Manual_IRGA_LI-6400XT-v6.2.pdf

8/17/2019 Manual_IRGA_LI-6400XT-v6.2.pdf

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Using the LI-6400

Portabl

Photosynthesi

System

V e r s i o n

6

LI-6400X


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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, INCLUDINGBUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR APARTICULAR 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 parof this document may be photocopied, reproduced, or translated to another language without prior written consenof LI-COR, Inc.

© Copyright 1998 - 2012, LI-COR, Inc.Publication Number 9806-122Printing History:

1st Printing July, 1998 - OPEN Software version 3.22nd Printing May, 1999 - OPEN Software version 3.33rd Printing Sept, 2000 - OPEN Software version 3.44th Printing Sept, 2001 - OPEN Software version 4.05th Printing July, 2002 - OPEN Software version 5.06th Printing Mar, 2003 - OPEN Software version 5.17th Printing June 2004 - OPEN Software version 5.28th Printing June 2005 - OPEN Software version 5.3

9th Printing Nov 2008 - OPEN Software version 6.110th Printing Dec 2011 - OPEN Software version 6.2

Macintosh® is a registered trademark of Apple, Inc.

New editions of this manual will incorporate all material since the previous editions. Update packages may be usebetween 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).

U.S. Patent Numbers: 5,332,901 & 5,340,987. Other patents pending in the U.S. and other countries.

LI-6400XT software is subject to the following license agreements:

•binutils, busybox, dbus, gcc, glibc, linux, module-init-tools, pcmciautils, rsync, samba, u-boot, udev: GNU GeneraPublic License Version 2•sysfsutils: GNU Lesser General Public License Version 2.1•boost: Boost Software License Version 1.0•howl: Apple Public Source License Version 2.0•openssh: OpenSSH License•openssl: OpenSSL License•xxd: (c) 1990-1998 by Juergen Weigert ([email protected])•zlib: A Free License• mDNSResponder: Apache License 2.0

Software license agreements are printed at the end of Book 4.

LI-COR Biosciences, Inc. • 4421 Superior Street • Lincoln, Nebraska 68504Phone: 402-467-3576 • FAX: 402-467-2819Toll-free: 1-800-447-3576 (U.S. & Canada)


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Using the LI-6400 / LI-6400XT Version 6

Contents

Welcome to the LI-6400XTA Bit of History -xiii

About this Manual -xv

Version 6.2 Summary -xvi

Part I: The Basics

1 System Description

What it is, what it does, and how it does it An Open System 1-2

The Flow Schematic 1-4

Equation Summary 1-7

The System Components 1-13

2 Assembling the LI-6400Putting it all togetherPreparations 2-2

Using a Tripod 2-6

6400-01 CO2 Injector Installation 2-7

External Quantum Sensor Installation 2-14

Attaching the LED Light Source 2-15

6400-40 Leaf Chamber Fluorometer 2-17

Powering the LI-6400 2-18

Installing System Software 2-22

3 Guided Tours

Learning how to make it work Before You Start 3-2

Tour #1: OPEN Overview 3-5

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Contents

iv Using the LI-6400 / LI-6400XT Version 6

Tour #2: New Measurements Mode Basics 3-15

Tour #3: Controlling Chamber Conditions 3-28

Tour #4: Matching 3-52

Tour #5: Logging Data 3-61Tour #6: Configuration Introduction 3-90

4 Making Measurements

The fundamentals of good measurementsPreparation Check Lists 4-2

Some Simple Experiments 4-8

Making Survey Measurements 4-21

Light Response Curves 4-24

CO2 Response Curves 4-29

Matching the Analyzers 4-33Stability Considerations 4-41

Leaks 4-44

Operational Hints 4-50

Answers to Questions 4-56

Part II: Useful Details

5 Standard Tools

Trees, Menus, Editors, and File DialogsTree Views 5-2

Standard Menu 5-3

Standard Line Editor 5-5

Standard File Dialog 5-9

Standard Edit 5-15

Low Battery Warning 5-18

The LPL Screen 5-19

Power ON Hooks 5-23

6 New Measurements Reference

Viewing real time data using text and graphicsReal Time Text 6-3

Real Time Graphics 6-14

Diagnostics 6-24

Stability Indicators 6-29

http://theprimer.pdf/http://-/?-http://-/?-http://theprimer.pdf/http://theprimer.pdf/


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Conten


Keyboard Summary 6-35

7 Environmental Control

How OPEN controls chamber conditionsOPEN’s Control Manager 7-2

Humidity Control 7-7

CO2 Control 7-14

Temperature Control 7-18

Light Control 7-20

8 Light Sources and Sensors

The most important parameter is the hardest to measure

Why Two Sensors? 8-2Specifying the Source and Sensor 8-3

6400-02 and -02B Light Sources 8-8

6400-18 RGB Light Source 8-11


Gallium Arsenide Phosphide (GaAsP) Sensor 8-24

9 Data Logging

What you want, where you want, when you want Basic Concepts 9-2

Getting Started 9-4Determining What is Logged 9-8

Prompts and Remarks 9-20

AutoPrograms 9-31

AutoProgram Details 9-34

Making Your Own AutoPrograms 9-47

Part III: Working With Files

10 The LPL File System

Managing your data storage spaceFiles and Directories 10-2

The Filer 10-4

Filer’s Directory Operations 10-8

Filer’s File Operations 10-10

Housekeeping 10-19



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Contents

vi Using the LI-6400 / LI-6400XT Version 6

Flash Memory 10-20

11 Connecting to a Computer

Retrieving your data, and remote controlSupport Software 11-2

Connecting with Ethernet 11-7

Connecting with RS-232 11-25

Remote Control 11-29

Getting Data From Serial Devices 11-51

12 GraphIt

A tool for viewing and graphing data files

Accessing GraphIt 12-2Data File Format 12-4

Defining Plots 12-5

Selecting Observations 12-10

Curve Fitting 12-14

Viewing Data 12-18

Measuring Graphs 12-21

PlotDef File Format 12-23

Storing and Retrieving Graphics Images 12-23

13 Recomputing Data Files

How to recompute data filesA Step-By-Step Example 13-2

The Details 13-6

Hints 13-8

Part IV: Configuration Issues

14 OPEN’s System Variables

Quantities provided by OPEN

Background Information 14-2Measured Variables 14-5

Computed Variables 14-12

Time and Logging Variables 14-14

Status Variables 14-15

Boundary Layer Variables 14-20



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List of Open 6.2 System Variables 14-23

IRGA Corrections 14-27

15 Defining User Variables Adding Your Own EquationsExtras 15-2

The ComputeList File 15-14

Excel File Considerations 15-34

The Default ComputeList 15-37

16 Configuration Topics

There must be some way to do this...

Managing Configurations 16-2The Config Menu 16-4

The Configuration Tree 16-15

Matching Variations 16-19

Defining Fct Keys 16-22

Specifying Default Control Settings 16-27

Configuring Spare Channels 16-29

Hooking Events 16-37

Adding an External Temp, RH Probe 16-43

Configuring for Alternative Materials 16-51

Interfacing Custom Chambers 16-56

Custom Chamber - Closed 16-73

17 Using an Energy Balance

Computing what you can’t measureThe Theory 17-2

Using Energy Balance in OPEN 17-6

Measuring Boundary Layer 17-9

Further Reading 17-11

Part V: Maintenance & Troubleshooting18 Calibration Issues

The difference between data and good data.Managing Calibration Data 18-2

CO2 and H2O Analyzers 18-10



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Contents

viii Using the LI-6400 / LI-6400XT Version 6

Flow meter 18-23

Zeroing the Leaf Temperature Thermocouple 18-24

6400-01 CO2 Mixer 18-25

Internal PAR Sensor (General) 18-296400-02(B) LED Source 18-30

6400-18 RGB Light Source 18-34


GaAsP Light Sensors 18-38

19 Maintenance & Service

The care and feeding of your new pet Chemical Tubes 19-2

6400-03 Batteries 19-8

System Console 19-10Real Time Clock 19-18

Cables 19-19

The Chamber Handle 19-20

Leaf Temperature Thermocouple 19-24

Leaf Chambers 19-26

LED Source Maintenance 19-28

Match Valve Maintenance 19-29

IRGA Maintenance 19-32

Servicing the External CO2 Source Assembly 19-38

Shipping The LI-6400 19-41Useful Part Numbers 19-42

20 Troubleshooting

When things go wrongPower On Problems 20-2

Real Time Clock Problems 20-5

New Measurements Mode Warning Messages 20-5

Unreasonable Results 20-9

Pump/Flow Problems 20-13

IRGA Problems 20-14Match Valve Problems 20-22

6400-01 CO2 Mixer Problems 20-24

Light Source / Sensor Problems 20-30

6400-18 RGB Source 20-34



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Chamber Problems 20-39

Finding Leaks 20-44

Soil Chamber Problems 20-49

Useful Information 20-50

21 Diagnostics and Utilities

Useful programsDiagnostics & Tests Menu 21-2

/Sys/Utility Programs 21-11

Part VI: Programming

22 Programming with LPL An introduction to the LI-6400’s programming languagOverview of LPL 22-2

Making Objects 22-7

Functions 22-12

Pointers 22-17

Public and Static 22-22

Compiler Directives 22-25

23 LPL Topics

Programming with LPLStack Control 23-2

Conditionals and Loops 23-4

Array Operations 23-6

Math Functions 23-18

Display Control 23-23

Keyboard Control 23-29

Clock 23-31

Event Handling 23-33

The Function Keys 23-36

I/O Programming 23-38

File System 23-47

Networking in LPL 23-51

Menus and Editors 23-53

ListBox 23-58

Real Time Graphics 23-59

http://-/?-http://-/?-http://-/?-


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x Using the LI-6400 / LI-6400XT Version 6

