LI-COR LI-6400 Primer
  1. Manuals
  2. Brands
  3. LI-COR Manuals
  4. Laboratory Equipment
  5. LI-6400
  6. Primer

LI-COR LI-6400 Primer

Portable photosynthesis system
Hide thumbs Also See for LI-6400:
Table of Contents

Advertisement

Quick Links

Download this manual
P
RIMER
LI-6400
Portable
Photosynthesis
System
®

Advertisement

Table of Contents
loading
Need help?

Need help?

Do you have a question about the LI-6400 and is the answer not in the manual?

Questions and answers

Subscribe to Our Youtube Channel

Related Manuals for LI-COR LI-6400

Summary of Contents for LI-COR LI-6400

  • Page 1 RIMER LI-6400 Portable Photosynthesis System ®...
  • Page 2 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.

  • Page 3: Table Of Contents

    Equation Summary ..........................Assembling the LI-6400 ........................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 CO Source Assembly ..............
  • Page 4 Section 3. Software Tour Overview............................Power On ............................Power Off ............................Using the Keypad ..........................Welcome Menu..........................About This Unit......................... Help Menu ..........................Tests and Diagnostics Menu ...................... Quit OPEN - IRGAs Left ON ....................Quit OPEN - IRGAs OFF ......................Configuration Menu ..........................
  • Page 5 Using the Auto Light Curve Program ..................4-23 Making a CO Response Curve ......................4-25 Preliminary Considerations ......................4-25 Manual Control AC Protocol..................... 4-25 Auto AC Protocol ........................4-28 Light Sensors Used in the LI-6400 ....................4-29 Gallium Arsenide Phosphide (GaAsP) Sensor ................4-30...
  • Page 6 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 ....................Using the FILER ..........................Opening and Closing the FILER ....................File Naming Conventions......................Directories ..........................
  • Page 7 Soda Lime/Desiccant Bottles in the Sensor Head ................6-19 Cleaning the Optical Bench ....................... 6-22 Servicing the External CO Source 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...
  • Page 8 Section 7. Troubleshooting Appendix A. Configuration List Appendix B. Specifications Appendix C. Connector Descriptions Warranty viii...

  • Page 9: What's What

    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.
  • Page 10 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.

  • Page 11: Optional Accessories

    Unpacking & Initial Inspection Optional Accessories There are several optional accessories, including: 6400-01 CO Injector The 6400-01 mounts on the LI-6400 console to provide a constant, regulated source of CO to the leaf chamber. The 6400-01 uses disposable CO cartridges to provide concentrations up to 2000 µmol mol...

  • Page 12: System Overview

    General Description ........... 2-20 Installation ..............2-20 Installation Using 4mm Copper Tubing ....2-22 System Overview Hardware Overview There are two major components of the LI-6400; the system console sensor head (Figure 2-1). The console has an environmentally sealed, 64-key, full ASCII...
  • Page 13 Section 2 Chicago character shows measured and computed values, LCD display software functions, and data plots. On the right side of the console are the , 6400-03 sensor head connectors battery , and compartments RS-232C connector scrubber attach to the left side of the console, along desiccant tubes with the optional 6400-01 assembly or...
  • Page 14 Sensor Head (optional) Figure 2-1. LI-6400 system console and sensor head. The LI-6400 Portable Photosynthesis System is an open gas exchange system. An open system has a net flow of air through the system. This system was designed to provide steady state light, CO O and temperature conditions for measurements.
  • Page 15 Vent Vent Figure 2-2. LI-6400 flow schematic (measurement mode). Figures 2-2 and 2-3 show flow schematics of the LI-6400. The pump draws air into the LI-6400 console. A variable amount of incoming air flow may be routed through chemical columns filled with a CO scrubber (soda lime) and a desiccant (Drierite).
  • Page 16 Control Control Desiccant Controller Vent Vent Figure 2-3. LI-6400 flow schematic (match mode). Pressure inside the leaf chamber is slightly positive to ensure that leaks are outward, so outside air does not affect the chamber CO and H O concentrations.

  • Page 17: Equation Summary

    Section 2 Chicago Equation Summary The governing equations for net photosynthesis, transpiration, total conductance to water vapor, stomatal conductance to water vapor, total conductance to CO , and intercellular CO concentration are given below. Transpiration (E) Net Photosynthesis (A) − −...
  • Page 18 Overview & Assembly = total conductance to CO , mol CO = total conductance to water vapor, mol H = (K + 1)/(K + 1) , where K is an estimate of the ratio of stomatal conductances of one side of the leaf to the other, dimensionless s = leaf area, cm = mole flow rate of air entering the leaf chamber, µmol s...

  • Page 19: Assembling The Li-6400

    Follow the same procedure with the desiccant tube. Indicating Drierite desiccant is provided in the spares kit. When the LI-6400 is in use, the CO scrub tube and desiccant tube should remain attached to the console at all times, except when changing chemicals.
  • Page 20 ON/OFF switch. Insert two 6400-03 batteries into the battery compartment and connect both batteries. The 6200B batteries used with other LI-COR instruments can also be used, but they will not fit into the battery compartment of the LI-6400. Overview & Assembly...
  • Page 21 Section 2 Chicago You will get better battery life when both batteries are connected. The system will sound a series of "beeps" when the batteries are low. One low battery can be removed and replaced with a fresh one while the system continues to run without interruption.

  • Page 22: 6400-02 Led Light Source Installation

    Overview & Assembly RS-232C connector Chamber connector IRGA connector Sample tube connection ON/OFF switch Air input Reference tube Battery jacks 6400-03 battery connection Figure 2-6. Console tubing and cable connections. 6400-02 LED Light Source Installation The optional 6400-02 LED Light Source is mounted to the sensor head by removing the upper half of the leaf chamber and replacing it with the lamp assembly.
  • Page 23 Section 2 Chicago half of the leaf chamber is secured by two long screws (Figure 2-7). Top View Connector O-rings GaAsP PAR sensor Upper leaf chamber cuvette Gasket Figure 2-7. Remove the two screws from the upper half of the leaf chamber.
  • Page 24 Overview & Assembly PAR sensor is attached to the connector near the rear of the analyzer housing, not to the log switch connector. LED Lamp Lamp Connector External Quantum Sensor BNC Leaf Temperature Connector Thermocouple Holder Air Hose PAR Sensor Connector Log Switch Connector...

