LI-COR LI-6400 User manual

PRIMER
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
consequential damages in connection with the furnishing, performance, or use of this material.
This document contains proprietary information which is protected by copyright. All rights are reserved. No part
of this document may be photocopied, reproduced, or translated to another language without prior written consent
of LI-COR, Inc.
© Copyright 1995, LI-COR, Inc.
Publication Number 9501-110
Printing History:
1st Printing January, 1995 - OPEN Software version 1.10
2nd Printing August, 1995 - OPEN Software version 2.0
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, Inc. • 4421 Superior Street • Lincoln, Nebraska 68504
Phone: [phone] • FAX: [phone]
Toll-free: 1-800-447-3576 (U.S. & Canada)

iii
Table of Contents
Section 1. Unpacking and Initial Inspection
What’s What ...................................................................................................................................... 1-1
Optional Accessories......................................................................................................................... 1-3
Section 2. Overview and System Assembly
System Overview............................................................................................................................... 2-1
Hardware Overview.................................................................................................................... 2-1
Equation Summary ............................................................................................................................ 2-6
Assembling the LI-6400 .................................................................................................................... 2-8
6400-02 LED Light Source Installation ............................................................................................ 2-11
Connecting the LI-6400 to Mains Power .......................................................................................... 2-14
Note on Battery Life .......................................................................................................................... 2-14
Mounting the Sensor Head on a Tripod ............................................................................................ 2-15
Installing the 6400-01 External CO2Source Assembly .................................................................... 2-17
General Description.................................................................................................................... 2-17
Installation .................................................................................................................................. 2-17
Using the CO2Tank Connector Block .............................................................................................. 2-20
General Description.................................................................................................................... 2-20
Installation .................................................................................................................................. 2-20
Installation Using 4mm Copper Tubing..................................................................................... 2-22

iv
Section 3. Software Tour
Overview............................................................................................................................................ 3-2
Power On........................................................................................................................................... 3-2
Power Off .......................................................................................................................................... 3-4
Using the Keypad .............................................................................................................................. 3-4
Welcome Menu.................................................................................................................................. 3-6
About This Unit... ...................................................................................................................... 3-6
Help Menu.................................................................................................................................. 3-7
Tests and Diagnostics Menu ...................................................................................................... 3-7
Quit OPEN - IRGAs Left ON .................................................................................................... 3-7
Quit OPEN - IRGAs OFF .......................................................................................................... 3-7
Configuration Menu .......................................................................................................................... 3-9
About the Compute List ............................................................................................................. 3-11
The Configuration Editor ........................................................................................................... 3-12
Calibration Menu............................................................................................................................... 3-16
New Measurements ........................................................................................................................... 3-17
About the New Measurements Screen ....................................................................................... 3-17
New Measurements Screen Function Keys................................................................................ 3-18
Changing the New Measurements Display ................................................................................ 3-19
Changing Display Definitions .................................................................................................... 3-21
Saving Display Definitions ........................................................................................................ 3-22
New Measurements Variables.................................................................................................... 3-23
About Status Variables............................................................................................................... 3-26
New Measurements Function Keys............................................................................................ 3-27
Using Strip Chart Mode..................................................................................................................... 3-32
Using the StdFileDialog Box............................................................................................................. 3-35
Utility Menu ...................................................................................................................................... 3-36
Access the FILER....................................................................................................................... 3-37
Configure the COMM Port ........................................................................................................ 3-37
File Exchange Mode................................................................................................................... 3-38
Graph Stored Data ...................................................................................................................... 3-38
Choosing and Editing the Axes........................................................................................... 3-40
New File (Editor)........................................................................................................................ 3-42
Recompute Stored Data.............................................................................................................. 3-42
Set the Time and Date ................................................................................................................ 3-45
Sleep mode ................................................................................................................................. 3-45

