inside. The leaf area inside chamber is LAI. gs and gl are soil con-
ductance and leaf conductance (m s-1 ). Ci is the intercellular CO2 mole fraction (mol
mol-1 ), Cs is the CO2 mole fraction of soil air (mol mol-1 ). Cc is the CO2 mole fraction
inside chamber (mol mol-1 ).

For a clear chamber, the mass balance for CO2 inside the chamber would be (see
equation 1-12 for more information);
1-23
where ρ c is the air number density inside the chamber (mol m -3 ), S is the surface
area inside the chamber (m 2 ), and wc is the chamber air water vapor mole fraction
(mol mol-1 ). Cc’ is chamber CO2 mole fraction corrected for water vapor dilution.
For soil CO2 flux fc:
1-24
Where fc is soil CO2 flux (mol m -2 s-1 ), and all variables have the same definitions
as described in the section for opaque chambers.
When you have living plants with leaf area index, (LAI, defined as the ratio of total
one-sided leaf area inside the clear chamber to ground area), the CO2 uptake rate
via photosynthesis (fp) would be:
1-25
Where fp is the photosynthesis rate (mol m -2 s-1 ), gl is the total leaf conductance
(mol m -2 s-1 ) including stomatal and leaf boundary layer conductance, Ci’ is inter-
cellular CO2 mole fraction (mol mol-1 ), is Ci/Ca ratio. We assume α to be constant
over a wide range of CO2 concentrations (around 0.6 for C3 species, and 0.3 for C4
species) (Wong et al., 1979; Morison, 1987; Xu and Hsiao, 2004).
1-26
where Rh is total above-ground biomass respiration. Rearranging equation 1-26, we

have
1-27
Let and
1-28
Equation 1-28 can be integrated to have

1-29
Let , we have
1-30
The following equation will be used to fit the time series of Cc’ (see earlier in this
section for an explanation of the origin of t0 )
1-31
Equation 1-28 is exactly the same as equation 1-15 for opaque chambers. For the
LI-8100A, we use a generic exponential equation to fit the time series of chamber
CO2 concentration. For a clear chamber, when Cm’ < C0 ’, net carbon uptake is
observed. When Cs’ > C0 ’ from fitted equation 1-28, net carbon release is observed.
The net carbon exchange then can be estimated using equation 1-12, with the
information from the initial slope of the time series of Cc’ (equation 1-29). Neg-
ative flux values will be reported for the cases of net carbon uptake and positive flux
will be reported for the cases of net carbon release. Note that Cm represents the
CO2 compensation point at which photosynthesis rate is equal to total respiration
rate inside the chamber.
The above derivation involved some assumptions to be able to solve the differential
equation 1-29 analytically. Not all assumptions are valid for all cases. For example,
we assume stomatal conductance is independent of air CO2 level, which clearly is
not the case. The purpose of this exercise is to provide a general view on how the
time series of chamber CO2 concentration behaves after the chamber is closed.
The considerations for setting up the configuration (dead band, observation length,
observation count, Pre-purge) for the clear chamber measurement are the same as
for other LI-COR opaque chambers (8100-101, -102, -103, -104).

450
t0 =17.1 s
400
C o = 349.1 ppm
C’c (µmol mol -1) 350 N = 0.01447 s-1
NCE = -13.0 µmol m-2 s-1
300
Dead band
250
200
Cm=176.3 ppm
150
0 20 40 60 80 100 120
Time (s)
Figure 1-5. Example of time series of Cc’ from one observation from the clear chamber over
a short grassland on the LI-COR campus. Values for various fitted parameters (t0 , Cm, and
N) from equation 1-31 are also shown. The observation length was 120 s with a dead band
of 20 s. The net carbon exchange (NCE) is -13 µmol m-2 s-1 .


Section 2.
Initial setup
You're probably eager to get started with some measurements or test the system. In
this section, we'll go over the basic operations and critical first steps to get you
ready to collect some actual field data.
First Things First

This section has some basic steps that will get you started with the system. Do this
the first time you power up the system.
1 Install the computer software

Download the latest LI-8100A software from the LI-COR web site:
www.licor.com/env/support. Install the software on your computer.
2 Connect the serial cable

The first time you power up the device, you'll need to communicate with it using a
PC and the RS-232 serial connection. Use the Serial-to-USB adapter for this1.
After some initial configuration, you'll be able to configure it with the Ethernet
connection or wirelessly (if enabled) for subsequent connections.
1Serial-to-USB adapters need the FTDI chipset. Other adapters are not compatible. LI-COR sells tested
adapters that will work, but we cannot guarantee adapters that are purchased elsewhere.

3 Install a battery
Grab a freshly-charged battery and plug it into either one of
the connectors in the analyzer control unit. The batteries are
charged prior to delivery, but if they have been sitting for a
long time, it is a good idea to charge them up before you start.
4 Connect a chamber
Attach the tubes and cable connector for a chamber. See Connecting a survey chamber
on page 2-24 or Connecting a long-term chamber on page 2-26 for details.
5 Power on the instrument

Press the ON/OFF button inside the analyzer control unit.
6 Connect to the LI-8100A

Launch the LI-8100A PC software, click the Connect button ( ), select the serial
port, and then click Connect.
To find the serial port number, open the Device Manager (press the Windows key
, type in Device Manager, then press Enter). Then click Ports (COM &
LPT). Look for USB Serial Port (COM#). Your serial port number is indicated by the
number.
7 Turn off the pump

Any time the LI-8100A powers on, the pump will begin running immediately. This
is a good thing if your system is making autonomous measurements in the field,
but if you're sitting in the lab, the pump might be annoying. To turn it off:
Click Utilities > Manual Controls > Flow, then click 8100 Flow Off.
8 Check the instrument's date and time

Under 8100 > Date and Time, set the date
and time. The date and time are logged
in your data files.

Get connected
There are six ways to connect your computer or mobile device to the LI-8100A. The
way that works best for you depends on the accessories in your instrument and
your computer configuration. We go through the possibilities below.
To connect using... ...see... ...you can...
Configure Transfer
Instrument Data
USB or serial to a Windows® Connecting over serial or USB ✔ ✔

computer below.
Ethernet directly to a Connecting directly over Ethernet ✔ ✔
Windows computer on the next page.
Ethernet to a Windows Connecting over a local area ✔ ✔
computer on a network network on page 2-5.
Wireless to a Windows Connecting to a computer over ✔ ✔
computer wireless on page 2-6.
Wireless to an older iOS Connecting with iOS version 8.4.1 ✔
device and older on page 2-8.
Wireless to a newer iOS or Connecting with the TP-Link ✔
Android device Wireless Router on page 2-10.
Connecting over serial or USB

These are both very dependable ways to connect with the instrument, and may be
required to configure the network connection settings. See First Things First on
page 2-1 for details.
Get connected 2-3

Connecting directly over Ethernet

You can connect to the LI-8100A using a network cable. You may need to connect
over the RS-232 serial connection to find the instrument IP address first (see First
Things First on page 2-1).
1 Configure your PC network settings.

A Press the Windows key ( ) and type IP Address.
B Click View Network Connections in the search results.
C Right-click the Local Area Connection and select Properties.
D Double-click the entry called Internet Protocol Version 4 (TCP/IPv4).
2 Select Use the following IP address and enter:
l IP Address: 172.24.24.44
l Netmask: 255.255.0.0
l Gateway: Leave this blank.
3 Click OK to dismiss the dialog boxes and implement the setting.
4 Connect the LI-8100A to your computer using the Ethernet cable.
5 Launch the LI-8100A PC software and click Connect.
6 Select TCP/IP and enter 172.24.24.43a and click Connect again.
You can connect using a PC as long as the PC has a static IP address.
Note: Setting the IP address on your computer will disable your internet con-
nection. Reset your computer settings to re-enable the internet connection.
aIf you have changed the IP address, use the address that you set previously. You may need to connect
over RS-232 serial or USB to find the IP address and change it.

Connecting over a local area network

In this configuration, your computer will be connected to a local network. You'll
connect the LI-8100A to a network terminal and configure the instrument using a
computer on that network.
1 Check the cable connections—be sure the network card is installed and connected to the internal
Ethernet cable under the LI-8100A access panel.
2 Connect to the instrument using a serial or USB connection.
See First Things First on page 2-1 for details.
3 Set the LI-8100A IP address.
Ask someone in your IT department to provide you with a static IP address for your
network. In the LI-8100A PC software, click 8100 > Networking and enter the fol-
lowing information:
l IP Address: The one provided by your IT department.
l Netmask: 255.255.255.0
The other settings can be left at the default values.
4 Restart the instrument after setting the IP address.
5 Launch the LI-8100A PC software again.
After the LI-8100A has powered up and the Ready light is on, click the Connect
button in the software.
6 Select TCP/IP and enter the IP address that your IT department provided.
7 Click Connect.
Connecting over a local area network 2-5

Connecting to a computer over wireless

You can connect to a wireless-enabled LI-8100A using your Windows computer's
wireless connection.
Note: The Cisco wireless card is not compatible with some modern devices and
software. Windows 10 does not support this connection. Use the TP-Link instead
(see Connecting with the TP-Link Wireless Router on page 2-10).
1 Check the LI-8100A wireless capability—be sure the Cisco wireless card is installed under the LI-
8100A access panel.
2 Connect to the instrument using serial or USB.
3 Set the LI-8100A IP address.
In the LI-8100A PC software, click 8100 > Networking and enter the following
information:
l IP Address: 192.168.100.101
l Netmask: 255.255.255.0
l Connection Type: Peer-to-Peer (ad-hoc)
l Network Name (SSID): Soil Network 1
l Channel: 1
The other settings can be left at the default values. Restart the instrument after set-
ting the IP address.

4 Configure your computer wireless settings.

This step differs depending upon your Windows version, but the steps below
should work in Windows 7 and newer versions:
A Press the Windows key ( ) and search for IP Address.
B Click View Network Connections in the search results.
C Right-click the Wireless Network Connection and select Properties.
D Double-click the entry called Internet Protocol Version 4 (TCP/IPv4).
Select Use the following IP address and enter:
l IP Address: 192.168.100.102
l Netmask: 255.255.255.0
5 Connect to the LI-8100 Network.
A Press the key and search for Sharing.
B Press enter to open the Network and Sharing Center .
C Click Connect or Disconnect.
D Connect to Soil Network 1.
6 In the LI-8100A PC software, click the Connect button in the software.
7 Select TCP/IP and enter the IP address: 192.168.100.101.
8 Click Connect.
Connecting to a computer over wireless 2-7

Connecting with iOS version 8.4.1 and older

You can use the LI-8100APP for iOS devices that run iOS version 8.4.1 and older if
your LI-8100A has a Cisco wireless card. Open the access panel inside the LI-8100A
and confirm that the wireless card is installed. To connect a device that runs iOS
version 9 or newer, follow the procedure described in Connecting with the TP-Link
Wireless Router on page 2-10
1 Connect the instrument using serial or USB.

2 In the LI-8100A PC software, click 8100 > Networking... and enter the following information:
l IP Address: 192.168.100.101
l Netmask: 255.255.255.0
l Connection Type: Peer-to-Peer (ad hoc)
l Network Name (SSID): Soil Network 1
l Channel: 1
Leave encryption unchecked. Click Set to apply the settings.
Then restart the LI-8100A.
3 In iOS, go to Settings > Wi-Fi and connect to Soil Network 1 (named
in the previous step).

4 Tap the network connection and tap Static .

Set the IP address and Subnet mask:
l IP Address: 192.168.100.100
l Netmask: 255.255.255.0
5 Launch the LI-8100APP and tap Connect to Instrument.
Tap New, then type in the LI-8100A's IP address
(192.168.100.101), and save it.
6 Select the IP address and tap Connect.
If your mobile device is set to automatically join the network,
all you need to do to connect is select the instrument
IP address and tap Connect in the future.
Connecting with iOS version 8.4.1 and older 2-9

Connecting with the TP-Link Wireless Router

A wireless router provides a simple way to connect to the LI-8100A wirelessly —
using the LI-8100APP for iOS and Android OS devices, or the Windows
PC software on a computer. Many different brands of battery-powered routers are
suitable. We provide the TP-LINK T-MR3040 (LI-COR part number 590-16299)
with new LI-8100A instruments. Other brands of wireless router are compatible as
well.
The router does not need an internet connection. It creates a wireless network (also
known as a wireless hotspot) that enables communication between the device and
the LI-8100A.
NOTE: Read all instruction guides and quick start guides for the wireless router.
TP-LINK TL-MR3040: http://www.tp-link.com/en/products/details/cat-4691_TL-
MR3040.html
1 Install the charged battery in the router and power it on. Verify that the power LED is green or
orange and not blinking.
2 Position the mode switch on the side of the TP-LINK to the position labeled WISP or 3G/4G.
3 Connect your computer to the router's network (be sure you computer has a dynamic IP address;
called Obtain an IP address automatically in Windows®):
l Either connect an RJ-45 Ethernet cable between the router and your computer,
l Or, connect to the wireless network. The network name (called SSID) and wireless password
are printed under the battery cover of the TP-LINK.
4 Open a web browser and type 192.168.0.1 in the address bar, then press Enter.

5 Log in. The default credentials are:

l Username: Admin
l Password: Admin
6 Click DHCP on the left of the setup page. Note the IP Address range of the DHCP server and the
Default Gateway. Typically they are:
l Start IP Address: 192.168.0.100
l End IP Address: 192.168.0.199
l Default Gateway: 192.168.0.1
7 If it is installed, remove the Cisco Systems wireless card that is under the LI-8100A access panel.
8 Connect to the LI-8100A using the serial or USB connection, as described in First Things First on
page 2-1.
9 In the LI-8100A software, under 8100 > Networking... configure the wireless settings.
Set the LI-8100A IP address so it is identical to the TP-LINK IP address for the first
three sets of numbers (as in, 192.168.0) and outside the start and end range for the
last set. So, 192.168.0.200 is a suitable IP address for the LI-8100A.
l IP Address: 192.168.0.200
l Netmask: 255.255.255.0 (this must be the same on the router and the LI-8100A)
Connecting with the TP-Link Wireless Router 2-11

l Gateway: 192.168.0.1 (this must be the same on the router and the LI-8100A)
l Connection Type: Access Point (infrastructure)
Leave encryption unchecked. Click Set to apply the settings.
10 Restart the LI-8100A.
11 Connect the router to the Ethernet port on the CompactFlash adapter under the access panel.
12 Connect your iOS or Android device to the network created by the TP-LINK.
The network name (called SSID) and wireless password are printed under the bat-
tery cover of the TP-LINK.
13 Launch the LI-8100APP and tap Connect to Instrument.
14 Tap New, type in the LI-8100A's IP address (192.168.0.200), and save it.
15 Select the IP address and tap Connect.
Once the connection is established, you may proceed with your measurements.
Other compatible wireless routers are configured similarly.

Exploring the analyzer control unit

The analyzer control unit is pretty simple. In this section we go over a few details
that you may find useful, and some others that you really need to know.
Batteries
The LI-8100A requires one 6400-03 battery to power the instrument. Alternatively,
you can power it with an external power source (10.5-28 VDC) through the aux-
iliary sensor interface.
l Each battery will provide about 3 to 4 hours of operation under normal con-
ditions.
l The battery fits inside the analyzer control unit.
l It can be connected to either of the two battery connectors.
l You can hot-swap the battery by attaching a second, fully charged battery before
removing the partially-discharged battery.
l The 6400-03 requires the LI-6020 Battery Charger, which charges up to four
6400-03 batteries at once.
Indicator panel
The indicator panel provides some basic information on the status and operation of
the system.
LOW BATTERY - On when the input
voltage drops below a factory-determined
threshold (approximately 10.94 volts). If
A
the voltage drops below 10.5 volts, the LOW BATTERY
instrument will turn off. ON/OFF ACTIVE
IRGA READY
ACTIVE - On when the LI-8100A is mak-
READY
ing a measurement.
POWER
IRGA READY - On when the IRGA has

Automated Soil
reached its operating temperature. This CO 2 Flux System
may take about 10 minutes after the
instrument is powered on. The instru- Figure 2-1. The indicator panel is inside
ment will function before the IRGA the Analyzer Control Unit.
Ready light illuminates; however,
Exploring the analyzer control unit 2-13

measurements should not be made until the optical bench has reached its oper-
ating temperature of 51 °C.
READY - On when the instrument is ready to communicate with a computer or
mobile device.
POWER - On when ON/OFF button is pushed, and indicates that power is applied
to the instrument.
The measurement flow path

A diaphragm pump inside the analyzer control unit provides a steady flow of air to
the survey chamber. The chamber shape provides mixing without using fans,
which could cause pressure gradients. Air returning from the chamber passes
through a filter before it enters the infrared gas analyzer in the analyzer control
unit. The infrared gas analyzer measures CO2 and H2 O concentrations sim-
ultaneously; these concentrations are then used to calculate flux rate.
Analyzer Control Unit
Diaphragm
Survey Chamber Pump
To Chamber
From Chamber
Infrared
Gas
Analyzer
Filter
Figure 2-2. The measurement flow path to the survey chambers.

PC adapter cards
The analyzer control unit has two slots for PC cards (PCMCIA). You can use an
Ethernet adapter (installed in the factory), CompactFlash memory card (also
installed at the factory), or a wireless card.
NOTE: You cannot simultaneously use two cards of the same type, such as two
CompactFlash cards or two wireless cards.
Figure 2-3. To remove the Ethernet adapter card, eject the card and disconnect the cable.
If you use the optional wireless package, you will need to eject either the Com-
pactFlash or Ethernet adapter card. The Ethernet adapter card is connected intern-
ally to a short cable that extends to the Ethernet connector on the analyzer control
unit side panel. If you choose to eject the Ethernet adapter card, simply remove the
cable at the junction shown below in Figure 2-3 above.
NOTE: Always eject the CompactFlash card before removing it. In the PC soft-
ware, go to Utilities > File Manager > Eject Card, or just power off the LI-800A. To
remove the card, press the eject button next to the card.
PC adapter cards 2-15

About data records and storage options

The LI-8100A has 18 megabytes of internal memory and a 1 GB CompactFlash
card. You can add memory by replacing the 1 GB card with a higher capacity card.
Although you can use larger capacity cards, the LI-8100A can only address 2 GB of
the available memory.
When logging all data values, each data record is approximately 190 bytes. Table 2-1
below summarizes the space required to log the largest data record at one second
intervals.
Table 2-1. Storage space1 required to log the largest data record at 1 second
intervals.
Data Logging Period Space Required
1 minute 11.1 K
1 hour 667.9 K
1 day 15.6 MB
Typically, you will not be recording data 100% of the time (except when used with
the multiplexer). Table 2-2 below illustrates some example observation con-
figurations and their respective durations based on internal storage.
Table 2-2. Examples of observation lengths2 and duration that can be stored to
internal memory.3
Observation Length Frequency Duration
Duration (days)
(minutes) (observations/hour) (hours)
3 15 102 4.25
2 15 153 6.3
3 4 384 16
2 4 576 24
3 2 768 32
2 2 1153 48
1100% duty cycle logging all data fields at 1 Hz.

2The observation length is defined to be the amount of time the chamber is closed and the system is
logging data.
3Possible long term protocols, logging all data fields at 1 Hz

Wireless card
An optional wireless package (part number 8100-565) enables you to control the
LI-8100A with a mobile device, such as an iPod, iPhone, or iPad. The wireless pack-
age includes a Type II PC card that can be inserted into either of the two PC card
slots in the analyzer control unit in place of either the Ethernet adapter card or
CompactFlash card.
NOTE: The wireless card included is the only card warranted for use with the LI-
8100A. Although other cards may be compatible, LI-COR cannot guarantee the
integrity of the data or performance of the system when other cards are used.
Air filters
There are two Balston air filters located inside the analyzer control unit. One of the
filters is on the flow path from the attached chamber. The other is on the bellows
air path. It is used only when a survey chamber is attached.
The air filter on the flow path will need to be replaced after about 3 months of con-
tinuous use, depending upon the conditions under which the instrument is used.
If the short section of tubing between the filter and the optical bench is con-
taminated, the filter and the tubing should be replaced. See Replacing the air filters
on page 9-3 for details.
Using soil collars

Although the ideal measurement would not alter the soil in any way, we've found
that soil collars present an acceptable and necessary tradeoff between affecting the
soil environment and measuring the actual gas flux. Soil collars have several advant-
ages over direct insertion of the chamber into the soil, including:
l The disturbance effect of insertion will not affect measurements conducted sev-
eral hours or days later.
l It is possible to make repeated measurements at the exact same location.
Make Your Own: You can make soil collars yourself if you can find the correct
size of pipe. See Making soil collars on page 10-4 for details.
Wireless card 2-17

Tips for installing and using soil collars

l Install soil collars several hours to one day before making a measurement. You
can test to see if the flux has stabilized by making a measurement immediately
after installing the collar, and then make subsequent measurements over time.
Note, however, that the soil surface CO2 flux depends on the time of day, and
the diurnal cycle can be quite large.
l In hard or compacted soils, you may need to create a channel around the collar
with a knife or trowel before insertion.
l For the larger 8" collars, you can lay a piece of wood across the collar and drive
the collar with a mallet.
Insertion depth
The optimal collar height will depend upon site conditions and the length of time
the collars will be used at a given site. At a minimum, the collar should be inserted
into the soil to a depth that gives a solid foundation so the collar does not move
when placing the chamber on the collar. As insertion depth is increased, lateral dif-
fusion of CO2 in the soil column below the chamber will be reduced. The advant-
age of this is that lateral diffusion can be a source of error in the measurement
(Healy et al., 1996), but the disadvantage is that as insertion depth increases, the
possibility of root shearing increases. Collars may become loose over time and
should be moved if this occurs.
Collars should extend a minimum of 2 cm above the soil surface for the survey
chambers, and 3 cm or more for the long-term chambers, depending on the slope
of the site. Collars can extend above the soil more than 2 or 3 cm, but with greater
extension there is increased shading and perturbation of air movement. Over the
long term, these perturbations could result in changes of evaporation rate, soil tem-
perature, and soil moisture.
Measuring the chamber offset

The chamber offset is used to determine the volume of air inside the soil collar,
which is in turn used to calculate the total system volume. The total system volume
is an important part of the flux calculation, so it should be determined as accurately
as possible.

