LI-COR LI7200RS User manual

Enclosed CO2/H2O
Gas Analyzer
Instruction Manual

LI-7200RS
Enclosed CO2/H2O Gas Analyzer
LI-COR Biosciences
4647 Superior Street
Lincoln, Nebraska 68504
Phone: [phone]
Toll free: 800-447-3576 (U.S. and Canada)
[e-mail]
Regional Offices
LI-COR Biosciences GmbH
Siemensstraße 25A
61352 Bad Homburg
Germany
Phone: [phone]
[e-mail]
LI-COR Biosciences UK Ltd.
St. John’s Innovation Centre
Cowley Road
Cambridge
CB4 0WS
United Kingdom
Phone: [phone]
[e-mail]
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.
The LI-7200/RS is covered by U.S. Patents 8,154,714; 8,125,626; 8,130,379; 8,300,218 and foriegn equivalents. Other patents
pending.
EddyPro and the SmartFlux System are trademarks of LI-COR, Inc. Microsoft® and Windows® are registered trademarks
of Microsoft Corporation. Eurofast® is a registered trademark of Turck, Inc. Campbell Scientific® is a registered trade-
mark of Campbell Scientific, Inc. Dropbox and the Dropbox logo are trademarks of Dropbox, Inc. All other trademarks
or registered trademarks are property of their respective owners.
Printing History
Publication Number 984-15810
© Copyright 2015 - 2018, LI-COR, Inc.
New editions of this manual will incorporate all material since the previous editions. Update packages may be used
between editions which contain replacement and additional pages to be merged into the manual by the user. The manual
printing date indicates its current edition. 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).
Version Number Publication Date Changes
1st Printing November, 2015 Not applicable.
2nd Printing October, 2016 Updates for the SmartFlux® 2 System
Updated on Wednesday, November 13, 2019.
ii

iii
CE Marking:
This product is a CE-marked product. For conformity information, contact LI-COR Support at [e-mail].
Outside of the U.S., contact your local sales office or distributor.
Doc. #53-16033-A
July 7, 2016
page 1 of 1
LI-7200RS Closed Path CO2/H2O Analyzer
Part Name Toxic and Hazardous Substances or Elements
(Pb) (Hg) (Cd) (Cr(VI)) (PBB) (PBDE)
PCBs)
Optics)
Cables and Wires)
(Metal Parts)
(Plastic Parts)
X
X
X
X
X
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).
O
O
O
O
O
O
O
O
O
O
O
O
O
X
O
O
O
O
O
O
O
O
X O O O O O
O
O
O
(Electro-
mechanical Parts)
LI-7200RS CO2 / H2O

A bit of history...
The LI-7200/RS model is the followup to the LI-7200, which is the enclosed ana-
lyzer that used technology from the original LI-7500. The LI-7200 began life
with the intention of being a component of homemade eddy covariance sys-
tems, but the built-in datalogging and networking capabilities enabled the
instrument to grow into the core component of a stand-alone, full-featured eddy
covariance system.
The RS models present improvements to the optical hardware, and these
improvements will directly affect the quality of data collected and the cleaning
frequency of optical components.
New instruments will provide a noticeable difference in measurements in many
circumstances. Older instruments can be upgraded to the new hardware. If you
don't want to purchase the upgrade, you can still update your instrument soft-
ware to the most current version—so you are not left behind by the new model
number.
Even if you do not upgrade your instrument hardware, you can use this manual
to guide your use of an original LI-7200. We invite you to install the new soft-
ware on older instruments. It is available for free from the LI-COR web site. We
also invite your feedback—what do you like? What do you dislike? What do you
want to measure that you can't measure now?
iv

v
Contents
A bit of history... iv
Section 1. General Information
What’s What 1-2
Spare Parts Kits 1-2
Cables 1-3
Calibration Certificate 1-5
The SmartFlux® 2 System 1-5
LI-7550 Analyzer Interface Unit 1-6
Section 2. Initial Setup
First Things First 2-1
Installing the Gas Analyzer and Components 2-4
Mounting the LI-7550 Analyzer Interface Unit 2-4
Using the Insulated Intake Tube 2-5
Using the Heated Intake Tube 2-6
Intake Tube Dimensions 2-9
Installing the 2-micron Dust Filter 2-9
Installing the Intake Cap 2-10
Mounting the Sensor Head and Intake Tube 2-12
Connecting the Sensor Head Cable 2-15
Tips for Success 2-16
Filtering 2-16
Cleaning 2-16
Vibrations 2-16
Operation in Cold Weather (<5 °C) 2-17
Extreme Humidity 2-17
Using the 7550-101 Auxiliary Sensor Interface 2-19
Mounting the ASI 2-19
Terminal Connections 2-20
Electrical Connections 2-21
Connecting Sensors to the ASI 2-21
Section 3. Operation
Installing the PC Software 3-1
Connecting with the Analyzer 3-1
Connect over Ethernet 3-1