Graphics 23-61

Serial Communications 23-69

Analog Measurements 23-71

Analog Output Control (D/A) 23-78Digital I/O 23-80

XML Support 23-82

Registered Variable Support 23-83

Curve Fitting Support 23-84

Application Tools 23-85

Excel Tools 23-89

Miscellaneous Tools 23-89

24 LPL Reference

Keyword SummarySyntax Summaries 24-2

Definitions 24-12

The Reference 24-17

25 AutoProgramming Reference

Making them do what you what them to doAutoprogram Format 25-2

Some AutoProgram Listings 25-4

Useful AutoProgram Commands 25-15

AutoPrograms and the Control Manager 25-30Low Level Control Tools 25-30

26 Customizing Open

“Cry ‘Havoc’ - and let slip the dogs of war”XML Templates 26-2

System Variable Definitions 26-9

Useful Variables 26-12

Open’s Hooks 26-14


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Part VII: Accessories

27 Leaf Chamber FluorometerUsing the 6400-40 Leaf Chamber FluorometerGetting Started 27-2

Background Information 27-3

Installing the LCF 27-11

Operational Summary 27-17

Using the MultiPhase Flash 27-40

LI6400XTerm and the LCF 27-48

Basic Experiments 27-53

Fluorescence AutoPrograms 27-71

Calibration Issues 27-73LCF Troubleshooting 27-82

LCF Reference 27-86

Chlorophyll Fluorescence References 27-93

28 Soil CO2 Flux Chamber

Using the 6400-09 Soil ChamberIntroduction 28-2

Attaching the Soil Chamber 28-7

Software 28-20

Making Measurements 28-29Data Files 28-35

Troubleshooting the Soil Chamber 28-39

Maintenance 28-41

Equation Derivation 28-44

Soil Chamber Specifications 28-49

A License Agreements

The fine print Apache A-2

GNU General Public License A-4GNU Lesser General Public License A-10

Boost Software License A-18

Apple Public Source License A-18

OpenSSH A-24

OpenSSL A-30

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Contents

xii Using the LI-6400 / LI-6400XT Version 6

Free License Agreement A-32

INDEX


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Welcome to the LI-6400XT

A Bit of HistoryThe LI-6400 is LI-COR’s third generation gas exchange system. In the bning was the LI-6000; it used a third-party CO2 analyzer having the nove

1983) features of small size, light weight, and low power. Photosynthesi

computed by measuring the rate of change of CO2 with time with a leaclosed in a relatively large chamber - a closed system. The LI-6000 was

ited by the signal noise of the analyzer (1-2 µmol mol-1) and an unfortuchoice of method for computing slopes. These problems were correct1986 in the LI-6200, which sported LI-COR’s first CO2 analyzer and m

improved software. It was still a closed system for CO2, but had the pote

for steady-state transpiration measurements. The steadiness of the state, ever, depended heavily on a motivated, attentive operator continually ading a knob.

While the LI-6200 was fairly well suited for survey measurements, a gronumber of customers (and potential customers) were looking to answer der questions. The deeper answers could be found in response curves, andmeant using a system that could control the environmental quantities imtant to photosynthesis: CO2, light, humidity, and temperature. Several

vators attempted to do various response curves with the LI-6200, varying degrees of success. Meanwhile, we were having a very hard timour attempts to transform that instrument into a next-generation system

By 1990, having abandoned the idea of enhancing the LI-6200, we restwith the question: “What would the ideal gas exchange system be likewould do response curves, of course, so it would need the ability to co

chamber conditions. To us, ideal response curves meant labor-free respcurves, so manual controls were out, computer controls were in. Respcurves should be seen, not imagined, so we needed built-in graphical capity. The ideal system would also do survey measurements: you should beto carry it around, clamp onto a leaf using only one hand (our previoustems needed two or three), and be done with the measurement quickly. Q


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Welcome to the LI-6400XT A Bit of History

xiv Using the LI-6400 / LI-6400XT Version 6

tions of weight, power, and compactness thus emerged. Could the capabilitieof a laboratory system (response curves) be squeezed into a field system (survey measurements)?

Challenges loomed, two of them formidable: CO2 and H2O control is don

best by having gas analyzers right in the leaf chamber, but suitable IRGAs didnot exist. Secondly, chamber CO2 could in principle be controlled by mixing

scrubbed air and pure CO2 (available in very portable 12 gram cylinders), bu

again, a suitable mixing device did not exist. So, we set about inventing them

Five years and one name change1 later, we shipped the first LI-6400 - andmany more since then. We’ve kept working on it, too, adding many innovations and enhancements, including soil respiration and a leaf chamber fluorometer.

In 2002 we changed the digital board (200 MHz processor, Linux operatingsystem, 128 MBytes memory, 64 MByte file system), and brought out version5 software, opening the door to many exciting new possibilities.

2007 brought the LI-6400XT, which was another digital board change, withversion 6 software, a 400 MHz processor, and an expansion slot for flashmemory or Ethernet connectivity, making possible remote control of multiplunits, and seamless integration of LI-6400XT consoles into local area networks. Data file recomputation got simpler: version 6 added the capability ogenerating data files as binary Excel files, with the equations built-in.

Old units continue to be upgradable. LI-6400s with the 200 MHz board (i.eversion 5 software) are able to run version 6 with just a software change. Iyou want the expansion slot capability, then you can turn any LI-6400 into anLI-6400XT with an upgrade kit. Thus, in the nearly 15 year history of theLI-6400, we haven’t left any users behind; their investment remains solid.

We thank you for your investment, and trust that this instrument will serveyou well. We stand ready with support and help as you put it to work. Welcome to the LI-6400XT.

1.It started out as the LI-6300.


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Welcome to the LI-6400X About this Man


About this ManualWhen confronted with a new instruction manual, most people turn to thetion named “About this manual” for one simple reason: to find out how mthey can skip. Since this manual has 28 chapters, you are probably eagskip most of them.

You’re in luck. You can.

Where to Start? Select the category that best describes you, and follow the suggested itary.

• Experienced with earlier versions of the LI-6400Read Version 6.2 Summary on page xvi.

• New to the LI-6400; new to gas exchange; methodical and thoroughWork through Chapters 1, 2, 3, and 4. You’ll understand the LI-6400 anfundamentals of making measurements fairly well by the end. Then, ifare also doing fluorescence, Chapter 27.

• New to the LI-6400; new to gas exchange and/or fluorescence; and fimpatientChapter 2: Assembling the system.Chapter 3: The minimum for learning the software is:

Tour #1, Stop after Step 5.Tour #2, The whole thing.Tour #3, Experiments 1, 2, and 5.Tour #4, Experiments 1 through 3

Chapter 4: Do the check lists, and the simple experiments.Chapter 27: Fluorescence.Having measured some leaves (and satisfied your impatience), you mwant to go back and pick up the parts you skipped in Chapters 3 and 4.

• New to the LI-6400, experienced at gas exchange measurementsSkim Chapter 1.Chapter 2: Assembling the system.Chapter 3: Tours 1 through 5.Chapter 4: The check lists are important; pick and choose after that.Chapter 27: How to connect and operate the LCF.

Electronic version This manual is also available as an Adobe® Acrobat® file, on CD and our web site (www.licor.com). All cross references in the text, table oftents, and index are hyper-linked, allowing one-click access.


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Welcome to the LI-6400XT Version 6.2 Summary

xvi Using the LI-6400 / LI-6400XT Version 6

Version 6.2 Summary

There are a number of interface changes that came with OPEN 6.2, and thmajor ones are summarized here. If you are familiar with earlier versions oOPEN, then this summary will get you started very quickly.

