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Using the LI-6400

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System

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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, INCLUDING,BUT 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 consequen-tial 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 partof this document may be photocopied, reproduced, or translated to another language without prior written consentof LI-COR, Inc.

© Copyright 1998 - 2004, 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

Macintosh

®

is a registered trademark of Apple Computer, Inc.

New editions of this manual will incorporate all material since the previous editions. Update packages may be usedbetween 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-COR Biosciences, Inc. • 4421 Superior Street • Lincoln, Nebraska 68504Phone: 402-467-3576 • FAX: 402-467-2819Toll-free: 1-800-447-3576 (U.S. & Canada)

Using the LI-6400 Version 5

iii

Contents

ContentsWelcome to the LI-6400

A Bit of History -xiiiAbout this Manual -xvVersion 5 Summary -xviVersion 5.2 Summary -xxivVersion 5.3 Summary -xxvii

Part I: The Basics

1 System Description

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

An Open System 1-2The Flow Schematic 1-4Equation Summary 1-7The System Components 1-12

2 Assembling the LI-6400

Putting it all together

Preparations 2-2Using a Tripod 2-66400-01 CO2 Injector Installation 2-7External Quantum Sensor Installation 2-14Attaching the LED Light Source 2-156400-40 Leaf Chamber Fluorometer 2-17Powering the LI-6400 2-18Installing System Software 2-22

Contents

iv


3 Guided Tours

Learning how to make it work

Before You Start 3-2Tour #1: OPEN Overview 3-4Tour #2: New Measurements Mode Basics 3-15Tour #3: Controlling Chamber Conditions 3-29Tour #4: Logging Data 3-50Tour #5: Configuration Introduction 3-69Tour #6: LPL 3-86

4 Making Measurements

The fundamentals of good measurements

Preparation Check Lists 4-2Some Simple Experiments 4-8Making Survey Measurements 4-21Light Response Curves 4-24CO2 Response Curves 4-29Matching the Analyzers 4-33Stability Considerations 4-40Leaks 4-43Operational Hints 4-48Answers to Questions 4-55

Part II: Useful Details

5 Standard Tools

Menus, Editors, and File Dialogs

Standard Menu 5-2Standard Line Editor 5-5Standard File Dialog 5-9Standard Edit 5-13Hot Keys 5-16Low Battery Warning 5-17The Boot Screen 5-18The LPL Screen 5-19Power ON Hooks 5-22

Contents


v

6 New Measurements Reference

Viewing real time data using text and graphics

Real Time Text 6-3Real Time Graphics 6-11Diagnostics 6-19Stability Indicators 6-25Keyboard Summary 6-29

7 Environmental Control

How OPEN controls chamber conditions

Open’s Control Manager 7-2Humidity Control 7-7CO2 Control 7-13Temperature Control 7-16Light Control 7-18

8 Light Sensor Considerations

The most important parameter is the hardest to measure

Why Two Sensors? 8-2Specifying the Source and Sensor 8-36400-02 and -02B Light Sources 8-76400-40 Leaf Chamber Fluorometer 8-9Gallium Arsenide Phosphide (GaAsP) Sensor 8-10

9 Data Logging

Storing what you want, where you want, when you want

Basic Concepts 9-2Getting Started 9-4Determining What is Logged 9-7Prompts and Remarks 9-15AutoPrograms 9-20AutoProgram Descriptions 9-23Making Your Own AutoPrograms 9-30

Contents

vi


Part III: Working With Files

10 The LPL File System

Managing your data storage space

Files and Directories 10-2The Filer 10-4Filer’s Directory Operations 10-7Filer’s File Operations 10-9Housekeeping 10-19

11 Connecting to a Computer

Retrieving your data, and remote control

Connecting the LI-6400 to a Computer 11-2Using the Comm Port 11-4Transferring Files 11-5Remote Control 11-12

12 GraphIt

A tool for viewing and graphing data files

Accessing GraphIt 12-2Data File Format 12-4Defining Plots 12-5Selecting Observations 12-10Curve Fitting 12-14Viewing Data 12-18PlotDef File Format 12-20Storing and Retrieving Graphics Images 12-20

13 Recomputing Data Files

How to recompute data files

Reasons to Recompute 13-2A Step-By-Step Example 13-2The Details 13-7Hints 13-14

Contents


vii

Part IV: Configuration Issues

14 OPEN’s System Variables

Quantities provided by OPEN

Background Information 14-2Measured Variables 14-4Computed Variables 14-9Time and Logging Variables 14-12Status Variables 14-12Boundary Layer Variables 14-17List of Open 5.3 System Variables 14-19Band Broadening Corrections 14-23

15 Defining User Variables

Equations, Constants, and Remarks

The ComputeList File 15-2ComputeList File Format 15-3Writing and Modifying ComputeList Files 15-7User Defined Constants and Remarks 15-13Importing RS-232 Data 15-14Useful Variables and Functions 15-16 The Default ComputeList 15-18Old Style vs. New Style 15-19

16 Configuration Basics

What you need to know to get by

A Definition of Terms 16-2Making Configuration Files 16-5Installation Menu: Behind the Scenes 16-10Modifying Config Files 16-13The Reset Menu 16-18Custom Chamber - Closed 16-20Matching Without the Match Valve 16-34Configuration Command Summary 16-36

17 Using an Energy Balance

Computing what you can’t measure

The Theory 17-2

Contents

viii


Using Energy Balance in OPEN 17-6Measuring Boundary Layer 17-9Further Reading 17-11

Part V: Maintenance & Troubleshooting

18 Calibration Issues

How much is good data worth?

CO2 and H2O Analyzers 18-3Flow meter 18-18View, Store Zeros & Spans 18-19Zeroing the Leaf Temperature Thermocouple 18-206400-01 CO2 Mixer 18-21Internal PAR Sensor (General) 18-256400-02(B) LED Source 18-266400-40 Leaf Chamber Fluorometer 18-29GaAsP Light Sensors 18-30Calibration and Configuration File Summary 18-32

19 Maintenance & Service

The care and feeding of your new pet

Chemical Tubes 19-26400-03 Batteries 19-8System Console 19-10Real Time Clock 19-18Cables 19-19The Chamber Handle 19-20Leaf Temperature Thermocouple 19-24Leaf Chambers 19-26LED Source Maintenance 19-28Match Valve Maintenance 19-29IRGA Maintenance 19-32Servicing the External CO2 Source Assembly 19-38Shipping The LI-6400 19-41Useful Part Numbers 19-42

Contents


ix

20 Troubleshooting

When things go wrong

Power On Problems 20-2Real Time Clock Problems 20-6New Measurements Mode Warning Messages 20-7Unreasonable Results 20-10Pump/Flow Problems 20-14IRGA Problems 20-15Match Valve Problems 20-236400-01 CO2 Mixer Problems 20-25Light Source / Sensor Problems 20-306400-40 Leaf Chamber Fluorometer 20-33Chamber Problems 20-34Finding Leaks 20-39Soil Chamber Problems 20-44Useful Information 20-45

21 Diagnostics and Utilities

Useful programs

Diagnostics & Tests Menu 21-2 /Sys/Utility Programs 21-12

Part VI: Programming

22 Programming with LPL

An introduction to the LI-6400’s programming language

Overview of LPL 22-2Making Objects 22-7Functions 22-12Pointers 22-17Public and Static 22-22Compiler Directives 22-25