Connect over Serial RS-232 3-3
Run Disconnected 3-4
Dashboard 3-6
Instrument Information and Logging 3-7
Instrument Status and Connectivity 3-8
Eddy Covariance Flux Graphs 3-10
Data Display 3-13
Configuring Eddy Covariance Measurements 3-16
Eddy Covariance Checklist 3-16
System Clock 3-19
Configuring the USB Log File 3-20
Entering the Site Description 3-21
Entering Anemometer Information 3-22
Entering CO2/H2O Analyzer Information 3-29
Configuring the Flow Module 3-31
Entering the Intake Tube Dimensions 3-32
Configure the Heated Intake Tube 3-33
Entering LI-7700 Information 3-33
Connect with an LI-7700 3-34
Enter analyzer information 3-34
Select variables 3-35
Entering Biomet System Information 3-36
Connecting to a datalogger 3-36
Connecting with the SmartFlux or SmartFlux 2 System 3-38
Begin Logging Data 3-44
About Data Files 3-45
About File Compression (USB Logging Only) 3-45
Transferring Logged Data 3-46
EddyPro Processing Modes on the SmartFlux System 3-48
Express Processing 3-48
Advanced Processing 3-48
SmartFlux Results Files 3-57
Section 4. User Calibration
How Stable are Zero and Span? 4-1
Checking the Zero 4-2
Checking the Span 4-3
Zero H2O 4-7
Secondary CO2 Span 4-8
Secondary H2O Span 4-9
What Actually Happens 4-9
Section 5. Maintenance
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vii
Eddy Covariance Site Maintenance Schedule 5-1
Cleaning the Optical Path 5-3
Opening the Optical Bench 5-3
Replacing the Internal Chemicals 5-4
Cleaning the Intake Cap and Screen 5-7
Maintaining the Filter 5-7
Replacing the Fuses 5-8
Power Supply Fuse 5-9
Accessory Fuse 5-9
Replacing the Thermocouples 5-9
Leak Test 5-11
Software Updates for Gas Analyzers 5-11
Embedded Instrument Software 5-12
Windows Software Update 5-14
Flow Module Maintenance 5-15
Section 6. Troubleshooting
LI-7200/RS is Identified as an LI-7500A/RS in the Software Interface 6-1
Power On Problems 6-1
Problems with the SmartFlux 2 System 6-2
Ethernet Connection Problems 6-3
Instrument not visible in software 6-3
RS-232 serial connection problems 6-4
"Port in use or does not exist" 6-4
"Not able to connect successfully" 6-4
“Parse Error” 6-4
Instrument software is unresponsive 6-5
Bad Temperature Readings 6-5
Bad Pressure Readings 6-6
Bad CO2 or H2O Readings 6-6
Section 7. Software Reference
Settings 7-1
Time 7-1
Network 7-4
Manual 7-7
Advanced—Chopper Housing Temperature 7-8
Integration 7-8
Menu Overview 7-10
Auxiliary Inputs 7-10
Outputs 7-12
RS-232 Output 7-13

Ethernet Output 7-14
DAC Configuration 7-15
SDM Output 7-16
Delay Time 7-18
Total System Delay Examples 7-19
Bandwidth 7-19
Diagnostic Value 7-20
Calibration Window Overview 7-21
Signal Strength Tab 7-22
Coefficients Tab 7-22
Manual Tab 7-23
History Tab 7-24
Changing Sensor Heads 7-24
By Hand 7-24
Automatic 7-24
PC Logging 7-26
Begin Logging Data 7-27
Note on Data Output Rates 7-27
Diagnostic Messages 7-27
General indicators 7-28
Test Point Values 7-29
Waveform 7-32
Configuration Files 7-34
Section 8. Theory of Operation
Relating Absorption to Concentration 8-1
Measuring Absorptance 8-2
Cross Sensitivity 8-3
Zero Drift 8-3
Equation Summary 8-4
LI-7200RS Implementation 8-6
A Note About Pressure And Temperature 8-7
Diagnostics 8-7
CO2 Signal Strength 8-7
Delta Signal Strength 8-10
LI-7200RS Transfer Functions and Signal Processing 8-11
Appendix A. Specifications
Appendix B. Pin Assignments
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ix
Appendix C. Suppliers
Appendix D. Configuration Grammar
Appendix E. Warranty
Appendix F. Index