Version 6.2 can run on either the third generation 400MHz LI-6400XT, or thsecond generation 200 MHz board (currently running version 5.x).

Controlling Flow, CO2, Temperature, LightThe “control panels” in New Measurements mode are a bit different in version 6.2. The differences are summarized below, and fully described in Interface Fundamentals on page 7-3.

Old Style: New Style:

1. It’s a modal dialog now.

2. Edit the Control node to getall the options.

3. The dialog adapts to theselected control type. Here isVPD, for example.

4. Shortcuts: T and O.O - (for Off): Turns off the control and exits.T - enter new target value, and exit.


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Welcome to the LI-6400XVersion 6.2 Summ


Constant CiOne of the CO2 Control options is to maintain a constant Ci.

You would use this option to try and maintain Ci while varying some

ronmental parameter (other than CO2) such as light. See Intercellular

on page 7-17.

New Log OptionsVersion 6.2 brings two new Log Options:

Means→→→→log fileNormally when you log data, the values recorded are averaged over a fshort time period, typically 4 seconds or less. When the Means→log filtion is enabled, what is logged can be much longer, such as the 15 seconthe above example. See ...Means→→→→Log File on page 9-16.

Control Changes

When the Control Changes option is enabled, anytime you have a logopen, and a control (flow, CO2, temperature, or light) changes, the chan

logged in the log file as a remark. See Control Changes on page 9-17.

Old Options: New Options:


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xviii Using the LI-6400 / LI-6400XT Version 6

AutoProgramsVersion 6.2 brings a number of changes to AutoPrograms, as summarized below. For details, see AutoPrograms on page 9-31.

‘Pick From List’ PromptsVersion 6.2 adds a new type of Prompt. This feature lets you pre-enter a lisof strings (complicated plot identifiers, etc.), and when you are prompted foone, you can pick it from the list. You can also modify your list on the fly. Se

‘Pick From List’ Prompts on page 9-25.



2. The input is contained in aneditable tree, with nodes you

can expand as needed.

5. Stability and Log Options arepart of the input setup.

4. New and improved matchingoptions (on, off, conditional).

3. The programs adapt to what-ever light source you are using.in this case, it is an LCF.

6. Read / Write your setup tonamed files.


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Welcome to the LI-6400XVersion 6.2 Summ


New Configuration BuilderThe interface for building configurations (Config Menu | New...) has evofrom sequential questions to a dialog.

Improved IRGA ZeroVersion 6.2 simplifies the method of zeroing that eliminates the long wai

the sample cell to flush (and dry) out. See Setting the CO2 and H2O on page 18-11.



2. Edit Material to generate a mass-based configurationany chamber. See The Material= Node on page 16-5

1. With the matchvalve off, zero thereference (only)analyzers.

2. With the matchvalve on, make thesample IRGAs matchthe reference.


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xx Using the LI-6400 / LI-6400XT Version 6


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1System Description

What it is, what it does, and how it does it

AN OPEN SYSTEM 1-2

Measuring Differentials 1-2

The Air Supply 1-3

Leaks 1-3

THE FLOW SCHEMATIC 1-4Matching the IRGAs 1-6

EQUATION SUMMARY 1-7

Transpiration 1-7

Total Conductance to Water Vapor 1-8

Stomatal Conductance to Water Vapor 1-9

Net Photosynthesis 1-9

Intercellular CO2 1-11

Everything Else 1-11

Summary of Symbols 1-12

THE SYSTEM COMPONENTS 1-13

The Standard Parts 1-14

The Optional Accessories 1-16


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System Description

1-2 Using the LI-6400 / LI-6400XT Version 6

1 This chapter acquaints you with the LI-6400XT’s operating principle, majocomponents, and how it computes gas exchange quantities.An Open System

Measuring Differentials

The LI-6400 is an open system, which means that measurements of photosynthesis and transpiration are based on the differences in CO2 and H2O in an ai

stream that is flowing through the leaf cuvette (Figure 1-1).

Sample IRGA

Reference IRGA

Flow x ∆CO2

AreaPhoto = Trans =

Flow x ∆H2O

Area

Figure 1-1. In an open system, photosynthesis and transpiration are computed from the differences in CO2 and H 2O between in-chamber conditions and pre-

chamber conditions. The equations are given in Equation Summary on page 1-7 .

Sample IRGA

Reference IRGA

FlowMeter

FlowMeter

Traditional Open System

LI-6400XT

Console

Console

Cuvette

Cuvette


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System Descripti An Open Sys


The LI-6400 improves upon traditional open systems by having the gaslyzers in the sensor head. This eliminates plumbing-related time delaysallows tight control for responding to leaf changes. For example, if sto

close, the control system immediately detects the drop in water vapor ancompensate. Similarly, a sudden change in light level will cause an immate change in photosynthetic rate, which will be detected as a change iCO2 concentration. The speed of detection is not a function of the syst

flow rate, as in traditional systems, since the sample IRGA is in the cuv

There is a second advantage of having the IRGAs in the sensor head. Thditional system has the potential for concentration changes (because of wsorption and CO2 diffusion) as the air moves from the reference IRGA t

chamber, and again from the chamber back to the sample IRGA. This ia problem for the LI-6400, because the IRGA measurements are made

the air has travelled through the tubing.

The Air SupplyOne strength of an open system is that the incoming air stream can be ctioned. That is, its humidity, CO2 concentration, temperature, etc. can b

tablished by some means prior to entering the system.

Regardless of what is done to the incoming air, however, one thing is cru

This is especially true for CO2, where the potential for fluctuations is

(your breath, for example, is typically 30,000 µmol CO2 (mol air)-1. Fl

ations in incoming concentration will cause concentration differences very erratic.

Leaks“Pressure inside the leaf chamber is slightly above ambient to ensureleaks are outward, so outside air does not enter the chamber and affec

CO2 and H2O concentrations.” This argument for the advantage of an system has been made for a long time, and it’s true - as far as it goes. Tis another process at work: diffusion. CO2 will always diffuse from h

concentrations toward lower, even against a pressure gradient, and islimited by the material through which it is moving. The black neoprenekets that we use on the LI-6400 (except for the light source) have the lo

Incoming concentrations must be stable.


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System Description The Flow Schematic


1

diffusivity to CO2 of all the gasket material we have tested, but it’s not per

fect. Diffusion effects are measurable at low flow rates when there is a largconcentration difference between chamber and ambient. See Diffusion

Leaks on page 4-44 for more details.

The Flow SchematicThe LI-6400 provides mechanisms for modifying the incoming air’s CO2 an

H2O concentrations (Figure 1-2 on page 1-5). There are chemical tubes fo

scrubbing CO2 and H2O, and air can be diverted through these tubes in any

proportion desired. CO2, however, is best controlled by scrubbing all of i

from the incoming air, and using the 6400-01 CO2 mixer to inject just enough

CO2 to provide a stable concentration at the desired value. If the 6400-01 i

not part of your system, you will need to use a buffer volume. For a morecomplete discussion of buffer volumes, see Air Supply Considerations onpage 4-50.

Humidity control in the leaf cuvette is achieved by regulating the flow ratthat is going though the cuvette. In units without a CO2 mixer, the pump

speed controls the flow, and in units with a CO2 mixer, a flow diverter regu

lates this flow.


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System DescriptiThe Flow Schem


75%

Flow

Flow Meter

Bypass Valve

Bypass Valve

Restrictors

Desiccant

CO2 Scrubber

Sample

Reference

Air In

Pump

25%

75%25%

CO2

FlowControl

AirFlowControl

Pump

CO2

Flow

Flow Meter

Vent

Bypass Valve

Bypass Valve

Liquid CO2

Vent

Restrictors

Desiccant

CO2 Scrubber

P u r e C O 2

Sample

Reference

Air In

Figure 1-2. LI-6400XT flow schematic, with and without a 6400-01 CO2 mixer.

Schematic with a 6400-01 CO2 Mixer

Schematic without a 6400-01 CO2 Mixer


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System Description The Flow Schematic


1

Matching the IRGAsThe heart of the computation of transpiration and assimilation is the measurement of the concentration differences. Since these differences are measured

by two independent infra-red gas analyzers, provisions must be made tocheck the IRGAs against one another. One way to do this is to compare theIRGAs when the leaf chamber is empty, and adjust one so that they matchMatching in this manner is a problem, however, because you don’t want toremove the leaf from the chamber in the middle of an experiment. ThLI-6400 provides a mechanism to match the IRGAs without disturbing theleaf: it is called match mode, and it is illustrated in Figure 1-3.

Match mode is something that you do at least once at the start of the day, andperiodically throughout the day. Matching is important when the ∆CO2 o

∆H2O value is small (low rates, small leaf areas). For example,

1 µmol mol-1 difference between the two CO2 IRGAs is trivial when th

∆CO2 is 75 µmol mol-1, but represents a significant error if the ∆CO2 is only

3 µmol mol-1.