23 LPL Topics

Programming with LPL

Stack Control 23-2Conditionals and Loops 23-4Array Operations 23-6

Contents

x


Math Functions 23-18Display Control 23-23Keyboard Control 23-29Clock 23-31Event Handling 23-33The Function Keys 23-37I/O Programming 23-39File System 23-47Menus and Editors 23-51ListBox 23-56Real Time Graphics 23-59Graphics 23-61Serial Communications 23-69Analog Measurements 23-71Analog Output Control (D/A) 23-78Digital I/O 23-80Application Tools 23-83Miscellaneous Tools 23-87

24 LPL Reference

Keyword Summary

Syntax Summaries 24-2Definitions 24-11The Reference 24-16

25 AutoProgramming Reference

Making them do what you what them to do

Autoprogram Format 25-2Some AutoProgram Listings 25-4Useful AutoProgram Commands 25-12AutoPrograms and the Control Manager 25-22Low Level Control Tools 25-22

26 Customizing Open

“Cry ‘Havoc’ - and let slip the dogs of war”

Using PATCH= 26-2Useful Variables 26-4Open’s Hooks 26-7New Style ComputeList Files 26-13

Contents


xi

Using Spare Channels 26-17

Part VII: Accessories

27 Leaf Chamber Fluorometer

Using the 6400-40 Leaf Chamber Fluorometer

Getting Started 27-2Background Information 27-3Installing the LCF 27-10Operational Summary 27-18Basic Experiments 27-41Fluorescence AutoPrograms 27-56Calibration Issues 27-59LCF Troubleshooting 27-68LCF Reference 27-72Chlorophyll Fluorescence References 27-82

28 Soil CO2 Flux Chamber

Using the 6400-09 Soil Chamber

Introduction 28-2Attaching the Soil Chamber 28-7Software 28-20Making Measurements 28-30Troubleshooting the Soil Chamber 28-35Maintenance 28-37Equation Derivation 28-39Partial Listing of Soil Efflux Eqns.LPL 28-43Soil Chamber Specifications 28-49

INDEX

Contents

xii



xiii

Welcome to the LI-6400

A Bit of History

The LI-6400 is LI-COR’s third generation gas exchange system. In the begin-ning was the LI-6000; it used a third party CO

2

analyzer having the novel (for1983) features of small size, light weight, and low power. Photosynthesis wascomputed by measuring the rate of change of CO

2

with time with a leaf en-closed in a relatively large chamber - a closed system. The LI-6000 was lim-ited by the signal noise of the analyzer (1-2 µmol mol

-1

) and an unfortunatechoice of method for computing slopes. These problems were corrected in1986 in the LI-6200, which sported LI-COR’s first CO

2

analyzer and muchimproved software. It was still a closed system for CO

2

, but had the potentialfor steady-state transpiration measurements. The steadiness of the state, how-ever, depended heavily on a motivated, attentive operator continually adjust-ing a knob.

While the LI-6200 was fairly well suited for survey measurements, a growingnumber of customers (and potential customers) were looking to answer deep-er questions. The deeper answers could be found in response curves, and thatmeant using a system that could control the environmental quantities impor-tant to photosynthesis: CO

2

, light, humidity, and temperature. Several inno-vators attempted to do various response curves with the LI-6200, withvarying degrees of success. Meanwhile, we were having a very hard time inour attempts to transform that instrument into a next-generation system.

By 1990, having abandoned the idea of enhancing the LI-6200, we restartedwith the question: “What would the ideal gas exchange system be like?” Itwould do response curves, of course, so it would need the ability to controlchamber conditions. To us,

ideal

response curves meant

labor-free

responsecurves, so manual controls were out, computer controls were in. Responsecurves should be seen, not imagined, so we needed built-in graphical capabil-ity. The ideal system would also do survey measurements: you should be ableto carry it around, clamp onto a leaf using only one hand (our previous sys-tems needed two or three), and be done with the measurement quickly. Ques-

Welcome to the LI-6400

A Bit of History

xiv


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

Challenges loomed, two of them formidable: CO

2

and H

2

O control is donebest by having gas analyzers right in the leaf chamber, but suitable IRGAs didnot exist. Secondly, chamber CO

2

could in principle be controlled by mixingscrubbed air and pure CO

2

(available in very portable 12 gram cylinders), butagain, a suitable mixing device did not exist. So, we set about inventing them.

Five years and one name change

1

later, we shipped the first LI-6400. Andmany more since then. We’ve kept working on it, too, adding many innova-tions and enhancements, including soil respiration and a leaf chamber fluo-rometer.

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. Old units areupgradable, so we haven’t left any users behind; their investment remains sol-id.

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. Wel-come to the LI-6400.

1.It started out as the LI-6300.

Welcome to the LI-6400About this Manual

Using the LI-6400 Version 5 xv

About this ManualWhen confronted with a new instruction manual, most people turn to the sec-tion named “About this manual” for one simple reason: to find out how muchthey can skip. Since this manual has 27 chapters, you are probably eager toskip most of them.

You’re in luck. You can.

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

• Experienced with earlier versions of the LI-6400Read Version 5 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 and thefundamentals of making measurements fairly well by the end. Then, if youare also doing fluorescence, Chapter 27.

• New to the LI-6400; new to gas exchange and/or fluorescence; and fairlyimpatientChapter 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.Chapter 4: Do the check lists, and the simple experiments.Chapter 27: Fluorescence.Having measured some leaves (and satisfied your impatience), you mightwant 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 fromour web site (www.licor.com). All cross references in the text, table of con-tents, and index are hyper-linked, allowing one-click access. (Version 4.0 ofAdobe® Acrobat® Reader is required. You can download this software forno charge from www.adobe.com)

Welcome to the LI-6400Version 5 Summary

xvi Using the LI-6400 Version 5

Version 5 SummaryThere are a number of interface changes that came with OPEN 5.0, and themajor ones are summarized here. If you are familiar with earlier versions ofOPEN, then this summary will get you started very quickly.

Version 5 runs on new hardware; there are 128 Mbytes of dynamic memory,and 64 Mbytes of flash memory (for files). The processor is faster (used to be16 MHz, 16 bit - now it’s 200 MHz, 32 bit), and the underlying operating sys-tem is now LINUX. Overall operation is much snappier, with minimal delays.And, no more coffee breaks while OPEN loads - the infamous bar chart nowgoes by in 5 seconds.

Real Time GraphicsThere are now 8 independent graphics displays for showing real time graph-ics in New Measurements mode, instead of just one. Each display can hold 1,2, or 3 independent strip charts or XY plots, as before. However, the scalingoptions are improved, and strip charts retain 10 minutes (or more - it’s userdefinable) worth of data, allowing you to scroll back in time, or zoom in andout (i.e. change time intervals). A typical real time graphics display is illus-trated on the next page.

Notice that there are 3 levels of function keys available while viewing thegraph for control and manipulation. Also, notice the A, B, C... indicator onthe right hand side. This shows which display is being viewed. Press the let-ters A through H to jump directly to a particular display. You can also use thearrow keys ↑ or ↓ to step through them sequentially.

In New Measurements mode, the level 4 function keys still control real timegraphics, but now they look like this:

GRAPH View GRAPH QuikPik Graph Setup

Pick a new group of display definitions. You can change all 8 at once.

