LI-COR LI-6400 - Part I: The Basics; System Description; Assembling the LI-6400; Guided Tours

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Using the LI-6400

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Contents

Welcome to the LI-6400

A Bit of History xi

About this Manual xiii

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

6400-02B LED Light Source Installation 2-15

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

Tour #2: New Measurements Mode Basics 3-14

Main Page

Default Chapter3
- Table of Contents3
- Welcome to the LI-640011
- A Bit of History11
- About this Manual13
Part I: the Basics15
1 System Description17
- An Open System18
- The Flow Schematic20
- Equation Summary23
- The System Components28
2 Assembling the LI-640033
- Putting It All Together33
- The CO2 Scrub and Desiccant Tubes34
- Preparations34
- Using a Tripod38
- 6400-01 CO2 Injector Installation39
- External Quantum Sensor Installation46
- 6400-02B LED Light Source Installation47
- Powering the LI-640050
  - Mains Power50
  - Batteries50
- Installing System Software51
3 Guided Tours53
- Learning How to Make It Work53
- Before You Start54
- Tour #1: OPEN Overview56
- Tour #2: New Measurements Mode Basics66
- Tour #3: Controlling Chamber Conditions72
- Tour #4: Logging Data93
- Tour #5: Configuration Adventures103
- Tour #6: Boot Screen and LPL111
4 Making Measurements119
- Preparation Check Lists120
- Some Simple Experiments126
- Making Survey Measurements139
- Light Response Curves142
- CO2 Response Curves148
  - Why Measure CO2 Response?148
  - Diffusion149
- Matching the Analyzers152
- Stability Considerations159
- Operational Hints165
- Answers to Questions171
Part II: Useful Details175
5 Standard Tools177
- Menus, Editors, and File Dialogs177
- Standard Menu178
- Cursor Keys180
- Standard Line Editor181
- Standard File Dialog185
- Standard Edit189
  - Tabs191
  - The Exit Menu191
- Hot Keys192
- Low Battery Warning193
  - Performing Without a Net193
  - Boot Screen Functions194
- The Boot Screen194
- The LPL Screen196
- Power on Hooks199
- The AUTOST File199
6 Real Time Data201
- Viewing Real Time Data Using Text and Graphics201
- Text Display202
- Real Time Graphics208
7 Environmental Control215
- How OPEN Controls Chamber Conditions215
- Open's Control Manager216
- Interface Fundamentals217
- Active Vs. Inactive Control Manger218
- Behind the Scenes218
- When Is the Control Manager Active?218
- Example: Tracking External Humidity219
- Variable Targets219
- Humidity Control221
- CO2 Control227
- Temperature Control230
- Condensation?231
- Light Control232
8 Light Sensor Considerations235
- The most Important Parameter Is the Hardest to Measure235
- Why Two Sensors?236
- Specifying the Source and Sensor237
- 6400-02 and -02B Light Sources240
- Gallium Arsenide Phosphide (Gaasp) Sensor241
9 Data Logging245
- Storing What You Want, Where You Want, When You Want245
- Basic Concepts246
- Getting Started248
- Determining What Is Logged251
- Prompts and Remarks256
- Autoprograms262
- Autoprogram Descriptions265
- Making Your Own Autoprograms277
Part III: Working with Files289
10 The LPL File System291
- Managing Your Data Storage Space291
- Files, Directories, and Disks292
- Defragmentation295
- The Filer296
- Troubleshooting311
- Out of Disk Space311
11 Downloading Files313
- Retrieving Your Data313
- Connecting the LI-6400 to a Computer315
- Typical Cable Connections315
- Using Winfx316
- To Transfer Files Using Winfx316
- File Exchange Mode316
- Using FX for DOS320
  - Making Directories320
  - Renaming Files or Directories320
- Using FX on Macintosh322
- To Transfer Files Using Fx/Macintosh323
- Using EW324
- Odds and Ends333
- Using a Data Capture Program335
12 Graphit341
- Accessing Graphit342
- Data File Format344
  - Finding the Label Line345
  - Finding the Data Lines345
- Defining Plots346
- Selecting Observations350
- Curve Fitting354
  - Configuring for Curves354
  - Viewing Curve Fit Results355
- Viewing Data357
- Plotdef File Format359
- Storing and Retrieving Graphics Images359
13 Recomputing Data Files361
- Reasons to Recompute362
- A Step by Step Example362
- The Details367
- Hints374
Part IV: Configuration Issues375
- Open's System Variables377
- Quantities Provided by OPEN377
- A Unique ID Number378
- Background Information378
- Measured Variables380
- Computed Variables385
- Time and Logging Variables387
- H2O Pump Flow Mixr Fan388
- Status Variables388
- Using Status Information from an LPL Program391