The chamber offset is measured differently for the survey and long-term chambers.
With the survey chambers, the chamber offset is measured by the distance between
the soil surface and the top of the soil collar.
Chamber Offset
for Survey Chambers
Soil Collar
Figure 2-4. Chamber offset for survey chambers is the distance between the soil surface and
the top of the coil collar.
With the long-term chambers, the chamber offset is measured by the distance
between the soil surface and the upper edge of the chamber base plate.
Long-Term Chamber Offset = A - B
B
A
Chamber
Base Plate Soil Collar
Figure 2-5. Chamber offset for long-term chambers is the distance from the soil surface to
the top of the chamber base plate.
In uneven or sloping soil conditions, measure the chamber offset at multiple points
within the collar and then average these measurements to represent the true offset
(see Figure 2-6 on the next page).
Measuring the chamber offset 2-19

Chamber Offset in Sloped Soil:

Average multiple measurements
A B
Figure 2-6. Chamber offset in sloped soil should be computed from an average of the off-
sets. Long-term chamber shown.
When setting the 10 cm survey chamber onto the collar, be careful not to let the
bottom edge of the chamber disturb the soil within the collar (this will not occur if
the collars extend more than 2 cm above the soil surface). Also, make sure the col-
lar is not disturbed when placing the chambers on or around them. The chamber
edge should be as close to the soil surface as practical (within 1-2 cm) so that air
flow within the chamber produces mixing near the soil surface.

More details on the survey chambers

The survey chambers (8100-102 10 cm and 8100-103 20 cm) are used to make
rapid measurements of soil gas flux that can be repeated over a number of loc-
ations, providing data to describe spatial variability.
The chamber itself is raised and lowered
with a bellows, which gently lowers the
chamber over the soil collar. The small
10 cm chamber is ideal for locations that
have many plant stems or rocks in the
soil. The larger 20 cm chamber is com-
patible with soil collars used for long-
term chambers.
Each chamber seals over the soil collar
with a thin gasket, and the chamber
volume seals with its own gasket when it
closes. This minimizes leaks and wind
effects. Each chamber has a pressure vent
to maintain ambient pressure under
windy conditions (Xu, et al., 2006). Figure 2-7. The 8100-102 10 cm Survey
Chamber.
More details on the survey chambers 2-21

Figure 2-8. The 8100-103 20 cm Survey Chamber.

The bellows flow path

Survey chambers are raised and lowered with a pneumatic bellows system. A dia-
phragm pump provides air flow to a series of valves controlled by a pressure trans-
ducer. Air fills the bellows and drives the chamber closed; a vacuum raises the
chamber.
Analyzer Control Unit
Diaphragm Pump
Check Check
Valve Valve
Chamber
To Bellows
Valve Valve
Filter
Pressure
Transducer
Vent
Figure 2-9. The bellows flow path to the survey chambers.
The bellows flow path 2-23

Connecting a survey chamber

The survey chambers have three tubes: AIR OUT is to the chamber, AIR IN is
returning from the chamber, and BELLOWS is air that drives the bellows.
Figure 2-10. Tube and cable connections for survey chambers. The tube with black shrink-
wrap connects to the AIR IN connector.
Notes on chamber connections:

l The cable fittings have fine threads. Make sure there is no debris on the fit-
tings before attaching the connectors, as the threads can be easily damaged.
l Inspect the pins in the cable connector to be sure that none of them are bent.
Straighten any bent pins before connecting the cable.
l Cover the connectors with the attached connector dust caps whenever the con-
nectors are not being used.
l If you swap between survey and long-term chambers connected to the Ana-
lyzer Control Unit you must power the instrument off and then back on, as
the type of chamber attached to the Analyzer Control Unit is recognized dur-
ing system startup.

More details on the long-term chambers

The 8100-104 and 8100-104C Long-Term Chambers are used to make continuous
measurements of soil gas flux at a single location for weeks or months at a time.
The chamber uses a motor-driven strut system to move the chamber bowl away
from the soil collar. This ensures that the sample location is subjected to normal,
undisturbed precipitation, temperature, and shading between measurements. It has
a pressure vent at the top of the chamber to prevent pressure spikes when the cham-
ber closes, and to maintain the chamber pressure at the ambient level under calm
and windy conditions (Xu, et al., 2006).
Each chamber has two gaskets: the chamber bowl seals to the base plate with a flex-
ible gasket, and the base plate seals to the soil collar with a second gasket.
Figure 2-11. 8100-104 Long-Term Chamber.
The 8100-104 and 8100-104C Long-Term Chambers are designed primarily for use
with the LI-8150 Multiplexer, but they can be used for long-term single chamber
measurements or as stand-alone devices with other analyzers.
NOTE: The 8100-104/C has three sensor inputs; sensors attached to these inputs
can only be monitored when the chamber is connected to the multiplexer. If the
8100-104/C is used in single chamber mode with the LI-8100A, auxiliary sensors
must be connected to the auxiliary sensor interface, not the chamber itself.
More details on the long-term chambers 2-25

The 8100-104/C moves away from the soil collar when the measurement is com-
plete. The 8100-104/C chamber raises slightly before it swings outward in a 180°
arc around the perimeter of the raised control panel (see Figure 2-14 on page 2-29).
Connecting a long-term chamber

The long-term chambers use only two tubes: AIR OUT is to the chamber, AIR IN is
returning from the chamber.
Figure 2-12. Tube and cable connections for long-term chambers. Insert the port plug (part
number 9981-118) into the bellows connector. The 2-meter tube and cable bundle (part
number 8100-704) connects to the long-term chamber.

Figure 2-13. The long-term chambers use a 2-meter or 15-meter cable bundle (part numbers
8100-704 and 8150-705 respectively).
Notes on chamber connections:

l When using a long-term chamber, the bellows port on the LI-8100A should
be plugged with part number 9981-118, found in the spare parts kit.
l If you swap between survey and long-term chambers connected to the ana-
lyzer control unit you must power the instrument off and then back on, as
the type of chamber attached to the analyzer control unit is recognized during
system startup.
Connecting a long-term chamber 2-27

Leveling the chamber

Each of the four legs should be adjusted so the chamber sits even over the soil col-
lar. To adjust a leg, loosen the handle and reposition the leg. Then tighten the
handle securely.
Changing the long-term chamber open position

The default open position is approximately 180° from the closed position, as shown
in Figure 2-14 on the facing page. You can choose from 5 other open positions to
avoid terrain or obstructions that interfere with the full 180° of movement. To
change the open position:
1 Press and hold the Open/Close button for 5 seconds.

Wait a few moments while the chamber positions itself.
2 Press the Open/Close button one time to move the chamber to its first open position (#5 in the dia-
gram below).
Continue to press the button one time to move the chamber to each of the other
five open positions.

3 When the chamber is in the desired open position, hold the Open/Close button for 5 seconds
again; the chamber will store the setting until it is reprogrammed.
3 2
4 1
14.5” 5
30.5”
Figure 2-14. The long-term chambers have six programmable open positions.
Press the Open/Close button twice in quick succession to park the chamber. When
parked, the chamber will raise slightly to prevent compression of the chamber gas-
ket.
CAUTION: Park the chamber before transporting it or placing it in long-term

storage. Handling the chamber while it is not parked can strain and potentially
damage the shaft and sealing mechanism.
Changing the long-term chamber open position 2-29

Tips for using the 8100-104C clear chamber

Below we provide some suggestions that will help you use the clear chamber.
Shading effects
The 8100-104C clear chamber should always be oriented so the LI-COR logo on
the base plate faces the equator. This will ensure that most of the shadows cast by
the structural elements are projected away from the collar area. Despite this key ori-
entation, the collar and chamber may shade the sample area.
Temporal variations in light intensity inside the collar area will occur due strictly
to shading effects. It is important to consider these temporal variations when
examining flux data. LI-COR has published a paper that describes the shadow
effects when using the 8100-104C Clear Chamber; request Application Note #131.
Measuring photosynthetically active radiation

When using the clear chamber for net carbon exchange (NCE) measurements,
you'll want to measure photosynthetically active radiation (PAR) to supplement
your measurements. Therefore, an LI-190 or LI-190R Quantum Sensor, amplifier,
and leveling stake is included with the NCE chamber packages.
l For single-chamber measurements (without the multiplexer), use the 2420-BL

amplifier.
l For multiplexed measurements, use the 2420-BLS amplifier.
Figure 2-15. The 8100-604 Leveling Stake is used to mount and level the LI-190 or LI-
190R Quantum Sensor for measuring PAR near the 8100-104C Clear Chamber.

Section 3.
Making single-chamber measurements
Assuming you have gone through the Initial setup on page 2-1, you are probably
ready to make some measurements. In this section we provide two tutorials: An
indoor tutorial, in which you measure respiration from a piece of fruit (good for
the office or a rainy day), and an outdoor tutorial, which is a survey measurement
in the field.
An indoor tutorial
For learning purposes, it might be useful to measure respiration of a piece of fruit.
An apple, banana, or orange (or whatever is available in your locale) will probably
work well, so long as the fruit is somewhat fresh and at room temperature.
With your instrument on the lab bench and connected to a PC:
1 Place the chamber over a piece of fruit

The chamber should be able to open and close freely without touching the fruit.
2 Set up the measurement (part 1)
In the LI-8100A PC software, click the Chamber button or press Ctrl+M.

Under Port Setup > Chamber :
l Select the chamber you have connected.

l Soil Area: Enter 80.1 cm 2 for 8100-102; 317.8 cm 2 for 8100-103.
l Chamber Offset: 0.0 cm since this is on the lab bench. Normally you will meas-
ure this in the field.
Under Port Setup > Observation:

l Treatment Label: It will be included in your data record.

l Observation Length: 40 to 60 seconds is fine for this tutorial.
l Dead Band: 0 seconds is fine for the tutorial. This is the time that passes
between the chamber closing and the measurement start.
l Observation Count: 5 is fine for the tutorial.
l Pre-purge: 0 seconds. Purge time before the chamber closes.
l Post-purge: 0 seconds. Purge time after the chamber opens.
3 Set up the measurement (part 2)

Upon clicking the Start Measurement button, you can set:
l Preset: Leave at Current Setting

l Measurement File: Enter a name for the file and choose whether to create a
new file or append an existing file.
l Comments: Comments are recorded in the file header.
l Set the Destination; either the instrument memory or the CompactFlash card.
l Measurement Start: Set to Start Immediately.
4 Start the measurement

Click the Start Measurement button to initiate the measurement.
5 View the data as it is logged

Click the Charting button. You may need to click the Start button to initiate the
data stream.
6 Transfer data from the LI-8100A to a computer

Click Utilities > File Manager... or the file manager button. You will see a list of
files that are saved to the internal memory and the CompactFlash memory of the
LI-8100A. Select the file you want to copy and then click Transfer to PC.
7 Chart data in SoilFluxPro™

After the file is transferred, you can open the data file in SoilFluxPro software. You
will see individual observations. Double click an observation to view the data and to
chart it. Select Fit #1 Cdry to view a plot of each observation. Click Help > View
SoilFluxPro Guide to learn more about the software.

An outdoor tutorial
Follow this tutorial to make a survey measurement. Be sure to go through Initial
setup on page 2-1 and An indoor tutorial on page 3-1 first.
1 Install the soil collars

Select a unbiased and representative locations for your measurements. Install the
soil collar, as described in Using soil collars on page 2-17.
2 Set up the measurement
In the PC Software: In the App:
Click the Chamber button (Ctrl+M). Tap Setup > Measurement Protocol:
Under Port Setup > Chamber : l Set Measurement Type: Chamber
l Obs. Length: 40 to 60 seconds
l Select the chamber you have con-
l Dead Band: 30 seconds is a good
nected
starting place.
l Soil Area: 80.1 cm 2 for 8100-102;
l Obs. Count: 5
317.8 cm 2 for 8100-103.
l Pre-Purge: 0 seconds.
l Chamber Offset: Enter the offset.
l Post-Purge: 0 seconds.
Under Port Setup > Observation: l Additional Log Fields: Set to all
l Treatment Label: It will be included unless you have limited data stor-
in your data record. age space.
l Observation Length: 40 to 60 Under Area and Volumes:
seconds.
l Chamber Offset: Enter the offset.
l Dead Band: 30 seconds is fine for the
l Soil Area: Select the 10 cm or 20
tutorial.
cm collar.
l Observation Count: 5 is fine for the
l Chamber Volume: Select your
tutorial.
chamber.
l Pre-purge: 0 seconds.
l Post-purge: 0 seconds.
An outdoor tutorial 3-3

3 Place the chamber over the collar

Gently set the chamber on the collar. Insert the soil temperature probe and/or soil
moisture probes at the desired depths and distances from the chamber.
Click Start Measurement: Tap Start Measurement:

l Preset: Leave at Current Setting l File Name: Enter a name.
l Measurement File: Enter a file name l Comments: Enter comments.
and choose whether to create a new l Chamber Offset: Enter the offset.
file or append an existing file. l Treatment Label: It will be
l Comments: Comments are recorded included in your data record.
in the file header. l Log To: Instrument memory or
l Set the Destination; either the instru- CompactFlash.
ment memory or the CompactFlash l Start At: Start immediately
card. l Repeat Meas.: Number of times to
l Measurement Start: Set to Start repeat.
Immediately .
5 Transfer the files

When you're done, you'll want to transfer the data to a computer. See Transferring
data from the LI-8100A on page 6-1 for details.
6 Get the most from your data

Although the results computed by the LI-8100A will be fairly accurate if you set up
the measurement correctly, you should always evaluate the computation in
SoilFluxPro software and recompute the results to get the most precise results pos-
sible.

Survey measurements checklist

Below is a checklist of things that you should do prior to making measurements.
The checklist will not take long to address, and can save you a lot of time and frus-
tration later.
A Instrument Time: Set correctly?

B Chamber Gaskets: Inspected and OK?
C Batteries: Charged and ready?
D Soil Temperature Probe: If using, connected and responding?
E Soil Moisture Probe: If using, connected and responding?
F Soil Collars: In place for at least several hours, but ideally 24 hours?
G Soil Collar Area: Entered in the software?
H Soil Collar Offset: Prepared to measure and enter in the software?
I Observations Configured: Observation length of 90 to 120 seconds. Dead band of 10 to 60
seconds. Purge times set?
Survey measurements checklist 3-5

Automatic restart function

For long-term measurements, either multiplexed or single-chamber, you'll want the
instrument to restart automatically if there is a disruption to the power supply.
Note: This function is available only when the LI-8100A is powered via the aux-
iliary sensor interface or from the multiplexer. It is not available when powered
by a battery inside the analyzer control unit.
There are two steps to enable the automatic restart: 1) Move a hardware jumper;
and 2) Configure the software.
1 Move the jumper

The jumper is located directly below the PC card slots in the analyzer control unit.
Remove the access panel to view the jumper. There are three pins aligned hori-
zontally on the underside of the circuit board, below the words “Power On."
Figure 3-1. Keypad jumper position (A) and Aux. In jumper position (B).
When configured at the factory, the jumper is on the leftmost and center pins (Fig-
ure 3-1 above). In this position, if power is interrupted, the instrument can only be
restarted by pressing the ON/OFF button on the keypad. Reposition the jumper so

that it covers the center and rightmost pins to configure the instrument to power
on after a power interruption.
WARNING: When the jumper is positioned to automatically restart, the LI-8100A

presents a potential shock hazard. If power is interrupted and the unit shuts off
and the user is unaware that a power interruption caused the instrument to shut
down, power could be automatically restored while the user is in contact with
these internal components. Therefore, we recommend that you always disconnect
the power supply from the instrument before servicing any internal components in the
analyzer control unit.
2 Enable the software auto restart function
Click 8100 > Instrument Settings and Tap on LI-8100A > Instrument Set-
enable the Resume measurement on tings and set Automatic Restart to
instrument restart (Figure 3-2 below). Enabled (Figure 3-3 below).
Figure 3-2. Automatic restart setting in the Figure 3-3. Automatic restart setting in
Windows® software. the LI-8100APP.
Automatic restart function 3-7

Using the auxiliary sensor interface

The auxiliary sensor interface attaches to the side of the analyzer control unit and
allows for connection of your choice of sensors or an alternative power supply. Data
from these sensors are logged in the data file under the headers V1 to V4 (voltage
inputs) and the headers T1 to T4 (thermocouple inputs).
The auxiliary sensor interface is O-ring sealed, and has connections for up to 4 ther-
mocouples (types E, J, or T, or raw), and 4 general purpose input voltage channels,
any of which can be configured to measure a soil moisture probe, thermistor, or
other voltage input.
Sensors can be powered externally or by the LI-8100A with a constant 5 VDC
source. There is also a switched 5 VDC power supply used for moisture sensors.
The auxiliary sensor interface also has a 10.5-28 VDC input (3 A minimum) for
use with external power.
Figure 3-4. Auxiliary sensor interface and connector.

Auxiliary sensor interface terminals

Open the box by loosening the 4 Phillips head screws in each corner of the aux-
iliary sensor interface module and remove the top cover.
Figure 3-5. Auxiliary sensor interface interior.
There are 2 terminal strips, with connections given in Figure 3-6 below.
GND
GND
GND
GND
GND
GND
+
+
-
V1 V2 V3 V4 T1 T2 T3 T4 -
+
+
-
V IN V OUT V OUT
10.5-28VDC 5VDC 5VDC
3A MAX 30mA 30mA
SWITCHED
Figure 3-6. Terminals with labels.
Table 3-1. Input terminals for analog sensors.

Terminal Label Description
1 V1+ Voltage input 1 positive
2 V1 GND Voltage input 1 ground
Auxiliary sensor interface terminals 3-9

Table 3-1. Input terminals for analog sensors. (...continued)

3 V2 + Voltage input 2 positive
9 GND Ground
10 GND Ground
11 T1 + Thermocouple input 1 positive
12 T1 - Thermocouple input 1 negative
Power in and out terminals are given in Table 3-2 below
Table 3-2. Terminals for power in and power out.

1 V IN + Voltage input positive
2 V IN - Voltage input negative
3 V OUT + 5 VDC output positive
4 V OUT - 5 VDC output negative
5 V OUT + 5 VDC output positive (switched)
6 V OUT - 5 VDC output negative (switched)

Connecting auxiliary sensors

There are 5 compression style strain relief cable glands on the auxiliary sensor inter-
face. To attach your sensor(s) or power supply to the auxiliary sensor interface:
1 Loosen the four screws and remove the top cover of the box.
2 Remove the cap from any of the 5 glands by turning counter-clockwise.
3 Pass the wires through the top of the gland cap first, and then through the gland.
Screw the cap on slightly, but don’t tighten yet. If the wire is too small, wrap it in
santoprene tubing to increase its diameter and to help seal it in the gland plug.
Note: When inserting wires through the gland plugs on the auxiliary sensor
interface, it is important that a water-tight seal is formed when the gland plug
cap is tightened. If you are have poor data from sensors that are connected to the
box, check to see if the wires are tightly sealed. If they are loose, you may need to
encase bare wires in a short piece of sheathing material to improve the seal.
4 Use a small slotted screwdriver to loosen the

appropriate screw terminal, insert the wire lead
into the terminal, and tighten the screw ter-
minals.
Make a note of which gland the wires
are passing through (A, B, C, D, or E),
and to which terminal the wires are con-
nected (e.g. A/T1, B/V3, etc.). This
information will be needed later when
you enter the sensor calibration coef-
ficients into software.

5 Pull gently on the wires to remove excess slack from inside the box, re-attach the interface top
cover, and tighten the gland cap.
When you have finished installing all of your sensors and/or a power supply, attach
the auxiliary sensor interface cable connector to the connector on the side panel of
the analyzer control unit labeled AUX SENSOR.
6 Snap the auxiliary sensor interface onto the console.
NOTE: In order to achieve a weather-tight seal, the interface cable connector

must be tightened until it completely covers the O-ring seal on the analyzer con-
trol unit connector. When the connector feels tight, push in and wiggle it while
continuing to tighten until the O-ring is covered.
7 Always leave plugs in place in any unused gland

plugs to prevent water and insects from getting
inside the box.

Connecting the Omega soil temperature probe

The 6000-09TC Omega soil temperature probe terminates with two bare wires for
connection to the auxiliary sensor interface. Thermocouple channels 1-4 (T1-T4)
can be used with the Omega soil temperature probe.
GND
GND
GND
GND
GND
GND
+
+
-
-
V1 V2 V3 V4 T1 T2 T3 T4
Red (negative)
OMEGA
E
CHROMEL
+CH
CONST
CONST
+
E
6000-09TC Omega Probe
Purple (positive)
Figure 3-7. Omega soil temperature probe (part number 6000-09TC) connection to aux-
iliary sensor interface.
Click Chamber Measurement (Ctrl + Tap LI-8100A > Auxiliary Inputs, the
M), then select Thermocouples. select the thermocouple to configure
(Thermocouple 1 in Figure 3-7
Select type E for the Omega probe for
above).
the specified channel (Thermocouple 1
in Figure 3-7 above). Select E for the Omega Probe.
Connecting the Omega soil temperature probe 3-13

Connecting the GS1 soil moisture probe

The GS1 soil moisture probe is compatible with voltage channels 1-4 (V1-V4). The
8100-205 model has red, bare, and white wires that connect to V4 (+), V4(GND),
and V OUT 5VDC Switched(+), respectively, as shown in Figure 3-8 below.
Bare (ground)
GND
GND
GND
GND
GND
GND
+
+
-
-
V1 V2 V3 V4 T1 T2 T3 T4
White (OLD) Red (OLD) GS1

Brown (NEW) Orange(NEW)
+
+
-
V IN V OUT V OUT
3A MAX 30mA 30mA
Figure 3-8. GS1 soil moisture probe connection to auxiliary sensor interface.
Click Chamber Measurement (Ctrl + Tap LI-8100A > Auxiliary Inputs, then
M) > Port Setup, then select the V4 tab select the voltage input to configure
(V4 in Figure 3-8 above). (V4 in Figure 3-8 above).
Select Soil Moisture Probe and enter m: Select SM (soil moisture) and
0.494 and b: -0.554. enterSlope: 0.494 and Offset: -0.554.

Connecting the EC-5 soil moisture probe

The ECH2O soil moisture probe is compatible with voltage channels 1-4 (V1-V4).
The 8100-202 model has red, bare, and white wires that connect to V4(+), V4(-),
and V OUT 5VDC SWITCHED(+), respectively, as shown in Figure 3-9 below.
GND
GND
GND
GND
GND
GND
+
+
-
-
V1 V2 V3 V4 T1 T2 T3 T4
Bare (ground)
Red ECH2O EC-5 Moisture Sensor

+
+
-
V IN V OUT V OUT
White (excitation)
3A MAX 30mA 30mA
SWITCHED
Figure 3-9. ECH2O EC-5 soil moisture probe connection to auxiliary sensor interface.
Select Soil Moisture Probe and enter1m: Select SM (soil moisture) and
0.488 and b: -0.272. enter1 Slope: 0.488 and Offset: -0.272.
1This slope and offset will provide a close approximation of soil moisture content. If a more accurate meas-
urement is needed, use a slope of 1 and an offset of 0 to record the voltage, and process the data in
SoilFluxPro using Transform > Decagon_EC-5(X) to compute Volumetric Water Content. SoilFluxPro
uses the following equation: .