v
Low Battery Warning ........................................................................................................................ 3-46
Humidity Warning............................................................................................................................. 3-46
Disk Full Warning ............................................................................................................................. 3-47
Adjusting the Display Contrast.......................................................................................................... 3-47
Section 4. Making Measurements
Overview............................................................................................................................................ 4-2
User Calibration................................................................................................................................. 4-2
Before Beginning Calibration Procedures.................................................................................. 4-3
Zero the CO2/H2O IRGAs.......................................................................................................... 4-3
Span the CO2/H2O IRGAs ......................................................................................................... 4-5
Independent Calibration of the Analyzers.................................................................................. 4-7
Flowmeter Zero .......................................................................................................................... 4-7
Storing the Zero and Span Values.............................................................................................. 4-7
Logging Data..................................................................................................................................... 4-8
Using the LogList....................................................................................................................... 4-9
Automatically Logging Data ...................................................................................................... 4-11
Using the Log Button ................................................................................................................. 4-12
Viewing Data..................................................................................................................................... 4-12
Recovering Lost Data ........................................................................................................................ 4-14
Changing the Flow Rate .................................................................................................................... 4-14
Null Balancing on Water Vapor................................................................................................. 4-14
Using Fixed Flow Rates ............................................................................................................. 4-16
Controlling Chamber Air and Leaf Temperatures............................................................................. 4-17
Matching the Analyzers..................................................................................................................... 4-18
Why Match? ............................................................................................................................... 4-19
When Do I Match? ..................................................................................................................... 4-20
Making a Light Response Curve ....................................................................................................... 4-22
Changing Light Intensity............................................................................................................ 4-22
Using the Auto Light Curve Program ........................................................................................ 4-23
Making a CO2Response Curve......................................................................................................... 4-25
Preliminary Considerations ........................................................................................................ 4-25
Manual Control ACiProtocol..................................................................................................... 4-25
Auto ACiProtocol ...................................................................................................................... 4-28
Light Sensors Used in the LI-6400.................................................................................................... 4-29
Gallium Arsenide Phosphide (GaAsP) Sensor........................................................................... 4-30

vi
Generating an Approximate GaAsP Sensor Calibration Using a Quantum Sensor and the
Quantum Sensor Chamber Mount.............................................................................................. 4-31
Section 5. File Management
Data Storage and File Management .................................................................................................. 5-2
Using the FILER................................................................................................................................ 5-3
Opening and Closing the FILER ................................................................................................ 5-3
File Naming Conventions........................................................................................................... 5-3
Directories .................................................................................................................................. 5-3
Directory Operations ......................................................................................................................... 5-4
Viewing and Changing Directories ............................................................................................ 5-4
Creating and Deleting Directories.............................................................................................. 5-4
File Operations .................................................................................................................................. 5-6
Viewing File Details................................................................................................................... 5-6
Viewing and Editing Files.......................................................................................................... 5-6
Tagging Files.............................................................................................................................. 5-7
Purging Files .............................................................................................................................. 5-9
Copying Files.............................................................................................................................. 5-9
Moving Files .............................................................................................................................. 5-9
Duplicating Files ........................................................................................................................ 5-10
Renaming Files........................................................................................................................... 5-10
Printing Files .............................................................................................................................. 5-10
Executing Programs.................................................................................................................... 5-11
Disk Operations................................................................................................................................. 5-11
About Flash Memory... .............................................................................................................. 5-11
Space Available.......................................................................................................................... 5-12
Defragmenting Disks.................................................................................................................. 5-12
Formatting Disks ........................................................................................................................ 5-13
Using the Hidden Disk ............................................................................................................... 5-14
Data Communications ....................................................................................................................... 5-15
Setting the Communications Parameters.................................................................................... 5-15
Cables......................................................................................................................................... 5-16
Sending Files to a Personal Computer........................................................................................ 5-18
Sending Files to a Macintosh®................................................................................................... 5-19

