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Using the LI-6400 Portable Photosynthesis System

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Using the LI-6400 Portable Photosynthesis System Using the LI-6400 Portable Photosynthesis System NOTICE The information contained in this document is subject to change without notice. LI-COR MAKES NO WARRANTY OF ANY KIND WITH REGARD TO THIS MATERIAL, INCLUDING, BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. LI-COR shall not be liable for errors contained herein or for incidental or 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 part of this document may be photocopied, reproduced, or translated to another language without prior written consent of LI-COR, Inc. © Copyright 1998,1999, LI-COR, Inc. Publication Number 9806-122 Printing History: 1st Printing July, 1998 - OPEN Software version 3.2 2nd Printing May, 1999 - OPEN Software version 3.3 3rd Printing Sept, 2000 - OPEN Software version 3.4 4th Printing Sept, 2001 - OPEN Software version 4.0 Macintosh® is a registered trademark of Apple Computer, Inc. Printing History New editions of this manual will incorporate all material since the previous editions. Update packages may be used between editions which contain replacement and additional pages to be merged into the manual by the user. The manual printing date indicates its current edition. The printing date changes when a new edition is printed. (Minor corrections and updates which are incorporated at reprint do not cause the date to change). 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 68504 Phone: 402-467-3576 • FAX: 402-467-2819 Toll-free: 1-800-447-3576 (U.S. & Canada) Contents Contents Welcome to the LI-6400 A Bit of History xiii About this Manual xv 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 1-12 2 Assembling the LI-6400 Putting it all together Preparations 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 2-19 3 Guided Tours Learning how to make it work Before You Start 3-2 Tour #1: OPEN Overview 3-4 Using the LI-6400 iii Contents Tour #2: New Measurements Mode Basics 3-14 Tour #3: Controlling Chamber Conditions 3-21 Tour #4: Logging Data 3-42 Tour #5: Configuration Adventures 3-52 Tour #6: Boot Screen and LPL 3-60 4 Making Measurements The fundamentals of good measurements Preparation Check Lists 4-2 Some Simple Experiments 4-8 Making Survey Measurements 4-21 Light Response Curves 4-24 CO2 Response Curves 4-30 Matching the Analyzers 4-34 Stability Considerations 4-41 Leaks 4-42 Operational Hints 4-47 Answers to Questions 4-53 Part II: Useful Details 5 Standard Tools Menus, Editors, and File Dialogs Standard Menu 5-2 Standard Line Editor 5-5 Standard File Dialog 5-9 Standard Edit 5-13 Hot Keys 5-16 Low Battery Warning 5-17 The Boot Screen 5-18 The LPL Screen 5-20 Power ON Hooks 5-23 6 Real Time Data Viewing real time data using text and graphics Text Display 6-2 Real Time Graphics 6-8 iv Using the LI-6400 Contents 7 Environmental Control How OPEN controls chamber conditions Open’s Control Manager 7-2 Humidity Control 7-7 CO2 Control 7-13 Temperature Control 7-16 Light Control 7-18 8 Light Sensor Considerations The most important parameter is the hardest to measure Why Two Sensors? 8-2 Specifying the Source and Sensor 8-3 6400-02 and -02B Light Sources 8-6 6400-40 Leaf Chamber Fluorometer 8-8 Gallium Arsenide Phosphide (GaAsP) Sensor 8-9 9 Data Logging Storing what you want, where you want, when you want Basic Concepts 9-2 Getting Started 9-4 Determining What is Logged 9-7 Prompts and Remarks 9-12 AutoPrograms 9-18 AutoProgram Descriptions 9-21 Making Your Own AutoPrograms 9-33 Part III: Working With Files 10 The LPL File System Managing your data storage space Files, Directories, and Disks 10-2 Defragmentation 10-5 The Filer 10-6 Filer’s Directory Operations 10-9 Filer’s File Operations 10-11 Filer’s Disk Operations 10-18 Recovery Operations 10-20 Troubleshooting 10-25 Using the LI-6400 v Contents 11 Downloading Files Retrieving your data Connecting the LI-6400 to a Computer 11-3 File Exchange Mode 11-4 Using WinFX 11-4 Using FX for DOS 11-8 Using FX on Macintosh 11-10 Using EW 11-12 Odds and Ends 11-21 Using a Data Capture Program 11-23 12 GraphIt A tool for viewing and graphing data files Accessing GraphIt 