Connecting the 8100-203 soil temperature probe

The 8100-203 soil temperature probe kit consists of a soil temperature probe (part
number 8150-203) and a cable adapter (part number 9981-150) that connects to the
probe. The cable adapter contains a resistor that allows the 8150-203 soil tem-
perature probe to be used with the auxiliary sensor interface on the LI-8100A.
GND
GND
GND
GND
GND
GND
+
+
-
-
V1 V2 V3 V4 T1 T2 T3 T4
Black (ground)
Red
(0-5VDC+)
9981-150 Soil Temperature
Probe Adapter
+
+
-
V IN V OUT V OUT
Orange
(V OUT 5VDC+)
3A MAX 30mA 30mA
SWITCHED
Figure 3-10. 8100-203 soil temperature probe connection to auxiliary sensor interface.
Select Thermistor Input and click Set to Select Therm (thermistor) and tap
Default or enter the coefficients: Set to Default or enter the coef-
ficients:
a=1.1259e-3
b=2.3459e-4
c=8.6329e-8

Connecting the Delta-T ThetaProbe

The 8100-204 Delta-T ThetaProbe has four bare wire leads for connection to the
auxiliary sensor interface voltage channels 1-4 (V1-V4). The cable has red, blue, yel-
low and green wires that are connected to V OUT 5VDC SWITCHED(+),V OUT
5VDC SWITCHED(-), V4(+), and V4(-) respectively, as shown in Figure 3-11 below.
Auxiliary Sensor Interface Terminal Strips
GND
GND
GND
GND
GND
GND
+
+
-
-
V1 V2 V3 V4 T1 T2 T3 T4
Green (ground)
Yellow (+V IN) o

Theta
Probe type ML2x
+
+
-
Blue (power supply -)

V IN V OUT V OUT
10.5-28VDC 5VDC 5VDC Red (power supply +)
3A MAX 30mA 30mA
SWITCHED
Figure 3-11. Delta-T ThetaProbe connection to the auxiliary sensor interface.
Select Soil Moisture Probe and enter m Select SM (Soil Moisture) and enter
(Slope) and b (Offset) from Table 3-3 on Slope and Offset from Table 3-3 on
the next page. the next page.
The 8100-204 uses different linearization coefficients, based on the organic content
of the soil into which the probe is inserted. In general, if the soil is classified as a
mineral soil, with < 7% organic content, the probe uses one set of coefficients, and
if the soil is classified as an organic soil, with > 7% organic content, the probe uses
a second set of coefficients.

Table 3-3. Delta-T ThetaProbe coefficients for mineral and organic soils.
Soil Organic Bulk density range Use for bulk Slope Offset
Type contents: (g cm-3) densities:
Mineral < 7% 1.25 - 1.5 g cm-3 > 1.0 g cm-3 0.529 -0.060
Organic > 7% 0.2 - 0.7 g cm-3 < 1.0 g cm-3 0.577 -0.026
It is possible to perform soil-specific calibration of the soil moisture probe to obtain

linearization coefficients; refer to the ThetaProbe ML2x instruction manual for
more information.
Placing soil temperature and moisture probes

In general, temperature and moisture measurements should be made in close prox-
imity to the CO2 flux measurement. Researchers have reported a strong correlation
between soil CO2 flux and soil temperature (e.g., Hanson et al., 1993, Norman et
al., 1992). Furthermore, soil temperature and moisture may vary significantly with
depth (Hillel, 1982), and both are dependent on a number of site characteristics,
such as exposure to light, shade, and wind.

Tips for success

Here are some things that may not be self-evident, but that may help you be suc-
cessful with the LI-8100A.
Store the instrument in low humidity conditions.
The LI-8100A can be stored in non-condensing conditions, but if it is exposed to

high humidity for a long period of time while it is powered off, the humidity can
temporarily affect measurements. You can identify this issue by observing unex-
pected drift that stabilizes after several days of operation, an offset in measurements,
or unresponsiveness. If your instrument exhibits these characteristics, verify the
issue by comparing raw detector outputs in data that was collected before and after
storage. If you don't have these data, contact LI-COR and we will provide the cal-
ibration data set for your instrument. In the PC interface software, observe the val-
ues for Raw CO2 Reference and Raw H2O Reference. If these values are lower than
the original values, power on the instrument and let it run (with the heaters on)
for several hours to several days. If the instrument has not fully recovered after sev-
eral days, you may need to disassemble the optical bench and heat the detector in
an oven at 65 °C (150 °F) for several hours. Reassemble the instrument and check
the measurements.
Work faster by saving a configuration for later.
You can save an instrument configuration for later. That way you do not have to set
it up each time you are making measurements.
Click the Chambers button (Ctrl + M) Go to Setup > Measurement Preset,

and select Presets. You can save a con- where you can save the current con-
figuration or load a saved one. figuration or load a saved one.
Tighten the cable connectors! Loose cables can cause data loss and damage to equip-
ment. Clean dust and dirt out of the connectors using compressed air. To tighten a
cable press the connector in and tighten, then repeat this several times. If a cable
will not tighten check for bent pins in the connector .

Warm it up. The infrared gas analyzer may take 10 minutes or more to warm up.
You know it is ready when the IRGA READY light is illuminated on the instrument
panel or it is indicated by the software. In cold environments, store the instrument
in a warm space to reduce the warm-up time.
What's in a name? You can name your instrument under 8100 > Instrument Set-
tings... . The default name is UNKNOWN (literally), but you can choose whatever
you want. HAL9000, T-1000, CHAPPiE, and Marvin are popular choices. The name
will be saved in the instrument and in each data file.
Getting an error? A good place to start is the Error Log. To open it:
The LI-8100A PC software indicates an The LI-8100APP indicates an error

error by placing a red flag in the dis- by placing an upper case E on the
play. To view the error details click right of the app display. Tap the E to
View > Error Log; or click the error flag retrieve the error log from the instru-
in the main window. ment.
Change the display variables. In the LI-8100A PC software, click a variable in the
data frame to select another variable.

Quickly view a record. To view a data record, select View > Summary Records.
Click Previous or Next to scroll through all observations.
Plot your data. To plot your data in the LI-8100A PC software, click View >
Reports. In the Report dialog, click File, and then select a data file that is stored on
the device or CompactFlash card.
l Under Observations View click View Observation. You can view all the data in
the record and select different observations.
l Under Flux Computation, click Plot Fluxes to chart the data.
l Values by Port is useful if you are using the multiplexer.
l Values by Observation shows individual observations.


Section 4.
Overview of the LI-8150 multiplexer
The LI-8150 Multiplexer is an accessory for the LI-8100A that makes it possible to
connect as many as 16 long-term chambers. Data from this configuration is useful
for characterizing spatial and temporal variation of soil gas flux. The LI-8150 can
also be connected to ordinary gas sampling lines for vertical profiling, custom
chambers, or other studies.
Figure 4-1. The LI-8150 Multiplexer supports up to 16 chambers, with a measurement dia-
meter of up to 30 meters.
What's what
If you have just taken delivery of your LI-8150 check the packing list to verify that
you received everything ordered, including the following items:
Cable and tube assembly

Contains one cable and two tubes for connecting the LI-8100A Analyzer Control
Unit to the LI-8150 Multiplexer.

Power cable
The power cable (part number 8150-706) is a 3 m cable with bare wire leads for
connection to a user-supplied DC power source (10.5-14.5 VDC).
Spare parts kit

This box contains replacement parts for your LI-8150. As you become familiar with
the system you will learn which items to keep close at hand and which items can
be stored away. Additional spares kits are packaged with the soil chambers, as well.
The spares kits include these commonly used items:

Multiplexer Spares Kit 1 9981-130
Urethane Tubing, 1/8” ID x 11” OD 3 ft. 222-00303
Hose Barb T-Fitting 2 300-02627
11” Quick Connect Plug 2 300-08151
3 Amp 250 V Fuse 1 439-04215
4 Amp 250 V Fuse 1 439-08516
Jumper Tube Assembly 1 9981-142
Filter Replacement Kit (set of 8) 1 or 21 8150-909
Optional accessories
Optional accessories may be provided, depending on the configuration you ordered.
AC to DC power supply
When used with the multiplexer, the AC to DC power supply (part number 8150-
770) provides power to both the multiplexer and the LI-8100A. The power supply
provides a constant 12 VDC source (4.5 A maximum) to the multiplexer and LI-
8100A. It is weather resistant, O-ring sealed, and is designed for long-term outdoor
deployment. It has a user-selectable input voltage range of 115-120 or 230-240 VAC.
Cable and tube extension

The extensions (part number 8150-705) are used to place the chamber up to 15
meters from the multiplexer.
1Two kits are included with the LI-8150-16 Multiplexer configuration.

NOTE: Only one extension is recommended for each chamber. Contact technical
support for more information about longer tube and cable runs.
Soil moisture probes

The 8150-202 ECH2O Model EC-5 soil moisture probe (Decagon Devices, Inc.,
Pullman, WA) is a 5 cm (2") dielectric sensor that measures volumetric water con-
tent of the soil. The 8150-202 probe has a plug for direct connection to the 8100-
104/C Long Term chambers.
The 8150-204 ThetaProbe has a connector pre-installed for direct connection to the
8100-104/C soil chambers.
Soil temperature thermistor

Part number 8150-203 has a 2 m (6') cable. It connects to the 8100-104/C Long-
Term Chamber. Accuracy: ±1.0 °C from –20 to 50 °C.
Soil moisture probes 4-3

How it works
The LI-8150 Multiplexer contains a pump and tubing to transport the sample gas
from one of the chambers (up to 16) to the IRGA in the LI-8100A. Air flows to and
from the chamber while maintaining the ambient pressure in the IRGA.
LI-8150 Multiplexer
Filter
LI-8100A Analyzer Control Unit
Flow
Meter
Open
Chamber
Diaphragm
Pump
Infrared
Gas
Closed Chamber LI-8150 Subsample Analyzer
Pump Loop
Filter
Open
Chamber
Solenoid Manifold
Figure 4-2. Flow paths and the major components of the multiplexed system. Solenoid
valves control flow to and from each chamber.
A diaphragm pump circulates the sample gas to and from the multiplexer and the
closed chamber. A flow sensor detects flow in the ‘chamber loop’ (between 1.5 and
3.5 lpm in normal operating conditions). The pump also circulates flow in a ‘sub-
sampling loop’, as it is in-line with both parallel loops. Flow restrictors in the ‘sub-
sampling loop’ restrict flow in comparison to the ‘chamber loop’ to control the
pressure in the LI-8100A IRGA. The LI-8100A, in turn, samples air from the ‘sub-
sampling loop’ using its own pump. Sample gas from the chamber is filtered before
it enters the solenoid, and again in the LI-8100A before it enters the IRGA.

The LI-8150 has connections for up to 8 chambers on each side. The left side
shown above (optional) has only chamber connections; the right side (not pic-
tured) also has power and LI-8100A connections. The power switch, chamber actu-
ator, and indicator panel are inside the LI-8150.
How it works 4-5

Power – Illuminates when power is applied to the

instrument, and the power switch is turned On.
Check Error Log – Illuminates when an error con-
dition is detected (a chamber failed to close, flow rate Power
is too low, etc.). The Error Log can be viewed in the
Check Error Log
Windows application software, under the View menu,
and in the mobile app by pressing the “E” indicator Activate All Chambers
when present. Active

Chamber
Activate All Chambers – Illuminates when Chamber
Actuator Button is pressed. All connected chambers
will close in series (4 at a time); (1-4), (5-8), (9-12), Active
Valve
and (13-16).
Active Chamber – Displays chamber that is currently V2 V3
performing a measurement.
Active Valve – Displays currently active (open) solen-
V4
oid valve. When a measurement is being performed,
this will always match the Active Chamber. When the
instrument is idle, however, a valve can be operated
independent of the chamber(s).
V2-V4 – Shows the port from which the indicated voltage output is coming.
Using the AC to DC power supply

The AC to DC power supply can be used with 115-120 or 230-240 VAC main
power.
WARNING: To protect against electrical shock, the power supply must be con-
nected to a grounded AC receptacle. We recommend that the mains power to the
instrument be supplied by a ground-fault circuit interrupter (GFCI). If an exten-
sion cord is to be used with the power supply, make sure that it is rated for out-
door use.

Figure 4-3. 8150-770 AC to DC Power Supply.
Setting the input voltage

Loosen the 4 screws in each corner on the top panel of the power supply. Slide the
top cover away from the supply; note that the cover is attached via a grounding
wire and cannot be fully removed. Verify that the switch is in the correct position
for your power supply voltage (choose 115 for 115-120 VAC, or 230 for 230-240
VAC).
If you move the voltage switch, you will need to change the fuse as well. Remove
the cap on the fuse holder and check to see that the proper fuse is installed. Spare
fuses are in the 8150-770 spares kit.

Figure 4-4. Location of voltage selector switch and fuse holder. When switching the input
voltage, be sure to replace the fuse with the correct one.
l A 1 A fuse (part number 439-08924) is used when the voltage selector switch is
in the 230 VAC position.
l A 2 A fuse (part number 439-08923) is used when the voltage selector switch is
in the 115 VAC position.
The AC to DC power supply includes a 2 m power cord that connects the power
supply to the LI-8150 Multiplexer (part number 9981-140). Connect the power cord
between the power supply and multiplexer before plugging the power supply into a
power outlet.
Tips for using the power supply in outdoor conditions

The AC to DC power supply can rest on the ground or on a platform. If it is
allowed to rest on the ground, and there is a possibility of water pooling around or
immersing the unit, we recommend placing the power supply on a platform or in
a shelter to reduce the possibility of shock hazard. Also be sure that the power sup-
ply cord will always be accessible, as this is the only way to completely remove
power from the instrument.

If the power supply is deployed outdoors for an extended period of time, it may be
subject to damage from weather and rodents. We recommend that you periodically
inspect the power supply and power cords for damage. In addition, check the gland
connector where the power cord passes through the power supply case to make
sure it is tight, so that water cannot leak into the case; tighten if necessary.
The power supply can be used in combination with the batteries inside the analyzer
control unit. If AC power is interrupted, the batteries will continue to power the
LI-8100A, but the system will collect bad data.

LI-8100A and LI-8150 cable connections

Cables and tubes connect to the left side of the LI-8100A Analyzer Control Unit.
These connectors (Figure 4-5 below) have slightly different uses when the LI-8150
Multiplexer is connected.
Figure 4-5. LI-8100A Analyzer Control Unit cable connection panel.
Two tube and cable bundles, which are included with the LI-8150, connect as
shown in Table 4-1 below and Figure 4-7 on the facing page. One of the tubes has a
piece of black shrink wrap; this tube attaches to the Air In fitting on the analyzer
control unit.
Table 4-1. LI-8100A and LI-8150 cable and tube connections.

AIR OUT I
AIR IN O
LI-8100A BELLOWS P
connector CHAMBER connects to CTRL on the LI-8150.
labeled... AUX. LI-8100
SENSOR
INTERFACE

Figure 4-6. Power and data cable for the multiplexer. In this configuration, the LI-8100A is
powered by the multiplexer.
Figure 4-7. Power cable, data cable, and tube connections to LI-8100A Analyzer Control
Unit.
Notes on multiplexer connections:

LI-8100A and LI-8150 cable connections 4-11

Connecting chambers
Each LI-8150 side panel has connectors
for 8 long-term soil chambers. The right
panel has ports 1-8, and the optional left
panel has ports 9-16. It is not necessary to
connect the chambers in sequential
order—a chamber can be connected to
any port. The port numbers are important
to note, however, as they are configured
in the software.
Each chamber connection has Air In and
Air Out connectors for each cor-
responding chamber. The bundled elec-
tronic cable connects to the fitting labeled
Figure 4-8. Cable connections for the LI-
CHBR. Figure 4-8 above shows some typ-
8150 and a soil chamber.
ical LI-8150 connections, including soil
chambers and gas sampling (vertical profiling) lines.
Unlike the auxiliary sensor interface that is used with the LI-8100A, the 8100-
104/C Long-Term Chambers have three connectors on the exterior of the chamber.
Soil temperature or soil moisture probes provide by LI-COR for use with the mul-
tiplexer, are fitted with connectors that connect directly to the chamber connectors.
For sensors from other manufacturers, an adapter cable with bare wire leads (part
number 392-08577) is available to attach the sensor’s wire leads. See Connecting
other sensors on page 5-18 for details.

Section 5.
Using the multiplexer
The following tutorial can be followed in the lab or field, wherever you happen to
be.
Do this first
This section assumes you are familiar with the system and that you have installed
the PC software on your computer or the LI-8100APP on your mobile phone.
If you assemble the system in the lab for later deployment in the field, or if you are
making continuous long-term measurements, configure the system to auto-
matically restart following a power interruption. See Automatic restart function on
page 3-6.
Multiplexed measurement tutorial

You will need a dependable power supply for long term measurements. A solar
power supply, deep cycle marine battery, or grid power are recommended for this
application.
The multiplexer and chambers are detected by the LI-8100A automatically and the
configuration options are activated in the software after the components are con-
nected, so you have to connect everything in order to configure multiplexed meas-
urements. The configuration is pretty straight forward, and once you have one
chamber set the way you like it, you can apply that configuration to the other cham-
bers with ease.

1 Install the soil collars and measure the offsets

See Using soil collars on page 2-17 for details. Remember that data collected within
24 hours of installation is not to be trusted.
2 Assemble the system and connect to a PC or mobile device

Connect the cables and power up the system (Figure 4-6 on page 4-11). Turn on the
multiplexer first, then power up the analyzer control unit. Connect to your com-
puter or mobile device. See Get connected on page 2-3 for details.
3 Connect the chambers

See Connecting chambers on page 4-12 for details.
Adjust the legs of each chamber so it is even over the soil collar, then record the off-
set of each chamber. Also insert the soil temperature probe, soil moisture probe, or
other sensor for each chamber. If the chambers do not have clearance to open and
close freely, adjust the chamber open positions to accommodate the situation (see
Changing the long-term chamber open position on page 2-28).

4 Configure the chamber on Port 1
Under Setup > Chamber Measurement Under Setup > Areas and Volumes,
(Ctrl+M); Port Setup > Chamber , select enter the following:
Port 1 (typically). l Chamber Offset: The offset meas-
l Chamber: Select the chamber. ured at the chamber.
l Temp Source: Typically you will use l Soil Area: Select the chamber to
the temperature inside the chamber, enter the area.
so select Chamber . l Chamber Volume: Select the
l Soil Area: 317.8 cm 2 for the 8100- chamber and temperature source
104/C Long-Term Chambers. ( Chamber , typically). Leave Cham-
l Chamber Offset: The offset measured ber Signals Closed set to on, then
at the chamber. tap Send Update.
l Extension Tube Volume: For the 15- l Ext. Tube Volume: For the 15-
meter tube enter 237 cm 2 . meter tube enter 237 cm 2 .
The remaining fields are preset. Tap

Send Update.
Section 5. Using the multiplexer 5-3

5 Configure the observation
Under Port Setup > Observation, enter a Under Setup > Measurement Pro-
Treatment Label that will be accompany tocol, enter a Treatment Label that
measurements from this chamber in will accompany measurements from
the data file. Configure the other para- this chamber in the data file. Con-
meters as shown: figure the other parameters:
l Observation Length: 2 minutes l Obs. Length: 2 minutes
l Dead Band: 25 seconds l Dead Band: 25 seconds
l Pre-purge: 30 seconds l Pre-Purge: 30 seconds
l Post-purge: 45 seconds l Post Purge: 45 seconds
Tap Send Update.
6 Select variables to log
Under Port Setup > Data Logging, click Under Setup > Measurement Pro-
Select All unless data storage space is an tocol, Additional Log Fields: All; or
issue. In that case, you may want to select variables if you have limited
identify the critical variables and log data storage space.
those.
Tap Send Update.

7 Configure the auxiliary sensors

If you are logging data from a soil temperature probe, soil moisture probe, or other
sensor with voltage output, configure the sensor.
Under the, V2, V3, or V4 tab, select Gen- Under LI-8100A > Auxiliary Inputs,
eral Purpose Input, Soil Moisture Probe, configure the inputs for Volt 2, 3, and
or Thermistor , and configure the chan- 4.
nel.
Tap Send Update.
For details on auxiliary sensors, see Connecting auxiliary sensors on page 5-9.
8 Configure the other ports

If the settings for your first port are applicable to the other ports and their cor-
responding chambers, you can easily copy the configuration to the other ports.
Under Port Tools you can copy the set- Under Setup > Areas and Volumes,
tings from one port to the others. tap Copy Ports. You can choose to
copy the Treatment Labels and
You can also quickly alter the Treat-
Chamber Offsets or not, then Pro-
ment Label and Chamber Offset for
ceed to Port Selection. Select the con-
each chamber under Quick Settings.
figured port, and then specify which
Click Apply to send the updated port ports to receive the configuration.
information. Tap Send Update.
Now you may wish to update the
Chamber Offset and Treatment Label
for the other ports under Setup >
Measurement Protocol.

9 Set the port sequence
Under the Port Sequence tab, the Under Setup > Start Measurement,
default sequence progresses from port 1 tap Port Sequence alter the sequence
to port 16 in order. Click Use as by keying in the order you prefer,
Sequence to set the sequence quickly. with digits separated by commas.
If you want to customize the order,
Tap Send Update when done.
simply key in the order you prefer, with
digits separated by commas.
10 Set the repeat time

A repeat time of 1 hour will provide 24 measurements per day.
Under the Repeat tab, enter the time Under Setup > Start Measurement,
that you want between measurement tap Repeat Meas and enter the time
sequences and the number of repeats. you wan between measurements. Set
Set as many repeats as you want - for as many repeats as you want - for
long-term continuous measurements, long-term continuous measurements,
click Set to Max . set the time you want.
Tap Send Update.

Under Chamber Measurement click Under Setup > Start Measurement

Start Measurement. enter a File Name and Comments and
change the Port Sequence if desired.
Use Preset: Current Settings
Specify a Log To destination and
Specify a Measurement File, Settings,
Start Time.
and specify a Destination.
You can alter the repeat sequence
Choose the start time (immediately, or
too.
at a defined date and time).
Tap the Start button.
Click the Start Measurement button.
Now the system should be running as specified, so just let it run until it is done.
After the system has recorded data for some time, you'll want to retrieve your data.
See Transferring data from the LI-8100A on page 6-1 to learn how.
12 Process the data in SoilFluxPro software

Process your data in SoilFluxPro™ software (formerly FV8100) for PC or Mac.
SoilFluxPro is an essential part of the LI-8100A system.
Get it free from http://www.licor.com/env/products/soil_flux/software.html.

Long-term measurements checklist

Below is a checklist of things that you should do prior to making measurements.
The checklist will not take long to address, and can save you a lot of time and frus-
tration later.
A Instrument Time: Set correctly?