vii
Section 6. Maintenance and Service
Recalibration...................................................................................................................................... 6-2
Filling the Desiccant Tube................................................................................................................. 6-2
About Drierite ............................................................................................................................ 6-2
Regenerating Drierite ................................................................................................................. 6-3
Ordering Information.................................................................................................................. 6-3
Filling the Scrubber Tube .................................................................................................................. 6-4
A Quick Soda Lime Test ............................................................................................................ 6-4
Replacing the Air Mufflers................................................................................................................ 6-5
Replacing the Leaf Temperature Thermocouple............................................................................... 6-6
Setting the Leaf Temperature Thermocouple Zero ........................................................................... 6-8
Recharging the 6400-03 Batteries ..................................................................................................... 6-9
Storing the 6400-03 Batteries..................................................................................................... 6-9
Replacing the Battery Fuse ........................................................................................................ 6-10
System Console ................................................................................................................................. 6-10
Cleaning and Removing the Card Cage ..................................................................................... 6-10
Replacing the Fuses.................................................................................................................... 6-11
Leaf Chamber Care............................................................................................................................ 6-14
Replacing the Leaf Chamber Foam Gaskets ..................................................................................... 6-14
Replacing the Upper Leaf Chamber Film.......................................................................................... 6-15
Internal Air Filter............................................................................................................................... 6-18
Soda Lime/Desiccant Bottles in the Sensor Head ............................................................................. 6-19
Cleaning the Optical Bench............................................................................................................... 6-22
Servicing the External CO2Source Assembly .................................................................................. 6-27
Oil Filter Replacement ............................................................................................................... 6-27
Making Your Own Filters .......................................................................................................... 6-28
If the Regulator Becomes Clogged ............................................................................................ 6-28
Shipping Your LI-6400...................................................................................................................... 6-32

viii
Section 7. Troubleshooting
Appendix A. Configuration List
Appendix B. Specifications
Appendix C. Connector Descriptions
Warranty

Unpacking and Initial Inspection 1-1
1
1
1
Unpacking &
Initial Inspection
Contents
What’s What ..................................................................... 1-1
Optional Accessories ........................................................ 1-3
What's What
If you have just taken delivery of your LI-6400 check the
packing list to verify that you received everything ordered,
including the following items:
Calibration Sheet
This data sheet is a copy of the calibration information entered
into the LI-6400 by LI-COR. Keep it in a safe place for future
reference.
Spare Parts Kit
This 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 which items can be stored away.

Section 1
1-2 Unpacking and Initial Inspection
External Scrubber and Desiccant Tubes
These tubes are used during operation. Several spare air
mufflers (located inside the tubes) have been included for
future use.
6400-03 Rechargeable Batteries
(10.5-16 VDC). The 6400-03 Rechargeable Batteries are
tested and fully charged before they leave the factory, but may
discharge during shipping. It is a good idea to test your
batteries to make sure they are charged. See "Recharging the
6400-03 Batteries" in Section 6 for instructions about testing
and charging batteries. The 6400-03 requires the LI-6020
Battery Charger for recharging. One 6400-03 battery provides
approximately 1-2 hours of battery life.
LI-6020 Battery Charger
(92-138/184-276 VAC, 47 to 63 Hz). The LI-6020 can charge
four 6400-03 Rechargeable Batteries simultaneously.
1000-90 Data Communications and Utility Software
This software can be used to communicate with PC-
compatible computers. The software is provided on a 3 1/2
inch diskette.
RS-232C Cables
(Part #’s 1800-04 and 1000-09). Use the 1000-09 to connect
the LI-6400 to a 25-pin DTE device; use both cables to
connect to a 9-pin computer serial port.
Field Stand
The LI-6400 field stand is mounted to the console. The four
legs can be attached to the underside of the LI-6400 to provide
a sturdy base for field measurements. When not in use, the
legs can be stored in the carrying case.
6400-50 System Software
The System Software disk is a complete backup of the system
software in your LI-6400. Keep this disk in a safe place in
case you need to re-install the system software.