x

Section 1.
General Information
The LI-7200/RS is a closed path, non-dispersive infrared CO2/H2O analyzer
designed for use in eddy covariance flux systems. Some of the LI-7200/RS's import-
ant features include:
Figure 1-1. Components of the
LI-7200/RS sensor head.
lOnboard computation of flux data in
the SmartFlux 2 System, which is
included as a standard component.
lSimultaneous, high-speed meas-
urements of CO2and H2O in the
sample cell (150 Hz) are digitally
filtered to provide true 5, 10, or 20 Hz
bandwidth.
lHigh speed measurements of pressure
in the sample cell and air temperature
at the cell inlet and outlet.
lInsulated intake tube and optional
heated intake tube.
The LI-7200/RS is designed for eddy cov-
ariance flux measurements, but it is also
suitable for profile measurements, relaxed
eddy accumulation measurements, gradi-
ent flux techniques, pCO2measurement
systems, or any other application that
depends on high-speed CO2gas or water
vapor measurements.
1-1LI-7200RS Enclosed CO₂/H₂O Analyzer

Section 1. General Information
The LI-7200/RS computes dry mole fractions of CO2or H2O in the air sample cal-
culated using high speed measurements. These variables account for changes in air
density due to the water vapor content, pressure, and temperature of the sample air.
CO2dry and H2O dry are computed as mole of gas per mole of dry air, and can be
used for computing eddy covariance fluxes without the need for density corrections
(Webb et al., 1980).
Important: There are fine-wire thermocouples that measure air temperature at
the air inlet and outlet ports. Do not insert long objects (e.g., narrow tubing or
screwdriver) into the inlet or outlet ports. Doing so will damage the ther-
mocouples.
What’s What
If you have just taken delivery of your LI-7200RS, check the packing list to verify
that you have received everything that was ordered.
Note: You need the PC software to configure the instrument. Download it from
the LI-COR technical support web site: www.licor.com/env/support. Select your
instrument and you'll find the software downloads.
Spare Parts Kits
The LI-7200/RS sensor head spare parts kit (part 7200-028) includes accessories and
replacement parts for the sensor head. The LI-7550 Analyzer Interface Unit also has
a spare parts kit (part 9975-023). It includes the cables and mounting bracket. As
you become familiar with the analyzer you will learn which items to keep close at
hand and which items can be stored away.
Description Qty. Part Number
LI-7200/RS Spares Kit 1 7200-028
Bev-a-line Tubing (4.6 m; 15 ft) 1 222-10770
Urethane Tubing (5.2 m; 17 ft) 1 222-00302
3/8-1/4” adapter 1 300-10771
Sensor Head Mounting Post (yellow dampers) 1 9972-046
Sock Tip Swabs 4 610-05315
Replacement Temperature Thermocouple 2 9972-007
1-2 LI-7200RS Enclosed CO₂/H₂O Analyzer

Description Qty. Part Number
Insulated Intake Tube (1 m) 1 9972-053
Intake Cap Assembly 1 9972-072
Swagelok 2-micron Dust Filter 2 9972-073
Hex Key (7/64") 1 610-03745
LI-7550 Analyzer Interface Unit Spares Kit 1 9975-023
Control Unit Mounting Kit 1 9979-022
RS-232 Cable 1 392-10268
Power Cable 1 9975-030
Analog Input/Output Cable 1 392-10109
Ethernet Cable (8-pin Turck® Connectors; 5 m; 16.4 ft) 1 392-10108
Ethernet Adapter Cable, 8-pin Turck to RJ45 1 392-10107
Standard Ethernet Cable (2.1 m; 7 ft) 1 616-06116
SDM Interface Cable 1 392-10093
5 Amp Fuse 2 439-04214
16 GB USB Flash Drive 1 616-10723
(Optional) Auxiliary Sensor Interface Spares Kit 1 9975-032
U-Bolt, ¼ x 20 2 184-09842
Hex Nut 4 163-00138
Santoprene (1/16” inside diameter; 0.6 m; 2 ft) 1 222-08325
Quick Connect Plug 10 300-07393
Cables
Most cables are 5 meters long. The sensor head cable can be extended to 10 meters.
The other cables can be ordered in custom lengths from the supplier (see Cables on
pageC-2) or homemade (see LI-7550 Analyzer Interface Unit on page1-6 for wire
assignments).
Power Cable
Part 9975-030. Connects to the POWER terminal on the analyzer interface unit con-
nector panel. The power cable is terminated with black (VIN-) and red (VIN+)
wires for connection to a user-supplied 10.5-30 VDC power supply (3 A or greater).
Sensor Head Cable
Part 9972-012. Connects the sensor head to the LI-7550 Analyzer Interface Unit.
One cable from the bundle connects into the connector labeled IRGA. The other
Section 1. General Information
1-3Cables