B Leak Test: Checked and OK?
C Soil Temperature Probe: Connected and responding?
D Soil Moisture Probe: Connected and responding?
E Soil Collars: In place for at least 12 hours?
F Soil Collar Area: Entered in the software (PC only)?
G Soil Collar Offset: Prepared to measure and enter in the software?
H Pre-purge: Set to at least 30 seconds?
I Post-purge: Set to at least 45 seconds?
J Dead Band: Configured for 10 to 20 seconds?
K Chamber Purge Period: Entered in the software?
L Automatically Restart After Power Interruption: Set as desired?

Connecting auxiliary sensors

The 8100-104 and 8100-104C Long-Term Chambers have sockets for connecting
three auxiliary sensors. The sealed connectors, labeled V2, V3, and V4, are 0-5 V
inputs. Data from these sensors are logged in the data file under the headers V2 to
V4 (voltage inputs) and the headers T1 to T4 (thermocouple inputs). The data
under the header V1, when using a multiplexer, is the multiplexer pump voltage.
Soil temperature and soil moisture probes that are pre-wired for direct connection
to the 8100-104/C are available from LI-COR.
You can connect auxiliary sensors to each chamber, or you can use measurements
from one auxiliary sensor for all chambers by enabling Fix to port. When you
enable Fix to port for a sensor, its data will be recorded for every port’s observation.
This works for sensors with continuous excitation voltages, such as a soil tem-
perature sensor or a quantum sensor. However, soil moisture sensors require a
switched excitation voltage. The chamber’s switched excitation voltage is only
turned on when that chamber is being sampled, so Fix to port does not work with
soil moisture probes.

Connecting the GS1 soil moisture probe

The GS1 soil moisture probe can be connected directly to the long-term chamber
V2, V3, or V4 inputs. The 8150-205 model has a connector that attaches directly to
the long-term chamber V2, V3, or V4 input. To connect it, simply plug it into the
terminal, then configure the software.
M) > Port Setup, then select the cor- select the corresponding voltage
responding voltage tab. input.
Select Soil Moisture Probe and enter m: Select SM (soil moisture) and enter
0.494 and b: -0.554. Slope: 0.494 and Offset: -0.554.
You can also perform soil-specific calibration to obtain linearization coefficients;

refer to the GS1 instruction manual for more information.

Connecting the EC-5 soil moisture probe

The ECH2O soil moisture probe can be connected directly to the long-term cham-
ber V2, V3, or V4 inputs. The 8150-202 model has a connector that attaches directly
to the long-term chamber V2, V3, or V4 input. To connect it, simply plug it into
the terminal, then configure the software.
responding voltage tab. input.
Select Soil Moisture Probe and enter1 Select SM and enter1 Slope: 0.488
m: 0.488 and b: -0.272. and Offset: -0.272.
1This slope and offset will provide a close approximation of soil moisture content. If a more accurate meas-
urement is needed, use a slope of 1 and an offset of 0 to record the voltage, and process the data in
SoilFluxPro using Transform > Decagon_EC-5(X) to compute Volumetric Water Content. SoilFluxPro
uses the following equation: .

Connecting the 8150-203 soil temperature probe

The 8150-203 soil temperature probe is a soil temperature sensor (part number
8100-203) without the cable adapter (part number 9981-150). The cable adapter
should be removed when the probe is connected directly to a long-term chamber
V2, V3, or V4 inputs. To connect it, simply plug it into the terminal, then con-
figure the software.
responding voltage input channel. input channel.
Select Thermistor Input and click Set to Select Therm and tap Set to Default
Default or enter the coefficients: enter the coefficients:
a=1.1259e-3
b=2.3459e-4
c=8.6329e-8

Connecting the Delta-T ThetaProbe

The 8150-204 Delta-T ThetaProbe is compatible with voltage channels 2-4. The
8150-204 model has a connector that attaches directly to the long-term chamber
V2, V3, or V4 inputs. To connect it, simply plug it into the terminal, then con-
figure the software.
M) > Port Setup, then select the cor- select the voltage input channel.
responding voltage input channel.
Select SM (Soil Moisture) and enter
Select Soil Moisture Probe and enter m Slope and Offset from Table 5-1
(Slope) and b (Offset) from Table 5-1 below.
below.
The ThetaProbe uses different linearization coefficients, based on the organic con-
tent of the soil into which the probe is inserted. In general, if the soil is classified as
a mineral soil, with < 7% organic content, the probe uses one set of coefficients,
and if the soil is classified as an organic soil, with > 7% organic content, the probe
uses a second set of coefficients.
Table 5-1. Delta-T ThetaProbe coefficients for mineral and organic soils.
Soil Organic Bulk density range Use for bulk Slope Offset
Type contents: (g cm-3) densities:
Mineral < 7% 1.25 - 1.5 g cm-3 > 1.0 g cm-3 0.529 -0.060
Organic > 7% 0.2 - 0.7 g cm-3 < 1.0 g cm-3 0.577 -0.026
It is possible to perform soil-specific calibration of the soil moisture probe to obtain

linearization coefficients; refer to the ML2x ThetaProbe instruction manual for
more information.

Connecting the LI-190R Quantum Sensor

The LI-190R-BL-2 Quantum Sensor with 2420-BLS Amplifier has four wire leads
connected to a terminal for connection to a long-term chamber.
Figure 5-1. Wire lead connections for the LI-190R-BL (left) and LI-190-BL (right) to the
2420-BLS Amplifier.
2420-BLS Amplifier Gain Settings

The amplifier provides 15 discrete gain settings to accommodate a variety of full-
scale light intensities and full-scale voltage ranges. This section shows how to
determine the correct gain setting for your application. Gather the following
information:
l Calibration constant for your light sensor (C)

l Maximum full-scale light intensity to be measured (Imax)
l Full-scale input voltage of the datalogger (Vmax = 5.0 V for the LI-8100A Auto-
mated Soil CO2 Flux System)
Follow these steps:
1 Calculate the ideal amplifier gain (Gideal).
Example: Consider a quantum sensor installation with the following parameters:

l Sensor calibration constant: C = 6.5 μA per 1000 μmol m –2 s–1
l Full-scale light intensity: Imax = 2000 μmol m –2 s–1

l LI-8100A full-scale channel voltage: Vmax = 5.0 V
2 Select the gain setting (G) from the Gain Settings Table (page 2) that is less than or equal to the
ideal gain from step 1.
Example: The ideal gain computed in step 1 is Gideal = 0.3846 V μA–1 . On the
table, the closest actual gain that is less than or equal to this value is G = 0.375 V
μA–1 .
3 Use a number 2 Phillips screwdriver to remove the amplifier lid. Alternate the four screws, pulling
the lid up as you go so that the screws do not bind with the lid.
4 Using a small screwdriver, set the switches in the center of the circuit board. Use the switch set-
tings from the gain settings table that correspond to the amplifier gain determined in step 2.
Example: The gain determined in step 2 (G = 0.375 V μA–1 ) requires all switches
to be in the off position:
G = 0.375; all switches off
Table 5-2. Gain settings for the amplifier.

DIP Switch Gain (V μA –1) DIP Switch Gain (V μA –1)
G = 0.375 G = 0.175
(all switches off)
G = 0.350 G = 0.150
G = 0.325 G = 0.125
G = 0.300 G = 0.100
G = 0.275 G = 0.075

Table 5-2. Gain settings for the amplifier. (...continued)

DIP Switch Gain (V μA –1) DIP Switch Gain (V μA –1)
G = 0.250 G = 0.050
G = 0.225 G = 0.025
G = 0.200 Do Not Use

(all switches on)
5 Re-install the lid. Torque the screws to 0.45 Nm (64 oz-in.) if using a torque screwdriver.
6 Calculate the voltage multiplier (M). The voltage multiplier is used to convert the voltage meas-
ured by the datalogger into a light intensity. For Quantum sensors, the units for M are μmol m–2
s–1 V–1.
Example: Calculate M using G = 0.375 V μA–1 from step 2 and C = 6.5 μA per
1000 μmol m –2 s–1 from step 1:
Connecting the LI-190R and amplifier to a chamber

The 2420-BLS amplifier comes prewired with an output cable. Plug this cable into
one of the auxiliary sensor ports on the side of the long-term chamber.
Figure 5-2. Amplifier output wiring.

M) > Port Setup, then select the V4 tab. select the voltage input to configure.
Select General Purpose Input and enter Select GP (general purpose) and
the slope calculated earlier for m and b: enter Slope (m): calculated earlier
0.0. and Offset: 0.0.
If you are using only one quantum If you are using only one quantum
sensor, select Fix to port and enter the sensor, select Fix to port and enter the
port number of the chamber that has port number of the chamber that has
the sensor attached. the sensor attached.
Click Apply to Port. Tap Apply to Port.

Connecting other sensors

Other sensors with bare wire leads are
connected with the adapter cable (part
number 392-08577). The software is con-
figured by setting the slope and offset as
needed to scale the readings from the
sensor.
It may seem obvious, but it is worth point-
ing out that when the multiplexer is
attached to the LI-8100A, the auxiliary
sensor interface cannot be attached to the
LI-8100A.
Connector on the Connector on the

8100-104/C Long- 392-08577 Cable
Term Chamber
1 7
2 8 6 6
7
8
1
2
Figure 5-3. Adapter cable with a ter-
3
4
5 5
4
3 minal and bare wire leads (part number
392-08577) is used to attach bare-wire
sensors to the 8100-104/C Long-Term
Chambers.
Table 5-3. The V2-V4 connectors on the long-term chambers terminal assignments.
Pin Number Signal Wire Color
1 0 v – 5 v In (+) Brown
2 5V_Ref Out (4 mA) Pink
3 +5 V Out (100 mA) Blue
4 N/C Grey
5 Unreg Out (50 mA) Red
6 Switched +5 V Out (30 mA) Yellow
7 0 v – 5 v In (-) Green
8 Gnd White

The leak test

Given the large amount of tubing and junctions in the multiplexer, there is a
chance that the system will develop leaks from time to time, especially as the sys-
tem ages1. Fortunately, it is relatively easy to perform a leak test and identify the
offending connection or tube and correct the leak2.
During the leak test, the bellows pump in the LI-8100A draws a vacuum on the sys-
tem. The pressure is monitored to determine the leak rate of the system. Upon com-
pletion of the leak check on each port, the system is purged to allow the next port
to be evacuated.
The leak test requires that; a) each mul-
LI-8150
tiplexer port is sealed to form a closed
loop, and b) one port is left open to allow
the system to purge itself.
Chamber Hose
The closed loop is made by disconnecting
Leak
the chamber and connecting the male Test Shunt
and female connectors to each other or
with the leak test shunt.
Figure 5-4. For the leak test, connect the
The leak test shunt (part number 9981- two ends of the chamber tube or install
142) is a short piece of tubing with male the leak test shunt to close the loop for
and female connectors. It is used to close each chamber. The shunt can help you
the loop between the air input and output determine whether a leak is in the
ports (Figure 5-4 above) when you are not external tubing or in the multiplexer.
testing the chamber tubing.
1 For each port to be tested, close the tubing loop.

A Join the male and female connectors on the chamber tube, or
B Connect the leak test shunt (part number 9981-142) between the air inlet and air outlet port
for a chamber.
Make sure that at least one port is left open; you can disconnect the tubing at the
chamber end, without joining the connectors, or simply disconnect at the mul-
tiplexer. Thus, the greatest number of ports that can be checked at one time is 7
1Not unlike the human body.

2Easier than with the human body, typically.
The leak test 5-19

with an 8-port system, or 15 with a 16-port system. The open port will need to be
checked for leaks after testing the other ports.
2 Start the Leak Test.
Go to Utilities > Manual Controls and Go to Utilities > Manual Controls and
select the Leak Test tab. tap Leak Test.
Check the boxes next to the ports to Tap Port Sequence and select the
test. Check 8100 to Mux to check the ports to test. Choose whether to test
lines between the two. LI-8100 to Multiplexer Lines.
Click Run Test. Results are: Tap Send Update to initiate the test.
Results are:
l p = pass
l f = fail
l x = canceled
l o = in queue
l - = not tested

Section 6.
Transferring data from the LI-8100A
Data files are stored in the LI-8100A memory, either in the instrument storage or
on a CompactFlash card in the instrument. Regardless of where it is stored, it is
simple to download data files from the instrument to your computer.
Transfer data over a serial, USB, or network

connection
1 Connect the instrument to a computer
l See First Things First on page 2-1 to transfer data over serial or USB.
l See Connecting directly over Ethernet on page 2-4 to transfer data over a wired Eth-
ernet connection.
l See Connecting over a local area network on page 2-5 to transfer data over a local
network.
l See Connecting to a computer over wireless on page 2-6 to transfer data over a wire-
less network connection.
2 Open the file transfer tool

Click Utilities > File Manager . You will see a list of files and folders on your PC, a
list of files stored in the LI-8100A internal memory, and a list of files stored in the
LI-8100A CompactFlash card.
3 Set the destination for the files

Under Local PC, select the folder where you want to store the files.

4 Select the files that you want to copy

Select one or multiple files using Shift + Click or Ctrl + Click.
5 Transfer the data

Click Transfer to PC to move the files.
WARNING: Do not click Delete or Delete All unless you are absolutely certain
that you do not want the data. Deleted files are not recoverable.
6 Open the files

SoilFluxPro software is for the next steps of processing, evaluating, and recom-
puting data logged to the LI-8100A.
SoilFluxPro™ software (formerly FV8100) is a free PC- and Mac-

compatible application for analyzing data from the LI-8100A. In
SoilFluxPro, you can recompute data sets, graph data, analyze res-
ults, and create .kml files for mapping georeferenced measurements.
SoilFluxPro is an essential part of the LI-8100A system.
Get it from http://www.licor.com/soilfluxpro.
Transfer data from the CompactFlash card

If you logged data to the CompactFlash card, you can simply eject it and copy data
from it in the same way you would from a USB drive, for example. Your computer
will need a CompactFlash card reader to do this.
The card is under the access panel. Power off the LI-8100A prior to ejecting the
card.

About data files

An LI-8100A data file consists of lines of tab-delimited text with one or more Obser-
vations. An Observation is preceded by Header information, and also contains Raw
Records, Summary Records, and Footer information as shown below.
Header
Raw Records
Summary Records
Footer
Header - The lines from "LI-8100A:" through "Labels_01:". See Header variables on
page 6-5.
Type - The first item in each record is called the Type, and it identifies the type of
record. The types are -1, 1, 2, 3, and 4.
About data files 6-3

Table 6-1. Record types and their definitions.

Type Description
-1 Warning record
1 Raw record
2 Initial value (regressed from first 10 seconds of data)
3 Mean value of raw records
4 Range value of raw records
Raw Records - A record of Type 1. These records represent measured data from the
time the chamber starts to close, to the time when it starts to open. See Raw records
and summary records on page 6-7.
Summary Records - A record of Type 2, 3, or 4. An Observation always has one of
each, for a total of three. See Raw records and summary records on page 6-7.
l Type 2 records for measured columns represent initial values based on a linear
regression with Etime of the first 10 seconds of data.
l Type 3 records for measured columns are the mean values of all the data.
l Type 4 records for measured columns are the ranges (max - min) of all the data.
Footer – The results of the analysis, including flux values. The footer won’t be
present for files logged with the “Compute Flux” option turned off. For these data,
a footer can be generated by recomputing the data in SoilFluxPro Software. See
Footer variables on page 6-10.
Observation – The Header + n Raw Records + 3 Summary Records + the Footer.
The Summary Records consist of a number of Measured Variables, some of which

appear in all Observations, (such as Date, Pressure, CO2 , H2 O) and some of which
are optional, and a number of Final Variables of Type 2, 3, or 4, as shown below.
Summary statistics of Measured Variables are identified by the column label, and a
prefix of “IV”, “Mean”, or “Range”. Thus, for example, “IV Cdry” means the Type 2
value of the Cdry column, and “Range Etime” means the Type 4 value of the Etime
column.

Header variables
above lists the LI-8100A variables, including the Label that appears in the Header
information, and a description of the variable. A summary of the method and equa-
tions used to compute the Measured Variables, including the appropriate slope of
Cdry, is given in Theory of operation on page 1-19.
Table 6-2. Header variables.

Label Description – Header Variables
LI-8100A 5 hexadecimal values giving the size of the header, label, raw data,
summary data, and footer
File Name File name stored on LI-8100A
Instrument User-entered instrument name
Name
Serial Number Instrument serial number
Software Version of embedded software in the instrument
Comment User-entered at time of data collection
Obs# Observation number
Port# Multiplexer port number (0 if not using multiplexer)
Label User-entered at time of data collection, same value in all records
Type The type of record
Pre-purge Wait time between observations
Observation Original observation length
Length
Flow8100 Reads zero at all times
FlowMux Pump setting in the LI-8150 Multiplexer
Tmux Multiplexer temperature at start of observation
Header variables 6-5

Table 6-2. Header variables. (...continued)

Label Description – Header Variables
Virga IRGA volume, in cm3
Vmux Volume of the multiplexer (if present), in cm3
Vext Volume of extension tubing, in cm3
Vcham Chamber and tubing volume, in cm3
Offset Collar offset dimension (cm)
Area Exposed soil area (cm2 )
Vtotal Total system volume, in cm3
V1 Info Information on how the voltage channel is configured; multiplexer
channel, slope, offset, etc.
V2 Info “
V3 Info “
V4 Info “
Labels_01 Number of columns in the raw data section

Raw records and summary records

The following variables are logged in data files. Additional variables may be present,
depending on the configuration.
Table 6-3. Variables logged by the LI-8100A.

Label Description Units
Type Type or record (see Table 6-1 on page 6-4) n/a
Etime Elapsed time of the measurement seconds
Date Full instrument time stamp, including date and time n/a
Tcham Air temperature inside the soil chamber during an active °C
measurement (if no measurement is active, displays
Multiplexer case temperature)
Pressure Atmospheric pressure in the optical bench kPa
H2O Chamber water vapor concentration, in mmol/mol mmol/mol
CO2 Chamber CO2 concentration in μmol/mol μmol/mol
CO2dry Chamber CO2 concentration, corrected for water vapor μmol/mol
dilution
Tbench Temperature of the optical bench °C
T1 Temperature measurement °C
V1 Voltage at auxiliary channel 1 (multiplexer flow to LI-
8100A when attached)
V2 Voltage at auxiliary channel 2
LATITUDE Decimal Degrees, + for the northern hemisphere, - for the
southern hemisphere
LONGITUDE Decimal Degrees, + for the eastern hemisphere - for the
western hemisphere
STATUS A indicates valid position; V indicates receiver warning
SPEED Speed over the ground; (0.0 to 1851.8 km/h) km/h
COURSE True course over ground; (0.0° to 359.9°) °
RH Relative humidity inside the soil chamber %
Tboard Temperature of the analyzer control unit board °C
Vin Input (battery) voltage volts
Raw records and summary records 6-7

Table 6-3. Variables logged by the LI-8100A. (...continued)

Label Description Units
CO2abs Absorption of photons in the optical bench due to the
presence of CO2
H2Oabs Absorption of photons in the optical bench due to the
presence of water vapor
Hour Hour of the day
Day of Year Day of the year DOY
RAWCO2 CO2 raw signal
RAWCO2REF A measure of the optical amplitude of the CO2 channel,
primarily for diagnostic purposes
RAWH2O H2 O raw signal
RAWH2OREF A measure of the optical amplitude of the H2 O channel,
primarily for diagnostic purposes
Annotation

System variables
The following variables are used in calculations. The corresponding variables meas-
ured by the LI-8100A system are indicated in the column called Name.
Table 6-4. Definitions of the variables used in the derivations and implemented in
the LI-8100A.
Variable Description Units Name
v Total Volume m3
V Total Volume cm3 "Vtotal"
s Total Surface Area m2
S Total Surface Area cm2 "Area"
fw Water Evaporation Rate mol m-2 s-1
p Pressure Pa
P Pressure kPa Type 1 "Pressure"
P0 Initial value of P kPa Type 2 "Pressure"
TK Absolute temperature K
T Temperature °C Type 1 "Tcham"
T0 Initial value of temperature °C Type 2 "Tcham"
R Gas Constant 8.314 Pa m3 K-1 mol-1
fc CO2 Flux mol m-2 s-1
Fc CO2 Flux μmol m-2 s-1 Exp_Flux
Lin_Flux
dC'/dt -1
Rate of change in water corrected CO2 μmol mol s -1 Exp_dCdry/dt
Lin_dCdry/dt
RH Relative Humidity % "RH"
wc Water Vapor Mole Fraction mol mol-1
W Water Vapor Mole Fraction mmol mol-1 Type 1 "H2O"
W0 Initial value of W Type 2 "H2O"
k Rate constant s -1
u Air flow rate out of the chamber mol s-1

ca CO2 mole fraction of air outside the mol mol-1
chamber
cs' Dilution-corrected CO2 mole fraction mol mol-1
of air in the soil
cc' Dilution-corrected CO2 mole fraction mol mol-1
of air inside the chamber
System variables 6-9

Table 6-4. Definitions of the variables used in the derivations and implemented in
the LI-8100A. (...continued)
Variable Description Units Name
ca' Dilution-corrected ambient CO2
concentration
ρcc The number density of CO2 in the mol m-3
chamber
ρcw The number density of water vapor in mol m-3
the chamber
ρc The total number density of air in the mol m-3
chamber
ρca The number density of dry air in the mol m-3
chamber
g Conductance to CO2 m s-1
a Rate Constant Exponential Coefficient s-1 Exp_a
t0 Time Zero Exp_t0
C'(t) Dilution-corrected CO2 μmol mol-1 "Cdry"
Cx' Asymptote parameter from μmol mol-1 Exp_cx
exponential fit
C' 0 Initial dilution-corrected CO2 μmol mol-1 Exp_Co
NOTE: Additional details on computations are provided in the SoilFluxPro user's

guide. Refer to that document for more information on final computations.
Footer variables
There may be several footers organized into columns in some files that have been
post processed. The GasColumnID variable specifies the variable that all the fol-
lowing footer variables were computed for. By default from the LI-8100A, the
GasColumnID will be Cdry. We added a dilution variable to define the source vari-
able for the dilution correction if one is needed. By default, this is none.
Table 6-5. Footer variables.

Label Description – Footer Variables
GasColumnID Specifies the variable that all the following footer variables were
computed from.
Dilution Specifies the source for the dilution correction.