Figure 1-3. In Match Mode, leaf chamber air is measured by both sample and ref-erence IRGAs, allowing the sample IRGA to be adjusted to match the reference IR-

GA.

SampleReference

Normal

SampleReference

Match


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System Descripti Equation Summ


Equation SummaryIf you are not interested in the details of the LI-6400’s gas exchange caltions, you can safely skip this section.

The equations for net photosynthesis, transpiration, etc. are essentially

derived by von Caemmerer and Farquhar1. Note also that these equationsresent the instrument’s defaults, and can be modified or replaced as deby the user (Chapter 15).

TranspirationThe mass balance of water vapor in an open system (Figure 1-4) is give

where s is leaf area (m2), E is transpiration rate (mol m-2 s-1), ue and u

incoming and outgoing flow rates (mol s-1) from the chamber, and we an

are incoming and outgoing water mole fractions (mol H2O mol air-1). S

we can write

1.S.von Caemmerer and G.D.Farquhar (1981) Some relationships betwee

biochemistry of photosynthesis and the gas exchange of leaves, Planta 153

387.

ue uo

E

Figure 1-4. Measuring fluxes in an open system. Transpiration rate (E) and ptosynthetic rate (a) change the water and CO2 concentrations of air as it pas

through the chamber. Transpiration also causes the exit flow uo to be greater t

the incoming flow rate (ue).

we wo

a

ce co

sE uowo uewe –=

uo ue sE +=

sE ui sE +( )wo uewe –=


28/1320

System Description Equation Summary


1

which rearranges to

(1-4

The relationships between the terms in (1-4) and what the LI-6400 measureare

(1-5

where F is air flow rate (µmol s-1), W s and W r are sample and reference wate

mole fractions (mmol H2O (mol air)-1), and S is leaf area (cm2). The equa

tion that the LI-6400 uses for transpiration is thus

(1-6

Total Conductance to Water VaporThe total (includes stomatal and boundary layer) conductance of the leaf gtw

(mol H2O m-2 s-1) is given by

(1-7

where W l is the molar concentration of water vapor within the lea

(mmol H2O (mol air)-1), which is computed from the leaf temperature T l (Cand the total atmospheric pressure P (kPa)

(1-8

E ue wo we –( )

s 1 wo –( )-----------------------------=

ue F 106

⁄ =

we W r 103

⁄ =

wo W s 103

⁄ =

s S 104 ⁄ =

E F W s W r –( )

100S 1000 W s –( )-------------------------------------------=

gtw

E 1000W l W s+

2-------------------- –

W l W s –------------------------------------------------=

W l

e T l( )

P------------ 1000×=


29/1320



The function e(T) is saturation vapor pressure (kPa) at temperature T (C)formula used by the LI-6400 is (14-24) on page 14-13.

Stomatal Conductance to Water VaporThe stomatal conductance gsw to water vapor (mol H2O m

-2 s-1) is obta

from the total conductance by removing the contribution from the bounlayer.

where k f is a factor based on the estimate K of the fraction of stomatal

ductances of one side of the leaf to the other (termed stomatal ratio throout this manual),

(

and gbw is the boundary layer conductance to water vapor (mol H2O m

from one side of the leaf. The boundary layer conductance correction thupends on whether the leaf has stomata on one or both sides of the leaf.

Net PhotosynthesisThe mass balance of CO2 in an open system is given by

(

where a is assimilation rate (mol CO2 m-2 s-1), ce and co are entering and

going mole fractions (mol CO2 mol air-1) of carbon dioxide. Using (1-2

can write

(

which rearranges to

gsw1

1

gtw--------

k f

gbw--------- –

-----------------------=

k f K

21+

K 1+( )2

---------------------=

sa uece uoco –=

sa uec

eu

esE +( )c

o –=


30/1320



1

(1-13

To write (1-13) in terms of what the LI-6400 measures, we use (1-5) and

(1-14

where C r and C s are sample and reference CO2 concentration

(µmol CO2 (mol air)-1), and A is net assimilation rate of CO2 by the lea

(µmol CO2 m-2

s-1

). Substitution yields

(1-15

Eqn (1-15) was used by the LI-6400 until version 6.0. To get to the new equation, we substitute for E from (1-6) to get

(1-16

which reduces to

(1-17

Why does transpiration (or W r and W s in (1-17)) appear in the equation fo

photosynthesis? (Asking this question means you didn’t follow the derivation…) The short answer is that it serves as a dilution correction; as the lea

adds water vapor to the chamber, it dilutes all other gasses, including CO2.

aue ce co –( )

s-------------------------- Eco –=

ce C r 106

⁄ =

co C s 106

⁄ =

a A 106

⁄ =

AF C r C s –( )

100S --------------------------- C s E –=

A

F C r C s – C sW s W r –

1000 W s –-------------------------

–

100S ------------------------------------------------------------------------=

A

F C r C s

1000 W r –

1000 W s –-------------------------

–

100S ------------------------------------------------------------=

http://-/?-http://-/?-


31/1320



Intercellular CO2The intercellular CO2 concentration C i (µmol CO2 mol air

-1) is given b

(

where gtc is the total conductance to CO2, and is given by

(

1.6 is the ratio of the diffusivities of CO2 and water in air, and 1.37 is the

ratio in the boundary layer.

Everything ElseThere are many other relationships that the LI-6400 uses (calibration etions for sensors, dew point temperatures, relative humidity, etc.), whicdocumented in Chapter 14.

C i

gtc E

2--- –

C s A –

gtc E

2---+

---------------------------------------=

gtc1

1.6

gsw

--------1.37k f

gbw

----------------+

--------------------------------=


32/1320



1

Summary of Symbolsa = net assimilation rate, mol CO2 m

-2 s-1,

A = net assimilation rate, µmol CO2 m-2

s-1

ce = incoming CO2 concentration, mol CO2 mol air-1.

co = outgoing CO2 concentration, mol CO2 mol air-1.

C s = mole fraction of CO2 in the sample IRGA, µmol CO2 mol-1 air

C r = mole fraction of CO2 in the reference IRGA, µmol CO2 mol-1 air

C i = intercellular CO2 concentration, µmol CO2 mol air-1

E = transpiration, mol H2O m-2 s-1

F = molar flow rate of air entering the leaf chamber, µmol s-1

gbw

= boundary layer conductance to water vapor, mol H2O m-2 s-1

gsw = stomatal conductance to water vapor, mol H2O m-2 s-1

gtc = total conductance to CO2, mol CO2 m-2 s-1

gtw = total conductance to water vapor, mol H2O m-2 s-1

k f = (K2 + 1)/(K + 1)2,

K = stomatal ratio (dimensionless); estimate of the ratio of stomatal conductances of one side of the leaf to the other

s = leaf area, m2

S = leaf area, cm2

ue = incoming flow rate, mol air s-1.

uo = outgoing flow rate, mol air s-1

.we = incoming H2O mole fraction, mol H2O mol air

-1.

wo = outgoing H2O mole fraction, mol H2O mol air-1.

W s = sample IRGA mole fraction of water vapor, mmol H2O mol air-1.

W r = reference IRGA mole fraction of water vapor, mmol H2O mol air-1.

W l = mole fraction of water vapor within the leaf, mmol H2O mol air-1.


33/1320

System DescriptiThe System Compon


The System ComponentsIf you have just taken delivery of your LI-6400XT check the packing lverify that you have received everything that you ordered. Or, if you’veinherited an LI-6400 from someone else, check to see that you have ething. Here’s a brief description of what should be there:

Figure 1-5. The LI-6400XT Portable Photosynthesis System.

Console

Sensor Head/IRGA

(Optional)

Chemical Tubes

Cable Assembly

CO2 Cartridge Holder and

Regulator (Optional)

6400-40 LCF


34/1320

System Description The System Components


1

The Standard Parts

Console

The console has an environmentally sealed, 64-key, full ASCII keypad and 8line × 40 character LCD. On the right side of the console are the sensor headconnectors, 6400-03 battery compartments, and RS-232C connector. CO

scrubber and desiccant tubes attach to the left side of the console, along withthe optional 6400-01 CO2 source assembly or CO2 tank connector block. A

field stand is normally attached to the underside of the console.

Sensor Head/IRGAThe sensor head/IRGA includes a leaf chamber, spring-loaded latching handle (squeeze and release to open, squeeze and release to close), two Peltiethermoelectric coolers, and the sample and reference gas analyzers. Up to two

light measurements are provided for: most leaf chamber tops have a GalliumArsenide Phosphide (GaAsP) PAR sensor, and a mounting fixture is providedfor a 9901-013 external quantum sensor, if desired. (For a discussion of thelogic of using two light sensors, see Why Two Sensors? on page 8-2.) Leatemperature is measured with a thermocouple held in the bottom of the 2x3and 2x6 cm leaf chambers; other chambers use energy balance to computeleaf temperature.