  • Page 25: Connecting The Li-6400 To Mains Power

    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 with a 6400- 03 will power the LI-6400 indefinitely. At maximum draw (with LED light source on, running the coolers, etc.), the LI-6400 will use about 3A.

  • Page 26: Mounting The Sensor Head On A Tripod

    Overview & Assembly Mounting the Sensor Head on a Tripod A mounting bracket is included in the spare parts kit for mounting the sensor head on a tripod. This is useful for making long-term measurements. The three screws included with the mounting bracket are threaded into holes on the right side of the analyzer housing on the sensor head (Figure 2-9) using the 3/32”...
  • Page 27 Section 2 Chicago Analyzer Housing (rear view) Tripod Mounting Bracket Tripod Head Figure 2-10. Mounting the sensor head with the tripod mounting bracket. 2-16 Overview & Assembly...

  • Page 28: General Description

    Controller, located in the LI-6400 console, the External CO Source Assembly (part no. 9964- 026), which is attached to the outside of the LI-6400 case, and the optional 9964-033 CO Tank Connector Block. These instructions pertain only to the installation of the External CO Source Assembly.
  • Page 29 Section 2 Chicago Figure 2-12. Location of external CO source assembly. Place a new O-ring in the groove in the piercing block (Figure 2-13). Use your finger to press the O-ring into the groove. If the O-ring is not in place when the CO cartridge is pierced, gas will rapidly vent out a hole on the underside of the mounting block.
  • Page 30 Overview & Assembly Piercing Block O-ring Vent Holes Piercing Pin Figure 2-13. Top view of piercing block showing the O-ring location. Important Note: Although the O-ring may perform properly for several cylinders, we recommend that it be replaced with each new cylinder. After being subjected to several high pressure cycles the O-ring weakens and becomes perforated, and easily tears or splits.

  • Page 31: Using The Co Tank Connector Block

    Connector Block between the CO and H O scrub tubes on the LI-6400 console. Make sure that the O-ring seal on the back of the block is properly seated. Insert a length of 1/8” copper tubing through the 1/8” connector nut and the ferrule (Figure 2-14). Important: Note the orientation of the ferrule.

  • Page 32: Installation Using 4Mm Copper Tubing

    220 PSIG. Installation Using 4mm Copper Tubing If you are unable to obtain 1/8” copper tubing, you can connect the Tank Connector Block to a CO source using 4mm tubing and the compression fitting (LI-COR part #300- Overview & Assembly 2-21...
  • Page 33 Section 2 Chicago 04439) included with the Tank Connector Block. Install the Tank Connector Block and the short length of 1/8” copper tubing (included) as described in steps 1-4 above. Use the 1/8” to 4mm compression fitting to connect the 1/8”...
  • Page 34 Overview & Assembly 1/8" Copper Tubing Connector Ferrule 1/8" Nut 1/8" Copper Tubing 1/8" Nut Ferrule 1/8" to 4mm Compression Fitting Ferrule 4mm Nut To CO Tank 4mm Copper Tubing Figure 2-15. Use the compression fitting to connect 1/8” and 4mm tubing.
  • Page 35 Software Tour Chicago Contents Overview................Power On ................Power Off ................Using the Keypad.............. Welcome Menu..............About This Unit............Help Menu ..............Tests and Diagnostics Menu ........Quit OPEN - IRGAs Left ON........Quit OPEN - IRGAs OFF .......... Configuration Menu ............

  • Page 36: Overview

    Power On Connect two 6400-03 Rechargeable Batteries, or use one 6400-03 and the LI-6020 Battery Charger, as described in Section 2. Turn the LI-6400 ON. You are prompted as to whether or not the sensor head is connected. Press (Yes) or (No).
  • Page 37 /User 10% full Tue Jun 27 1995 13:31:56 12.00V Welcome Config Calib Utility Menu Menu Menu Msmnts Menu labels labels Figure 3-1. OPEN screen. Chicago You can safely power the LI-6400 off when the OPEN screen is displayed. Software Tour...

  • Page 38: Power Off

    If the system is inadvertently powered off before closing an open data file, the data are stored in a file named "Unknown". When the LI-6400 is powered back on, you may see a message stating that the Unknown file has been written to the disk that was being used to log data at the time of the power failure.
  • Page 39 Software Tour Chicago aaaaaa LI-6400 Portable Photosynthesis System LI-6400 Photosynthesis System home pgup home pgup OPEN 2.00 /User 10% full Tue Jun 27 1995 13:31:56 12.00V Welcome Config Calib Utility pgdn pgdn Menu Menu Menu Msmnts Menu labels labels &...

  • Page 40: Welcome Menu

    OPEN application (Figure 3-4). About This Unit... The display shows a number of system parameters, including the LI-6400 serial number, date of last factory service, software version numbers, and available system memory. Press to dismiss the "About" display.

  • Page 41: Help Menu

    Enter Tests and Diagnostics Menu The Tests and Diagnostics menu contains system tests that verify the integrity of the LI-6400. Quit OPEN - IRGAs Left ON Quits the OPEN application, and leaves the infrared gas analyzers (IRGAs) ON. This is useful for running other applications when you intend to make further measurements, as you will not have to wait for the IRGAs to warm up again.
  • Page 42 Section 3 Chicago Chicago Editor Filer Kbdexec Run Stream Xchng LPL 2.0 Copyright 1995 LI-COR, inc. /User 163654 bytes labels labels Figure 3-5. LPL Operating System screen. Chicago NOTE: Use the 'Sleep mode' function in the Utility menu to temporarily power the IRGAs off for sensor head connection or disconnection, .

  • Page 43: Configuration Menu

    Software Tour Chicago Configuration Menu Chicago LI-6400 Photosynthesis System OPEN 2.00 /User 10% full Tue Jun 27 1995 13:31:56 12.00V Welcome Config Calib Utility Menu Menu Menu Msmnts Menu labels labels Configuration Programs "Config Editor" "Reset to Factory Defaults" "Reset to User Defaults"...

  • Page 44: About The Compute List

    Section 3 Chicago Select ... to ... Config Editor Access the Configuration file and the Master list, where you can edit the default parameters, or select a different Config- uration file. Reset to Factory Defaults Reset all configuration items to the factory defaults.
  • Page 45 Configuration File, and appears as ComputeList="filename". The Config Editor is used to change the active Compute List File. LI-6400 Technical Note #2 contains a more complete description of how to modify and implement your Compute List File(s). Software Tour...