Table 6-5. Footer variables. (...continued)

Label Description – Footer Variables
CrvFitStatus Curve fit solution. “Exp” means the exponential fit was better than the
linear fit (Exp_SSN<Lin_SSN). “Lin” means the linear fit was still better
after the maximum number of iterations, and the non-linear
coefficients have therefore been derived from the linear fit
Exp Flux Flux computed from Exponential Fit
Exp_FluxCV Coefficient of variation (%) of Exp Flux
Exp_dCdry/dt Slope of the Exponential Fit at time t0 (Equation 1-20)
Exp_R2 Correlation coefficient for Exponential Fit
Exp_SSN Normalized sum of squares of residuals for Exponential Fit
Exp_SE Standard error (%) of the Exponential Fit
Exp_a The a term in the Exponential Fit
Exp_Cx The C term in the Exponential Fit
Exp_Co The C0 term in the Exponential Fit. Usually the IV value of Cdry, but if
followed by *, indicates it has been manually set.
Exp_t0 The t0 term in the Exponential Fit
Exp_Iter Number of iterations used in the Exponential Fit
Exp_MaxIter Maximum number of iterations allowed for the Exponential Fit. This is
fixed to 10 in the LI-8100A (but can be adjusted in the SoilFluxPro
software)
Lin Flux Flux computed from Linear Fit
Lin_FluxCV Coefficient of variation (%) of Lin Flux
Lin dCdry/dt Slope of the Linear Fit
Lin_R2 Correlation coefficient for the Linear Fit
Lin_SSN Normalized sum of squares of residuals for Linear Fit
Lin_SE Standard error (%) of the Linear Fit
Crv_Domain Time span (s) used in the curve fit
Crv_#Smp Number of data points used for curve fitting
Dead Band Time (s) after the chamber closes that are skipped by the analysis, in
the latest (re-)computation
TimeClosing Time, in seconds, it took the chamber to close
Footer variables 6-11


Section 7.
Calibrating the LI-8100A
The gas analyzer in the LI-8100A is calibrated at the factory using precision gases at
controlled temperatures. The calibration function for CO2 uses a rectangular hyper-
bola and also corrects for temperature and pressure, as well as band broadening and
cross-sensitivity to water vapor. The calibration function for water vapor uses a third
order polynomial and also corrects for pressure and temperature. The Coefficients
pages of the Windows and mobile software display the factory-determined cal-
ibration coefficients, and they are also recorded on a calibration sheet that comes
with the instrument.
Like all infrared gas analyzers, the LI-8100A optical bench zero and span may drift
over time with changes in temperature, cleanliness of the optical bench, and other
factors. The zero and span procedure discussed in this section is used to correct for
any drift that may occur. Setting zero and span makes the instrument meas-
urements conform to expected values.
Zero and span should be checked periodically, the frequency depending upon accur-
acy requirements and the variability of the environment in which the LI-8100A is
used. The majority of the analyzer drift is corrected by setting the zero, so this
should be the highest priority. It is also a good idea to verify analyzer performance
by periodically checking the span. If you begin checking these on a daily basis and
keep a log of zero and span adjustments, you will learn how much your analyzer
drifts and how frequently you need to zero and span.
The calibration of the instrument shifts if the optical path gets dirty. Most of this
shift is corrected by setting the zero and span, but the calibration curve linearity
may also change if the optical path becomes extremely dirty. Linearity can be tested
using two span gases and a zero gas. Set the zero and span as usual, and then meas-
ure a known intermediate gas concentration. The concentration measured should

be within the instrument specification, taking into account the known accuracy of
the intermediate gas. If that is not the case, clean the optical path as described in
Cleaning the optical bench on page 9-4. Linearity changes are small even when the
cell becomes quite dirty, so frequent cleaning of the optical path should not be
necessary, especially if the filters are kept clean.
Carbon dioxide and water vapor gas standards

Tanks of compressed air with known CO2 concentration and specified accuracy are
readily available from commercial suppliers. Such tanks can provide convenient
standards for checking the CO2 span of the LI-8100A; however, tanks are not avail-
able that contain a known water vapor concentration for checking the span of the
water vapor channel. The LI-610 Portable Dew Point Generator can be used to
provide air with a known dew point for the primary calibration of new analyzers.
The span of the analyzer in the LI-8100A is stable when the zero is set on a regular
basis, and soil CO2 flux measurements are not very sensitive to errors in the water
vapor measurement. For these reasons, we recommend that you do not alter the
span of the water vapor channel unless an LI-610 or similar equipment is used to
produce an accurate H2 O span gas.
Zero gases
Either CO2 -free air or CO2 -free nitrogen can be used as a zero gas. It is best to use a
column filled with a chemical CO2 scrubbing agent downstream of the tank, how-
ever, as even "CO2 -free" gases at times contain 10 or 20 ppm of CO2 . Note that the
scrubber may add significant H2 O vapor, so you may want to use a water vapor
scrubber downstream from the CO2 scrubber.
A suitable CO2 zero scrub is soda lime (part number 9964-090) and an H2 O scrub
is Drierite (part number 622-04299). When using chemical scrubbers, it is import-
ant to make sure that the chemicals are fresh. Always be sure to have a particulate
filter installed in the air flow path between the chemicals and the instrument.
Compressed cylinders may be at pressures of several thousand pounds per square
inch; before using them for calibration, they should be fitted with a regulator to
reduce the pressure to around 15 pounds per square inch (101 kPa).

Carbon dioxide span gases

To set either the primary or secondary CO2 span, a cylinder of CO2 in air, verified
to be accurate to within at least 1%, is ideal. Be cautious with a new cylinder, as the
stated value of the calibration cylinder may be significantly different from the
actual gas concentration, if the tank is mislabeled, for example.
For the primary span gas, choose a gas with a CO2 concentration slightly greater
than the highest concentration encountered during measurements. The span and
secondary span concentrations should be as far apart as possible, and they should
bracket the concentration range of interest to you (e.g., 200 and 20,000, or 300 and
1500, etc.).
Water vapor span gases

For known water vapor concentrations, the LI-COR LI-610 Portable Dew Point Gen-
erator provides a stable dew point. To avoid condensation problems, choose a dew
point temperature that is about 3 to 5 °C below the ambient temperature. Also,
since water vapor sorbs and desorbs from surfaces, minimize the sorbing surface
area (minimize tubing lengths), and allow plenty of time for the reading to sta-
bilize. It is important not to rush through water vapor calibrations; give the sur-
faces 15 to 20 minutes to equilibrate to large changes in water vapor concentration.
Carbon dioxide span gases 7-3

Setting the zeros

NOTE: Read "Using CO2 and H2 O Scrubbers with LI-COR Gas Analyzers" for
important information about the interactions between scrub chemicals and the
air. See https://www.licor.com/documents/7i418s3uhd2uamoxfmjd.
1 Plumb the LI-8100A. See Figure 7-1 below for tank gas and Figure 7-2 below for scrubbers.
If you are using tank gas, use a flow splitter to vent the excess gas to the atmo-
sphere. Turn the instrument pump on and set flow from the tank to 2 to 2.5 lpm.
Vent the instrument outlet to the atmosphere to prevent pressurizing the analyzer.
If you are using chemical scrubbers, plumb everything and then turn the instru-
ment pump on.
Rotameter
ter
in
× 100 cc/min
25
20
To LI-81
LI-8100A
15 Air In
10
Zero Gas Regulator 5
Vented to
Atmosphere
Figure 7-1. Typical plumbing configuration for setting the instrument zero using a zero gas.
Always use dry, CO2 -free air.
CO2 Scrubber H2O Scrubber Particulate Filter
To LI-8100A
Air In
Figure 7-2. Typical plumbing configuration for setting the instrument zero using gas scrub-
bers. Soda lime and Ascarite II® are good CO2 scrubbers. Drierite® and magnesium per-
chlorate are good water vapor scrubbers.

2 Monitor CO2 and H2O concentra`tions. Allow 1-2 minutes for the CO2 concentrations to stabilize
and 15-20 minutes for the H2O concentration to stabilize near zero.
3 Calibrate:
Configure the Data view to show CO2 Go to Utilities > Calibration, then tap
(µmol/mol) and H2 O (mol/mol); (click Perform: Zero.
a variable to change it).
Under the CO2 tab, tap Send Com-
Go to Utilities > Calibration and go to mand when the CO2 reading is
the Zero tab. stable.
When H2 O concentrations are stable, Under the H2O tab, tap Send Com-
click Zero H2O. mand when the H2 O reading is
stable.
When the CO2 concentration is stable,
click Zero CO2.
Setting the zeros 7-5

Setting the span: Carbon dioxide

Note: Always set the zero before setting the span.
1 Plumb the LI-8100A as shown in Figure 7-3 below.

Attach a tank containing a known concentration of CO2 to the LI-8100A air inlet.
Use a flow splitter to vent the excess gas to the atmosphere. Vent the instrument
outlet to the atmosphere to prevent pressurizing the analyzer. Turn on the pump
and set flow from tank at 2 to 2.5 lpm.
Rotameter
ter
in
× 100 cc/min
25
20
To LI-81
LI-8100A
15 Air In
10
CO2 Regulator 5
Span Gas
Vented to
Atmosphere
Figure 7-3. Typical plumbing configuration for a CO2 span gas.
2 Monitor CO2 concentration.

When CO2 concentration is stable proceed to the next step. Allow 1-2 minutes for
the CO2 concentrations to stabilize.
3 Calibrate:
(µmol/mol) and H2 O (mol/mol). Perform: Span.
Go to Utilities > Calibration, go to the Under the CO2 tab, enter the span
Span tab, and enter the span gas con- gas concentration.
centration.
When the CO2 reading is stable, tap
When the CO2 concentration is stable, Send Command.
click Span CO2.

Setting the span: Water vapor

Note: Always set the zero before setting the span.
To set the H2 O span, use an air stream containing a known, stable H2 O con-
centration. This is best achieved by using an instrument such as the LI-610 Dew
Point Generator. If the proper equipment is not available, we strongly recommend
that you do not adjust the span of the H2 O channel.
1 Verify that the LI-8100A pump is turned on. Turn it on if needed.

2 Plumb the LI-8100A to the water vapor source, such as the LI-610.
Split the output of the LI-610 using a Y-adapter. Connect one side to the LI-8100A
Air In port and vent the other to the atmosphere.
To LI-81
LI-8100A
Air In
LI-610
Dew Point
Generator Vented to
At
Atmosphere
Set up the LI-610 to provide an air stream with a known dew point. Set the LI-610
flow rate as high as possible (usually between 1.5 and 2.0 lpm.). This will provide
extra calibration air that will vent out the "Y" connector, providing adequate flow
to the LI-8100A and eliminating pressure changes in the optical bench.
3 Calibrate:
(µmol/mol) and H2 O (mmol/mol). Perform: Span.
Go to Utilities > Calibration and go to Under the H2O tab enter the dew
the Span tab and enter the dew point. point and tap Send Command when
the H2 O reading is stable.
When the H2 O concentration is stable,
click Span H2O.
Setting the span: Water vapor 7-7

Two point span

If you find that after zeroing then spanning at one concentration, the instrument is
not within specifications at a different concentration, a secondary span may be in
order. The optical bench in the LI-8100A uses a span value that is a linear function
of absorptance, with two parameters; a slope and an offset. The normal span func-
tion adjusts the offset and leaves the slope alone. Setting the secondary span ( Span
2 tab) adjusts the slope, and then adjusts the offset value for the new slope value.
The slope and offset values can be viewed under the Manual tab in the Calibration
window. Span offset values (CO2 Span and H2 O Span) are typically 1.0 ± 0.1.
Span slope values (CO2 Span 2 and H2 O Span 2) are typically 0 ± 0.1. When they
are exactly zero, then slope is a constant, and not a function of absorptance.
The CO2 span slope value is first determined at the factory by setting the span at
200 ppm, and doing a secondary span close to 20,000 ppm. This value should
remain valid for some time. Things that are likely to make it change include chan-
ging the source and/or detector, a dirty optical cell, and possibly when taking the
optical bench apart for cleaning.
Considerations for performing a secondary span

1 Zero the instrument first, then do a normal span.
2 The span and secondary span concentrations should be as far apart as possible, and they should
bracket the concentration range of interest to you (e.g. 200 and 20,000, or 300 and 1500, etc.).
“Far apart” means in absorptance, not concentration. We recommend absorptance
differences of at least 0.1 when choosing concentrations for setting span and sec-
ondary span (Figure 7-4 on the facing page).

0.7
0.6
0.1
CO 2 Absorptance
0.5
0.4
0.1
0.3
0.2
0.1 0.1
0.0
100 1000 10000 100000
CO 2 (ppm)
Figure 7-4. CO2 absorptance differences for typical LI-8100A optical bench.
For CO2 , the difference in absorptance between 200 and 1000 ppm is typically
about 0.1. There is also a 0.1 absorptance difference between 3500 and 7000 ppm,
and between 15,000 and 40,000 ppm. For H2 O, it is a little harder to get a 0.1
absorptance difference. If you want to do a secondary span at room temperature, the
two span values would need to be 5 °C or less, and 22 °C, for example, as shown
below.
0.4
H2O Absorptance
0.3
0.2
0.1
0.1
0
-30 -20 -10 0 10 20 30 40
Dew Point Temp (°C)
You can perform multiple secondary spans after a normal span. For example, span
at 200, then do a secondary span at 3000 ppm. Then, if you don’t like the result,
you can do another secondary span at 2000 ppm. As long as the secondary span is
Two point span 7-9

well away (in absorptance) from the previous normal span, it is OK to do as many
consecutive secondary spans at various concentrations as you’d like.
Setting the second span
(µmol/mol) and H2 O (mmol/mol). Perform: Zero.
Go to Utilities > Calibration and go to Under the H2O tab, tap Send Com-
the Span 2 tab. mand when the H2 O reading is
stable.
When the H2 O or CO2 concentration is
stable, click Span 2 H2O or Span 2 CO2. Under the CO2 tab, tap Send Com-
mand when the CO2 reading is
stable.
Remember that it may take 15 to 20 minutes for the water vapor to stabilize.

Section 8.
Troubleshooting
When things are not going as planned, this section is here to help (hopefully) you
find a solution to the problem.
System will not power on or powers on

incompletely
Power supply inadequate? The system power supply should be strong enough to
power the system. Check to be sure that it supplies adequate current for the instru-
ments (see Table A-1 on page A-6).
Cables tightened properly? If you are using the Multiplexer or Auxiliary Sensor
Interface, press in on the 27-pin cable and tighten it. If the cable is loose it may not
work properly.
NOTE: In order to achieve a weather-tight seal, the interface cable connector

must be tightened until it completely covers the O-ring seal on the analyzer con-
trol unit connector. When the connector feels tight, push in and wiggle it while
continuing to tighten until the O-ring is covered.
Fuse blown? Check the fuses, as described below, and replace any blown fuses.
If you are using the AC to DC power supply, start with the power supply system.
Even if the power supply fuse is good, the wrong fuse can lead to power supply
problems. See Using the AC to DC power supply on page 4-6 and confirm that the cor-
rect fuse is installed and that it is not blown.

If you are powering the LI-8100A analyzer control unit from the battery, the power
circuit has two fuses: one in the battery and one in the analyzer control unit.
Troubleshoot the circuit:
l If you are not able to charge a battery or power up the instrument from the bat-
tery, check the fuse inside the battery. See Replacing the battery fuse on page 9-13.
l If the battery fuse is OK, check the fuse for battery power, which is inside the
analyzer control unit. See Analyzer control unit fuses on page 9-10.
If you are using the LI-8150 multiplexer, the power circuit has two fuses: one in
the LI-8150, and one in the analyzer control unit. Troubleshoot the circuit:
l If neither the multiplexer nor the analyzer control unit will power on, see Mul-
tiplexer fuses on page 9-39 and check the fuse labeled LI-8100.
l If the multiplexer will power on but the analyzer control unit will not, check
the fuse for auxiliary power, which is inside the analyzer control unit. See Ana-
lyzer control unit fuses on page 9-10.
l If the multiplexer will not power on but the analyzer control unit will, see Mul-
tiplexer fuses on page 9-39 and check the fuse labeled LI-8150.
If you are powering the LI-8100A analyzer control unit through the auxiliary
sensor interface, the power circuit has two fuses: one in the auxiliary sensor inter-
face, and one in the analyzer control unit. Troubleshoot the circuit:
l Check the auxiliary sensor interface fuse. See Auxiliary sensor interface fuse on
page 9-10.
l Check the fuse for auxiliary power, which is inside the analyzer control unit.
See Analyzer control unit fuses on page 9-10.
Connection and communication problems

This section addresses problems communicating over a computer or mobile device.
Cannot connect to the instrument over wireless

Power up cycle complete? The instrument takes 1 or more minutes to power up.
During this time you will not be able to connect. Wait until the Ready light is illu-
minated, then try connecting.

Wireless card installed? Check to be sure the wireless card is installed in the LI-
8100A under the access panel. If it is loose or not installed, restart the instrument
after installing it.
Network settings of the instrument configured properly for your connection?
Attempt to connect using the RS-232 serial or USB connection, as described in First
Things First on page 2-1. Make sure the IP address of the computer or mobile device
are identical for the first three octets and unique in the last. Configure the network
settings and try again.
Restrictive network security policy? Some network settings may prohibit this type of
connection.
Some devices my not support the type of connection. Contact LI-COR technical
support to find a solution.
Cannot connect to the instrument over Ethernet

Power up cycle complete? The instrument takes 1 or more minutes to power up.
During this time you will not be able to connect. Wait until the Ready light is illu-
minated, then try connecting.
Network card installed? Check to be sure the Ethernet card is installed and the Eth-
ernet cable is connected under the access panel inside the LI-8100A.
Computer and the instrument on the same network? The devices need to be on the
same local network.
Computer using WiFi? Disable WiFi on the computer.
Network settings of the instrument configured properly for your connection?
Attempt to connect using the RS-232 serial or USB connection, as described in First
Things First on page 2-1. Configure the network settings and try again.
Cannot connect over RS-232 serial or USB

Using the correct com port number on your computer? Open the Device Manager
(press the Windows key , type in Device Manager, then press Enter). Then
click Ports (COM & LPT). Look for USB Serial Port (COM#). Your serial port number
is indicated by the number.
Compatible serial-to-USB adapter? It must have an FTDI chipset.
Cannot connect to the instrument over Ethernet 8-3

Compatible software versions? Check the LI-8100A PC software version you are
running on your computer. You can download updated software from the LI-COR
support site at www.licor.com/env/support/
LI-8100A will not recognize the multiplexer

Powered on in the right order? Be sure to turn on the multiplexer first. Power off
the LI-8100A. Then power on the multiplexer. If the LI-8100A does not power on
automatically, press the power button.
Cable connections tight? Be sure the large 27-pin cable is attached securely. Press
on the connectors and tighten each connection.
Chamber issues
See this section for issues related to a chamber.
Long-term chamber will not close or open

Debris in the chamber? Check for debris that may block the movement of the
chamber.
Cable connections tight? Check the cable connections. Press in on each connector
and tighten each one.
Attempt to activate the chamber using the software under Utilities > Manual Con-
trols.
If you have a multiplexer, connect the chamber to a different port and try to open
or close it. Also try to use a different cable to determine if the cable is damaged. If
cables solves the problem, you may have a faulty or poorly attached cable. If switch-
ing ports solves it, you may have a poorly connected cable or a problem with the
internal connections.
Survey chamber will not close or open, or does so very

slowly
Bad cable? Check the cable. Pins number 1 and 4 should have 0 ohms (Ω) res-
istance. If there is 1 ohm of resistance, the cable is damaged and should be
replaced.

Leaking bellows? If so, replace the bellows. See Replacing the bellows on the 10 cm
chamber on page 9-18 or Replacing the bellows on the 20 cm chamber on page 9-23
Leaky tube? Check that the bellows tube for leaks. Confirm that it is connected to
the correct connector on the LI-8100A. See Connecting a survey chamber on page 2-24
for details.
Bad or dirty check valves? See The bellows flow path on page 2-23.
Measurements stop immediately after starting

Adequate power supply? Check the power supply to be sure that is powerful
enough to run the system. If it is not powerful enough, the instruments will shut
off when there is a load on the power supply (see Table A-1 on page A-6).
Instrument settings? Is the system configured to stop automatically under humid
conditions? Check the humidity threshold in the software and disable the setting or
choose a higher humidity threshold.
Data and measurement issues

See this section for problems related to data quality or measurements.
Unexpected drift, shift in data values, or lack of

responsiveness
Instrument stored in humid conditions? These symptoms may be expressed if the
instrument has been stored in high-humidity conditions while powered off, which
can cause humidity to saturate the detector. Let the instrument sit for several days
powered on and the issue should resolve itself. If not, disassemble the gas analyzer
and place the detector in an oven at 65 °C (150 °F) for several hours. Reassemble
the instrument and check measurements.
Noisy data
Chamber sealing properly around the collar? Check for obstructions that interfere
with the chamber. Check the gaskets on the chamber and replace any damaged or
hardened gaskets.
Measurements stop immediately after starting 8-5

Cable and tube connections OK? Check the tubing and be sure everything is con-
nected.
Leaky tube? Check the tubes for leaks, especially near the connectors.
Bad pump? Disconnect the tubes and feel for air movement. If you don't feel air
movement, a call to technical support is a good idea.
475 475 475
A B C
460 460 460
CO2 Concentration (ppm)

445 445 445
430 430 430
415 415 415
400 400 400

0 20 40 60 80 100 120 0 20 40 60 80 100 120 0 20 40 60 80 100 120
Seconds Seconds Seconds
Figure 8-1. Normal data (A) shows a steady increase in CO2 concentration in the chamber.
Noisy data (B) with a response indicates a small leak in the tubing or chamber. Data with
no response (C) indicates that there is a major leak or that the soil is not respiring.
Dirty or failed optical source? If the CO2 concentration is fluctuating wildly (espe-
cially going negative, which is physically impossible) or stuck on a certain con-
centration and not changing—even when you breathe into the Air In (especially -
50 ppm), then open and clean the optical path first, as described in Cleaning the
optical bench on page 9-4. If the issue continues, then check View > Instrument
Status in the software or the app. If Operating Hours (or On Time Hours in the
app) is around 18000, then you need to purchase a new 8100-902 infrared source.
The infrared source starts to fail after about 18000 hours (around 2 years con-
tinuous use). Installation instructions are provide with the replacement, and can be
downloaded from https://licor.com/documents/ihemfe24orwk232tikja.
High initial carbon dioxide concentrations

CO2 concentrations should be near ambient levels at the start of a measurement
(around 400 ppm).
If using the multiplexer, is the pre-purge set to long enough? Lengthen this period
and see if the problem is corrected.
Dead band set properly? Try to lengthen the dead band and see if that resolves the
issue.

Low flow rate

Clogged filter? If you haven't replaced it in a while, it might be time.
Blockage or liquid water in a tube? Check all the tubes for water.
Bad pump? Disconnect the tubes and feel for air movement. If you don't feel air
movement, a call to technical support is a good idea.
Unreasonable RH readings
The long tubes that connect the chamber to the multiplexer and gas analyzer, can
affect H2 O readings, especially because water vapor can adhere to the tube walls.
This also means that there is a long distance from where water vapor is measured
and where the temperature is measured. Therefore, the system can compute RH
<100% sometimes, even if there is no problem.
Poor water vapor calibration? Check the zero and span, as described in Setting the
zeros on page 7-4. Set them if necessary.
Accurate temperature measurements? If a temperature sensor is not working, or if
the calibration values are incorrect, the temperature data may be incorrect. Incor-
rect temperature values may lead to inaccurate RH computations.
Unreasonable chamber temperature readings

Chamber cable not fully connected? Tighten the connector.
Chamber thermistor broken? If you are using the multiplexer, try swapping ports,
chambers, and cables to isolate the problem.
Still having trouble?