Enter graphics viewing mode (same as before).

View and edit the configuration of the 8 displays


Using the LI-6400 Version 5 xvii

Scroll back and forth in time. Resume brings you back to the present (StripCharts)

Expand or shrink the time axis (StripCharts)

Mark an event on this screen.

Mark charts on all graphics screens

Change this screen.

Hide the function key labels.

Clear all data from this screen

Clear all data from ALL screens

Graphics Function Keys. Press la-bels or 1, 2, 3 to make them visible.

8 displays available. Navigate by pressing A, B, ...H.


xviii Using the LI-6400 Version 5

The GRAPH Setup key allows the 8 real time graphics displays to be config-ured individually, or all at once.

Editing a particular graphics display brings up an editor that is illustrated onthe next page. This is also the editor accessed by pressing the EDIT functionkey while viewing a real time graphics display.

GRAPH View GRAPH QuikPik Graph Setup

Graph A: PHOTO, CONDGraph B: CO2R, CO2SGraph C: H2OR, H2OS, FlowGraph D: Tblk, Tair, TleafGraph E: Photo-Ci, Photo-PARiGraph F: no plotsGraph G: no plotsGraph H: no plots

Real Time Graphics Displays

+ +Edit ♦ ReadOne♦ SaveOne♦ ♦ Done

+ + ♦ ReadAll♦ SaveAll♦ ♦ Done

Edit high-lighted entry

Read or Save definition for highlighted display

Read or Save all 8 definitions


Using the LI-6400 Version 5 xix

+ ♦ TurnON ♦ Read ♦ ♦ Done

97.08 12 1499 2.84

28.56 29.02 29.13TBlock°C Tair°C Tleaf°C

Prss_kPa ParIn_µm ParOutµm BLC_molg

h

→

Program ProgPrgs FwMxCrLp totalCV%k 00:00:12 5/10 1 1 1 1 3.26

Plot #1 < none >Plot #2 < none >Plot #3 < none >

Graph F

+ Edit ♦ ♦ ♦ Cancel ♦ Done

97.08 12 1499 2.84

28.56 29.02 29.13TBlock°C Tair°C Tleaf°C

Prss_kPa ParIn_µm ParOutµm BLC_molg

h

→

Program ProgPrgs FwMxCrLp totalCV%k 00:00:12 5/10 1 1 1 1 3.26

Plot #1 < none >Plot #2 < none >Plot #3 < none >

Graph F

Y Axis = Min=(0), Max=(1), ∆=1X Axis = (Strip Chart Time) Buffer: 10 mins

Plot #1

Press this key to enable a plot. You then choose between StripChart and XY Plot

Axes variables are se-lected from a list. (For StripCharts, only the Y axis variable is select-able).

Scaling options. There are four, shown below. When a min or max is ’Auto’ (automatically scaled), you specify a minimum change increment. That is, do you want it changing by 10, 1, 0.5, etc.For StripCharts, you can pick how many minutes of data to retain.

F: Fixed Min, Fixed MaxN: Auto Min, Fixed MaxX: Fixed Min, Auto MaxD: Fixed DeltaA: Auto Min, Auto Max

Scaling Option

Default


xx Using the LI-6400 Version 5

Stability TestingSystem stability was formerly determined by the coefficients or variation offlow and the IRGA differentials. In Version 5, it is completely user definable.You can pick a list of variables (system or user) and the stability criteria foreach, including rate of change, standard deviation, and/or coefficient of vari-ation.

In New Measurements mode, there is a function key on level 5 named DefineStability. This accesses a list of the current stability criteria, which you canedit, store, read, etc. Stability criteria can be stored as part of a system config-uration.

1 CO2R: 20s Slp


Using the LI-6400 Version 5 xxi

You can monitor some variables in New Measurements mode that indicatethe state of system stability. In addition to this, statistical details can beviewed in a diagnostic screen, described in the next section.

Diagnostic ScreensIn New Measurements mode, there is a new set of screens called DiagnosticScreens, that provide some behind-the-scenes information that is not normal-ly available for viewing. To get there, press the left square bracket key ([).There are 7 of diagnostic screens, labelled A through G, and you can navigateby typing A through G. When done, press [ or escape to leave.

Perhaps the most useful diagnostic screen is A, from which you can view allof the system stability information (discussed above).

3/4 0.75 1110 Stable StableF CHPC

e→

First letter from each of the variables checked for stabil-ity. In this case, it is CO2S, H2OS, Photo, and Cond.

3 of the 4 variables are stable

Numerical equivalent

(A) Stability Status = 2/3 1)CO2R 2)CO2S* 3)Tleaf

Sec 20 20 20 Mn 0.1234 5.8642 25.13SDv 1.1E-01 5.1E+00 2.8E-02%CV 8.9E+01 1.1E-01 1.1E-03Slp 1.1E-02 -3.2E-00 5.4E-03

Not Stable

Period,Mean,StdDev,%CV,and rate of change (slope)


xxii Using the LI-6400 Version 5

Log OptionsThere is a dialog named Log Options, available from the Logging Control Di-alog, or from the New Measurements screen (f4 level 5). (The key in eitherlocation is shown only if there is no log file open. You can’t change your logoptions in the middle of logging.)

HeaderThe choice is "Embedded (normal)" or "Separate .HDR file". The latter caseputs all the header entries (which normally go before the column labels) intoa separate file. This file has the same name as your log file, but with .HDRappended.

RemarksThe choice is "Embedded (normal)" or "Separate .REM file". The latter caseputs all remarks (including fluorescence actions) into a separate file (samename as log file, but with .REM appended), instead of interspersing them inthe data records.

Stability DetailsThe choice is "Not logged", or "Logged". Stability details refers to the list ofvariables that you are using to define system stability. Setting this option to"Logged" will cause extra data columns to be appended in your log file. Foreach variable in the stability list, you’ll get a sample count, mean, standarddeviation, coefficient of variation, and the rate of change. Each has a columnlabel, so you’ll know what they are.

StatisticsChoices are "None (normal)" or "-> .STATS file". The latter case will causestatistics (mean and standard deviation over a user-entered time period) to becomputed for each variable in your log list. This information is logged in aseparate file (same name as log file, but with .STATS appended).

Header: Embedded (normal)Remarks: Embedded (normal)Stability Details: Not loggedStatistics: -> .STATS file

Log Options


Using the LI-6400 Version 5 xxiii

User Definable Log ButtonWhat the log button does when pressed (while in New Measurements mode)is now user definable. f5 level 5 lets you select possible actions from a menuof choices:

The FilerThe file system has changed, and no longer requires periodic defragmenta-tion. Purging files moves them to a trash directory, and when the trash is emp-tied, the space is recovered.

The Filer function keys are shown below:

Changes are:

fiLter Short-cut key changed from F to L

Normal LogLog only (no prompts)Do NothingMeaureToggle_OnOffFarRedToggle_OnOffActinicToggle_OnOffDo FmDo FoFmDo FsFm’Do Fo’Do FsFm’Fo’Flash (no assign)Dark (no assign)

Log Button Action

Available when configured for the LCF

+ Dir ♦ fiLter♦ Sort ♦ Tag ♦ purGe

+ Copy ♦ Move ♦ dUplct ♦ Rename♦ Print

+ View ♦ Bview ♦ Edit ♦ grapH ♦ Working

+ space ♦ trAsh ♦ eXecute♦ Find ♦ re-scaN

Welcome to the LI-6400Version 5.2 Summary

xxiv Using the LI-6400 Version 5

The dialog for choosing directories has a slightly different look. It can showdirectories in a tree format or traditional full name format. Also, directoriescan be expanded or collapsed.