Cable AssemblyThe cable assembly has two electrical cables and two air flow hoses, and connects the console to the sensor head / IRGA. These are held together with a

flexible, outer wrapping.

Spare Parts KitThis box contains replacement parts for your LI-6400. As you become familiar with the system you will learn which items to keep close at hand and whichitems can be safely stored away.

Chemical TubesThese tubes are used during operation to remove CO2 and water vapor from

the incoming air stream. One tube should contain soda lime, and the othetube should contain Drierite, a desiccant. Each tube has an adjustment valveat the top for partitioning the flow through the chemical contained in the tube

6400-03 Rechargeable BatteriesThe 6400-03 Rechargeable Batteries are shipped tested and fully chargedBecause they slowly self-discharge with time, it is a good idea to test youbatteries periodically. Leaving them discharged for an extended period canresult in damage. (See 6400-03 Batteries on page 19-8 for instructions con


35/1320



cerning testing and charging batteries.) One 6400-03 battery provides appimately 1-2 hours of operational life. Recharge them with the LI-6020 BaCharger.

LI-6020 Battery ChargerThe LI-6020 can charge four 6400-03 Rechargeable Batteries simultanly. It runs on 92-138/184-276 VAC, 47 to 63 Hz, but a selector switch oback of the LI-6020 must be set to the appropriate mains voltage. Theships with no fuse installed - install the correct fuse based on your mainsage (0.5A for 115 V, 0.25 A for 230 V).

RS-232C CablePart number 9975-016 has a 9 pin to 9 pin cable, and a separate 9 to 25adapter. Figure 11-27 on page 11-25 illustrates how to use it.

6400-25 Compact Flash Memory CardCan be installed in the expansion slot in the XT console.

6400-26 Ethernet Adapter CardFor use in the expansion slot in the XT console.

Field StandWhen shipped from the factory, the LI-6400’s field stand base plate tached to the bottom of the console. It normally remains there, and youattach or detach the legs as needed. Store the legs in the narrow front slthe carrying case.

6400-60 CDThe CD contains a hyper-linked, electronic version (.pdf file) of this maplus a number of support programs for tasks such as (re-)installing instrusoftware, and remotely controlling the LI-6400 from a computer. Seeport Software on page 11-2. Note: New versions of all of our softwarreleased periodically. You can get the most recent version by contaLI-COR, or by downloading it from our web site (www.licor.com).

Calibration SheetThis data sheet lists the calibration information entered into the LI-6400

factory. Keep it in a safe place for future reference.

Carrying CaseThe hard-shell, foam padded carrying case can hold the console, sensor cables, some batteries, legs, and a few other accessories.

http://www.licor.com/http://www.licor.com/http://www.licor.com/http://www.licor.com/http://www.licor.com/http://www.licor.com/


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1

The Optional AccessoriesThere are several optional accessories that you may have ordered with youLI-6400. Any of them can also be purchased later, and (with the exception o

the 6400-01 CO2 Mixer), they do not require factory installation:

6400-01 CO2 MixerThis consists of three components:

• A control module that is inside the consoleThis part is factory installed in the console.

• A cartridge holder and regulatorFor use with the disposable 12 gram CO2 cartridges, this part is user-install

able between the chemical tubes on the outside of the console (see Figure 2-

on page 2-8).

• An adapter block for CO2 tanks

This alternative to the cartridge holder and regulator allows tanks of compressed pure CO2 to be used instead of the 12 gram cartridges (see Figure 2-

on page 2-11).

6400-02B LED Light SourceThe 6400-02B replaces the top half of the standard leaf chamber and provide

light from 0 to over 2000 µmol quanta m-2 s-1. The intensity of the light i

software adjustable to a resolution of 1 µmol m-2 s-1. The 6400-02B replace

the 6400-02, which used only red LEDs. See Spectral Considerations onpage 8-8 for a comparison of the 6400-02 and 6400-02B.

6400-05 Conifer ChamberA cylindrical chamber suitable for short-needled shoots. Leaf temperature iobtained by energy balance, for which an external PAR sensor reading is required. (External PAR sensor not included with this option.)

6400-07 Needle ChamberA 2x6 cm chamber with Propafilm® top and bottom windows. Leaf temperature is not measured, but is computed using an energy balance. A GaAsPlight sensor is included.

6400-08 Clear-Bottom ChamberA 2x3 cm chamber bottom with a Propafilm® window. Leaf temperature icomputed using an energy balance. This chamber can be used with any 2xcm chamber top (such as the fluorometer adapters) or 6400-02 or -02B LEDsource.


37/1320



6400-09 Soil ChamberFor measuring soil CO2 efflux.

6400-11 Narrow Leaf ChamberA 2x6 cm chamber with a Propafilm® top window, and an opaque bothat holds the 6400-04 leaf temperature thermocouple. A GaAsP light seis included.

6400-13 Thermocouple AdapterAllows a type E thermocouple to be connected to the 37 pin connector oLI-6400 console. This adapter is included with the 6400-09 Soil Chamb

6400-15 Extended Reach 1 cm ChamberThis is a chamber designed for Arabidopsis and other small leaves. The

ture is 1.0 cm in diameter, and has a Propafilm® top and bottom. No lighsor is included. Leaf temperature comes from an energy balance analysiwhich an external quantum sensor is necessary (but not included).

6400-17 Whole Plant Arabidopsis ChamberCircular chamber, 7 cm diameter, for whole plant measurements of plansmall pots.

6400-18 RGB Light SourceDesigned for the 6400-17 chamber, but can be used on other chambers.

6400-22 Opaque Conifer Chamber

Accommodates short needle shoots. Designed for use with the 6400-18 Light Source. Top shell of chamber is clear, bottom is opaque.

6400-24 Bryophyte ChamberThis is the 7 cm diameter 6400-17 with a solid bottom, making it suitabmeasuring unattached clumps of whatever material you’d care to drop in

6400-40 Leaf Chamber FluorometerChapter 27 covers installation and operation of this accessory.

6400-70 AC Adapter

This optional accessory fits in the battery compartment, and allowLI-6400 to be powered from mains power. It can simultaneously (but slorecharge one battery.

9901-013 External Quantum SensorA LI-COR LI-190SA quantum sensor can be mounted on the sensor h(The 9901-013 is an LI-190SA with a short cable.)


38/1320



1

Display BacklightIf installed, the display backlight is toggled on and off by holding down shif+ ctrl then pressing home.


39/1320


2Assembling the LI-6400

Putting it all together

PREPARATIONS 2-2

The CO2 Scrub and Desiccant Tubes 2-2

Cables And Hoses 2-3

Connecting the Chamber / IRGA 2-5

USING A TRIPOD 2-6

6400-01 CO2 INJECTOR

INSTALLATION 2-7

Using CO2 Cartridges 2-8

External CO2 Tanks 2-10

EXTERNAL QUANTUM SENSOR

INSTALLATION 2-14

ATTACHING THE LED LIGHT

SOURCE 2-15

6400-40 LEAF CHAMBER

FLUOROMETER 2-17

POWERING THE LI-6400 2-18

LI-6020 Battery Charger 2-18

6400-03 Batteries 2-18

Other Batteries 2-19

6400-70 AC Module 2-20

INSTALLING SYSTEM SOFTWARE 2-22

Hardware Requirements 2-22


40/1320

Assembling the LI-6400


2 This chapter guides you through the assembly and preparations necessary tooperate the LI-6400.Preparations

This section explains how to prepare the console and sensor head for operation.

The CO2 Scrub and Desiccant TubesThe CO2 scrub and desiccant tubes can remain attached to the console at al

times, except when changing chemicals. Figure 2-1 shows the position othese tubes.

Caution: Never unscrew the top cap while a tube is full of chemicals. Tochange the chemical, grasp the tube barrel (not the top cap) and unscrew thbottom cap. If the top cap is unscrewed with chemicals inside, damage to thair mufflers will occur.

Remove the bottom cap of the CO2 scrub tube, and fill the tube with soda lim(in the spares kit) to within 1 cm of the tube’s end. Replace the bottom capand attach the tube to the console using the lower of the two knurled knobs.

Follow the same procedure with the desiccant tube. Indicating Drierite desiccant is provided in the spares kit.

Complete information on maintenance and service of the chemical tubes ifound on page 19-2.

Keep the threads on the end cap and barrel clean

Do not over-tighten the attachment screws (Figure 2-1). Slightly

snug (finger power only - never pliers) is sufficient. The O-rings dothe sealing.