Contact LI-COR technical support:
l www.licor.com/env/support
l envsupport@licor.com
l Telephone: 1-402-467-3576
Or contact your local distributor.
Low flow rate 8-7


Section 9.
Maintenance
This section describes maintenance and repair procedures for the analyzer control
unit, multiplexer, and chambers.
Analyzer control unit maintenance

This section describes basic maintenance and repair procedures for the analyzer con-
trol unit.
Updating the instrument software

The LI-8100A instrument software is programmed into the instrument internal
memory. It can be updated using an updater application available from the LI-COR
technical support website at http://www.licor.com/env/support.
We recommend running the most current software, if possible, unless there is a
function that you need that is not supported by the current software (such as com-
patibility with Palm or Windows Mobile devices). Refer to the Software compatibility
table on page B-1 for more details.
NOTE: The update may require 20-30 minutes to complete. If you are using the
battery to power the LI-8100A, be sure that you have sufficient charge to operate
the LI-8100A for 30 minutes or more.
1 Turn the LI-8100AOFF.

Make sure the computer and the LI-8100A are connected via the serial cables
included, as described in First Things First on page 2-1.
2 Locate the LI8100_update program, and double-click on the icon to start the program.
3 Choose the serial port on your computer to which the LI-8100A is connected using the arrow keys.

4 Click the Connect button.

5 Turn the LI-8100A ON.
6 The update will begin.
A series of messages will appear in the window, as shown in Figure 9-1 below.
Figure 9-1. Progress messages appear in the Update window.
7 Wait for the message ‘Action Successful’ to appear.

In some cases, the ‘Action Successful’ message will not appear even though the
update was successful; follow the steps below, and then start the LI-8100A Win-
dows or mobile software application. Go to the View > Instrument Status to view
the Embedded software version number to see if the version that you were updating
was installed. If it was not, you may need to run the LI-8100_update program
again.
8 Close the LI-8100A Update window.
9 Turn the LI-8100A OFF, and then back ON.
10 Wait 2 minutes or so, until the green Ready light on the LI-8100A keypad turns on.
The LI-8100A instrument software is now ready to use.

NOTE: You should always run computer software that is compatible with the
instrument software. Check the Software compatibility table on page B-1 for more
information.
Replacing the air filters

There are two Balston air filters located inside the analyzer control unit. One of the
filters is on the flow path to the attached chamber, and the other is on the bellows
air path, and is used only when the survey chamber is attached. The bellows air
path draws air from outside of the analyzer control unit through a port on the front
panel. This port also has a built-in filter, so the air filter on this line should not
need to be changed with any regularity, if at all.
The air filter on the flow path will need to be replaced after about every three
months of continuous use, depending upon the conditions under which the instru-
ment is used. You can look at the clear Bev-a-line tubing to get a visual indication
of how much dirt is present in the line, or alternatively, if the instrument zero and
span settings are fluctuating widely (see Calibrating the LI-8100A on page 7-1), it
may be time to change the filter. Follow these steps to replace the Balston air filters
(there are two in the spares kit under part number 300-01961):
CAUTION: Never swap the bellows filter and the gas analyzer filter. Airflow
through the bellows air circuit is bi-directional, meaning dirt can be introduced
into the filter in both directions. If this filter is inserted into the gas analyzer air
path, dirt can be blown into the gas analyzer, which will affect the calibration.
1 Power the instrument off and disconnect the bat-

tery or external power source.
2 Open the analyzer control unit case and remove
the access panel by loosening the four thumb-
screws.
3 Remove the air filters by pressing the orange
part of the quick-connect fittings toward the
white part of the connector and pulling the filter
out. Figure 9-2. The gas analyzer air filter
4 Insert the new filters as shown in Figure 9-2 (left) and bellows pump air filter
above. (right).
Replacing the air filters 9-3

Cleaning the optical bench

There is a Balston air filter in-line on the flow path leading to the IRGA optical
bench. It is very important that incoming air be filtered. This is because any dirt in
the optical cell will cause an immediate zero shift.
The optical bench can be removed and cleaned if necessary. If the optical path
becomes dirty it may become difficult to span the analyzer. Excessive zero drift may
also be observed if the optical path becomes dirty. If significant dirt accumulates in
the optical bench, linearity errors that exceed the stated specifications can also res-
ult.
Follow these steps to clean the optical bench:
NOTE: Make sure that you are properly grounded to avoid any electro-static dis-
charge events that can damage the internal components.
1 Remove the air filters as described in Replacing the air filters on the previous page.
2 There are three electrical connectors that must be removed.
Two of them are just to the right of filters. Pull straight out on the connectors to
remove them. The third is a large "D" connector.
3 Remove the two screws that hold the tube connectors to the top of the manifold.

4 Remove the twelve screws around the outer edge of the white panel, as shown below.

5 Lift the analyzer control unit from out of the yellow case.
Turn the control unit upside down. It will appear as shown below.
6 Remove the six screws from the optical bench cover, as shown above.
The optical bench will appear as shown below.

7 Leave the tubes connected to the optical bench, and lift the bench out of the foam casing.
8 There are four screws on the source and detector circuit boards that must be removed.
Remove the four screws in the corners of the source housing circuit board, as
shown below. Do not remove the remaining four screws.
Remove the four screws from the detector housing cover, as shown below. Note
that there are some small standoffs inserted over the screws behind the cover; tilt
the housing down when removing the cover so these standoffs don't get lost.

9 The optical bench can now be removed.
Note that there are O-rings on both ends of the optical bench. It is a good practice
to replace the O-rings when cleaning or replacing the optical path.
10 Swab the optical path.
There are a number of swabs in the spare parts kit. Dip one end of a swab into a
50:50 ethanol/water solution and carefully swab both ends of the optical bench,
until there is no more visible residue. A mild solution of dish washing soap and
water will also work. Do not use abrasive cleansers, as they can irreparably damage
the gold plating on the optical bench.
11 Use a reflector swab and carefully swab the gold-plated concave surface of the source housing, if
necessary.
If you need to clean out the hose barbs and/or replace the tubing connected to the
source and detector housings, use a small pair of diagonal cutters to remove the
tubing from the hose barbs. Use the cutters to pinch the tubing parallel to the hose
barb axis, and then pivot the cutters over the hose barb tip; the tubing will pull off

of the hose barb. Be very careful not to cut the tubing or scratch the hose barb with
the cutters, as subsequent tubing connections may leak.
12 Let the optical bench dry.
13 Re-assemble the bench, making sure the O-rings are in place on both ends of the bench.
Note that the orientation of the cylinder is not important; either end can be inser-
ted into the source or detector housing.
14 Re-assemble the LI-8100A case.
Make sure that the foam insulation on the inside top cover is positioned over the
optical bench; it is required for thermal stability.
15 Perform zero and span calibrations as described in Calibrating the LI-8100A on page 7-1.

Fuses
If your LI-8100A fails to turn on when you press the power button, there is a pos-
sibility that a fuse has blown. There is one fuse inside each 6400-03 battery, one
insed the auxiliary sensor interface, two fuses in the analyzer control unit, and two
fuses in the Multiplexer. See Replacing the battery fuse on page 9-13 if the battery
will not charge or power the LI-8100A. See Multiplexer fuses on page 9-39 if the
instrument powers up from the battery, but will not power up from the Mul-
tiplexer. Continue in this section if the problem stems from the Auxiliary Sensor
Interface or the Analyzer Control Unit.
Auxiliary sensor interface fuse

A fuse is located inside the auxiliary sensor interface. It protects the instrument
from overcharges due to improper connection of an external power supply. To
check this fuse, simply loosen the four screws on the auxiliary sensor interface
cover and remove the cover.
The screws on the 8100-663 Auxiliary Sensor Interface cover are "captive" screws,
meaning they are retained in the cover so they can't fall out. Loosen them until
you can lift the cover off. If the fuse is blown, replace it with a spare 250V, 3A fast-
blow fuse in the spare parts kit (part number 439-04215).
Analyzer control unit fuses

There are two fuses inside the analyzer control unit. One fuse protects the circuitry
when powered from a battery attached to the LI-8100A battery connectors. The
other protects the circuitry when powered from the auxiliary sensor interface or the
multiplexer. In most cases these fuses will not blow; we recommend that you test

the battery to make sure it is fully charged before attempting to check the fuses. If
you have eliminated all other possibilities, follow these steps to check the analyzer
control unit fuses:
1 Troubleshoot the power issue:

l If the LI-8100A cannot be powered by the battery (and the battery is working properly), but can
be powered through the auxiliary sensor interface or multiplexer, then the battery power fuse
may have blown. In this case, follow this procedure and check the fuse for battery power .
l If the LI-8100A can be powered by the battery, but cannot be powered through the auxiliary
sensor interface, then the auxiliary fuse may have blown. In this case, follow this procedure
and check the fuse for auxiliary power .
2 Power the instrument off and remove the battery or other external power source.
3 Open the analyzer control unit case and remove the access panel by loosening the four thumb-
screws.
4 Mark one of the Balston air filters with a marker or piece of tape so you are able to return them
to their original locations when reassembling the system.
CAUTION: Never swap the bellows filter and the gas analyzer filter. Airflow
through the bellows air circuit is bi-directional, meaning dirt can be introduced
into the filter in both directions. If this filter is inserted into the gas analyzer air
path, dirt can be blown into the gas analyzer, which will affect the calibration.
Remove both air filters by pressing the orange part of the quick-connect fittings
toward the white part of the connector and pulling the filter out.
Fuses 9-11
5 There are three electrical connectors that must be removed.

Two of them are on a single wiring harness, just to the right of filters in the photo
above; the third is about two inches further back from them, just beyond the edge
of the access panel, as shown below. Pull straight out on the connectors to remove
them. The large connector under the access panel can be difficult to reach; you can
gently pull on the wire harness and slowly rock the connector back and forth to
remove it, if necessary. When reinserting the connector, make sure that you check
the pin alignment before pushing the connector into place, as the upper right hand
side pins can easily become bent if misaligned.
6 Remove the two screws that hold hoses onto the air manifold.
7 Remove the twelve screws around the outer edge of the white panel.
8 Lift the analyzer control unit from out of the yellow case.
The battery power fuse (part number 439-04215) is located on the back of the con-
trol unit as you face the instrument. The circuit board is labeled 3A 250V at the loc-
ation of the fuse.
The auxiliary power fuse is located on the right hand side of the control unit as you
face the instrument. It is a 4A 250V fuse (part number 439-04482).
9 Inspect the fuse and check it using an ohm meter. If a fuse has blown, replace it with an identical
fuse from the spare parts kit.
10 Test the system by powering it up. Then re-assemble the analyzer control unit.

6400-03 batteries
Batteries are normally charged with the LI-6020 battery charger. To charge the bat-
teries:
1 Select the proper voltage.

Make sure that the voltage selector slide switch on the back of the LI-6020 battery
charger is set to the appropriate line voltage (115 or 230 VAC) and the correct fuse
is in place.
2 Plug the charger into mains power.
The AC indicator light will illuminate. If the charge indicator lights up instead,
you’ve got the wrong voltage selected.
3 Connect the batteries.
The CHARGE indicator illuminates if any of the batteries connected to the charger
are being charged. One method for testing a battery’s charge is to connect it to the
charger when no other batteries are attached. If it is charged, the CHARGE light
comes on for only a few seconds, if at all. If the CHARGE light does not come on,
either the battery is fully charged, or the battery’s fuse has blown. (To test, plug the
battery by itself into the LI-8100A, and power it on. If nothing happens, then the
problem is the fuse or the battery is dead.)
A fully discharged 6400-03 battery requires about three hours to recharge. Four dis-
charged batteries connected simultaneously require approximately 10 to 12 hours
to recharge. Do not leave a battery on the charger for more than 24 hours after the
charge light has gone out.
Storing the 6400-03 batteries

Store batteries fully charged, and in a cool place, if possible. For long term storage,
place the batteries on the charger overnight every three months.
Replacing the battery fuse

There is a 10A automotive fuse located inside the metal cover of the 6400-03 bat-
tery. If the battery fails to power the LI-8100A, and will not light the charge indic-
ator on the battery charger, check to see if the fuse has blown.
6400-03 batteries 9-13

1 Cut the black tape between the two halves of the battery.
2 Remove the top half of the battery (the half with the connector), and lay it to the side with the
wires still attached.
3 Look at the fuse or check it with an ohm meter to determine if it has blown.
4 Replace the fuse (part number 438-03142) if needed.
5 Tape the battery covers together with black electrical tape.

10 cm survey chamber maintenance

Replacing the gaskets
The 10 cm Survey Chamber uses a series
of three gaskets to seal the chamber to
the soil collar. The first gasket is a black
neoprene "rolled" type gasket that is loc-
ated on the bottom of the moveable part
of the chamber; in most cases this gasket
will not need to be replaced unless it is
inadvertently damaged. The second gas-
ket (foam seal gasket) rests against the
soil collar. It may need to be changed
more regularly. The gasket kit is avail-
able (part number 8100-622; see Gasket
kit on page 1-9).
The foam seal gaskets can become
cracked or lose their shape relatively
quickly, depending upon the conditions
they are used in, and the pressure with
which they are placed over the soil col-
lar. Inspect the foam seal gasket before you start making measurements each day; if
it appears that it might not form a tight seal against the soil collar, you should
replace it.
l To replace the gaskets:
1 Remove the 18 Phillips head screws from the metal plate on the bottom of the survey chamber.
Set the plate aside.
Caution: Handle the plate carefully and be sure not to bend it.
2 If you need to replace the foam seal gasket, simply pry it out with a knife or a screwdriver.
3 Discard the damaged gasket.
4 Insert the new foam seal gasket by working the gasket with your fingers into the recessed area of
the flange.

It may help to work the gasket in with the inside edge first. Press in opposite sides
of the gasket to prevent stretching it. Make sure the gasket is seated all the way
down into the flange, and that it lays flat without warping.
5 Align the soil collar gasket holes with the holes in the flange.
There is a top and bottom to the soil collar gasket; if it does not align with the
holes on the flange, turn the gasket over and try again.

6 Insert the screws on opposite sides of the flange, but do not fully tighten until all screws are star-
ted.
7 Partially tighten the screws on opposite sides, and work your way around the ring so that the
metal plate lays flat and does not bow.
The screws should not be fully tightened, as this will distort the gasket - tighten
until the gasket begins to deform, and then back off slightly.
Replacing the gaskets 9-17

Replacing the bellows on the 10 cm chamber

If the bellows on the Survey Chamber is punctured or is otherwise damaged and
develops a leak, it will not operate properly. You can replace it with the optional Bel-
lows Kit (part number 8100-623).
1 Remove the handle from the chamber.

When the handle is in a horizontal position, it can be removed by pulling out on
both sides of the handle.
2 Remove the four thumbnuts from the top plate of the pres-
sure relief valve assembly.
The top plate and attached tube can stay attached to
the manifold; it will hang along side the chamber
during this procedure.
3 Remove the four standoffs from the lower plate of the pres-
sure vent.
4 Remove the eight screws that attach the top plate to the
chamber supports and the four screws near the center of the
plate that attach to the top of the bellows.
Note that the 4 screws nearest the center of the plate
are slightly larger than the other 8 and have a small
red o-ring seal on them. Make sure these o-rings are
present and are not damaged when re-assembling
the chamber. Replace if necessary.
5 Now you can remove the bellows and chamber from the
assembly.
Note the orientation of the upper plate. There are
screw inserts on the underside of this plate; it is
important to re-insert this plate in the proper ori-
entation during re-assembly. Note, too, that there is
a thin film of silicone lubricant along the top edge
of the bellows. This helps seal the bellows against
the chamber top plate. There is a tube of silicone
lubricant in the bellows kit that you can apply to the new bellows during re-
assembly.

Insert your finger between the bellows and the black plate and pry the plate out.
6 There are two more plates at the bottom of the bellows. Remove the four screws from the base
plates and remove the bellows.
Note that there is a film of silicone lubricant applied to the bottom of the bellows,
which helps seal it against the outer black plate. Remove the inner plate from the
bellows, and discard the old bellows.
7 To re-assemble the bellows, insert the lower black plate into the new bellows, by running your fin-
ger along the edge of the plate, as shown below.
8 Apply a thin film of silicone lubricant around the edge of the bellows, and place the second black
plate over the bellows.
9 Align the holes between the two black plates.
If the manifold gasket is torn or otherwise damaged, there are two spares in the
spare parts kit. Align the bellows with two attached plates with the holes in the
manifold (above). There is a seam on the bottom edge of the bellows. Before tight-
ening the screws, align the seam in the bellows with one of the long edges of the
manifold and attach with the four screws removed in Step 7 above. In other words,
do not align the seam in the bellows with any of the corners of the manifold.
10 Insert the black plate into the top of the bellows as shown.

Note that the screw inserts should be on the underside of the plate. Apply a film of
silicone lubricant around the top edge of the bellows. The screw inserts are on the
underside of the top plate. They face downward, into the center of the bellows.
11 If the chamber was removed earlier, re-insert it into the strut assembly.
Make sure that the tubes are positioned between two of the struts with adequate
clearance. Place the chamber top plate on top of the struts, align the screw holes,
and secure the top plate to the struts with the eight screws.
12 Attach the bellows to the chamber top plate.
Lift up on the bottom of the chamber to compress the bellows to verify placement
and clearances, and rotate slightly until the four screw holes on the chamber top
plate and the bellows top plate align.
13 Re-attach the lower plate from the pressure vent using the four standoffs with attached star
washers.
Attach the upper plate with the four thumbnuts. Re-attach the handle. Connect the
chamber to the Analyzer Control Unit and manually open and close the chamber a
few times to verify that there are no leaks.

20 cm survey chamber maintenance

The 20 cm survey chamber uses a series of three gaskets to seal the chamber
against air leaks between the soil collar and the chamber. The first gasket is a black
neoprene gasket (part number 224-07606) that is located on the bottom of the
moveable part of the chamber; in most cases this gasket will not need to be
replaced unless it is inadvertently damaged. The other two gaskets are located on
the underside of the chamber, beneath the metal flange that envelopes the soil col-
lar. These two gaskets, and in particular the white foam gasket, may need to be
changed with some regularity.
The black rubber
gasket is referred
to as the soil col-
lar gasket; four
spares are
included in the
spares kit under
part number 6581-
108.
The white foam
gaskets are
referred to as foam
seal gaskets; a
package of 20 is
included in the
8100-632 gasket
kit, or individually
under part num-
ber 6581-107.
Foam seal
gasket
The foam seal gasket can become cracked or lose its shape relatively quickly,
depending upon the conditions they are used in, and the pressure with which they
are placed over the soil collar. Inspect the foam seal gasket before you start making

measurements each day; if it appears that it might not form a tight seal against the
soil collar, you should replace it.
It is not necessary to remove the soil collar gasket when replacing the foam seal gas-
ket. The collar plates do not need to be removed from the chamber.
If you need to replace the foam seal gasket, simply pry it out with a knife or a screw-
driver and discard the damaged gasket. In some cases you can simply flip the gasket
over and use the reverse side before replacing.
Insert the new foam seal gasket by working the gasket with your fingers into the
recessed area of the flange. It may help to work the gasket in with the inside edge
first, as shown below. Press in opposite sides of the gasket to prevent stretching it.
Make sure the gasket is seated all the way down into the flange, and that it lays flat
without warping.
Soil collar gasket

The soil collar gasket should not need to be replaced unless it is torn. To replace
the gasket, loosen the six screws on the chamber bottom plate. Remove the plate
and gasket. Align the new gasket with the screw holes and reassemble.
The 6 screws on the bottom plate are captive; they need only be loosened, not com-
pletely removed.
Chamber gasket
The bottom of the soil chamber "bowl" has an attached adhesive gasket that seals
the chamber against the bottom plate. This gasket has a long life, and should be
replaced only if it is damaged and does not form a tight seal.
1 Remove the four nuts from the bottom of the chamber supports, as shown below.
2 Bend the supports out slightly to remove the bottom plate assembly.
3 Use a knife or razor blade to remove the old gasket. Clean the rim of the chamber with alcohol if
necessary to remove any adhesive residue.
4 Remove the adhesive backing from the new gasket and install around the rim of the chamber.
Trim the gasket as needed so that the ends are touching.
5 Apply a small amount of Loctite to glue the ends together.

Replacing the bellows on the 20 cm chamber

If the bellows on the 20 cm Survey Chamber is punctured or is otherwise damaged
and develops a leak, it will not operate properly. If the chamber fails to raise or
lower when the bellows pump is operating, the bellows and/or the Bev-a-line
tubing on the bellows air path may be damaged. Check the Bev-a-line tubing first
to see if it has developed a leak, and replace if necessary. If you have determined
that the bellows is damaged, you can replace it using the optional bellows kit (part
number 8100-623). Follow these steps to replace the 20 cm Survey Chamber bel-
lows.
1 Remove the four nuts from the bottom of the chamber supports.
2 Gently move the supports out slightly to remove the bottom plate assembly.
3 Remove the four screws from the inside of the chamber, and remove the chamber bowl from
between the chamber supports.
This will expose the manifold and bellows assembly.

4 Remove the four #10 Kep nuts in each corner of the bellows assembly with a 3/8" nut driver.
5 Remove the four thumb screws from the top plate of the pressure vent assembly and lift the top
plate off (optional).
6 Remove the four screws from the bellows mounting plate.

7 Note the orientation of the black plate at the top of the bellows - the screw inserts on the under-
side of this plate face down.
There is a thin film of silicone lubricant along the top edge of the bellows. This
helps seal the bellows against the bellows mounting plate.
8 Insert your finger between the bellows and the first circular black plate and pry the plate out.
9 There are two more plates at the bottom of the bellows.

Remove the four screws from the two remaining circular base plates (inside the bel-
lows) and remove the bellows from the manifold. Again, note that there is a film of
silicone lubricant applied to the bottom of the bellows, which helps seal it against

the outer black plate. Remove the inner plate from the bellows, and discard the old
bellows.
10 To re-assemble the bellows, insert the lower black plate into the new bellows, by running your fin-
ger along the edge of the plate.
11 Apply a thin film of silicone lubricant around the edge of the bellows, and place the second black
plate over the bellows.
12 Align the holes between the two black plates. If the manifold gasket (below) is torn or otherwise
damaged, there is a spare in the bellows kit.
13 Align the bellows and two attached plates with the holes in the manifold.
There is a seam on the bottom edge of the bellows. Before tightening the screws,
align the seam in the bellows with one of the long edges of the manifold and
attach with the four screws removed earlier. In other words, do not align the seam
in the bellows with any of the corners of the manifold. Make sure that the bellows
remains centered with respect to the two clamping plates.
14 Insert the remaining black plate into the top of the bellows.
The screw inserts should be on the underside of the plate (inserts shown below).
Apply a film of silicone lubricant around the top edge of the bellows.
The screw inserts are on the underside of the top plate, and face downward, into
the center of the bellows.
15 Align the screw holes in the clamping plate with the tubing and control cables attached to the
manifold, as shown below.
16 Reattach the bellows mounting plate.