Version 5.2 SummaryVersion 5.2 brought additional changes:

Backlight ON at startupA new program has been added to the folder “/Sys/Autostart” named Back-LightON. (All files in this folder execute when LPL starts running at power

Bview Binary view. For viewing binary files, ortext files. Shows hex codes for each byte ofthe file.

space Gets the space on both file system parti-tions.

trAsh Empty the trash.

Find Find (global search) a file name.

P/P/User"P/User/JoeP/User/ConfigsR/User/Configs/AutoProgs

Select a Directory

+ Find ♦ fnd Nxt♦ Currnt♦ View ♦ Rename

+ R/P ♦ Add ♦ Purge ♦ CANCEL♦ SELECT

P/User-Joe-Configs

AutoProgs

View (or V) alternates between the full path names (above) and a tree view (left)

P

P

R

Open / Close directories. Directories that do not contain other directories are always shown as open (P).


Using the LI-6400 Version 5 xxv

up.) BackLightON is a very short program that simply turns on the displaybacklight (if present).

:FCT main{ 1 BACKLIGHT}

If you do not wish for this to happen, edit BackLightON, and change the 1 toa 0. Or, simply move the file to the trash.

The backlight can be toggled on and off at any time by pressing ctrl shifthome simultaneously.

New System Variable: TotalCVNew system variable TotalCV (id number -74) has been added in version 5.2.It is on display line ‘e’ by default.

TotalCV is the sum of the CVs (%) of all stability variables presently defined.For more on stability variables, see Stability Variables on page 14-11.

New System Constant: Oxygen%Another new system variable (actually a user-entered constant) is Oxygen%(id number -52). This value defaults to 21, but can be adjusted by you by put-ting it into the prompts list (Prompt Control on page 9-15). You can then beprompted for it in New Measurements mode (f5 level 3).

The purpose of Oxygen% is to account for O2 concentration in the computa-tion of CO2R and CO2S, the reference and sample CO2 concentrations, andon H2OR and H2OS, the reference and sample water vapor concentrations.

The impact of O2 on the CO2 measurement is a band broadening effect thatfits the theory fairly well (See Carbon Dioxide Concentrations on page14-6, and Band Broadening Corrections on page 14-23). For water vapor,with its much more saturated bands, the effect is entirely empirically deter-mined. See Water Concentrations on page 14-5.

New Configuration Parameter: LogOption=The Log Options (Log Options on page 9-9) can now be made part of a con-figuration file, and changes to them (done in New Measurements mode orfrom Logging Control) will trigger the CONFIG change flag in Open’s MainScreen.


xxvi Using the LI-6400 Version 5

Fan Control in IRGA Zero and SpanChamber fan control has been added to the IRGA zero and span routines. Thishas been done to allow these routines to be used with large chambers whichare attached directly to the IRGA sample cell. In this configuration, the cham-ber fan is the connection between the chamber’s volume and the IRGA’s cell.Turning the fan off allows the cell to measure incoming concentration withlittle influence from the chamber.

Typing ‘f’ will increment the fan speed through “Fast”, “Slow”, and “off”.See CO2 and H2O Analyzers on page 18-3.

Soil Respiration EnhancementsThe soil respiration chamber configuration has several improvements.

Logging RatePrior to version 5.2, raw readings were logged at 2 Hz, and an internal bufferof 50 pairs (rate of change and concentration) was filling up in about 30 sec-onds, leading to early termination of each cycle in some low flux / large deltacases. In 5.2, logging occurs once every two seconds, and the buffer size ismuch larger, so early termination should not be a problem.

All Settings in One PlacePrior to 5.2, the soil respiration configuration had settings accessed via sev-eral different function keys. Now, you can access them all from one place: f5level 7

Storable SettingsIn addition to being in one place, these settings are now storable. This featureis also accessed via f5 level 7.

These settings are saved (by default) in a new directory named /User/Con-figs/SoilParams. The default file is named /User/Configs/SoilParams/Std Settings,as defined in the default soil respiration configuration file:

SoilParams= “Std Settings”

If you use Save or Open in the soil settings editor to change this file, or if youmake a change to one or more of these settings and don’t update the file, theCONFIG flag will appear in the main screen, and the Config Status displaywill show the reason: an unsaved file, or a different file name.


Using the LI-6400 Version 5 xxvii

New Configuration: Custom Chamber - ClosedA new configuration builder is available in the Installation menu, named"Custom Chamber - Closed". The fundamental assumption here is that fluxmeasurements are to be made in a closed (non-flow through) chamber basedon a time rate of change of CO2. The program will guide you through a seriesof questions, and build an appropriate configuration based on your responses.See Custom Chamber - Closed on page 16-20

New Configuration Parameter: MatchType=OPEN 5.2 adds the option of an alternative matching scheme, useful for turfand soil chambers operating in open mode. See Matching Without theMatch Valve on page 16-34.

Version 5.3 Summary

MultiLevel Flash Option for the LCFVersion 5.3 adds support for doing multilevel saturation flashes with the6400-40 LCF. This technique allows the fluorescence at saturation to be mea-sured without actually achieving saturation. This type of flash has three dif-ferent intensity levels, and the saturated value of F is computed by plotting Fagainst 1/Q, and finding the 1/Q intercept. See Saturating Flashes on page27-22.

Interfacing OptionsVersion 5.3 add remote control capability, using a computer connected to theRS-232 port, or over the internet. See Control via Terminal Software(LTerm / iTerm) on page 11-16.

Version 5.3 makes it very simple to incorporate data coming in the RS-232port into user variables in OPEN. See Importing RS-232 Data on page15-14.

Incoming data can also be treated as commands to be compiled and executed.This allows other devices to exchange data with - as well as have some con-trol over - the LI-6400. See Control via LPL Commands on page 11-20.

Minor ChangesVersion 5.3 has a number of minor changes, including


xxviii Using the LI-6400 Version 5

• Tab is the defaultThe tab character is now the default delimiter in log files, instead of a comma.This can be changed with a configuration command, if you wish.

• Logged Data can be simultaneously echoed to the Comm PortPrior to version 5.3, you could log to a file or to the Comm port. Now you cando both. See Using the Comm Port on page 11-4.

Part I

The Basics

Using the LI-6400 Version 5 1-1

1System DescriptionWhat it is, what it does, and how it does it

AN OPEN SYSTEM 1-2Measuring Differentials 1-2The Air Supply 1-3Leaks 1-3

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

EQUATION SUMMARY 1-7Transpiration 1-7Total Conductance to Water Vapor 1-8Stomatal Conductance to Water Vapor 1-9Net Photosynthesis 1-9Intercellular CO2 1-10Everything Else 1-11Summary of Symbols 1-11

THE SYSTEM COMPONENTS 1-12The Standard Parts 1-13The Optional Accessories 1-14

System Description

1-2 Using the LI-6400 Version 5

1This chapter acquaints you with the LI-6400’s operating principle, majorcomponents, and equations.