41/1320

Assembling the LI-64Preparat


Cables And HosesAir inlet and outlet ports and electrical connectors are located on the righ(end) of the console (Figure 2-2).

Electrical ConnectorsPlug the female 25-pin connector into the receptacle labeled IRGA, anmale 25-pin connector into the receptacle labeled CHAMBER. These contors are gender specific, and cannot be interchanged. Tighten (slightlyscrews on the connectors, but be careful: these screws can break off if tened too much. See Replacing Connector Screws on page 19-19.

Air InletThe port labeled INLET is located to the right of the ON/OFF switch. Tthe intake through which the pump draws in the air that flows through thetem.

If your system does not have a CO2 injector, attach tubing from a buffer

ume to the INLET port. The buffer volume can be as simple as a clean, dliter plastic soft drink bottle. The larger the volume, the better. For mortails, see Air Supply Considerations on page 4-50.

Figure 2-1. Desiccant and CO2 scrubber tubes.

Desiccant Tube

CO2 Scrub Tub

Air Passage Holes

O-Rings

Open This End

Don’t Over-Tighten


42/1320

Assembling the LI-6400 Preparations


2

Air OutletsThe two sections of Bev-a-line tubing attached to the sensor head must beconnected to the console air outlet ports. One of the tubes has a black band

near the end of the hose. Attach this hose to the SAMPLE port of the consoleAttach the other hose to the REF port.

Figure 2-2. Console tubing and cable connections.

RS-232

Air Inlet

Sample

ReferencePower Switch


43/1320

Assembling the LI-64Preparat


Connecting the Chamber / IRGAThe sensor head/IRGA end of the electrical cables attach as showFigure 2-3. Be careful not to overtighten the screws on the 26 pin D con

tor. To plug in the round connector, first line up the red dots, then pusconnector all the way in until the red dots meet and there is a click.

Figure 2-3. Electrical connectors, air hoses, and tripod bracket mounting hoon the sensor head / IRGA.

Red Dots

To Sample

To Reference

IRGA Connector

Chamber Connector

Tripod BracketMounting Holes

Interchanging IRGAs? Don’t.If you have more than one LI-6400 at your disposal, can you interchathe IRGA/chambers? The simple answer is (probably) no; they are notsigned to do it. Each LI-6400 console is adjusted at the factory for a pticular head. If you mismatch them, you may not able to zero the IRGA


44/1320

Assembling the LI-6400 Using a Tripod


2

Using a TripodA mounting bracket is included in the spare parts kit for mounting the sensohead on a tripod. A tripod is a virtual requirement when making long-termmeasurements in the absence of cooperative graduate students.

The three screws included with the mounting bracket are threaded into holeon the right side of the analyzer housing on the sensor head (Figure 2-4). Thtripod mounting bracket is threaded for use with standard 3/8-16 and 1/4-20tripod heads.

Figure 2-4. Mounting holes for the tripod bracket are found on the right side of

the sensor head.

Tripod Head

Tripod MountingBracket

Analyzer Housing (rear view)

122-04276


45/1320

Assembling the LI-646400-01 CO2 Injector Installa


6400-01 CO2 Injector Installation

Figure 2-5. 9964-026 External CO2Source Assembly

The optional 6400-01 CO2 Injector consists of a controller tis factory installed within the LI-6400 console, and an exterpart that attaches between the chemical tubes on the end of console. This external part can be either

• the 9964-026 Source Assemblywhich uses 12 gram CO2 cartridges (described below), or

• the 9964-033 Tank Connector Blockfor using a tank of pure CO2 with a regulator, described on p

2-10.

Warning: CO2 cylinders contain 12 grams of high pres-

sure liquefied CO2. Follow the handling precautions on

the cylinder and cylinder cover carefully.

Note: 12 gram CO2 cartridges last about 8 hours from the

time they are pierced, regardless of whether the system isin use or not. However, every once in a while - say, every100 or 200 cylinders - you might encounter one that pro-vides considerably less, such as only 1 or 2 hours.

WARNI N G:

Hi gh P r e s s ur e

WARNING:

Pressure Liquefied Gas

SLOWLY

Regulator

O-ring

CO2 Cylinder

CO2 Cylinder Cover

CO2 Cylinder Piercing Block

Piercing Pin

CO2 Source Mounting Block

V en t


46/1320

Assembling the LI-6400 6400-01 CO2 Injector Installation


2

Using CO2 Cartridges

■■■■ To install the 9964-026 Source Assembly

1 Attach the assembly block. Is the O-ring present?Make sure that the O-ring seal on the mounting block is properly seatedTighten the two knurled knobs on the mounting block to secure the assemblyto the console.

2 Unscrew the CO2 cylinder cover.

3 Install a new O-ring in the groove around the piercing block.Use your finger to press the O-ring into the groove (Figure 2-7). If the O-ringis not in place when the CO2 cartridge is pierced, gas will rapidly vent out a

hole on the underside of the mounting block.

Figure 2-6. Location of external CO2 source assembly.

Check for O-rings inthese two locationsCylinder Cover

12 gram cylinder

CO2 source at-taches here.

Oil Filter


47/1320



Important Note: Although the O-ring may perform properly for severainders, we recommend that it be replaced with each new cylinder. After bsubjected to several high pressure cycles the O-ring weakens and becperforated, and easily tears or splits. If the O-ring is slightly torn or perfed, gas slowly leaks through the vent hole shortening the life of the cyliIf the O-ring is split, gas rapidly vents until the cylinder is empty.

4 Check the oil filter (every 3 or 4 cylinders)It’s actually a cigarette filter that is located in the “T” fitting on the rear osource assembly (Figure 2-6). It’s a good idea to unscrew the cap (beforinstall the cylinder!) and look down in at the end of the filter to check fooil accumulating on the white filter material. If the filter is getting discolchange the filter. See Servicing the External CO2 Source Assemblpage 19-38 for more details. (With LI-COR cylinders, the filter should la25 cylinders. We have encountered other cylinders, however, that comuch more oil, notably Copperhead™ and Curtis™ brands, so beware.

5 Place a new CO2 cylinder into the cylinder cover

The cylinder goes in large end first, although one of our engineers accide

ly got one to work the other way around.1

Figure 2-7. Top view of piercing block showing the O-ring location.

Piercing BlockO-ring

Vent HolesPiercing Pin

1.He’s now in management.

Warning: Use only the proper size 12 gram cartridges.


48/1320



2

6 Screw the cylinder cover onto the piercing block.You may feel some resistance as the piercing pin contacts the cylinder. Ashort burst of venting CO2 may occur as the cylinder is pierced; the leak i

minimal if you continue to quickly tighten the cylinder cover. Tighten thecover until snug; there’s no need to overtighten.

Using other sizesThe mixer cap is designed for a 12g CO2 cylinder, which is 83 mm in length

You can also use a shorter cylinder, such as the 8g ones readily available inEurope, by inserting a spacer into the cylinder cap. The spacer’s length shouldbe such that the cylinder plus the spacer is 83mm (+/- 2 mm).

External CO2 TanksThe Tank Connector Block replaces the 6400-01 External CO

2 Source As

sembly, and is useful in situations where CO2 tanks or other high volume sup

plies are available.

The tank connector block is designed for use at pressures between 180 and

220 PSIG (lbs in-2 gauge pressure) of CO2. Use a regulator, and do not ex

ceed 250 PSIG CO2, as the pressure relief valve may vent your source.

The Tank Connector Block uses a 1/8” male NPT to 1/8” tubing fitting. Thi

fitting has a flow restrictor installed (10 cm3 min-1). Do not remove this fitting. A 1/8” to 4mm compression union is also provided for users who may

be unable to obtain 1/8” copper tubing. Directions for installing the TankConnector Block to a CO2 source using 4mm copper tubing are given in In

stallation Using 4mm Copper Tubing on page 2-11.

■■■■ To install the 9964-033 Assembly

1 Mount the CO2 Tank Connector Block

Use the two knurled knobs to mount the block between the CO2 and H2O

scrub tubes. Make sure that the O-ring seal on the back of the block is properly seated.

2 Insert copper tubingInsert the 1/8” copper tubing between the 1/8” connector nut and the ferrul(Figure 2-8).

Important: Note the orientation of the ferrule. One of the tapered ends of thferrule is longer than the other; the long end must be oriented toward the connector on the mounting block. When the nut is tightened onto the connector


49/1320



the ferrule will be permanently crimped to the copper tubing, and you wibe able to remove it.

3 Tighten the nut until snug, plus 3/4 of a turn.

4 Connect your CO2 source.

The other end of the copper tubing connects to your CO2 source. Adjust

regulator pressure to between 180 and 220 PSIG.