  • Page 46: The Configuration Editor

    Section 3 Chicago The Configuration Editor The Configuration Editor accesses two distinct lists; the Configuration file and the Master list. The Master list contains default parameters for configuring the hardware and software. The Master list is not edited but is used to copy parameters to the Configuration file where the desired changes are made.
  • Page 47 Software Tour Chicago Close the Configuration menu and implement any changes made. Disable Insert comment indicators (//) in front of the selected item (below). Disabled items in the Configuration menu will be ignored by the system. Enable Remove comment indicators from the selected item.
  • Page 48 Section 3 Chicago Example 1. Assume that your measurements are typically made on a plant species with hypostomatous leaves. Because the stomatal ratio affects the calculation of boundary layer conductance, you want to change the default stomatal ratio parameter (STOMRAT) from 1 to 0. Press at the OPEN main screen.
  • Page 49 Software Tour Chicago Appendix A lists the items found in the Configuration and Master lists. More details and examples are found in LI-6400 Technical Note #3. Software Tour 3-15...

  • Page 50: Calibration Menu

    Section 3 Chicago Calibration Menu Chicago LI-6400 Photosynthesis System OPEN 2.00 /User 10% full Tue Jun 27 1995 13:31:56 12.00V Welcome Config Calib Utility Menu Menu Menu Msmnts Menu labels labels Calibration Programs "Flow Meter Zero" "IRGA Zero" "IRGA Span"...

  • Page 51: New Measurements

    Software Tour Chicago New Measurements Chicago LI-6400 Photosynthesis System OPEN 2.00 /User 10% full Tue Jun 27 1995 13:31:56 12.00V Welcome Config Calib Utility Menu Menu Menu Msmnts Menu labels labels Figure 3-9. Press f4 to access the New Measurements screen.

  • Page 52: New Measurements Screen Function Keys

    Section 3 Chicago Chicago Display list label → CO2S_µml H2OS_mml Tair °C Tleaf °C Variables 22.0 22.3 ∆CO2_µml ∆H2O_mml Flow_µml RH_S_% Function key labels Photo Cond Trmmol 17.5 13.0 5.76E-03 VIEW CLEAR Match Function key REMARK level labels labels Figure 3-10. New Measurements screen. New Measurements Screen Function Keys The New Measurements screen is unique, in that the seven sets of function key definitions (viewed by pressing...

  • Page 53: Function Key Descriptions

    Software Tour Chicago Chicago Press... to view these function key labels... VIEW CLOSE Match Log control and matching FILE FILE REMARK Flow, CO , temperature, *PAR= *Flow= *CO2R= *BlkT= <range> 1000µml and light control 500µms 400µml 20.0C AREA= STOMRT= LeafFan Fan control and constants 6.00 1.00...
  • Page 54 Section 3 Chicago label becomes View File (below) if you are logging to a file. View File Allows you to view the observations in the active file or plot the data. Clear Pad Deletes all observations from the scratch pad. This label becomes Close File (below) if you are logging to a file.
  • Page 55 Software Tour Chicago Flow = Opens the humidity control and target value menu, where you can select flow control options. You can set the air flow rate at a constant value, constant mole fraction of water, constant RH, or constant VPD of the leaf or air. The current setting is displayed in the function key label.
  • Page 56 Section 3 Chicago intensity (µmol m ) of the artificial light source. Set the value between 0 and 2000 µmol m . You must have selected 'LightSource = 6400-02 LED Source' in the Configuration file before you can set an intensity value. You can also set the lamp to output a constant control voltage, if desired.
  • Page 57 Software Tour Chicago Strip chart control CHART <view CHART CHART Chart QuikPik chart> Editor Help is OFF Chart is ON/OFF Turns on the strip chart recorder and takes you to graphics mode to observe the chart(s). Press to return to Escape the New Measurements screen.
  • Page 58 Section 3 Chicago LogList Editor Opens the Log Editor, where you can select variables to be logged. Display control Display Display Display Display What's QuikPik List Editor Help What Display QuikPik Opens a menu from which you can select a pre-defined list of variables to be displayed in the New Measurements screen.
  • Page 59 Software Tour Chicago Mixer Help Opens a Help file related to operating the 6400-01 CO injector accessory. Flow Help Opens a flow control Help file. cago Software Tour 3-25...

  • Page 60: Changing The New Measurements Display

    Section 3 Chicago Changing the New Measurements Display Each of the three lines of variables on the display can be customized individually, and the entire display of 12 variables can also be customized and saved as a unit. As many as 26 custom variable lines can be defined for the New Measurements screen.
  • Page 61 Software Tour Chicago Press a-z or ← or → to change the variables shown on this line → CO2R_µml CO2S_µml H2OR_mml H2OS_mml 22.0 22.3 ∆CO2_µml ∆H2O_mml Flow_µml RH_S_% Photo Cond Trmmol 17.5 13.0 5.76E-03 VIEW CLOSE Match New variables FILE FILE REMARK labels...

  • Page 62: Changing Display Definitions

    Section 3 Chicago Changing Display Definitions The sixth set of function key labels in the New Measurements screen lets you perform functions that define the row of variables that appears when a through z is pressed on the keypad. Press at the New Measurements screen, or press successively until the following function key labels are labels...

  • Page 63: Saving Display Definitions

    Software Tour Chicago . Press (f2) to add an additional display line. You can also press Edit (f1) to change the currently highlighted line. . Use the arrow keys to scroll the list of variables until RH_S_% is highlighted. Press (f5).

  • Page 64: New Measurements Variables

    Section 3 Chicago Press Escape to return to the OPEN screen. Press select "Config Editor" to open the Configuration file. Scroll down the list and note that the Displays= menu reflects the file named in step 1. . Press , then .
  • Page 65 Software Tour Chicago ObsTime Elapsed time (s) since the first measurment was logged in the current file or pad. ParIn_µm Photosynthetically Active Radiation (PAR), input, measured by the GaAsP sensor, or by the silicon photodiode in the artificial light source, in µmols m ParOutµm PAR measured by external quantum sensor (optional), in µmols m...