17 Re-insert the bellows assembly into the support frame.

Make sure that the plastic standoffs are still present on the four studs on the sup-
port frame. Note too that the gray control cable should extend around the outside
of one of the support struts, as shown below.
18 Re-attach the chamber bowl, making sure to insert the sensor wire through the small hole at the
center of the bowl.
19 Re-attach the bottom mounting plate with the four nuts removed earlier.
20 Re-attach the top plate of the pressure vent using four thumb screws.

Long-term chamber maintenance

The 8100-104 and 8100-104C long-term chambers are designed to require minimal
maintenance. The black neoprene collar gasket can be easily replaced if it becomes
damaged; two spare gaskets (part number 6581-060) can be found in the long-term
chamber gasket kit (part number 8100-612). Instructions are also given for repla-
cing the tubing/cable assembly, replacing the thermistor assembly, and replacing
the shaft seal assembly.
Replacing the collar gasket

The Soil Collar Gasket should not need to be replaced unless it is cracked, brittle,
or otherwise worn. To replace the gasket, move the chamber to its open position.
Loosen the 24 screws on the chamber gasket plate. Remove the plate and gasket.
Align the new gasket with the screw holes and re-assemble. Tighten the screws to 4
lb.-in (0.45 newton meters) of torque.
Replacing the tubing and cable assembly

The tubing and cable assembly (part number 9981-141) may need replacement if
the tubing becomes cut or damaged (most often by rodents).

l Follow these steps to replace the tubing and cable assembly:
1 Disconnect the temperature thermistor cable from the side of the enclosure by loosening the
thumb nut and pulling the cable connector straight out.
2 Remove the two cable clamps with an 11/32” nut driver.
3 Disconnect the temperature thermistor cable from the top of the chamber by loosening the thumb
nut and pulling the cable connector straight out.
4 Remove the two right-angle fittings by loosening the nuts on the underside of the chamber bowl
with a 3/8” nut driver.

5 Cut the four cable ties that secure the tubing/cable assembly to the arm assembly, and remove
the tubing and cable assembly.
6 On the new tubing and cable assembly, locate the end containing the right-angle fittings.
Use a cable tie to loosely attach the tubing and cable assembly to the end of the
arm nearest the pressure vent. The portion of the tubing and cable assembly that
splits into three separate cables should be attached so that it is approximately even
with the end of the arm.
7 Loosely install the three remaining cable ties to secure the tubing and cable assembly to the arm.
Verify that the assembly is positioned properly, and tighten the cable ties.

8 Trim the excess end from the cable ties.

Make sure the O-rings are present in the temperature cable connector and right-
angle fittings. Install the two right-angle fittings by tightening the nuts on the
underside of the chamber bowl with a 3/8” nut driver (it does not matter which fit-
ting goes into each hole).
9 Connect the temperature cable; make sure the connector is fully seated and the outer thumbnut is
tight (you should feel a slight snap as it locks into place).
10 Place the control cable cap retainer over the stud.
11 Align the portion of the tubing and cable assembly that divides into three separate cables with
the edge of the base plate.
12 Loosely install the bottom cable clamp.
13 Connect the temperature cable.
Make sure the connector is fully seated and the outer thumbnut is tight. You
should feel a slight snap as it locks into place.
14 Loosely install the upper cable clamp.
15 Adjust the clamps if necessary, and tighten the nuts.

Replacing the thermistor assembly

The thermistor in the long-term chamber may need to be replaced if it becomes
damaged or stops working. The procedure is the same for both the 8100-104 and
8100-104C chambers, but the chambers use different thermistors.
Chamber Thermistor Part Number

8100-104 Opaque Long-Term Chamber 9981-125
8100-104C Clear Long-Term Chamber 9981-172
l Follow these steps to replace the temperature thermistor assembly:
1 Disconnect the temperature thermistor cable from the top of the chamber by loosening the thumb
nut and pulling the cable connector straight out.
2 Remove the plastic retaining nut with a 5/8” open-end wrench.
3 Make sure the rubber seal is present on the bottom of the new thermistor connector body, and
then install the new thermistor.
4 Tighten the plastic retaining nut just enough to compress the rubber seal.
5 Do not over tighten the nut (torque to 5 lb.-in. or 0.56 newton-meters).
6 Connect the temperature cable; make sure the connector is fully seated and the outer thumb nut
is tight (you should feel a slight snap as it locks into place).

Replacing the shaft seal assembly

The shaft seal assembly (part number 8100-928) has a recommended replacement
cycle of three years. Replace the seal if the arm mechanism squeals or shudders dur-
ing motion.

1 With the chamber powered on, press the

OPEN/CLOSE button twice in succession to move
the chamber to its “Park” position. Disconnect
the cable so the chamber is no longer powered.
2 Using a 3/8" socket, remove the arm mounting
nuts on the underside of the arm that hold the
bowl assembly.
3 Remove the two hex screws on the drive
column adapter using a 9/64” hex wrench.
4 Remove the four screws and washers from the
shaft seal assembly .
5 Remove the shaft seal assembly from the
drive column. It may be stuck on, so grasp it
firmly and twist it loose.
6 Replace the gasket (part number 6581-163).
Begin by cleaning any residue off of the top of
the housing. Use a mild detergent, if needed. Do
not use sharp objects, and be careful not to dam-
age the finish. Make sure the sealing surfaces
are clean and smooth before installing the new
gasket.
7 Lubricate the new shaft seal assembly with oil
and grease from the shaft seal assembly kit.
l Apply the full 1.5 ml of lubricant from the syr-
inge to the felt washer inside the shaft seal
assembly.
l With your finger or a cotton-tipped swab, Figure 9-3. Components that secure the
apply a generous coat of grease to the
shaft seal. Corresponding dis-assembly
O-ring and rubber seal.
steps are indicated in the figure.

8 Install the new shaft seal assembly on the shaft. You may need to press firmly and twist the
assembly to get past the main shaft O-ring and seal, but use caution and be sure not to cut, pinch,
or gouge the O-ring or seal. If the O-ring or seal is damaged, water may leak into the mechanism,
causing damage.
9 Apply a droplet of Loctite® (from the spares kit; part number 208-08233) to each of the four
screws that were removed in Step 4, then install the screws, lock washers, and flat washers
as shown in Figure 9-3 on the previous page. Tighten the screws to 4 lb.-in.
Important: Wipe any oil or grease off of the top of the shaft before installing the
drive column adapter .
10 Re-install the drive column adapter . The slotted side goes toward the chamber openining.
Torque hex screws to 40 in-lbs.
11 Re-install the bowl and arm assembly using the nuts and washers removed in Step 2.
12 Tighten the nuts only finger tight, and then adjust the chamber bowl so that it is centered over
the soil collar gasket.
13 Tighten the two arm mounting nuts to 40 lb.-in.

Changing the clear and opaque chamber bowls

The 8100-104 Long-Term Chamber's opaque "bowl" can be swapped out with the
clear bowl from the 8100-104C Long-Term Chamber, and vice versa. Upgrade pack-
ages are also available from LI-COR that contain all of the hardware required to
upgrade either chamber. The upgrades requires a 3/8" combination wrench and an
11/32" combination wrench or nut driver.
l Follow these instructions to change the chamber bowl on the 8100-104 or

8100-104C:
1 Make sure that the chamber drive column is in the "Park" position before starting.
If the chamber is not parked, press the OPEN/CLOSE button twice to park.
2 Use the 11/32" wrench or nut driver to remove the two hex nuts that secure the cable/tubing
assembly to the side of the motor housing, as shown below.
Unscrew the nut and disconnect the thermistor cable.
3 Use the 3/8" wrench to remove the arm mounting nuts and washers.
4 Remove the arm assembly.

For storage, reinstall the flat washer, split washer, and hex nut on each of the PEM
studs on the underside of the arm assembly.
5 Remove the mounting hardware from the underside of the new arm assembly.
6 Place the arm assembly into position on the mounting flange and install the flat washer, split
washer, and hex nut finger tight.
The nuts should be tight enough to hold the arm flat against the mounting flange,
but should still allow some lateral movement.
Changing the clear and opaque chamber bowls 9-37

7 Adjust the position of the arm assembly so that the bowl is centered over the gasket.
8 When centered, tighten the mounting nuts.
9 Use the cable clamps provided to attach the cable/tubing assembly to the motor housing.
Note that the dust cap connector is placed under the lower cable clamp.
10 Plug in the thermistor cable and tighten the nut.

Multiplexer maintenance
The LI-8150 Multiplexer is designed to require little or no routine maintenance.
Most of the LI-8150 components are modular, and are designed to be easily
replaced should the need arise. The discussion below describes basic maintenance
and repair of user-replaceable items; contact LI-COR for information on repair of
items not described below.
Multiplexer fuses
There are two fuses on the LI-8150 main circuit board that protect the LI-8100A
and LI-8150. Spare fuses can be found in the LI-8150 spares kit. The fuses are loc-
ated under the access panel at the front edge of the white lower plate assembly, as
shown in Figure 9-4 below. The proper fuse sizes are labeled on the circuit board;
the leftmost fuse protects the LI-8100A power supply (3A Fast 250V 5x20, part num-
ber 439-04215), and the rightmost fuse protects the LI-8150 power supply (4A Fast
250V 5x20, part number 439-08516). If the LI-8150 and/or LI-8100A fail to power
up, check to see if either of these fuses has blown. Loosen the thumbnuts on the
access panel and lift off to access the fuses. You may need to unplug the two con-
nectors above the fuses to access the fuses.
Figure 9-4. Remove the access panel to replace the fuse(s).
Multiplexer maintenance 9-39

Tubing
The urethane tubing used for air connections within the LI-8150 is 1/8” ID x 11”
OD; a 3’ length of this tubing can be found in the spare parts kit under part num-
ber 222- 00303. If any of the internal tubing should become clogged or otherwise
damaged, simply remove it by pressing in on the orange quick-connect fittings, cut
a new piece of the same length, and replace.
Air filters
The air filters are located on the air lines connected to each of the eight (or sixteen)
air input ports. The filters are translucent to more easily see dust and dirt buildup.
Check the filters periodically (yearly or more often, depending on operating envir-
onment). Replace the filters when they become dirty, or if low, or no, flow rates are
present on the associated chamber. A filter kit (8 each) can be found in the spares
kit under part number 8150-909; additional kits can be ordered from LI-COR.
Remove dirty or damaged filters by pressing on the quick-connect fittings and
pulling the tubing straight out; discard the tubing and old filter. Note the ori-
entation of the new filter; the arrow pointing toward the wider end of the filter
should point toward the solenoids. Attach the tubing near the solenoid first. The
tubing on the other end of the filter is longer than is required; route the tubing
toward the connector on the multiplexer case, leaving a bit of slack, and cut to
length.

Solenoid valves
Under normal operation the solenoid valves should not need to be replaced. If how-
ever, a solenoid fails to open, it can be easily replaced. Note that each solenoid has a
manual override that can be used to test the mechanical opening of each solenoid
(they are normally closed). If it appears that a solenoid is not opening (no flow),
turn the blue screw on the top of the solenoid valve with a small flathead screw-
driver a quarter turn in either direction to manually open the solenoid. If the solen-
oid does not open manually, it should be replaced. Solenoid valves are available
from LI-COR under part number 300-08249 (1 each). Follow these steps to replace
a solenoid:
1 Power the LI-8150 off and open the lid.

2 Remove the single screw on the wired valve connector, pinch the top of the connector, and
remove.
3 Remove the two screws on the top of the solenoid valve, remove the solenoid, and discard.
4 Make sure the manifold gasket is in place, and install the new solenoid valve.
Figure 9-5. Remove the electrical connector, remove the valve, and make sure the manifold
gasket is in place before installing new valve.
Solenoid valves 9-41

Figure 9-6. Note orientation of filters. Attach nearest the solenoids first, and cut the tubing
at the other end to length.

Section 10.
Customizations and other applications
This section describes ways to use the LI-8100A that are beyond the basic soil gas
flux capabilities. For some applications, we direct you to supplementary documents
on the procedure.
Trace gas flux measurements

For gases such as NO2 , N2 O, CH4 , or isotopologues, you can add a trace gas ana-
lyzer to the LI-8100A system, log the data in the LI-8100A, and process the data in
SoilFluxPro™ software. Download the application note called "Capturing and Pro-
cessing Soil GHG Fluxes Using the LI-8100A" from the LI-COR support site:
www.licor.com/env/support and select the LI-8100A.
Download the Application Note:
https://www.licor.com/documents/zbjt20wkx738drzu19et
Flask measurements
You can configure the LI-8100A and LI-8150 multiplexer to measure gas exchange
from discrete samples such as soil samples, fruit, or small animals in flasks or cus-
tom chambers. This is described in detail in an application note called "Meas-
urement of CO2 Evolution in a Multiplexed Flask System."
https://www.licor.com/documents/rdt83ib1nlj70zpgrg2r

Profile measurements
You can configure the system to measure concentrations across a vertical or hori-
zontal profile. This is described in the document called "Atmospheric CO2 Profile
Measurements Using the LI-8100A/LI-8150 System."
https://www.licor.com/documents/gc4evxucnhzp69eeevg3
Trace gas sampling kit

The trace gas sampling kit (part number 8100-664) is used to collect air samples
from the same air stream used by the LI-8100A Automated Soil CO2 Flux System.
The collected sample can be analyzed to measure trace gases such as methane
(CH4 ), ammonia (NH3 ), nitrous oxide (N2 O), isotopologues.
https://www.licor.com/documents/od4g3wjp9dgxmr2c9nl8
Chamber control kit

The chamber control kit (part number 8100-401) enables you to use a long-term
chamber with a home-made controller and third-party gas analyzer.
Download the Technical Note:
https://www.licor.com/documents/tcikluk3o0cc3foz406o
The GPS accessory

The optional 8100-405 CO2 Mapping Kit can be used without a soil chamber in
continuous measurement mode to map CO2 concentrations across a transect. You
can make a single measurement of up to 24 hours. A user-provided intake tube is
required; tubing and fittings are provided in the spare parts kit to aid in con-
struction of the intake tube. Considerations and guidelines for sampling height,
intake tube construction, and concentration mapping can be found in Application
Note #135, entitled “Mapping CO2 Concentrations and Fluxes with the LI-8100A”.
Download the Mapping Kit Instructions:
https://www.licor.com/documents/xg18h1n174tt08kewk4s

XML communication
You can view the XML monitor in the PC software any time: Click Utilities > XML
Monitor . From this window, you can also send XML commands.
XML outputs
Under 8100 > Outputs you can select variables to output to an external data logger
or terminal program, either over RS-232 serial or Ethernet communication. The
variables available are essentially the same, the difference being that you do not
have geographical (GPS) data available over RS-232 because the GPS accessory occu-
pies the RS-232 port.
There are several options available when configuring the outputs:
Remove XML from data: Select this to remove the markup from the data stream.
The resulting data set is a data stream where each value is separated by a space.
Add CRC to data: Select this to enable the Cyclic Redundancy Check (CRC). CRC
is an algorithm that is used to verify the integrity of the data. Before each data
packet is sent by the LI-8100A, a CRC is calculated (pre-transmission) for that
packet, and then appended to the packet. When the client (e.g. the computer)
receives the packet, it strips off the appended CRC and calculates its own CRC
(post transmission). If the two CRC values match, it is assumed that the packet was
transmitted correctly. When CRC values are appended to the data packet, the value
is automatically marked up. A typical CRC will appear as
<CRC>3067450353</CRC>
Disable the Add CRC to data check box to remove CRC from the data.
Terminal program
You can also communicate with the LI-8100A using a command line program
such as Tera Term. When you communicate with the LI-8100A with a Trans-
mission Control Protocol (TCP) connection, connect with the instrument using
the IP Address. The LI-8100A uses port number 1562.
If you connect with the RS-232 serial port, simply select the COM port that you
used to connect your LI-8100A.
XML communication 10-3

Logging data to a computer

In addition to the data storage available in the LI-8100A, you can also configure log-
ging directly to a personal computer. You will want to configure measurements the
same way as for any survey or long-term measurement.
1 Click Utilities > PC Data Logging.

2 Select the Data Values to log.
3 Set the field delimiter. Typically choose Tab.
4 Set the Log Frequency (number of measurements per second).
5 Start logging—This will begin creating the file. Data will be written to the file until you Stop
Logging.
The data file that is created will be delimited text file. You can open it in most text
editors or spreadsheets, depending upon the formatting of the logged file.
Making soil collars

You can make your own soil collars with materials that are widely available in the
United States. In other countries you may need to special order materials.
10 cm collars
9.9 cm (3.9") minimum inside diameter
The 10 cm (4 inch) collars are made from 11.4 cm (4.5”) maximum outside diameter
thin-walled polyvinyl chloride (PVC) sewer
pipe. The pipe must have an inside dia-
meter of 10 cm (3.930 inches) minimum
and an outside diameter of 11.4 cm (4.5
inches) maximum. Cut a section approx- 3.5"
(8.9 cm)
imately 8.9 cm (3.5 inches) or longer,
depending on requirements for your meas-
urement. Bevel the bottom edge with a
grinder or coarse file.

20 cm collars
21.34 cm (8.4") outside diameter
The 20 cm (8 inch) collars
are constructed from thick-
walled 8 inch SDR 35 PVC
pipe. Use a grinder, coarse
file, or an extremely large
lathe to bevel the bottom edge 11.43 cm
to an angle of 24°. (4.5")
24°
Making soil collars 10-5


Appendix A.
Specifications
Mobile device requirements

OS: Apple iOS V4.0 or greater; Android; Windows Mobile (older software).
Wireless: 802.11b/g.
Analyzer control unit

Memory: 32 MB flash memory total (18 MB for data collection)
CompactFlash: Type I industrial grade, 1 GB with adapter sleeve included
Wireless PC Card: Fixed wireless networking Type II PC Card. Cisco Systems Airon-
et® 350 Series 11 Mbps DSSS for Wi-Fi (802.11b) networking
RS-232
Signal output rate: 1 Hz
Baud rate: 57,600 bps (instrument software <V4.0), 38,400 (instrument soft-
ware V4.0 or greater)
Pressure Sensor
Measurement Range: 15-115 kPa
Accuracy: 1.5% over 0 to 85 °C
Maximum Gas Flow Rate: 1.7 liters/min (permanently affixed to max.)
Power Requirements
Auxiliary Input Voltage: 10.5-28 VDC
Battery Input Voltage: 10.5-15 VDC
3A @ 12V (36W) maximum usage during warm-up with heaters on 1A @ 12V
(12W) average usage after warm-up with heaters on
Operating Range
Temperature: –20 °C to 45 °C
Relative Humidity: 0 to 95% RH, non-condensing
Weatherproof Rating: Tested to IEC IP55 standard
Dimensions: 29 cm L × 38.1 cm W × 6.5 cm H (11.4" × 15" × 6.5")
Using the LI-8100A A-1

Weight: 5.3 kg (11.8 lb.) without battery; 6.7 kg (14.8 lb.) with battery
Battery Weight: 1. 4 kg (3.0 lb.)
Infrared Gas Analyzer

Measurement Principle: Non-Dispersive Infrared
Traceability: Traceable to WMO standards for CO2 .
NIST traceable LI-610 Portable Dew Point Generator for H2 O
CO2
Measurement Range: 0-20,000 ppm
Accuracy: 1.5% of reading
Calibration Drift
Drift at 0 ppm: <0.15 ppm/°C and <1 ppm/day
Span Drift1: < 0.03 %/°C
Total Drift at 370 ppm: <0.4 ppm/°C
RMS Noise at 370 ppm with 1 sec signal averaging: <1 ppm
Sensitivity to water vapor: < 0.1 ppm CO2 /mmol/mol H2 O
H2O
Measurement Range: 0-60 mmol/mol
Accuracy: 1.5% of reading
Calibration Drift
Drift at 0 ppt: <0.005 mmol/mol/°C and <0.1 mmol/mol/day
Span Drift1: <0.006 mmol/mol/°C
Total Drift at 10 ppt: <0.016 mmol/mol/°C
RMS Noise at 10 ppt with 1 sec signal averaging: <0.01 mmol/mol
Sensitivity to CO2: <0.0001 mmol/mol H2 O/ppm CO2
Auxiliary sensor interface

Dimensions: 10.2 cm L × 3.8 cm W × 6.4 cm H (4" × 1.5" × 2.5")
Inputs: 4 Thermocouple channels (Type E, J, T, or raw)
4 General input channels (0-5 VDC)
Power Out: 0-5 VDC
Power In: 10.5-28 VDC
Connections: Terminal strip with screw posts
1Residual error after zero correction
A-2 Using the LI-8100A

10 cm survey chamber: 8100-102

Chamber Volume: 835.2 cm 3
Soil Area Exposed: 80.1 cm 2 (13 in.2 )
Dimensions: 15.2 cm L × 15.2 cm W × 25.4 cm H (6" × 6 " × 10")
Air temperature thermistor
Operating Range: –20 to 45 °C
Accuracy: ± 0.2 °C from 0 to 50 °C, ± 0.3 °C from -20 to 0 °C
Cable length: 1. 01 m (40")
Weight: 1.6 kg (3.5 lb.)
20 cm survey chamber: 8100-103

Chamber Volume: 4824 cm 3
Soil Area Exposed: 317.8 cm 2 (49.3 in.2 )
Dimensions: 28.7 cm L × 28.7 cm W × 29.2 cm H (11.3" × 11.3" × 11.5")
Cable length: 1. 01 m (40")
Weight: 2.9 kg (6.4 lb.)
Appendix A. Specifications A-3

Survey and single-chamber accessories

The following accessories are for use with the LI-8100A for single-chamber and sur-
vey measurements.
10 cm (4") soil collar

Part number: 6581-157
Material: Thin-walled PVC pipe
Inside Diameter: 10 cm (3.930")
Outside Diameter: 11.4 cm (4.50")
Height: 8.9 cm (3.5")
20 cm (8") soil collar

Part number: 6581-044
Material: PVC pipe; SDR 35
Inside Diameter: 20.3 cm (8")
Outside Diameter: 21.34 (8.4")
Height: 11.43 cm (4.5")
Note: See Making soil collars on page 10-4 for more details on soil collars.