An Open System

Measuring DifferentialsThe LI-6400 is an open system, which means that measurements of photosyn-thesis and transpiration are based on the differences in CO2 and H2O in an airstream that is flowing through the leaf cuvette (Figure 1-1).

Sample IRGA

Reference IRGA

Flow x ∆CO2Area

Photo = Trans =Flow x ∆H2O

Area

Figure 1-1. In an open system, photosynthesis and transpiration are computedfrom the differences in CO2 and H2O 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-6400

Console

Console

Cuvette

Cuvette

System DescriptionAn Open System


The LI-6400 improves upon traditional open systems by having the gas ana-lyzers in the sensor head. This eliminates plumbing-related time delays, andallows tight control for responding to leaf changes. For example, if stomataclose, the control system immediately detects the drop in water vapor and cancompensate. Similarly, a sudden change in light level will cause an immedi-ate change in photosynthetic rate, which will be detected as a change in theCO2 concentration. The speed of detection is not a function of the system’sflow rate, as in traditional systems, since the sample IRGA is in the cuvette.

There is a second advantage of having the IRGAs in the sensor head. The tra-ditional system has the potential for concentration changes (because of watersorption and CO2 diffusion) as the air moves from the reference IRGA to thechamber, and again from the chamber back to the sample IRGA. This is nota problem for the LI-6400, because the IRGA measurements are made afterthe air has travelled through the tubing.

The Air SupplyOne strength of an open system is that the incoming air stream can be condi-tioned. That is, its humidity, CO2 concentration, temperature, etc. can be es-tablished by some means prior to entering the system.

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

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

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

ations in incoming concentration will cause concentration differences to bevery erratic.

Leaks“Pressure inside the leaf chamber is slightly above ambient to ensure thatleaks are outward, so outside air does not enter the chamber and affect theCO2 and H2O concentrations.” This argument for the advantage of an opensystem has been made for a long time, and it’s true - as far as it goes. Thereis another process at work: diffusion. CO2 will always diffuse from higherconcentrations toward lower, even against a pressure gradient, and is onlylimited by the material through which it is moving. The black neoprene gas-kets that we use on the LI-6400 (except for the light source) have the lowest

Incoming concentrations must be stable.

System DescriptionThe 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 largeconcentration difference between chamber and ambient. See DiffusionLeaks on page 4-43 for more details.

The Flow SchematicThe LI-6400 provides mechanisms for modifying the incoming air’s CO2 andH2O concentrations (Figure 1-2 on page 1-5). There are chemical tubes forscrubbing CO2 and H2O, and air can be diverted through these tubes in anyproportion desired. CO2, however, is best controlled by scrubbing all of itfrom the incoming air, and using the 6400-01 CO2 mixer to inject just enoughCO2 to provide a stable concentration at the desired value. If the 6400-01 isnot part of your system, you will need to use a buffer volume. For a morecomplete discussion of buffer volumes, see Air Supply Considerations onpage 4-48.

Humidity control in the leaf cuvette is achieved by regulating the flow ratethat is going though the cuvette. In units without a CO2 mixer, the pumpspeed controls the flow, and in units with a CO2 mixer, a flow diverter regu-lates this flow.



75%Flow

Flow Meter

Bypass Valve

Bypass Valve

Restrictors

Desiccant

CO2 Scrubber

SampleReference

Air In

Pump

25%

75%25%

CO2FlowControl

AirFlowControl

Pump

CO2

Flow

Flow Meter

Vent

Bypass Valve

Bypass Valve

Liquid CO 2

Vent

Restrictors

Desiccant

CO2 Scrubber

Pur

e C

O2

SampleReference

Air In

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

Schematic with a 6400-01 CO2 Mixer

Schematic without a 6400-01 CO2 Mixer



1

Matching the IRGAsThe heart of the computation of transpiration and assimilation is the measure-ment of the concentration differences. Since these differences are measuredby 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 match.Matching in this manner is a problem, however, because you don’t want toremove the leaf from the chamber in the middle of an experiment. TheLI-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 or∆H2O value is small (low rates, small leaf areas). For example, a1 µmol mol-1 difference between the two CO2 IRGAs is trivial when the

∆CO2 is 75 µmol mol-1, but represents a significant error if the ∆CO2 is only3 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

System DescriptionEquation Summary


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

The equations for net photosynthesis, transpiration, etc. are essentially thosederived by von Caemmerer and Farquhar1. Note also that these equations rep-resent the instrument’s defaults, and can be modified or replaced as desiredby the user (Chapter 15).

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

(1-1)

where s is leaf area (m-2), E is transpiration rate (mol m-2 s-1), ui and uo are

incoming and outgoing flow rates (mol s-1) from the chamber, and wi and woare incoming and outgoing water mole fractions (mol H2O mol air

-1). Since

(1-2)

we can write

(1-3)

1.S.von Caemmerer and G.D.Farquhar (1981) Some relationships between thebiochemistry of photosynthesis and the gas exchange of leaves, Planta 153:376-387

ui uo

E

Figure 1-4. Measuring fluxes in an open system. Transpiration rate (E) and pho-tosynthetic rate (a) change the water and CO2 concentrations of air as it passesthrough the chamber. Transpiration also causes the exit flow uo to be greater thanthe incoming flow rate (ui).

wi wo

a

ci co

sE uowo uiwi–=

uo ui sE+=

sE ui sE+( )wo uiwi–=



1

which rearranges to

(1-4)

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

(1-5)

where F is air flow rate (µmol s-1), Ws and Wr are sample and reference water

mole fractions (mmol H2O (mol air)-1), and S is leaf area (cm-2). 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 Wl is the molar concentration of water vapor within the leaf

(mmol H2O (mol air)-1), which is computed from the leaf temperature Tl (C)

and the total atmospheric pressure P (kPa)

(1-8)

Eui wo wi–( )s 1 wo–( )

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

ui F 106⁄=

wi Wr 103⁄=

wo Ws 103⁄=

s S 104⁄=

EF Ws Wr–( )

100S 1000 Ws–( )-------------------------------------------=

gtw

E 1000Wl Ws+

2--------------------–

Wl Ws–------------------------------------------------=

Wle Tl( )

P------------ 1000×=



The function e(T) is saturation vapor pressure (kPa) at temperature T (C). Theformula used by the LI-6400 is (14-22) on page 14-10.

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

-2 s-1) is obtainedfrom the total conductance by removing the contribution from the boundarylayer.

(1-9)

where kf is a factor based on the estimate K of the fraction of stomatal con-ductances of one side of the leaf to the other (termed stomatal ratio through-out this manual),

(1-10)

and gbw is the boundary layer conductance to water vapor (mol H2O m-2s-1)

from one side of the leaf. The boundary layer conductance correction thus de-pends 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

(1-11)

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

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

we can write

(1-12)

which rearranges to

gsw1

1gtw--------

k fgbw---------–

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

k fK

21+

K 1+( )2---------------------=

sa uici uoco–=

sa uici ui sE+( )co–=



1

(1-13)

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

(1-14)

where Cr and Cs are sample and reference CO2 concentrations

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

(µmol CO2 m-2 s-1). Substitution yields

(1-15)

Why does transpiration appear in the equation for photosynthesis? (Askingthis question means you didn’t follow the derivation…) The short answer isthat it serves as a dilution correction; as the leaf adds water vapor to the cham-ber, it dilutes all other gasses, including CO2.