  • Page 66: About Status Variables

    Section 3 Chicago STS_H2O Status of H O analyzer. STS_Pump Pump status. STS_Flow Flow status. STS_Mixr injector status. STS_Fan Fan status. uc_20_mV User channel 20 mV reading. uc_21_mV User channel 21 mV reading. uc_22_mV User channel 22 mV reading. uc_23_mV User channel 23 mV reading.
  • Page 67 Software Tour Chicago As an example, if the CHPWMF variable is displaying 111204, it indicates that the CO and H O analyzers and the pump are functioning normally, the flow rate is Low, the CO mixer is not present (or is off), and the fan speed is Slow. 1 (OK) 1 (OK) 0 (Off)

  • Page 68: Using Strip Chart Mode

    Section 3 Chicago Using Strip Chart Mode Strip chart mode can display graphical strip charts of up to three different variables simultaneously. To use strip chart mode, you first choose the variable(s) to be monitored, the time scale range on the X axis, and the Y axis range over which the data are plotted.
  • Page 69 Software Tour Chicago highlight the parameter to be edited and pressing Edit (f1). For example, if you press Edit Enter ) while one of the variables is highlighted, a list of variables will appear. Use the arrow keys to highlight the variable that you want to monitor and press Enter Time (s) is the number of seconds of data that will be...
  • Page 70 Section 3 Chicago . Press the right arrow key again to highlight the time parameter. Press Edit , delete the text and enter 60. Press . You are finished defining the plot. To name this Enter definition press , then .

  • Page 71: Using The Stdfiledialog Box

    Software Tour Chicago Using the StdFileDialog Box In most cases, when you are asked to select a file or enter a filename, the Standard File Dialog (StdFileDialog) box is displayed. In this dialog box you can enter a filename and change the directory to which the file will be saved, if desired.

  • Page 72: Utility Menu

    Section 3 Chicago Utility Menu Chicago LI-6400 Photosynthesis System OPEN 2.00 /User 10% full Tue Jun 27 1995 13:31:56 12.00V Welcome Config Calib Utility Menu Menu Menu Msmnts Menu labels labels Utility Menu "Access the FILER" "Configure the COMM port"...

  • Page 73: File Exchange Mode

    File Exchange Mode Enters file exchange mode, where you can transfer files to and from the LI-6400 with the FX software or EW.EXE (see Technical Note #8). In file exchange mode, the LI-6400 becomes a “slave” to the computer. A DOS version of FX is currently available (part #6400-20).
  • Page 74 Section 3 Chicago Measurements screen can be plotted on an X,Y or X,Y,Y graph. When you select Graph Stored Data you are prompted to choose the file to plot. Select a file from the StdFileDialog box and press (f5) or Select Enter Select...
  • Page 75 Software Tour Chicago Table 3-1. QuikPlot definitions. X Axis Left Y Axis Right Y Axis (Z) A Ci curve Photosynthesis rate Ball-Berry Relation AHs/Cs Conductance Light curve PAR(In) Photosynthesis rate Photo, Cond vs Obs Observation # Photosynthesis rate Conductance A representation of a 'Light curve' QuikPlot is shown in Figure 3-19.

  • Page 76: Choosing And Editing The Axes

    Section 3 Chicago Choosing and Editing the Axes In addition to the predefined QuikPlots, you can choose any variable in the data set to define a plot. Press and select labels the ‘Edit Axes’ function key. Choose the axis to modify (X, Y, or Z) and a list of the available variables is displayed (Figure 3-20).
  • Page 77 Software Tour Chicago Chicago File: /USER/Data Size: 1129 bytes (stored) X Axis: *,*, PARi Y Axis: 0, *, + : Photo Store DRAW VIEW Edit Config GRAPH DATA Axes labels labels Figure 3-21. Press f4 to draw the plot with the axis definitions shown. Example.

  • Page 78: New File (Editor)

    Section 3 Chicago New File (Editor) Opens a text editor screen in which you can create a new file. Enter the text and press Escape when you are finished; you will be prompted with the Exit menu, where you can save the file, if desired.
  • Page 79 Software Tour Chicago Recompute OPEN files SourceFile: -undefined- LeafArea: No change StomatalRatio: No change BLCond: Computed Destination: Write to buffer Edit HELP quit labels labels Figure 3-22. Recompute menu. Chicago Highlight and press (f1). The LeafArea LeafArea Edit menu appears on the screen: Chicago Recompute OPEN files Leaf Area...

  • Page 80: Set The Time And Date

    Section 3 Chicago . Select to leave the Prompt for each Obs No change parameter unchanged. . After the file is recomputed, you will have the opportunity to plot the new data, if desired. Follow this same procedure to recompute the data set with new values for stomatal ratio and/or boundary layer conductance, if desired.

  • Page 81: Sleep Mode

    When you exit the Utility menu, the unit will power up again. Low Battery Warning When the LI-6400 battery voltage drops below 11V, a low battery warning appears on the top line of the display, regardless of what application (if any) is running. The message appears every 2 seconds until the voltage rises above 11V, at which time a “Battery OK”...

  • Page 82: Disk Full Warning

    Section 3 Chicago To prevent water condensation in the analyzers when the relative humidity in the leaf chamber (based on the lowest of the analyzer block, leaf, or air temperatures) exceeds 95%, a warning will appear on the display. The warning will remain on the display until the RH falls below 95%.

  • Page 83: Overview

    Making Measurements Contents Overview................User Calibration ..............Before Beginning Calibration Procedures ....Zero the CO O IRGAs......... Span the CO O IRGAs ........Independent Calibration of the Analyzers ....Flowmeter Zero ............Storing the Zero and Span Values ......Logging Data ..............Using the LogList ............

  • Page 84: Before Beginning Calibration Procedures

    These coefficients are quite stable over time, but we recommend that they be checked every two years by returning the LI-6400 to LI-COR for recalibration. You should check the zero after about 20 minutes of warmup, and every hour in the face of large temperature changes.

  • Page 85: Zero The Co 2 /H 2 O Irgas

    Making Measurements air temperature, refer to "'Controlling Chamber Air Temperature" later in this section. After adjusting temperature and fan speed, close the cuvette and check the flow rate; it should be 500 µmol s . Route all of the air flow through the CO scrubber and the desiccant (see Figure 2-2) by turning the flow adjustment knobs (Figure 2-5) on top of the CO...