- Boundary Layer Variables393
- List of System Variables395
- System Variables - Labels and Variable Names395
- Band Broadening Correction for Water Vapor399
15 Defining User Variables403
- Equations, Constants, and Remarks403
- The Computelist File404
- Where Do They Come From?404
- Computelist File Format405
- Writing and Modifying Computelist Files409
- User Defined Constants and Remarks414
- Examples415
  - To Add Water Use Efficiency to the Current Computelist415
  - Water Use Efficiency415
- Useful Variables and Functions417
- The Default Computelist418
- Old Style Vs. New Style419
16 Configuration Basics421
- What You Need to Know to Get by421
- A Definition of Terms422
- Making Configuration Files424
- Installation Menu: Behind the Scenes430
- Modifying Config Files432
- The Reset Menu436
- Configuration Command Summary438
17 Using an Energy Balance443
- Computing What You Canõt Measure443
- The Theory444
- Using Energy Balance in OPEN448
  - Absorbed Energy450
  - Wall Temperature450
- Energy Balance and Boundary Layer451
  - Recomputation Considerations451
  - Transpiration Rate451
- Further Reading453
Part V: Maintenance & Troubleshooting455
18 Calibration Issues457
- How Much Is Good Data Worth457
- CO2 and H2O Analyzers457
- View, Store Zeros & Spans474
- Zeroing the Leaf Temperature Thermocouple475
- 6400-01 CO2 Mixer476
- 6400-02(B) LED Source480
  - LED Source Calibration481
  - LED Source Warmup481
- Gaasp Light Sensors484
- Calibration and Configuration File Summary486
19 Maintenance & Service490
- Chemical Tubes490
- Cleaning the End Cap Threads491
- Replacing the Air Mufflers491
- Chemical Tubes491
- The Desiccant Tube: Use Drierite492
- The CO2 Scrub Tube: Use Soda Lime492
  - A Quick Soda Lime Test492
  - Reattaching493
  - Chemicals to 1 CM of the Top493
  - Not too Tight493
- Chemical Tube Flow Control494
  - To Disassemble and Service a Flow Adjustment Assembly494
  - Removing the Flow Adjust Knob494
  - Remove the Outer and Center Pieces495
- Charging the 6400-03 Batteries496
- Storing the 6400-03 Batteries496
- Replacing the Battery Fuse496
- System Console497
- Opening the Console497
- Internal Air Filter Replacement497
- To Remove the Console Cover497
- Replacing the Fuses498
- Replacement Fuse Sizes for the Flow and Backplane Boards498
- Real Time Clock500
- Cables500
- Insulation500
- Replacing Connector Screws500
- The Chamber Handle502
- Handle Maintenance502
- Latch Maintenance502
- Chamber Doesn't Unlatch Reliably503
- Latch Return Spring504
- Handle Removal504
  - To Remove the Chamber Handle Assembly505
  - Remove the Handle Screws505
- Leaf Temperature Thermocouple506
- Thermocouple Maintenance506
- Thermocouple Replacement506
  - To Replace the 6400-04 Leaf Temperature Thermocouple506
  - Pull out the Holder507
  - Insert the New Holder507
  - Plug in the Connector507
  - Position the Holder507
- Leaf Chambers508
- Foam Gasket Care508
- Foam Gasket Replacement508
- Propafilm Replacement508
  - To Replace the Propafilm509
  - Detach the Affected Chamber Part509
  - Remove the Old Propafilm and Tape509
  - Prepare the New Tape509
- LED Source Maintenance510
- Fluorescence Chamber Tops510
- Match Valve Maintenance511
- Unsticking the Match Valve511
  - Exercise511
  - Match Valve Test Program511
  - Orthoscopic Surgery512
  - Open Heart Surgery512
- IRGA Maintenance514
- Chemical Bottles514
  - To Change the Sensor Head Soda Lime/Desiccant Bottles514
  - Insert the New Bottles515
  - Wait before Use515
- Cleaning the Optical Bench516
  - To Remove and Clean the Mirrors516
  - Opening the Optical Bench517
  - To Disassemble the Sensor Head and Clean the Optical Path517
  - Reassemble the Sensor Head519
- Servicing the External CO2 Source Assembly520
- Oil Filter Replacement520
- To Install the Filter520
- If the Flow Restrictor Becomes Clogged521
- Servicing the External Co2 Source Assembly521
- Getting to Know Your Mixer521
  - To Replace the Flow Restrictor and Clean the Copper Supply Tube522
  - Clean the Supply Tube522
  - Replace the Flow Restrictor522
- Shipping the LI-6400523
- If Shipping to LI-COR for Repair or Recalibration523
- Useful Part Numbers524
20 Troubleshooting527
- When Things Go Wrong527
- Power on / Start-Up Problems528
- Real Time Clock Problems532
  - Doesn't Keep Time When Power off532
  - Clock Stopped Message532
- New Measurements Mode Warning Messages533
- Unreasonable Results535
- Pump/Flow Problems539
- IRGA Problems540
- Match Valve Problems547
- 6400-01 CO2 Mixer Problems549