Intercellular CO 2The intercellular CO2 concentration Ci (µmol CO2 mol air

-1) is given by

(1-16)

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

(1-17)

aui ci co–( )

s------------------------- Eco–=

ci Cr 106⁄=

co Cs 106⁄=

a A 106⁄=

AF Cr Cs–( )

100S--------------------------- CsE–=

Ci

gtcE2---–

Cs A–

gtcE2---+

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

gtc1

1.6gsw--------

1.37k fgbw

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

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



1.6 is the ratio of the diffusivities of CO2 and water in air, and 1.37 is the sameratio in the boundary layer.

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

Summary of Symbolsa = net assimilation rate, mol CO2 m

-2 s-1,

A = net assimilation rate, µmol CO2 m-2 s-1

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

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

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

Cr = 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

kf = (K2 + 1)/(K + 1)2,K = stomatal ratio (dimensionless); estimate of the ratio of stomatal conduc-tances of one side of the leaf to the others = leaf area, m2

S = leaf area, cm2

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

uo = outgoing flow rate, mol air s-1.

wi = incoming H2O mole fraction, mol H2O mol air-1.

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

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

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

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

System DescriptionThe System Components


1

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

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

Console

Sensor Head/IRGA

Quantum Sensor(Optional)

Chemical Tubes

Cable Assembly

CO2 Cartridge Holder and Regulator (Optional)

2x3 Chamber



The Standard Parts

ConsoleThe 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. CO2scrubber and desiccant tubes attach to the left side of the console, along withthe optional 6400-01 CO2 source assembly or CO2 tank connector block. Afield stand is normally attached to the underside of the console.

Sensor Head/IRGAThe sensor head/IRGA includes a leaf chamber, spring-loaded latching han-dle (squeeze and release to open, squeeze and release to close), two Peltierthermoelectric coolers, and the sample and reference gas analyzers. Up to twolight 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.) Leaftemperature 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 con-nects the console to the sensor head / IRGA. These are held together with aflexible, outer wrapping.

Spare Parts KitThis box contains replacement parts for your LI-6400. As you become famil-iar 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 fromthe incoming air stream. One tube should contain soda lime, and the othertube 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 charged.Because they slowly self-discharge with time, it is a good idea to test yourbatteries periodically. Leaving them discharged for an extended period canresult in damage. (See 6400-03 Batteries on page 19-8 for instructions con-



1

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

LI-6020 Battery ChargerThe LI-6020 can charge four 6400-03 Rechargeable Batteries simultaneous-ly. It runs on 92-138/184-276 VAC, 47 to 63 Hz, but a selector switch on theback of the LI-6020 must be set to the appropriate mains voltage.

RS-232C CablePart number 9975-016 has a 9 pin to 9 pin cable, and a separate 9 to 25 pinadapter. Figure 11-1 on page 11-3 illustrates how to use it.

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

6400-55 CDThe CD contains a hyper-linked, electronic version (.pdf file) of this manual,plus a number of Windows® and Macintosh® support programs for taskssuch as (re-)installing instrument software, running the LI-6400 from a com-puter, and doing data file transfers. Note: New versions of this software arereleased periodically. You can get the most recent version by contactingLI-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 at thefactory. Keep it in a safe place for future reference.

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

The Optional AccessoriesThere are several optional accessories that you may have ordered with yourLI-6400. Any of them can also be purchased later, and (with the exception ofthe 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 2-6on page 2-8).

• An adapter block for CO 2 tanksThis alternative to the cartridge holder and regulator allows tanks of com-pressed pure CO2 to be used instead of the 12 gram cartridges (see Figure 2-8on page 2-11).

6400-02B LED Light SourceThe 6400-02B replaces the top half of the standard leaf chamber and provideslight from 0 to over 2000 µmol quanta m-2 s-1. The intensity of the light issoftware adjustable to a resolution of 1 µmol m-2 s-1. The 6400-02B replacesthe 6400-02, which used only red LEDs. See Spectral Considerations onpage 8-7 for a comparison of the 6400-02 and 6400-02B.

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

6400-06 PAM 2000 AdaptorThis chamber top is designed for 8 mm fluorometer probes such as is used onthe PAM 2000 (Heinz Walz GmbH, Effeltrich, Germany) and Hansatech In-struments, Ltd (Norfolk, England). It can be used with the standard 2x3 cmopaque chamber bottom, or the 6400-08 Clear Bottom Chamber. A GaAsPlight sensor is included.

6400-07 Needle ChamberA 2x6 cm chamber with Propafilm® top and bottom windows. Leaf temper-ature 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 iscomputed using an energy balance. This chamber can be used with any 2x3cm chamber top (such as the fluorometer adapters) or 6400-02 or -02B LEDsource.



1

6400-09 Soil ChamberFor measuring soil CO2 efflux.

6400-10 MiniPAM AdaptorThis is a 2x3 cm chamber top that is designed to hold a 2 mm fiber probe, suchas is used by the MiniPAM fluorescence system (Heinz Walz GmbH, Effel-trich, Germany). A GaAsP light sensor is included.

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

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

6400-14 Opti-Sciences AdapterThis is a 2x3 cm chamber top that is designed to accommodate the 10 mm tri-furcated fiber probe used by Opti-Sciences fluorometers (Opti-Sciences,Tyngsboro, MA). A GaAsP light sensor is included.

6400-15 Arabidopsis ChamberThis is a chamber designed for Arabidopsis and other small leaves. The aper-ture is 1.0 cm in diameter, and has a Propafilm® top and bottom. No light sen-sor is included. Leaf temperature comes from an energy balance analysis, forwhich an external quantum sensor is necessary (but not included).

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

6400-70 AC AdapterThis optional accessory fits in the battery compartment, and allows theLI-6400 to be powered from mains power. It can simultaneously (but slowly)recharge one battery.

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

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


2Assembling the LI-6400Putting it all together

PREPARATIONS 2-2The CO2 Scrub and Desiccant Tubes 2-2Cables And Hoses 2-3Connecting the Chamber / IRGA 2-5

USING A TRIPOD 2-6

6400-01 CO2 INJECTOR INSTALLATION 2-7Using CO2 Cartridges 2-8External 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 2-18LI-6020 Battery Charger 2-186400-03 Batteries 2-18Other Batteries 2-196400-70 AC Module 2-20

INSTALLING SYSTEM SOFTWARE 2-22Hardware Requirements 2-22What To Do 2-23

Assembling the LI-6400


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

PreparationsThis section explains how to prepare the console and sensor head for opera-tion.

The CO2 Scrub and Desiccant TubesThe CO2 scrub and desiccant tubes can remain attached to the console at alltimes, except when changing chemicals. Figure 2-1 shows the position ofthese 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 thebottom cap. If the top cap is unscrewed with chemical inside, damage to theair mufflers will occur.

Remove the bottom cap of the CO2 scrub tube, and fill the tube with soda lime(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 desic-cant is provided in the spares kit.

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

Keep the threads on the end cap and barrel clean

Do not over-tighten the attachment screws (Figure 2-1). Slightlysnug (finger power only - never pliers) is sufficient. The O-rings dothe sealing.