  • Page 86: Span The Co 2 /H 2 O Irgas

    Section 4 warmup procedure. If the CO and H O values are not stable after 10-15 minutes of scrubbing you should change chemicals and/or check for leaks. To view IRGA stability graphically: To view IRGA stability select the function key. A list of Plot available plots appears (below).
  • Page 87 LI-610 manual instructions to ensure that the proper pressure corrections are applied to the mole fraction of water vapor measured by the LI-6400 sample and reference H O analyzers. Select IRGA Span...

  • Page 88: Independent Calibration Of The Analyzers

    Section 4 Press from the Span screen to change the display from O adjustment. Use the ↑ or ↓ arrow keys to to H adjust the readout so that it matches the incoming dew point (or Shift + ↑ or ↓ to make coarse adjustments). It may take 10 minutes or more for the water vapor mole fraction to stabilize.
  • Page 89 Making Measurements system defaults. Once you have stored these values, you do not need to store them again; they can be useful, however, in viewing and characterizing the change in zero and span values from day to day. Making Measurements...

  • Page 90: Logging Data

    Section 4 Logging Data Data are logged in three different ways; 1) by pressing the function key (f1) in the New Measurements screen, 2) by using an automatic logging program, or 3) with the sensor head log button. When is pressed for the first time, you are prompted to enter a file name in the StdFileDialog box (see Section 3, "Using the StdFileDialog Box"), followed by a prompt to enter any remarks.

  • Page 91: Using The Loglist

    Making Measurements Using the LogList The LogList is a list of variables to be logged. This list can be modified, stored and read from disk. This is useful for quickly changing the logged variables for specific applications. The LogList is accessed in the New Measurements screen by pressing , followed by (f5).
  • Page 92 Section 4 To edit the LogList: To change a variable, press Change (f1). You will be prompted to select a new variable. Scroll the list until the desired variable is highlighted and press (f5) or Select . You can press to exit the Log Editor Enter Escape...

  • Page 93: Automatically Logging Data

    Making Measurements Automatically Logging Data Data can also be logged automatically using the AutoProgram named AutoLog. Autolog prompts for the interval (in seconds) at which to log data, the number of observations to log, and whether or not you want to match the analyzers after a given number of observations have been logged.

  • Page 94: Using The Log Button

    Section 4 Enter the number of observations to log. These obser- vations are in addition to any observations that are already stored in the active file or scratch pad. Press Enter Enter the interval at which you want to automatically match the analyzers, if desired.
  • Page 95 Making Measurements /User/LightCurve "Start: Thr Jun 9 09:45:53 1994" "LightCurve" "Obs","Time","Photo","Cond","Ci","Trans","Area","StmRat","BLCond","Tair" 1,0.0,21.6,0.276,201,0.00516,6,1,2.84,34.32,31.97,377.1,345.5,21.40,28.19, 2,133.0,30.7,0.287,153,2.1,0.00576,6,1,2.84,34.39,32.51,388.5,347.9,21.26 3,201.0,34.5,0.295,137,2.26,0.00636,6,1,2.84,34.44,33.08,391.9,350.1,21.16 labels labels Figure 4-3. View data screen (data shown as stored). /User/LightCurve "Start: Thr Jun 9 09:45:53 1994" "LightCurve" "Obs" "Time" "Photo" "Cond" "Ci" 21.6 0.276 133.0 30.7 0.287...

  • Page 96: Recovering Lost Data

    ‘Unknown’. (Directory updates occur on exiting new measurements mode and on closing a file). When the LI-6400 is powered back on, you may see a message stating that the Unknown file has been written to the disk that was used to log data at the time of the power failure.
  • Page 97 Making Measurements constant pump speed, and will still keep the vapor pressure very near the target. You may need to experiment when setting the null point to find a value at which the flow rate will be adequate for your measurement protocol. As an example, if the null point is set too high (e.g.
  • Page 98 Section 4 → Tair °C Tleaf °C CO2S_µml H2OS_mml 22.3 H2O_sample ∆CO2_µml RH_S_% 20.0 mml/s Photo Cond CHPWMF 17.5 13.0 111101 DelLn ClrEnd DelChar CapLock AnyChar labels labels Figure 4-5. Enter the H O target value. Fixing the Flow Rate The flow rate can also be fixed at a constant rate.

  • Page 99: Controlling Chamber Air And Leaf Temperatures

    Making Measurements → Tair °C Tleaf °C CO2S_µml H2OS_mml 22.3 Flow rate ∆CO2_µml RH_S_% 500 µmol/s Photo Cond CHPWMF 17.5 13.0 111101 DelLn ClrEnd DelChar CapLock AnyChar labels labels Figure 4-6. Enter the flow rate, in µ mol s Controlling Chamber Air and Leaf Temperatures Peltier thermoelectric coolers control the analyzer block temperature, which in turn dominates the chamber air temperature.

  • Page 100: Matching The Analyzers

    Section 4 highlighting Leaf Temp and pressing (or by Enter pressing Chicago → Tair °C Tleaf °C CO2S_µml H2OS_mml 22.3 Block Temp ∆CO2_µml RH_S_% 20.0 °C Photo Cond CHPWMF 17.5 13.0 111105 DelLn ClrEnd DelChar CapLock AnyChar labels labels Figure 4-7. Enter the target temperature, in degrees C. Matching the Analyzers There is a matching valve on the bottom of the sensor head.

  • Page 101: Why Match

    Making Measurements Why Match? Matching the analyzers improves the accuracy of your measurements, especially when working with low photo- synthesis rates. Recall from Section 2, the equation for net photosynthesis rate A is − − where A = net photosynthesis, µmol CO = mole flow rate of air entering the leaf chamber, µmol s = mole fraction of CO...

  • Page 102: When Do I Match

    Section 4 483.6 (388.5 - 346.9 − 346 9 0 00576 . ( . 31 5 100 (6) As you can see, a ∆CO error of 1 ppm resulted in a 3% error in net photosynthesis rate. If all other variables remain equal, and the leaf is assimilating less CO , so that the value for c becomes 368.9, the equation...
  • Page 103 Making Measurements Offsets Elapsed time since last match IRGA Match Mode CO2A_µml CO2B_µml H2OA_mml H2OB_mml 350.10 350.30 20.30 20.20 Prev: 00:09:32 CO2 = 0.1 H2O = 0.02 MATCH exit labels labels Figure 4-8. IRGA Match Mode screen. To match the analyzers: In the New Measurements screen, press ) until labels...