Installation Using 4mm Copper TubingIf you are unable to obtain 1/8” copper tubing, you can connect the Tank nector Block to a CO2 source using 4mm tubing and the compression f

(LI-COR part #300-04439) included with the Tank Connector Block.

Figure 2-8. Insert tubing through nut and ferrule. Note proper orienta-

tion of ferrule.

250 PSIG Pressure

Relief Valve

1/8" Tubing Connector

Knurled Knob

Ferrule

Tank Mounting Block

1/8" Nut

O-ring Seal

1/8" Copper Tubing

To CO2 Tank

Washer


50/1320



2

1 Install the Tank Connector Block and copper tubingThis is described in steps 1-4 above.

2 Connect the 1/8” and 4mm tubingUse the 1/8” to 4mm compression fitting to connect the two pieces of tubing(Figure 2-9). Be sure to orient the ferrules correctly; the narrow tapered endof each ferrule must be oriented toward the compression fitting. Tighten thnuts on the compression fitting until snug, plus 1 1/4 turn.

3 Connect the 4mm tubing to your CO2 source.

Adjust the regulator’s pressure to between 180 and 220 PSIG.


51/1320



Figure 2-9. Use the compression fitting to connect 1/8” and 4mm tubing.

1/8" Nut

Ferrule

1/8" Copper Tubing Connector

1/8" Copper Tubing

4mm Copper Tubing

To CO2 Tank

Ferrule

Ferrule

1/8" to 4mmCompression Fitting

1/8" Nut

4mm Nut


52/1320

Assembling the LI-6400 External Quantum Sensor Installation


2

External Quantum Sensor InstallationThe external quantum sensor is held in its mounting bracket with a small sescrew (turned with a 0.050” hex key provided in the spares kit). The BNCconnector plugs in at the rear of the chamber.

If the LI-6400 was shipped from the factory with an external quantum sensorits calibration factor will have already been entered into the instrument. Otherwise, you will have to do this. See View / Edit Accessories on page 18-8

Figure 2-10. The external quantum sensor installed.

BNC

Connector

Set screw


53/1320

Assembling the LI-64 Attaching the LED Light Sou


Attaching the LED Light SourceThe optional 6400-02 or -02B LED Light Source is mounted to the sehead by removing the upper half of the leaf chamber and replacing it witlamp assembly. Follow these steps to install the lamp:

1 Remove the tripod mounting bracketThis is necessary to access the connector for the in-chamber PAR senso

2 Disconnect the light sensorPull the connector straight out (don’t wiggle side to side) with a pair ofnose pliers (or your fingernails) gripping the connector (Figure 2-11).

Or, just grasp both wires with your fingers and pull straight out. The wwill bring the connector with it.

Figure 2-11. Disconnecting the in-chamber PAR sensor connector.

Log switch connector

Light sensor connector


54/1320

Assembling the LI-6400 Attaching the LED Light Source


2

3 Remove the top leaf chamberUse the 3/32” hex key provided in the spare parts kit to remove the two longscrews that hold the chamber top in place (Figure 2-12).

4 Install the O-ringsEnsure that there are O-rings in the air passage holes.

Figure 2-12. The top and bottom chamber halves are held on with two hex head

bolts. Use the 3/32 inch hex key to loosen and tighten them.

Gasket

GaAsP PAR sensorConnector O-rings

Upper leafchamber cuvette

Top View

140-04251

192-04357

192-04356


55/1320

Assembling the LI-646400-40 Leaf Chamber Fluorom


5 Install the lamp assemblyAttach the lamp connector and PAR sensor connector as showFigure 2-13. Ensure that the PAR sensor is attached to the connector nea

rear of the analyzer housing, not to the log switch connector.

If the LED source was purchased with the LI-6400, its calibration factor

have been installed in the console. Otherwise, you will have to do thisExample: 6400-02B LED Source on page 16-6 for how to do this.

6400-40 Leaf Chamber FluorometerInstallation and operation are described in Chapter 27.

+ CH

C ON S T

E

C H R O M E L

C O N S T

E O M E G A

+

+

Figure 2-13. Attach the lamp and PAR sensor connectors.


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Assembling the LI-6400 Powering the LI-6400


2

Powering the LI-6400

LI-6020 Battery ChargerThe LI-6400 cannot be operated from mains power alone using this batterycharger. (For independent mains power operation, see 6400-70 AC Modulon page 2-20.) It can, however, be operated with the charger and a singl6400-03 Rechargeable Battery. To use the LI-6020, plug a fully charged6400-03 battery into one of the LI-6400 battery jacks, and plug the LI-6020into the other jack using the 9960-062 cable (in spares kit).

Note: This will not provide indefinite operation. The battery will slowly discharge, and eventually need to be swapped. (Procedure to swap: Disconnecthe plug from the charger, plug in a fresh battery, then disconnect the old bat

tery and reconnect the plug from the charger.)

6400-03 BatteriesTwo battery jacks are located beneath the ON/OFF switch. Insert two6400-03 batteries into the battery compartment and connect both batteriesThe 6200B batteries used with other LI-COR instruments can also be usedbut with less convenience since they will not fit into the battery compartmenof the LI-6400.

The 6400-03 batteries have a capacity of approximately 3 Amp-hours eachThe LI-6020 Battery Charger produces about 1.5A. The LI-6400, on average

draws 1.5A; therefore, if the LI-6400 is drawing 1.5A, the LI-6020 used witha 6400-03 will power the LI-6400 indefinitely. At maximum draw (with LEDlight source on, running the coolers, etc.), the LI-6400 will use about 3AWithout the light source, it will draw about 2A. Table 2-2 shows the approximate battery life when the LI-6400 is used with two 6400-03 batteries or withthe LI-6020 Battery Charger and one 6400-03.

• Two batteries are better than oneYou will get better battery life when they are used in pairs.

Table 2-1. Approximate hours of battery life for 6400-03 batteries (at 25 °C ambient).

Power Supply Power requirement of LI-6400

1.5A 2A 3A

Two 6400-03 Batteries 4 Hours 3 Hours 2 HoursLI-6020 and one 6400-03 Indefinite 6 Hours 3 Hours


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Assembling the LI-64Powering the LI-6


• At least one battery is requiredYou cannot run the system using only the LI-6020 charger.

•You are warned when the batteries are lowThe system will beep regularly when the batteries are low, and there areplay indicators as well (see Low Battery Warning on page 5-18). Onebattery can be removed and replaced with a fresh one while the systemtinues to run without interruption. Immediately replace the second lowtery with a freshly charged battery to ensure maximum operation time.

Note that you can also power the LI-6400 using any 12 volt battery withficient capacity; a car battery, for example, will run the system for 24 hours before recharging is necessary.

Other BatteriesYou can power the LI-6400 with any 12 V battery (car, marine, etc.) thaat least a 1.5 Amp-hour capacity. To connect an alternative battery to thesole, you’ll need a 318-02031 connector (the kind that is on the 6400-03tery). One simple way to get this connector already attached to a cable

remove it from a dead 6400-03 battery. Alternatively, you can order connectors by themselves, or else order part number 9960-120, which iconnector attached to 10 feet of cable, or else obtain a 9960-062 (the cthat runs between the console and an LI-6020 charger), and cut it in haget two short (2.5 ft.) versions of a 9960-120.

The 6400-03 batteries are protected with a 10 Amp automotive fuse (seeplacing the Battery Fuse on page 19-9). You might wish to do the sameyour alternative battery.

Shooting yourself in the foot…When you are swapping batteries on a running, data-collecting instrumbe careful not to bump the on/off switch with your thumb as you unplbattery. It’s easy to do (I speak from experience), and it quickly brings measurements to an abrupt halt.


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Assembling the LI-6400 Powering the LI-6400


2

6400-70 AC ModuleThis optional accessory allows the LI-6400 to be powered from mains powerIt consists of a transformer, and a battery-shaped box that can fit in the con

sole (Figure 2-14).

■■■■ Notes on using the 6400-70 AC Module

• A battery is not requiredThe module will power the LI-6400 by itself. However, plugging a battery

into the module will provide 1 or 2 hours continued operation in case of mainpower failure.

• Use both plugs - most of the timeThe AC module has two plugs that go into the console’s battery connectorsFor normal operations, plug both of them in.

• Hot swappingYou can switch from AC operation to battery operation by unplugging one othe module’s plugs from the console, and replacing it with a fresh batteryThen disconnect the other plug, and replace it with second battery if you wishReverse the process to switch from battery to AC operation.

Either way, observe the caution in Figure 2-15.

Figure 2-14. The 6400-70 AC Module fits in a battery compartment inthe console. If you install a battery in the other compartment, and plug

it into the module (as shown here), that battery will trickle charge, but more importantly, provide continued operation for 1-2 hours in theevent of a mains power failure.