Omega soil temperature probe

LI-COR part number: 6000-09TC
Sensor type: Type E thermocouple
Probe length: 25.4 cm (10")
Cable length: Up to 1.5 m (5')
ECH2O model EC-5 soil moisture probe

LI-COR part number: 8100-202
Sensor type: Dielectric sensor
Sensor length: 5.5 cm (2.25")
Cable length: 4.6 m (15')
Operating temperature range: -40 to +50 °C
LI-COR soil temperature thermistor

Sensor type: Thermistor
Sensor length: 6 cm (2.375")
Delta-T ML2x ThetaProbe soil moisture probe

Cable length: 2 m (6.6')
Operating temperature range: 0 to +70 °C
GS1 soil moisture sensor

Sensor length: 5.2 cm (2")
Cable length: 5 m (16')
LI-8150 Multiplexer
Dimensions: 40.6 cm L × 57.2 cm W × 21.1 cm H (16” × 22.5” × 8.3”)
Weight
8 port version: 9.4 kg (20.7 lb)

16 port version: 11.2 kg (24.8 lb)

Operating Range
Temperature: –20 to 45 °C
Humidity: 0 to 95% RH, non-condensing
Coverage Area
Maximum radius from LI-8150 to chambers: 15.0 m (49.2 ft) with one exten-
sion tube.
Maximum diameter of measurement circle: 30.0 m (98.4 ft) with one extension
tube on each chamber.
Plumbing
Flow rate to/from chambers: ~2-3 lpm
Flow rate between LI-8100A and LI-8150: 1.7 lpm
Pump in the LI-8100A subsamples air stream in the LI-8150
LI-8150 Pump Type: Diaphragm
Display
Four LED Indicators: Power, Check Error Log, Manual Chamber Activation
Indicator, Active Chamber Error
Five 7-segment LED Displays: Active Chamber, Active Valve, three voltage chan-
nel indicators
Power Requirements: 10.5 – 14.5 VDC (120 VAC and 240 VAC with optional
power supply). Power supplied through the LI-8150; the LI-8150 powers the
LI-8100A when connected. See Table A-1 below for total system power require-
ments.
Table A-1. Total system power requirements in different sampling configurations.

LI-8100A + Sampling: No Sampling: Two Warm-up: Up to four
LI-8150 + chamber chambers move at chambers move at
n Chambers movement once once
n Chambers Amps @ Watts Amps @ Watts Amps @ Watts
12.5 VDC 12.5 VDC 12.5 VDC
1a 1.0 12.5 3.0 37.5 3.0 37.5
2 2.0 25.0 3.8 47.5 3.8 47.5
4 2.1 26.3 3.8 47.5 4.8 60.0
8 2.1 26.3 3.8 47.5 4.8 60.0
16 2.3 26.8 3.8 47.5 4.8 60.0
aMultiplexer not required.

8150-770 AC to DC power supply

Power Requirements: 115-120 VAC or 230-240 VAC, 50/60 Hz, 230 W.
Output Voltage: 12 VDC, 4.5 A
Operating Temperature Range: -20 to 50 °C (-4 to 122 °F)
Environmental Operating Conditions: Tested to IP55 for dust and water ingress.
Dimensions: 18.1 cm D × 28 cm L × 10.2 cm T (7.125” × 11” × 4”)
Weight: 31 kg (14.05 lbs.)
2-meter cable and tube

Length: 2 m (6.6')
15-meter chamber cable and tube

Length: 15 m (49')
Volume: 237 cm 3
Long-term chamber: 8100-104

Chamber Volume: 4076.1 cm 3
Dimensions: 48.3 cm L × 38.1 cm W × 33.0 cm H (19" × 15" × 13")
Weight: 5.9 kg (13 lb.)
Clear long-term chamber: 8100-104C

Chamber Volume (serial numbers 2024 and below): 4076.1 cm 3
Chamber Volume (serial numbers 2025 and above): 3876.1 cm 3
Dimensions: 48.3 cm L × 38.1 cm W × 33.0 cm H (19" × 15" × 13")
Weight: 5.9 kg (13 lb.)

Multiplexer accessories
The following accessories are for use with the LI-8150 Multiplexer for long-term
measurements.
ECH2O model EC-5 soil moisture probe

Sensor length: 5.5 cm (2.25")
LI-COR soil temperature thermistor

Sensor type: Thermistor
Delta-T ML2x ThetaProbe soil moisture probe

Cable length: 2 m (6.6')
Operating temperature range: 0 to +70 °C
GS1 soil moisture sensor

Sensor length: 5.2 cm (2")
Cable length: 5 m (16')

Appendix B.
Software compatibility table
The LI-8100 embedded instrument software and LI-8100A PC software are updated
periodically to add new features and fix bugs. Any LI-8100 or LI-8100A can run the
most up-to-date software. If you update an LI-8100 embedded instrument software
to the LI-8100A embedded instrument software, you will need to set the zero and
span of the instrument, however, it is best to get a full factory recalibration.
NOTE: Always run the corresponding versions of instrument and PC software to

prevent compatibility problems.
Instrument Compatible Mobile Devices Supported

Software PC Software
Palma Windows Mobilea iOSb Android OSb
1.0.0 1.0.1 Yes No No No
1.0.1 1.0.2 Yes No No No
1.2.0 1.2.0 Yes No No No
2.0.0 2.0.0 No Yes No No
3.0.1c 3.0.0 / 3.0.1 No No Yes No
4.0.0 / 4.0.5 4.0.0 No No Yes Yes
aSerial cable adapters, the wireless communication package, or a user-supplied battery-powered wireless
router are required for these devices.
bWireless communication package or a user-supplied battery-powered wireless router is required for these
devices.
cSoftware version 3.0.0 is the first LI-8100A version. Installing this software on an LI-8100 instrument will
require a zero and span calibration, but it is best is to do a factory recalibration due to changes to the gas
measurement algorithms. You will need to install a PCMCIA Ethernet adapter to use the Ethernet
functionality.
Using the LI-8100A B-1

Appendix B. Software compatibility table
B-2 Using the LI-8100A

Appendix C.
Pin assignments
The LI-8100A uses a round Turck connector on the side panel for RS-232 serial out-
put. An RS-232 serial cable (part number 392-10587) with a round Turck con-
nector and a DB-9 connector attaches to the LI-8100A RS-232 serial port. The pin
assignments for the DB-9 connector on the 392-10587 cable are given below; note
that not all pins are used for communication between the LI-8100A and a com-
puter. If you want to make a custom cable for use with the LI-8100A, follow the list
below for the proper connections.
The 392-10587 RS-232 cable pin assignments are as follows:
392-10587
To Analyzer
Control Unit
Using the LI-8100A C-1

Appendix C. Pin assignments
C-2 Using the LI-8100A

Appendix D.
References
1 Hanson, P.J., S.D. Wullschleger, S.A. Bohlman and D.E. Todd. 1993. Seasonal and topographical
patterns of forest floor CO2 efflux from an upland oak forest. Tree Physiology. 13:1-15
2 Healy, R.W., R.G. Striegl, T.F. Russell, G.L. Hutchinson, and G.P. Livingston. 1996. Numerical
evaluation of static-chamber measurements of soil-atmosphere gas exchange: Identification of
physical processes. Soil Sci. Soc. Am. J. 60:740- 747.
3 Hillel, D. Introduction to Soil Physics, 366 pp., Academic Press Inc. San Diego, 1982.
4 Morison, J.I.L., 1987. Intercellular CO2 concentration and stomatal response to CO2. In: Zeiger,
E., Farquhar, G.D. and Cowan, I.R. (Eds.), Stomatal Function. Stanford University Press, Stan-
ford, California, pp. 229-251.
5 Norman, J.M., R.L. Garcia and S.B. Verma. 1992. Soil surface CO2 fluxes and the carbon budget
of a grassland. J. Geophys. Res. 97(D17):18845-18853.
6 Wong, S.C., Cowan, I.R., Farquhar, G.D., 1979. Stomatal conductance correlates with pho-
tosynthetic capacity. Nature 282, 424-426.
7 Xu, L., M. D. Furtaw, R. A. Madsen, R. L. Garcia, D. J. Anderson, and D. K. McDermitt. 2006.
On maintaining pressure equilibrium between a soil CO2 flux chamber and the ambient air, J.
Geophys. Res., 111, D08S10, doi:10.1029/2005JD006435.
8 Xu, L-K and Hsiao TC, 2004. Predicted vs. measured photosynthetic water-use efficiency of crop
stands under dynamically changing field environments. Journal of Experimental Botany.
55:2395-2411.
Using the LI-8100A D-1

Appendix D. References
D-2 Using the LI-8100A

Appendix E.
Warranty
Each LI-COR, Inc. instrument is warranted by LI-COR, Inc. to be free from defects
in material and workmanship; however, LI-COR, Inc.'s sole obligation under this
warranty shall be to repair or replace any part of the instrument which LI-COR,
Inc.'s examination discloses to have been defective in material or workmanship
without charge and only under the following conditions, which are:
1 The defects are called to the attention of LI-COR, Inc. in Lincoln, Nebraska, in writing within one
year after the shipping date of the instrument.
2 The instrument has not been maintained, repaired or altered by anyone who was not approved by
LI-COR, Inc.
3 The instrument was used in the normal, proper and ordinary manner and has not been abused,
altered, misused, neglected, involved in an accident or damaged by act of God or other casualty.
4 The purchaser, whether it is a DISTRIBUTOR or direct customer of LI-COR or a DISTRIBUTOR'S cus-
tomer, packs and ships or delivers the instrument to LI-COR, Inc. at LI-COR Inc.'s factory in Lincoln,
Nebraska, U.S.A. within 30 days after LI-COR, Inc. has received written notice of the defect.
Unless other arrangements have been made in writing, transportation to LI-COR, Inc. (by air
unless otherwise authorized by LI-COR, Inc.) is at customer expense.
5 No-charge repair parts may be sent at LI-COR, Inc.'s sole discretion to the purchaser for install-
ation by purchaser.
6 LI-COR, Inc.'s liability is limited to repair or replace any part of the instrument without charge if
LI-COR, Inc.'s examination disclosed that part to have been defective in material or workmanship.
There are no warranties, express or implied, including but not limited to any
implied warranty of merchantability of fitness for a particular purpose on
underwater cables or on expendables such as batteries, lamps, thermocouples,
and calibrations.
Using the LI-8100A E-1

Appendix E. Warranty
Other than the obligation of LI-COR, Inc. expressly set forth herein, LI-COR,
Inc. disclaims all warranties of merchantability or fitness for a particular pur-
pose. The foregoing constitutes LI-COR, Inc.'s sole obligation and liability with
respect to damages resulting from the use or performance of the instrument
and in no event shall LI-COR, Inc. or its representatives be liable for damages
beyond the price paid for the instrument, or for direct, incidental or con-
sequential damages.
The laws of some locations may not allow the exclusion or limitation on implied
warranties or on incidental or consequential damaged, so the limitations herein
may not apply directly. This warranty gives you specific legal rights, and you may
already have other rights which vary from state to state. All warranties that apply,
whether included by this contract or by law, are limited to the time period of this
warranty which is a twelve-month period commencing from the date the instru-
ment is shipped to a user who is a customer or eighteen months from the date of
shipment to LI-COR, Inc.'s authorized distributor, whichever is earlier.
This warranty supersedes all warranties for products purchased prior to June 1,
1984, unless this warranty is later superseded. To the extent not superseded by the
terms of any extended warranty, the terms and conditions of LI-COR’s Warranty
still apply.
DISTRIBUTOR or the DISTRIBUTOR's customers may ship the instruments dir-
ectly to LI-COR if they are unable to repair the instrument themselves even though
the DISTRIBUTOR has been approved for making such repairs and has agreed with
the customer to make such repairs as covered by this limited warranty.
Further information concerning this warranty may be obtained by writing or tele-
phoning Warranty manager at LI-COR, Inc.
E-2 Using the LI-8100A

Appendix F.
Index
# A
# AC to DC Power Supply, 4-2, 4-6
392-08577, 5-18 Air Filter
392-09436, 1-3 Replacing in the LI-8100A, 9-3
392-10587, 1-3 Replacing in the LI-8150, 9-40
6000-09TC, 1-6 Android, 1-2
604-10643, 1-4 Connecting, 2-10
6400-26, 1-3 App, 1-2
6400-27, 1-3 Automatic Restart Function, 3-6
8100-102, 1-9, 2-21 Auxiliary Sensor Interface, 1-3, 3-8, 3-9, 3-11
8100-103, 1-10, 2-22
8100-104, 1-12, 2-25, A-7 B
8100-104C, 1-12, 2-25, A-7 Balston Filters, 9-3
8100-202, 1-7, 4-3 Battery, 1-6
8100-204, 1-7, 4-3 About, 2-13
8100-405, 1-8 Fuse, 9-13
8100-554, 1-4 Indicator, 2-13
8100-565, 1-8 Installation, 2-2
8100-663, 1-3 Battery Charger, 1-6
8100-704, 2-26 Bev-a-line Tube, 1-14
8150-202, 1-7, 4-3
8150-203, 4-3 C
8150-204, 1-7, 4-3 Cable
8150-705, 2-26, 4-2 RS-232, 1-3
8150-706, 4-2 Serial, 1-3
8150-770, 4-2 Calibration
9981-078, 1-7 Calibration Sheet, 1-4
9981-160, 1-7 Data Online, 1-4
9981-185, 1-8
Appendix F. Index F-1

Appendix F. Index
Gas Standards, 7-2 Transferring to a PC, 6-1

Span 2, 7-8, 7-8 Data Files, 6-3
Setting, 7-10 Data Logging
Spans, 7-3, 7-3, 7-7 To a PC, 10-4
Zero, 7-4 Date, 2-2
Zero Gas, 7-2 Dead Band, 1-14
CH4, 10-1 Decagon Devices, 4-3
Chamber Single Chamber Measurements, 3-15
Connecting Long-Term, 4-12 Delta-T Theta Probe, 1-7
Open Position, 2-28 Multiplexed Measurements, 5-13
Chamber Control Kit, 10-2 Single Chamber Measurements, 3-17
Chamber Offset, 2-18 Destination, 1-14
Chamber Shaft Seal
Replacing, 9-33 E
CHAPPiE, 3-20 ECH2O, 1-7, 4-3
Checklist Single Chamber Measurements, 3-15
Survey Measurements, 3-5 Error Log, 3-20
Clear Chamber, 2-30 Ethernet, 2-4
CO2 Calibration Ethernet Cable, 1-3
Zero, 7-4 Ethernet Card, 1-3
Collar, A-4 Extension tube volume, 1-14
Making, 10-4
Communicate F
Android, 2-10 File Manager, 6-1
Ethernet, 2-4 Files
iOS Device, 2-8 81x, 6-3
Network, 2-5 Transferring to a PC, 6-1
Wireless to PC, 2-6 Filters, 2-14, 2-17
CompactFlash Memory Card, 1-4 Replacing in the LI-8100A, 9-3
Connecting Replacing in the LI-8150, 9-40
Android, 2-10 Flask Measurements, 10-1
Ethernet, 2-4 Flow Path, 2-14, 4-4
iOS, 2-10 Fuse, 1-5, 4-2
iOS Device, 2-8 AC Power Supply, 4-7
Network, 2-5 Auxiliary Sensor Interface, 9-10
Wireless to PC, 2-6 Battery, 9-13
Copying Files, 6-1 LI-8100A, 9-10
CRC, 10-3 LI-8150, 9-39
Cyclic Redundancy Check, 10-3 FV8100, 1-2, 5-7, 6-2
D G
Data Gasket
Storage Options, 2-16 10 cm Chamber, 9-15
F-2 Using the LI-8100A

Appendix F. Index
20 cm Chamber, 9-21 What Happens, 1-13

Long-Term Chamber Collar Gasket, 9-28 Measurement File, 1-15
GPS, 1-8 Memory, 1-4
GS1, 3-14, 5-10 Methane, 10-1
Moisture
H Soil, 1-7
H2O Calibration Morison, 1987, 1-29, D-1
Zero, 7-4 Multiplexer
HAL-9000, 3-20 Specifications, A-5
Hanson, et al., 1993, 3-18, D-1
Healy, et al., 1996, 1-19, 2-18, D-1 N
Hillel, 1982, 3-18, D-1 Name, 3-20
Net Carbon Exchange Measurements, 2-30
I Networking, 2-4, 2-8
iOS, 2-8 Nitrogen Dioxide, 10-1
connecting, 2-10 NO2, 10-1
IP Address, 2-4, 2-5, 2-6, 2-8, 2-10 Norman, et al., 1992, 3-18, D-1
iPad, 1-2, 2-8
iPhone, 1-2, 2-8 O
IRGA, 2-14 Observation Count, 1-15
IRGA Ready, 2-14, 3-20 Observation Length, 1-15
Isotopologues, 10-1 Omega Soil Temperature Probe
Multiplexed Measurements, 5-11
L Single Chamber Measurements, 3-13
Leak Test Open Position, 2-28
LI-8150, 5-19
LI-190R, 2-30 P
LI-6020, 1-6 PC Adapter Cards, 2-15
LI-COR Soil Temperature Probe PC Logging, 10-4
Multiplexed Measurements, 5-12 Post purge, 1-16
Single Chamber Measurements, 3-16 Power
Local Area Network, 2-5 On/Off, 2-14
Logging Power Cable, 4-2, 4-11
To a PC, 10-4 Power Supply, 4-2
Long-Term Chamber, 2-25, 2-26 Specifications, A-7
Open Position, 2-28 Pre-purge, 1-16
Low Battery Indicator, 2-13 Profile measurements, 10-2
Pump
M On/Off, 2-2
Mapping Kit, 1-8
Marvin, 3-20 Q
Measurement Quantum Sensor, 2-30
Tutorial, 3-1, 3-3
Appendix F. Index F-3

Appendix F. Index
R 20 cm Gasket Kit, 1-11
Remove XML from data, 10-3 T

Repeat, 1-17
T-1000, 3-20
Restart
Terminal Program, 10-3
Automatic Restart Function, 3-6
Thermistor
RJ45, 1-3, 1-3
Replacing, 9-32
RS-232 Cable, 1-3, 2-1
Thermocouples, 3-8
S ThetaProbe, 1-7, 4-3
Time, 2-2
Serial Cable, 1-3, 2-1 Trace Gases, 10-1
Serial Port Number Sampling Kit, 10-2
Finding, 2-2, 2-4, 8-3 Transferring Data, 6-1
Shoulder Strap, 1-4 Treatment Label, 1-18
Soil Collars, 2-17, 2-18, 3-3 Tube Volume, 1-14
Chamber Offset, 2-18 Turn off pumps between measurements,
Inserting, 2-18 1-18
Making, 10-4
Specifications, A-4 U
Soil Moisture Probes, 1-7, 3-14, 5-10
Placing, 3-18 USB to RS-232 Adapter, 1-3
Soil Temperature Probes, 1-6
Multiplexed Measurements, 5-12, 5-13
V
Placing, 3-18 Volume
Single Chamber Measurements, 3-16, Chamber Offset, 2-18
3-17 Tube, 1-14
SoilFluxPro, 1-2, 3-2, 5-7, 6-2
Span Calibration, 7-3, 7-3, 7-6, 7-7
W
Spare Parts, 1-5 Water Vapor Calibration, 7-7
Specifications Wireless
10 cm Chamber, A-3 to PC, 2-6
20 cm Chamber, A-3 Wireless Card, 2-17
Accessories, A-4, A-8 Wireless Communication Package, 1-8, 2-17
Long-Term Chambers, A-7 Wireless Hotspot, 2-10
Multiplexer, A-5 Wong, et al., 1979, 1-29, D-1
Power Supply, A-7
System, A-1 X
Start Measurement, 1-15 XML Monitor, 10-3
Stop Observation if RH Reaches..., 1-18 Xu and Hsiao, 2004, 1-29, D-1
Survey Chamber Xu, et al., 2006, 2-21, 2-25, D-1
10 cm, 1-9, 2-21
10 cm Gasket Kit, 1-9 Z
20 cm, 1-10, 2-22 Zero Calibration, 7-2, 7-4
F-4 Using the LI-8100A

LI-COR Biosciences
4647 Superior Street
Lincoln, Nebraska 68504
Phone: +1-402-467-3576
Toll free: 800-447-3576 (U.S. and Canada)
envsales@licor.com
Regional Offices
LI-COR Biosciences GmbH

Siemensstraße 25A
61352 Bad Homburg
Germany
Phone: +49 (0) 6172 17 17 771
envsales-gmbh@licor.com
LI-COR Biosciences UK Ltd.

St. John’s Innovation Centre
Cowley Road
Cambridge
CB4 0WS
United Kingdom
Phone: +44 (0) 1223 422102
envsales-UK@licor.com
LI-COR Distributor Network:

www.licor.com/env/distributors
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Using the LI-8100A

Soil Gas Flux System

with support for

LI-COR Biosciences GmbH

LI-COR Biosciences UK Ltd.

LI-COR Distributor Network:

Warning Warnings must be followed carefully to avoid bodily injury.

Part Name Toxic and Hazardous Substances or Elements

(Pb) (Hg) (Cd) (Cr(VI)) (PBB) (PBDE)

Section 1. Getting started

Section 2. Initial setup

Section 3. Making single-chamber measurements

Section 4. Overview of the LI-8150 multiplexer

Section 5. Using the multiplexer

Section 6. Transferring data from the LI-8100A

Section 7. Calibrating the LI-8100A

Section 10. Customizations and other applications

Appendix B. Software compatibility table

Appendix C. Pin assignments

What is the LI-8100A?

The LI-8100A PC Software

Using the LI-8100A 1-1

Analyzer control unit

1-2 Using the LI-8100A

Auxiliary sensor interface

RS-232 serial cable

Auxiliary sensor interface 1-3

CompactFlash® memory card

The CompactFlash memory card (part

Shoulder strap kit

1-4 Using the LI-8100A

Spare parts kit

Description Qty. LI-COR Part No.

Spare parts kit 1-5

6400-03 Rechargeable battery

LI-6020 Battery charger

Soil temperature probes

1-6 Using the LI-8100A

Soil moisture probes

8100-104 and 8100-104C conversion kits

Optional accessories 1-7

Wireless communications package1

GPS mapping kit

1May not be available in all areas.

1-8 Using the LI-8100A

Table 1-3. The bellows kit components.

1-10 Using the LI-8100A

Table 1-6. The bellows kit components.

20 cm survey chamber 1-11

Chamber spares kit

1-12 Using the LI-8100A

The measurement cycle

Chamber Chamber Observation Chamber Chamber Observation

Pre-purge Dead Data Post- Pre-purge Dead Data

Figure 1-1. A typical measurement cycle.

The measurement cycle 1-13

Extension tube volume

l For a long-term single-chamber measurements, connect the chamber to the ana-

1-14 Using the LI-8100A

General purpose input

register a count up to 0 from seconds until 0 (in older versions of software it

Optional data fields

1-16 Using the LI-8100A