  • Page 104: Making A Light Response Curve

    Section 4 Making a Light Response Curve Changing Light Intensity The optional 6400-02 LED Light Source offers a convenient way to control the light intensity inside the leaf chamber for obtaining light response curves, or for avoiding variations in natural illumination. Light intensity can be adjusted from 0 (Off) to approximately 2000 µmols m To change the light intensity in the leaf chamber: Install the 6400-02 as described in Section 2 at 6400-02...

  • Page 105: Using The Auto Light Curve Program

    Making Measurements Using the Auto Light Curve Program The light intensity in the chamber can also be adjusted automatically, using the AutoProgram entitled "LightCurve - stable check". With this program, you can select the light intensities at which you want to log data, the minimum and maximum times that the system will wait to log the next observation, and how stable the chamber conditions should be before the measurement is made.
  • Page 106 Section 4 An asterisk appears above the menu level number on the bottom of the display (below), indicating that an AutoProgram is in progress. VIEW CLOSE Match FILE FILE REMARK You can view the progress of the AutoProgram by displaying the ProgPrgs variable (press in the New Measurements screen with the Std Display file open).

  • Page 107: Making A Co 2 Response Curve

    AC curves. Diffusion occurs to a greater or lesser extent with all of the gasket materials that LI-COR has tested; Volara type "A" (expanded propylene), silicon rubber, and neoprene. Diffusion leaks cause the computed C value to be slightly high. This is a potential problem for all photosynthesis systems.

  • Page 108: Manual Control Ac I Protocol

    To make your AC response curve measurements: Make sure your soda lime and desiccant are fresh. Turn on the LI-6400 and allow several minutes for it to warm up. Calibrate the analyzers as described earlier in this section, if you have not already done so.

  • Page 109: Auto Ac I Protocol

    Making Measurements Match the analyzers. Log a measurement after the photosynthesis and C values have stabilized. Turn the knob on the CO scrubber tube to draw down the level to the next measurement point in the series. Match the analyzers again after CO concentrations stabilize and log another measurement.
  • Page 110 Escape the program (a) or trigger another step (t). LI-6400 Light Sensors Three light sensors may be used with the LI-6400. The optional External Quantum Sensor (part # 9901-013) measures photosynthetically active radiation (PAR) over the 400nm to 700nm waveband. The External Quantum Sensor gives...

  • Page 111: Gallium Arsenide Phosphide (Gaasp) Sensor

    The spectral properties and calibration of the GaAsP sensor are discussed below. The third light sensor used in the LI-6400 is a silicon diode that monitors and controls the optional 6400-02 LED Light Source. The silicon diode light sensor has a wide response that covers the red LED emission range.

  • Page 112: Generating An Approximate Gaasp Sensor Calibration Using A Quantum Sensor And The Quantum Sensor Chamber Mount

    Section 4 Quantum Sensor Chamber Mount (part # 9864-111) found in the spare parts kit. Generating an Approximate GaAsP Sensor Calibration Using a Quantum Sensor and the Quantum Sensor Chamber Mount An approximate calibration of the GaAsP sensor in the leaf chamber can be performed for light sources not included in the Light Source menu in the Configuration list, or for other special circumstances.
  • Page 113 Making Measurements Compute ParOutµm ÷ parIn_mV and enter the resulting value as CalParGaAs = value using the configuration editor. We do not recommend using a quantum sensor to calibrate, or even accurately measure, the optional LED Light Source PAR output because the dropoff in quantum sensor sensitivity near 700nm is similar to the long wave edge of the LED emission spectrum.
  • Page 114 File Management Chicago Contents Data Storage and File Management ........Using the FILER ............... Opening and Closing the FILER ....... File Naming Conventions .......... Directories..............Directory Operations ............Viewing and Changing Directories ......Creating and Deleting Directories ......File Operations ..............Viewing File Details ..........

  • Page 115: Data Storage And File Management

    To check the available memory after OPEN is loaded, open the Welcome Menu and select About this unit For storing data files, the LI-6400 has 1.5 MB of non-volatile “flash memory”. An application called the FILER (below) manages these data files.

  • Page 116: Using The Filer

    FILER by pressing Escape File Naming Conventions File names in the LI-6400 can be any length and are case insensitive. Thus, Test, test, and TEST are identical file names. File extensions are not used for data files, although a period is a valid character, and can be used if desired.

  • Page 117: Directory Operations

    Section 5 Directory Operations Viewing and Changing Directories To view or change directories: From the FILER main screen, press the function key (f1), or simply press . The FILER scans the system and displays a list of all directories on all disks. Use the arrow keys to scroll the list up or down.

  • Page 118: File Operations

    File Management File Operations Many file operations require that files or directories be selected (“tagged”) before the command can be executed (See Tagging Files below). Some of the operations that require files to be tagged include purging, copying and printing files. Press the Space Enter...

  • Page 119: Tagging Files

    Section 5 save the file with a new name, to execute the file (LPL source code files only), or to quit the Editor and return to the FILER. chicago Exit Menu "Star <esc> - Resume editing 4" "" U - Update file TestData "Obs"...
  • Page 120 File Management chicago This file is "tagged" /User MyData Filter= TestData Total: 4 ACiCurve Bytes: 5384 LightCurve Tagged: 0 Tag options Bytes: 0 Tag all Clr all Retag Invert tag One labels labels Figure 5-3. Tag function keys. The Tag function keys perform the following functions: Press...

  • Page 121: Purging Files

    Section 5 Purging Files To remove files, you must first tag them (above), and then press the key (or ). Press (Yes) at the prompt to Purge delete the file(s). Purged files are placed in the /User/Trash directory on the parent disk. The disk must be defragmented to actually remove old files and free up disk space.

  • Page 122: Duplicating Files

    File Management Duplicating Files To make duplicate files: Tag the file(s) to be duplicated. Press dUplct ). The file is duplicated and placed in the current directory; the filename is appended with "copy" (i.e., data copy). Renaming Files To rename a file: Select the file to be renamed.

  • Page 123: Disk Operations

    Disk Operations About Flash Memory... The LI-6400 file system uses a type of memory called Flash memory. Flash memory is very stable, in that it can only be erased by exposing it to an electrical charge. Powering the instrument off, or sudden power failures have no effect on Flash memory.

  • Page 124: Formatting Disks

    Do not format the /SYS disk, as it contains system operating files that affect the operation of the LI-6400. These files can be reloaded from the system floppy disk, but any changes made to the system defaults will be lost.