Section 1. General Information
cable plugs into the connector labeled SENSOR, and the hose plugs into the con-
nector labeled PRESSURE.
A 5-meter extension (part 9972-032)(part 392-13984) can be connected to extend
the distance between the sensor head and the LI-7550 Analyzer Interface Unit to 10
meters. Only one extension cable can be used.
Ethernet Cables
Ethernet cables are included for connection to a Local Area Network (LAN) or dir-
ectly to a computer. Part 616-06116 is a standard Ethernet cable (RJ45 connector
on both ends), 2.1 meters in length. This cable can be used to connect a computer
to the system Ethernet switch or to a port inside the LI-7550 Analyzer Interface
Unit. Part 392-10108 is a 5-meter cable terminated on both ends with a male 8-pin
Turck®connector; one end plugs into the LI-7550 Analyzer Interface Unit, and the
other end plugs into the Ethernet Adapter Cable. Part 392-10107 is a short Ethernet
adapter cable that is terminated with an RJ45 connector, and is used to connect the
5-meter Ethernet cable to an Ethernet wall socket or into your computer’s Ethernet
port.
RS-232 Serial Cable
This 5-meter null modem cable has a 6-pin female circular connector that plugs
into the RS-232 connector on the LI-7550 Analyzer Interface Unit. The other end
has a standard DB-9 female connector for direct connection to a computer. Most
modern computers will require an RS-232-to-USB adapter to use this cable. LI-COR
provides an RS-232-to-USB adapter (part 6400-27) that has been tested to work with
all LI-COR devices.
SDM Cable
Part 392-10093, for connecting to Campbell®Scientific, Inc.(Logan, UT) data-
loggers for Synchronous Device for Measurement (SDM) communications. For
more information on using this instruction refer to SDM Output (SDM Output on
page7-16) and the instruction manual for your datalogger. The SDM cable con-
nects to the connector labeled SDM on the Analyzer Interface Unit connector
panel. The other end connects to the control ports on the datalogger.
1-4 LI-7200RS Enclosed CO₂/H₂O Analyzer

Analog Input and Output Cable
Part 392-10109. Used to connect external sensors to LI-7550 analog inputs; or for
analog outputs.
When used with external input devices, this cable plugs into the connector labeled
AUXILIARY INPUT on the LI-7550 Analyzer Interface Unit connector panel. When
used for outputs, the cable plugs into the connector labeled DAC OUTPUT on the
LI-7550 Analyzer Interface Unit. If you intend to use both the Auxiliary Input and
DAC Output ports on the LI-7550, you will need the 7550-101 Auxiliary Sensor
Interface and an additional 392-10109 cable.
Calibration Certificate
Provides the calibration coefficients for your sensor head. These values are unique
to each sensor head and have been entered into the corresponding LI-7550 at the
factory. Keep this sheet in case you need to re-enter these values. You can also
acquire a copy of your calibration certificate from the LI-COR support web site.
The SmartFlux® 2 System
The SmartFlux 2 System comes standard
with your analyzer. It mounts inside a sys-
tems enclosure or another suitable enclos-
ure. This digital system includes a
computer that runs EddyPro®software for
on-site, real-time flux processing in an
eddy covariance system.
Your sonic anemometer plugs directly
into one of the three serial ports and
provides digital data and diagnostics. Gas
analyzer and biomet data is provided
through an Ethernet connection. For
more information, see the SmartFlux 2
System Instruction Manual.
Section 1. General Information
1-5Calibration Certificate

Section 1. General Information
LI-7550 Analyzer Interface Unit
The LI-7550 Analyzer Interface Unit houses the gas analyzer electronics and a con-
nector for the USB flash drive. A 16 GB industrial-rated drive is included with the
instrument. There are three Ethernet connectors inside the LI-7550, two of which
are connected to the external ports.
Figure 1-2. LI-7550 interior.
Note: Only use an industrial rated USB flash drive. Standard flash drives can fail,
causing you to lose data.
The connector panel has connectors for the sensor head and other cables.
1-6 LI-7200RS Enclosed CO₂/H₂O Analyzer

Figure 1-3. LI-7550 connector panel.
Figure 1-4. Pin assignments and wire colors for Power, SDM, Auxiliary Input and DAC
Output cables. The lower left section describes blink patterns given by the USB indicator
LEDs.
Section 1. General Information
1-7LI-7550 Analyzer Interface Unit

Section 1. General Information
1-8 LI-7200RS Enclosed CO₂/H₂O Analyzer