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Assembling the LI-64Powering the LI-6


SAMPLE

REF

INLE T

!UNPLUG BA T T

ERIES

BEFORE SER VICING.

O l

CHG PWR

B ATTERY

INPUT - 12VDC

CH ARGE- 14.8VDC

0.65 A M AX.

INPUT

17-24VDC

72W

OUTPUT

14.8VDC

4.0 A M AX.

MODEL 6400-70

SAMP

REF

INLE T

!UNPLUG BA T T

ERIES

BEFORE SER VICING.

O l

CHG PWR

B ATTERY

INPUT - 12VDC

CH ARGE- 14.8VDC

0.65 A M AX.

INPUT

17-24VDC

72W

OUTPUT

14.8VDC

4.0 A M AX.

MODEL 6400-70

Battery Battery

Battery safely trickle charges, and isavailable to run the instrument if mainspower fails.

Battery is being charged in an uncontrolled maner. Damage could result to the battery and/orthe transformer.

Figure 2-15. Avoid extended (more than a minute) operations with a battery and one of the ACmodule’s plugs connected to the console. In this configuration, you will be providing uncontrolled charging of the battery, which could damage the battery and/or the transformer.

Safe for extended operations Don’t do this for more than a minut

To minimize shock hazard:

The 6400-70 AC Module MUST be connected to an electrical ground through a three-con-ductor power cable, with the third wire firmly connected to an electrical ground (safetyground) at the power outlet.

Any interruption of the protective (grounding) conductor or disconnection of the protectiveearth terminal may result in a potential shock hazard at the LI-6400 instrument chassis thatcould result in personal injury.

ALSO: If you connect an analog output from the LI-6400 to the LI-610 Dew Point Generator,and are powering both units by AC power, a “ground loop” can develop, causing unwantedsignal noise that can affect the operation of the LI-610. If you are using the LI-6400 andLI-610 in this manner, we recommend that you isolate the two circuits by operating one orboth of the instruments with battery power.

Important Safety Notice


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Assembling the LI-6400 Installing System Software


2

Installing System SoftwareNote: Installing software is not something you have to do to make the LI-6400work when you get it from the factory. It comes with software installed andready to use. We change this software periodically, to fix bugs and add en

hancements2, and to take advantage of these changes, you have to install thnew software into the LI-6400. To see what version of software you have installed, select “About this unit” in the Home Menu (see Figure 3-6 on pag3-9). You can see what the latest available system software is (and downloadit) by checking our web site: www.licor.com.

Hardware RequirementsVersion 6.x runs on either the current 400 MHz board (LI-6400XT), or theolder 200 MHz board (version 5.x software). If an LI-6400 has version 3.x o

4.x, it has the original digital board (18 MHz). Any LI-6400 can be upgradedto an LI6400XT via part number 6400-926. Any version 5.x LI-6400 can install and run version 6.x software, but will not have any of the flash memoryor Ethernet capability.

2.Or fix enhancements and add bugs…

http://www.licor.com/http://www.licor.com/http://www.licor.com/http://www.licor.com/http://www.licor.com/http://www.licor.com/


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Guided Tours


3 This chapter teaches you a) how to operate the LI-6400, and b) how theLI-6400 accomplishes its tasks. We do this with a series of guided tours. Wrecommend that you follow along on your instrument or LI6400Sim simulator. You won’t need plant material for these tours - that will come in Chapte4.

Before You StartHere are some things you should know about the display and keypad(Figure 3-1 on page 3-3).

Cursor Control KeysThe cursor control keys (↑, ↓, ←, →, pgup, pgdn, home, and end) appear oneither side of the front panel. The left group does the same thing as the righgroup, and it doesn’t matter which you use. Similarly, there are two entekeys and two labels keys.

Function KeysKeys labeled f1 through f5 below the display are called function keys, and often have labels associated with them on the bottom line(s) of the displayWhen there are multiple definitions for these keys, the labels key can be usedto cycle through them (and shift + labels to go backwards). Sometimes, thlabels remain hidden even though function keys are defined and active; pressing labels will make the labels temporarily appear.

DisplayThe display has independent text (8 lines, 40 characters per line) and graphic(64 dots high, 240 dots wide) modes. In this tour we will use both.

You can adjust the contrast by pressing ctrl + shift + ↑ and ctrl + shift + ↓Also, if it is so equipped, you can toggle the display backlight on and off bypressing ctrl + home. All the hot keys are listed in Table 3-1 on page 3-3.


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Guided Tou Before You S


Figure 3-1. The LI-6400 keypad. The cursor control keys, labels, and enter are paired to facilitate access

either hand.

Cursor control keys.

Function keys

A S D F G H J K L

Z

ctrl

X C V B N M

PQ W E R T Y U I O {[

} ]

:;

"’

\ space

_- +=

~ |

<,

>.

?/ shift

escape

shift

!1 @2 #3 $4 %5 ^ 6 &7 *8 (9 )0

enterenter

pgdnend

pguphome

pgdnend

pguphome

labels labelsf1 f2 f3 f4 f5

Table 3-1. Hot key combinations - valid anytime.

Press... To Do...

ctrl shift ↑ Darkens display contrast.

ctrl shift ↓ Lightens display contrast.

ctrl shift home Toggles display backlight (if installed).

ctrl shift → Turns graphics mode on. If already on, turns text moff.

ctrl shift ← Turns text mode on. If already on, turns graphics moff.

ctrl escape Aborts the current application.

ctrl shift escape Reboots.

ctrl shift end (XT Only) Unmounts compact flash card (if inserte


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Guided Tours Before You Start


3

Table 3-2. New Measurements key summary.

Press... To Do...

[ Enters/Exits Diagnostics Mode

] Enters/Exits Graphics Mode

a..z(Text) Selects display line.(Diagnostics) Selects display screen (a - i).(Graphics) Selects graphics screen (a - h).

0..9 (Text and Graphics) Selects function key level.

homeend

pguppgdn

(Text) Implements a Display Group key.

ctrl homectrl endctrl pgupctrl pgdn

(Text) Defines a Display Group key.

↑ ↓ (Text) Selects new display line.(Graphics) Selects new display screen.

← → (Text) Changes to next display on selected line.(Graphics) Changes chart selection.

ctrl z Toggles warning messages on/off.ctrl s (Graphics) Stores current graphics display to /User/Im-

ages/RTG_ yyyy-mm-dd_hh-mm-ss.(Text & Diagnostics) Stores a system snapshot (vari-ables, values, settings, etc.) to a text file names /Us-er/Snapshot_ yyyy-mm-dd_hh-mm-ss.


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Guided TouTour #1: OPEN Overv


Tour #1: OPEN Overview

Running OPENOPEN is the name of the program that controls normal operation oLI-6400XT and the one you’ll be running most of the time. This programgins to run automatically after you power on (unless you intervene), aswill see in the following steps.

1 Turn the LI-6400 ON

About 10 seconds will pass while the display shows1:

INITIALIZING.

followed by a series of start up messages. Eventually, you should see:

2 Press enter or wait

If you press escape, you’ll prevent OPEN from loading, and will accesLPL screen (The LPL Screen on page 5-19). If you press enter (or nearlother key), OPEN is loaded (Figure 3-3), which takes about 5 seconds.

1.If your LI-6400 doesn’t behave as described here, refer to Power On Prob

on page 20-2.

Figure 3-2. OPEN’s Autostart countdown is 5 seconds long. Press

enter to skip it, or press escape to prevent OPEN from loading.

Countsdown to 0

Figure 3-3. OPEN’s bar chart is displayed while loading.


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Guided Tours Tour #1: OPEN Overview


3

3 If asked, select a ConfigurationOnce OPEN’s bar chart finishes, you might be asked to pick a configurationfile (Figure 3-4). If there is only one configuration file on your instrumen

(e.g. a new instrument), then you won’t be asked to do this.

A configuration file contains settings and values used by OPEN. Configuration files are easy to create and modify. There is an introductory tour later inthis chapter on page 3-90.

For now, however, select FactoryDefault_6.2.When it is highlighted, press enter

4 Power up the IRGAs.After a few more seconds, and several more messages, you’ll be asked

Press Y when you have both electrical cables between the console and the sensor head connected.

OPEN’s Main ScreenAfter some more messages, OPEN’s main screen appears (Figure 3-5). Thi

screen represents the home base of operations for OPEN. The function key(f1 through f5) have 2-line labels above them on the display, which are usedto access the various menus and routines available in OPEN.

Normally at this point, one would do a series of checks before making measurements, and these are described in Preparation Check Lists on page 4-2We’ll skip these checks for purposes of our tours.

Documents

Manual_IRGA_LI-6400XT-v6.2.pdf