Assembling the LI-6400Preparations


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

Electrical ConnectorsPlug the female 25-pin connector into the receptacle labeled IRGA, and themale 25-pin connector into the receptacle labeled CHAMBER . These connec-tors are gender specific, and can not be interchanged. Tighten (slightly) thescrews on the connectors, but be careful: these screws can break off if tight-ened 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. This isthe intake through which the pump draws in the air that flows through the sys-tem.

If your system does not have a CO2 injector, attach tubing from a buffer vol-ume to the INLET port. The buffer volume can be as simple as a clean, dry 2-liter plastic soft drink bottle. The larger the volume, the better. For more de-tails, see Air Supply Considerations on page 4-48.

Figure 2-1. Desiccant and CO2 scrubber tubes.

Desiccant Tube

CO2 Scrub Tube

Air Passage Holes

O-Rings

Open This End

Don’t Over-Tighten



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 bandnear the end of the hose. Attach this hose to the SAMPLE port of the console.Attach the other hose to the REF port.

Figure 2-2. Console tubing and cable connections.

RS-232

Air Inlet

Sample

ReferencePower Switch



Connecting the Chamber / IRGAThe sensor head/IRGA end of the electrical cables attach as shown inFigure 2-3. Be careful not to overtighten the screws on the 26 pin D connec-tor. To plug in the round connector, first line up the red dots, then push theconnector 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 holeson 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 interchangethe IRGA/chambers? The simple answer is (probably) no; they are not de-signed to do it. Each LI-6400 console is adjusted at the factory for a par-ticular head. If you mismatch them, you may not able to zero the IRGAs.

Assembling the LI-6400Using a Tripod


2

Using a TripodA mounting bracket is included in the spare parts kit for mounting the sensorhead 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 holeson the right side of the analyzer housing on the sensor head (Figure 2-4). Thetripod 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 ofthe sensor head.

Tripod Head

Tripod Mounting�Bracket

Analyzer Housing (rear view)

122-04276

Assembling the LI-64006400-01 CO2 Injector Installation


6400-01 CO2 Injector Installation

Figure 2-5. 9964-026 External CO2Source Assembly

The optional 6400-01 CO2 Injector consists of a controller thatis factory installed within the LI-6400 console, and an externalpart that attaches between the chemical tubes on the end of theconsole. 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 page2-10.

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 thetime 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.

WA

RN

ING

:�H

igh Pressure�

�

WARNING:�Pressure Liquefied Gas�SLOWLY

Regulator

O-ring

CO2 Cylinder

CO2 Cylinder Cover

CO2 Cylinder �Piercing Block

Piercing Pin

CO2 Source �Mounting Block

Vent



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 seated.Tighten the two knurled knobs on the mounting block to secure the assemblyto the console.

2 Unscrew the CO 2 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 ahole on the underside of the mounting block.

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

Check for O-rings in these two locationsCylinder Cover

12 gram cylinder

CO2 source at-taches here.

Oil Filter



Important Note: Although the O-ring may perform properly for several cyl-inders, we recommend that it be replaced with each new cylinder. After beingsubjected to several high pressure cycles the O-ring weakens and becomesperforated, and easily tears or splits. If the O-ring is slightly torn or perforat-ed, gas slowly leaks through the vent hole shortening the life of the cylinder.If 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 of thesource assembly (Figure 2-6). It’s a good idea to unscrew the cap (before youinstall the cylinder!) and look down in at the end of the filter to check for anyoil accumulating on the white filter material. If the filter is getting discolored,change the filter. See Servicing the External CO2 Source Assembly onpage 19-38 for more details. (With LI-COR cylinders, the filter should last for25 cylinders. We have encountered other cylinders, however, that containmuch more oil, notably Copperhead™ and Curtis™ brands, so beware.)

5 Place a new CO 2 cylinder into the cylinder coverThe cylinder goes in large end first, although one of our engineers accidental-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.



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 isminimal 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 CO2 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 and220 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. Thisfitting has a flow restrictor installed (10 cm3 min-1). Do not remove this fit-ting. A 1/8” to 4mm compression union is also provided for users who maybe 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 CO 2 Tank Connector BlockUse the two knurled knobs to mount the block between the CO2 and H2Oscrub tubes. Make sure that the O-ring seal on the back of the block is prop-erly seated.

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

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



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

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

4 Connect your CO 2 source.The other end of the copper tubing connects to your CO2 source. Adjust yourregulator 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 Con-nector Block to a CO2 source using 4mm tubing and the compression fitting(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



2

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

2 Connect the 1/8” and 4mm tubing Use 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 thenuts on the compression fitting until snug, plus 1 1/4 turn.

3 Connect the 4mm tubing to your CO 2 source. Adjust the regulator’s pressure to between 180 and 220 PSIG.



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 4mm�Compression Fitting

1/8" Nut

4mm Nut

Assembling the LI-6400External Quantum Sensor Installation


2

External Quantum Sensor InstallationThe external quantum sensor is held in its mounting bracket with a small setscrew (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 sensor,its calibration factor will have already been entered into the instrument. Oth-erwise, you will have to do this. See The Installation Menu on page 16-5.

Figure 2-10. The external quantum sensor installed.

BNCConnector

Set screw

Assembling the LI-6400Attaching the LED Light Source


Attaching the LED Light SourceThe optional 6400-02 or -02B LED Light Source is mounted to the sensorhead by removing the upper half of the leaf chamber and replacing it with thelamp 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 sensor.

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

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

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

Log switch connector

Light sensor connector

Assembling the LI-6400Attaching the LED Light Source


2

3 Remove the top leaf chamber Use 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 lips are held on with two hex headbolts. Use the 3/32 inch hex key to loosen and tighten them.

Gasket

GaAsP PAR sensorConnector O-rings

Upper leaf�chamber cuvette

Top View

140-04251

192-04357192-04356

Assembling the LI-64006400-40 Leaf Chamber Fluorometer


5 Install the lamp assemblyAttach the lamp connector and PAR sensor connector as shown inFigure 2-13. Ensure that the PAR sensor is attached to the connector near therear of the analyzer housing, not to the log switch connector.

If the LED source was purchased with the LI-6400, its calibration factor willhave been installed in the console. Otherwise, you will have to do this. SeeExample: 6400-02B LED Source on page 16-6 for how to do this using theInstallation Menu.

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

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

Lamp Connector

PAR Sensor�Connector

External Quantum�Sensor BNC�Connector

Log Switch�Connector

LED Lamp

Leaf Temperature�Thermocouple Holder

Air Hose

�

+C

HC

ON

ST

E

CH

RO

ME

L

CO

NS

TEO

ME

GA

+

+

140-04251

Assembling the LI-6400Powering 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 Moduleon page 2-20.) It can, however, be operated with the charger and a single6400-03 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 dis-charge, and eventually need to be swapped. (Procedure to swap: Disconnectthe 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 batteries.The 6200B batteries used with other LI-COR instruments can also be used,but with less convenience since they will not fit into the battery compartmentof the LI-6400.

The 6400-03 batteries have a capacity of approximately 3 Amp-hours each.The 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 3A.Without the light source, it will draw about 2A. Table 2-2 shows the approx-imate 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 Hours

LI-6020 and one 6400-03 Indefinite 6 Hours 3 Hours



• 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 are dis-play indicators as well (see Low Battery Warning on page 5-17). One lowbattery can be removed and replaced with a fresh one while the system con-tinues to run without interruption. Immediately replace the second low bat-tery with a freshly charged battery to ensure maximum operation time.