  • Page 125: Using The Hidden Disk

    Section 5 Select to erase the disk, or to abort the Proceed Cancel process. After the formatting is finished, the disk is empty except for about 70 bytes of file system infor- mation. NOTE: If you reformat the /USER disk, run the program /SYS/OPEN/ConfigInstall to put the necessary directories and files back onto the /USER disk.

  • Page 126: Data Communications

    File Management To hide the temporary disk: Press the Disk function key (or ) to display the Disk function keys labels. Press the function key (or ) to display a list of HideDsk the disks. Select the disk to be hidden and press .

  • Page 127: Cables

    LI-6400 is a null modem cable. Your computer is probably a DTE (or 9-pin AT) device, although there is no guarantee of this. The LI-6400 is a 9-pin AT device, so you must use a null modem cable to com- municate with your computer.
  • Page 128 File Management LI-6400 Computer 1000-09 9 pin AT 25 pin DTE LI-6400 Computer 1000-09 1800-04 9 pin AT 9 pin AT LI-6400 Modem 1800-04 9 pin AT 25 pin DCE LI-6400 Macintosh Hayes Modem cable 1000-09 9 pin AT Modem port Figure 5-4.

  • Page 129: Sending Files To A Personal Computer

    ). You are prompted to print header information and form feeds. The header information includes the file name as entered in the LI-6400. If you send multiple files at one time or if the file names don't follow DOS conventions you will want to include headers. The tagged file(s) are sent to the RS-232C port.

  • Page 130: Sending Files To A Macintosh

    ‘LI-6400 Photosynthesis System’ from the Instrument menu, and set the Communications parameters in the LI-6400 to 9600, 8, 1, N. In earlier versions of the 1000-91 program, select ‘General...’ from the Instrument menu and set the parameters as shown above.
  • Page 131 Soda Lime/Desiccant Bottles in the Sensor Head .... 6-19 Cleaning the Optical Bench ..........6-22 Servicing the External CO Source 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 Maintenance and Service...

  • Page 132: Recalibration

    Company, P.O. Box 460, Xenia, OH 45385) as the recom- Open this end BOTTOM mended desiccant for use with the LI-6400. Drierite is anhy- drous calcium sulfate (CaSO ), which is chemically inert ex- cept toward water, is safe, economical, and can be regenerated.

  • Page 133: Regenerating Drierite

    Note that the color of the indicating Drierite may become less distinct after successive regenerations. Ordering Information Indicating Drierite can be ordered from LI-COR (1 lb. bottle) under part #622-04299, or from W.A. Hammond Drierite Company (P.O. Box 460, Xenia, OH 45385. Phone: 513-376- 2927) under stock number 24001.

  • Page 134: Filling The Scrubber Tube

    Section 6 Filling the Scrubber Tube The external soda lime tube is used to scrub CO from the air entering the system. CO can be scrubbed from ambient to 0 Flow Control Knob ppm for the purpose of zeroing the CO analyzers during calibration.

  • Page 135: Replacing The Air Mufflers

    Maintenance and Service Replacing the Air Mufflers There are two air mufflers attached to the air hoses inside the soda lime and desiccant tubes (Figure 6-3). These mufflers may become clogged, restricting air flow through the tubes. To replace the mufflers, remove the bottom cap, empty the chemicals and then unscrew the top cap.

  • Page 136: Replacing The Leaf Temperature Thermocouple

    Section 6 Replacing the Leaf Temperature Thermocouple The leaf temperature thermocouple will last a long time if you are careful with it. If the thermocouple is broken, the leaf temperature will always read the same as the air temperature. To replace the leaf temperature thermocouple: The leaf temperature thermocouple is mounted in a plastic holder that is inserted from below the bottom half of the leaf chamber (Figure 6-4).
  • Page 137 Maintenance and Service Connect the new assembly by re-inserting the male ther- mocouple connector, and carefully insert the plastic ther- mocouple holder up through the bottom of the leaf cham- ber. Be careful not to pinch the thermocouple wires when inserting the holder.

  • Page 138: Setting The Leaf Temperature Thermocouple Zero

    Section 6 Setting the Leaf Temperature Thermocouple Zero Remove the male thermocouple connector by pulling straight out. Configure the New Measurements screen so that you can view both the leaf temperature and block temperature variables (Tleaf °C and Tblock °C, respectively). In the default display configuration you can view these variables by pressing There is a small adjustment screw located on the under-...

  • Page 139: Recharging The 6400-03 Batteries

    There is a 10A automotive type fuse located inside the metal cover of the 6400-03 battery. If the battery fails to power the LI-6400, and will not light the charge indicator on the battery charger, check to see if the fuse has blown.

  • Page 140: System Console

    Disconnect all cables and hoses from the console and remove the batteries. Remove the eight screws (nine screws on console serial numbers PSC101-160) on both sides of the LI-6400 con- sole case with a Phillips head screwdriver. Grip the carrying handle and lift the card cage straight up and out of the case.
  • Page 141 Maintenance and Service Figure 6-7. Location of flow board fuses F1-F3 and backplane fuse F1. Maintenance and Service 6-11...
  • Page 142 Section 6 Figure 6-8. Location of backplane board fuses F2 and F3. Table 6-1. Replacement fuse sizes for the flow and backplane boards. Flow Board Fuse Size Protects... F1 (Circ. fan) 3A Fast blow, 250V Circulating fan F2 (TEC-) 5A Fast blow, 125V Thermoelectric coolers F3 (TEC+) 5A Fast blow, 125V...

  • Page 143: Leaf Chamber Care

    Maintenance and Service Leaf Chamber Care It is important to take care of the foam gaskets on the leaf chambers. Never latch the chamber closed when it is not in use, as the foam will stay compressed if you leave the chamber closed for several hours.

  • Page 144: Replacing The Upper Leaf Chamber Film

    Wilmington, DE) over the upper leaf chamber if it becomes torn or punctured, or excessively dirty. Replacement Propafilm (LI-COR part #250-01885) and double-sided tape (part #212-04341) can be found in the spare parts kit. To replace the Propafilm: Unhook the PAR sensor connector from the port on the side of the sensor head by gently pulling straight out.
  • Page 145 Maintenance and Service Top View Connector O-rings GaAsP PAR sensor Upper leaf chamber cuvette Gasket Figure 6-9. Remove the two screws from the upper half of the leaf chamber. Remove the old Propafilm and the tape from the chamber surface. The tape has a fairly strong adhesive; if it does not peel off readily, use a mild solvent (i.e., acetone) to help dissolve the adhesive.
  • Page 146 Section 6 Lower the top surface of the chamber onto the tape and press firmly. Trim the tape around the outer and inner edges of the chamber (Figure 6-10). To get a clean cut, use a fresh blade (an Exacto knife works well) and make your first cut as close to the edge as possible.