- Light Source / Sensor Problems556
- Chamber Problems559
- Finding Leaks561
- Soil Chamber Problems565
- Useful Information568
21 Diagnostics and Utilities574
- Diagnostics & Tests Menu574
- Sys/Utility Programs582
Part VI: Programming593
22 Programming with LPL595
- An Introduction to the LI-6400Õs Programming Language595
- Overview of LPL596
  - A Simple Example597
  - The View from the Stack598
- Making Objects601
- Functions606
- Pointers611
- Public and Static616
  - Using PUB616
  - Using STATIC617
- Compiler Directives619
  - General Purpose Compiler Directives619
  - Boardsoff Listing621
23 LPL Topics623
- Programming with LPL623
- Stack Control624
  - Basic Stack Manipulation625
  - Stack Size, Status, Errors625
- Conditionals and Loops626
- Flow Control Keyword Summary626
- Array Operations628
  - Array Keyword Summary628
  - Array SIZE and READY Values628
  - Manipulating Arrays630
  - Address to Value Conversion631
  - APP, PICK, AMOVE, and SUBSET Illustrated631
  - Searching and Comparing Arrays632
  - Dynamic Allocation632
  - Using MAKE and FREE634
  - Illustration of VAL and PVAL636
  - FIND and PFIND Illustrated637
  - FIND with Subscripts638
- Math Functions640
  - Math Keyword Summary640
  - Single Object Transforms642
  - Two Object Transforms643
  - Two Object Transform Combinations644
- Display Control645
  - Trig Functions645
  - Display Size646
  - Text Windows646
  - Text and Cursor Attributes648
  - Manipulating Text650
- Keyboard Control651
  - Keyboard Behavior651
  - Keyboard Codes651
  - Example Key Codes652
  - Non Ascii Key Codes: High Byte652
- Clock653
  - Clock Keyword Summary653
  - Real Time654
  - Time Since Power on654
- Event Handling655
  - Illustration of the Hard Way to Detect Events656
  - Programming for Events in LPL656
  - Events Supported by LPL657
  - Function Key Keyword Summary659
  - Defining Function Keys660
- I/O Programming661
  - GLOBALKEYS on661
  - GLOBALKEYS off661
  - I/O Keyword Summary661
  - Paths663
  - Path Registers664
  - PATH Status Registers664
  - Path Filters664
  - Transferring Data666
  - Simple Filter Example666
  - I/O Errors667
  - Formatted ASCII I/O667
  - Simple Terminal Emulator667
  - I/O Error Codes667
- File System668
  - File System Keywords668
  - Hierarchical Structure669
  - The Trash Directory671
  - The LI-6400 File System671
- Menus and Editors673
  - LPL Menu and Editor Keywords673
  - Standard Menus and Editors673
  - Programming with STDMENU674
  - Single Line Editor675
  - STDMENU Example: Knowing What was Selected675
  - Customized Editors and Menus676
  - Multiple Line Editor676
- Graphics678
  - Graphics Keyword Summary678
  - Graphics Hardware679
  - Windows and Coordinates680
  - Drawing and Labelling681
  - GLORG Locations for a Graphics Label Relative to Pen Location682
  - Labelling in Graphics Mode683
  - Drawing Modes684
  - Labelled Cosine Curve684
  - Graphics Drawing Modes684
  - Illustration of Drawing Modes685
- RS-232 Communications686
- Graphics Image Handling686
- Analog Measurements688
  - Analog Measurement Keyword Summary688
  - Groups and Channels688
  - Setting It up689
  - Complete A/D Example692
  - LI-6400 Analog Channels693
  - LI-6400 Analog Input Channels693
  - LI-6400 Reference Channel Descriptions694
- Analog Output Control (D/A)695
  - Hardware Consideration695
  - D/A Control Keywords695
- Digital I/O697
  - Ports and Pins697
  - Low Speed Counters698
  - High Speed Counter698
  - Digital Errors699
- Application Tools700
  - LPL Keywords for Running Applications700
  - Running Applications701
  - ID Numbers701
  - Garbage Collection701
  - Modules701
  - Debugger702
  - Debugging Tour702
  - Picking the Target Application702
  - The Function List of /Sys/Open/Start703
- Battery and Power704
24 LPL Reference705
- Keyword Summary705
- Syntax Summaries706
- Definitions715
- The Reference720
25 Autoprogramming Reference779
- Making Them Do What You What Them to Do779
- Autoprogram Format780
- Some Autoprogram Listings782
- Useful Autoprogram Commands790
- Autoprograms and the Control Manager797
- Low Level Control Tools797
26 Customizing Open803
- Òcry Ôhavocõ - and Let Slip the Dogs of Waró803
  - Using PATCH=804
  - How to Add a Patch= Command to a Configuration File804
- Useful Variables806
- New Style Computelist Files818
- Using Spare Channels824
Index831

LI-COR LI-6400 - Part I: The Basics; System Description; Assembling the LI-6400; Guided Tours

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