Note that you can also power the LI-6400 using any 12 volt battery with suf-ficient capacity; a car battery, for example, will run the system for 24 to 48hours before recharging is necessary.

Other BatteriesYou can power the LI-6400 with any 12 V battery (car, marine, etc.) that hasat least a 1.5 Amp-hour capacity. To connect an alternative battery to the con-sole, you’ll need a 318-02031 connector (the kind that is on the 6400-03 bat-tery). One simple way to get this connector already attached to a cable is toremove it from a dead 6400-03 battery. Alternatively, you can order theseconnectors by themselves, or else order part number 9960-120, which is thisconnector attached to 10 feet of cable, or else obtain a 9960-062 (the cablethat runs between the console and an LI-6020 charger), and cut it in half toget two short (2.5 ft.) versions of a 9960-120.

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

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



2

6400-70 AC ModuleThis optional accessory allows the LI-6400 to be powered from mains power.It 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 batteryinto the module will provide 1 or 2 hours continued operation in case of mainspower failure.

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

• Hot swappingYou can switch from AC operation to battery operation by unplugging one ofthe module’s plugs from the console, and replacing it with a fresh battery.Then disconnect the other plug, and replace it with second battery if you wish.Reverse 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 plugit into the module (as shown here), that battery will trickle charge, butmore importantly, provide continued operation for 1-2 hours in theevent of a mains power failure.



SAMPLE

REF

INLET!

UNPLUG BATTERIES

BEFORE SERVICING.

O l

CHG PWR

BATTERYINPUT - 12VD

C

CHARGE - 14.8VDC 0.65A M

AX.

INPUT17-24VDC72W

OUTPUT14.8VDC4.0A MAX.

MODEL 6400-70

SAMPLE

REF

INLET!

UNPLUG BATTERIES

BEFORE SERVICING.

O l

CHG PWR

BATTERYINPUT - 12VD

C

CHARGE - 14.8VDC 0.65A M

AX.

INPUT17-24VDC72W

OUTPUT14.8VDC4.0A MAX.

MODEL 6400-70

Battery Battery

Battery safely trickle charges, and is available to run the instrument if mains power fails.

Battery is being charged in an uncontrolled man-ner. Damage could result to the battery and/or the 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 uncon-trolled 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 minute

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

Assembling the LI-6400Installing 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 thenew software into the LI-6400. To see what version of software you have in-stalled, select “About this unit” in the Welcome Menu (see Figure 3-6 onpage 3-9). You can see what the latest available system software is (anddownload it) by checking our web site: www.licor.com.

Hardware Requirements

Version 5.0 and aboveVersion 5.0 and above requires the new digital board, which began shippingwith serial number PSC-1214. Any LI-6400 can be upgraded to this board.The upgrade is part number 6400-915. To determine which board an LI-6400has, see Figure 2-16.

2.Or fix enhancements and add bugs…

INITIALIZING.BOOTING PAUSEDUSE THE LI-6400 UPDATE PROGRAM

Welcome to LI-6400(R)un(U)pload(C)heck CRC(B)ps = 115200(T)erminal

Select:_

(V)oltages(S)ave parms(+/-/UP/DOWN) contrast(D)ebug: OFF

New Board (uses version 5)

Old Board (cannot use version 5)

Figure 2-16. To determine which digital board an LI-6400 has, power up withthe escape key held down, and see which display is shown.



Version 4Version 4.x requires the 6MB flash memory board, which has been standardon all units from about serial number PSC-350 until the shift was made to thenew digital board. Any old-board unit can be upgraded to this memory board.(Part number 6400-906.).

Version 3What’s left is version 3.x, which can be installed on any old-board LI-6400.

Note: The 6400-40 Leaf Chamber Fluorometer requires at least Version 4(old board) or Version 5 (new board).

What To DoThe latest system software (3.x, 4.x, or 5.x) is available on the 6400-55 CD,and also from our web site (www.licor.com). The version 5 installer requiresWindows®, while the Version 3 or 4 can be done with Macintosh® or Win-dows® computers.

1 Obtain the system softwareSystem software is on the CD, or can be downloaded from our web site.

2 Power the LI-6400 on while pressing escape.This will access the Boot Screen (Figure 2-16 on page 2-22).

3 Connect the computer to the LI-6400Connection instructions are on page 11-2.

4 Run the installation programTwo pieces of software are installed: LPL and the /Sys directory. LPL is theoperating system that supports the programs that run on the LI-6400, and the/Sys directory contains those programs. The installation should not affect anyother file system information, other than updating the factory default files(listed in Table 16-3 on page 16-19) in the /User/Configs directory.



2


3Guided ToursLearning how to make it work

BEFORE YOU START 3-2Cursor Control Keys 3-2Function Keys 3-2Display 3-2

TOUR #1: OPEN OVERVIEW 3-4Running OPEN 3-4Alert Messages in OPEN’s Main Screen 3-7The Welcome Menu 3-9The Config Menu 3-11The Calib Menu 3-12The Utility Menu 3-14New Measurements 3-14

TOUR #2: NEW MEASUREMENTS MODE BASICS 3-15Function Keys 3-17Text Display 3-19Graphics Displays 3-23

TOUR #3: CONTROLLING CHAMBER CONDITIONS 3-29Fixed Flow Operation 3-29Fixed Humidity Operation 3-33Dynamic Response of Humidity Control 3-36CO2 Control - Without a 6400-01 3-42CO2 Control - With a 6400-01 3-43Temperature Control 3-45Lamp Control 3-48Control Summary 3-49

TOUR #4: LOGGING DATA 3-50Logging Data Manually 3-50Viewing Stored Data 3-52Automatically Logging Data 3-59Stability 3-61Log Options 3-67

TOUR #5: CONFIGURATION INTRODUCTION 3-69Configuration Basics 3-69Equations, Displays, LogLists 3-76Using The Installation Menu 3-81

TOUR #6: LPL 3-86The LPL Screen 3-86

Guided Tours


3The purposes of this chapter are to teach you a) how to operate the LI-6400,and b) how the LI-6400 accomplishes its tasks. We do this with a series ofguided tours. We recommend that you follow along on your instrument. Youwon’t need plant material for these tours - that will come in Chapter 4.

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 rightgroup, and it doesn’t matter which you use. Similarly, there are two enterkeys and two labels keys.

Function KeysKeys labeled f1 through f5 below the display are called function keys, and of-ten have labels associated with them on the bottom line(s) of the display.When there are multiple definitions for these keys, the labels key can be usedto cycle through them. Sometimes, the labels remain hidden even thoughfunction keys are defined and active; pressing labels will make the labelstemporarily appear.

DisplayThe display has independent text (8 lines, 40 characters per line) and graphics(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.

Guided ToursBefore You Start


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

Cursor control keys.

escape key

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 f1 f1 f1 f1

LI-6400 Photosynthesis SystemOPEN 5.3

/User 2% fullThr Jun 3 2004 09:46:55 12.01V

WelcomeMenu

ConfigMenu

CalibMenu

NewMsmnts

UtilityMenu

Guided ToursTour #1: OPEN Overview


3

Tour #1: OPEN Overview

Running OPENOPEN is the name of the program that you’ll be running most of the timewhen you use the LI-6400. This program begins to run automatically afteryou power on (unless you intervene), as you’ll see in the f

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