12-2 Data File Format 12-4 Defining Plots 12-6 Selecting Observations 12-10 Curve Fitting 12-14 Viewing Data 12-18 PlotDef File Format 12-20 Storing and Retrieving Graphics Images 12-20 13 Recomputing Data Files How to recompute data files Reasons to Recompute 13-2 A Step By Step Example 13-2 The Details 13-7 Hints 13-14 Part IV: Configuration Issues 14 OPEN’s System Variables Quantities provided by OPEN Background Information 14-2 Measured Variables 14-4 Computed Variables 14-9 Time and Logging Variables 14-12 Status Variables 14-12 vi Using the LI-6400 Contents Boundary Layer Variables 14-17 List of Open 4.0 System Variables 14-19 Band Broadening Correction for Water Vapor 14-24 15 Defining User Variables Equations, Constants, and Remarks The ComputeList File 15-2 ComputeList File Format 15-3 Writing and Modifying ComputeList Files 15-7 User Defined Constants and Remarks 15-13 Examples 15-14 Useful Variables and Functions 15-16 The Default ComputeList 15-17 Old Style vs. New Style 15-18 16 Configuration Basics What you need to know to get by A Definition of Terms 16-2 Making Configuration Files 16-4 Installation Menu: Behind the Scenes 16-10 Modifying Config Files 16-12 The Reset Menu 16-16 Configuration Command Summary 16-18 17 Using an Energy Balance Computing what you can’t measure The Theory 17-2 Using Energy Balance in OPEN 17-6 Energy Balance And Boundary Layer 17-9 Further Reading 17-11 Part V: Maintenance & Troubleshooting 18 Calibration Issues How much is good data worth? CO2 and H2O Analyzers 18-3 Flow meter 18-17 View, Store Zeros & Spans 18-18 Using the LI-6400 vii Contents Zeroing the Leaf Temperature Thermocouple 18-19 6400-01 CO2 Mixer 18-20 6400-02(B) LED Source 18-24 6400-40 Leaf Chamber Fluorometer 18-27 GaAsP Light Sensors 18-28 Calibration and Configuration File Summary 18-30 19 Maintenance & Service The care and feeding of your new pet Chemical Tubes 19-2 6400-03 Batteries 19-8 System Console 19-9 Real Time Clock 19-12 Cables 19-12 The Chamber Handle 19-14 Leaf Temperature Thermocouple 19-18 Leaf Chambers 19-20 LED Source Maintenance 19-22 Match Valve Maintenance 19-23 IRGA Maintenance 19-26 Servicing the External CO2 Source Assembly 19-32 Shipping The LI-6400 19-35 Useful Part Numbers 19-36 20 Troubleshooting When things go wrong Power On / Start-up Problems 20-2 Real Time Clock Problems 20-6 New Measurements Mode Warning Messages 20-7 Unreasonable Results 20-9 Pump/Flow Problems 20-13 IRGA Problems 20-14 Match Valve Problems 20-21 6400-01 CO2 Mixer Problems 20-23 Light Source / Sensor Problems 20-30 6400-40 Leaf Chamber Fluorometer 20-32 Chamber Problems 20-33 Finding Leaks 20-35 Soil Chamber Problems 20-40 viii Using the LI-6400 Contents Useful Information 20-43 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 22-2 Making Objects 22-7 Functions 22-12 Pointers 22-17 Public and Static 22-22 Compiler Directives 22-25 23 LPL Topics Programming with LPL Stack 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 23-37 I/O Programming 23-39 File System 23-46 Menus and Editors 23-51 Graphics 23-56 RS-232 Communications 23-64 Analog Measurements 23-66 Analog Output Control (D/A) 23-73 Digital I/O 23-75 Application Tools 23-78 Using the LI-6400 ix Contents Battery and Power 23-82 24 LPL Reference Keyword Summary Syntax Summaries 24-2 Definitions 24-11 The Reference 24-16 25 AutoProgramming Reference Making them do what you what them to do Autoprogram Format 25-2 Some AutoProgram Listings 25-4 Useful AutoProgram Commands 25-12 AutoPrograms and the Control Manager 25-20 Low Level Control Tools 25-20 26 Customizing Open “Cry ‘Havoc’ - and let slip the dogs of war” Using PATCH= 26-2 Useful Variables 26-4 Open’s Hooks 26-7 New Style ComputeList Files 26-16 Using Spare Channels 26-22 Part VII: Accessories 27 Leaf Chamber Fluorometer Using the 6400-40 Leaf Chamber Fluorometer Background Information 27-2 Installing the LCF 27-9 Executive Summary 27-16 Basic Experiments 27-36 Fluorescence AutoPrograms 27-53 Calibration Issues 27-55 LCF Troubleshooting 27-63 LCF Reference 27-67 Chlorophyll Fluorescence References 27-76 INDEX x Using the LI-6400 Welcome to the LI-6400 A Bit of History The LI-6400 is LI-COR’s third generation gas exchange system.
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