  • Page 147: Internal Air Filter

    The frequency with which the Balston air filter needs to be replaced depends upon the operating environment; it generally needs replacement after about 1 year, unless the LI-6400 is used in a very dusty environment. The filter is located inside the LI-6400. Disassemble the con- sole as described above at "Cleaning and Removing the Card...

  • Page 148: Soda Lime/Desiccant Bottles In The Sensor Head

    Section 6 Soda Lime/Desiccant Bottles in the Sensor Head There are two small plastic bottles containing a mixture of anhydrous magnesium perchlorate and soda lime inserted into the analyzer housing that keep the detectors free of CO water vapor. These bottles should be recharged with fresh chemicals on an annual basis.
  • Page 149 Maintenance and Service Housing Cover Bottle Cover Figure 6-11. Remove the two screws that secure the housing cover. Filter Before removing the bottles, prepare the new bottles (in spares kit) by filling them with equal parts soda lime and magnesium perchlorate. Fill the bottles half full with soda lime first, followed by the magnesium perchlorate.
  • Page 150 Section 6 Bottle Cover/O-Ring Soda Lime/Desiccant Bottles Cover Analyzer Housing Soda Lime Mg(ClO Figure 6-13. Insert the new bottles lid first, followed by the bottle cover/o-ring and housing cover. Magnesium perchlorate is the recommended desiccant since it does not interact with CO .

  • Page 151: Cleaning The Optical Bench

    Maintenance and Service Cleaning the Optical Bench Because the LI-6400 contains open path analyzers, it is possi- ble for air-borne debris to enter the system and contaminate the sample optical path. If the analyzers become so dirty that the optical path is affected, you will see a message on the console display indicating that the IRGAs are not ready.
  • Page 152 Section 6 Remove the 3 screws located on the back side of the han- dle, as shown in Figure 6-15, using a #1 Phillips head screwdriver. Note that the middle screw is shorter than the other two. Rear View Handle Quantum sensor holder Remove these...
  • Page 153 Maintenance and Service Remove the upper half of the leaf chamber. Remove the 2 screws from the hinge on the rear of the upper half of the leaf chamber (Figure 6-16). The upper portion of the leaf chamber can now be moved aside; unhook the connector from the PAR sensor or LED Light Source, if necessary.
  • Page 154 Section 6 Top View Gasket Lower leaf chamber cuvette Hex head screws (8) Figure 6-17. Remove the 8 cap screws. 6-24 Section 6...
  • Page 155 Maintenance and Service Moisten a cotton swab and swab the 2 optical windows (Figure 6-18). Leaf Chamber Adjustment Nut Optical Windows Figure 6-18. Clean the two optical windows. You can also remove and clean the 2 gold plated optical mirrors by unscrewing the 6 cap screws on each mirror. Allow to air dry before reassembling the sensor head.

  • Page 156: Servicing The External Co Source Assembly

    Section 6 Servicing the External CO Source Assembly Oil Filter Replacement Inside the CO cylinders there is a small amount of residual oil from the manufacturing process. When the CO cylinder is pierced, some of this oil is released along with the CO .

  • Page 157: Making Your Own Filters

    Maintenance and Service To install the filter: Remove the CO cylinder cover. After depressurizing the CO cylinder, remove the filter cap to reveal the filter (Figure 6-19). Use the filter hook included to carefully remove the old filter, being careful not to scratch the O-ring seat. Cylinder Cover Remove the paper from around the new filter.
  • Page 158 Section 6 concentrations, and you are using a fresh CO cylinder and oil filter, it may indicate that the flow restrictor is clogged. The flow restrictor must be replaced if it becomes clogged. The restrictor is pressed into the fitting connected to the top of the copper supply tube (Figure 6-20), and can not be removed;...
  • Page 159 (i.e., acetone) that leaves no residue. Remove the fitting containing the flow restrictor and dis- card. Install the new fitting/restrictor (LI-COR part #9964-042). Note that the fitting is wrapped at one end with teflon tape (Figure 6-21). Insert this end into the mounting block and tighten securely.
  • Page 160 Section 6 Teflon tape Remove this fitting and replace Ferrule "T" fitting Ferrule Copper supply tube Figure 6-21. Reassemble the supply tube as shown. 6-30 Section 6...

  • Page 161: Shipping Your Li-6400

    Maintenance and Service Shipping Your LI-6400 If you need to return your LI-6400 to LI-COR for any reason, or need to transport the instrument in its shipping case over long distances, we recommend that you secure the sensor head handle in the closed position. Close the leaf chamber and use a piece of string or a cable tie to prevent the spring-loaded handle from opening.
  • Page 162 Troubleshooting Hardware Problems Problem Possible Cause Solution Does not power ON. Low batteries. Check voltage, recharge if necessary. Batteries not connected Plug in battery jacks. Fuse blown. Check fuse F2 on backplane board. LED lamp is connected, but LEDSource=6400-02 not Set LEDSource=6400-02 in Lamp function key is not selected in Configuration...
  • Page 163 Section 7 There are a variety of software error messages that may appear on the screen if you try to perform a function that is not allowed. Some of these messages indicate that an error was made when you tried to perform a function;...
  • Page 164 Troubleshooting Displayed Message Error/Warning Explanation <filename> is a system device Error Attempted to open a system device. only. Only the operating system can use a system device. <filename> is a system file Error Attempted to open a system file. Only only.
  • Page 165 Cannot copy directory Error Attempted to copy a directory like an <directoryname> ordinary file. Cannot copy to or from /. Error Cannot copy files to or from the root directory "/". On the LI-6400, files cannot be stored in "/". Troubleshooting...
  • Page 166 Cannot move a file to itself. Error Cannot move from a file to the same file. Cannot move to or from /. Error Cannot move files to or from the root directory "/". On the LI-6400, files cannot be stored in "/". Troubleshooting...
  • Page 167 Section 7 Displayed Message Error/Warning Explanation Cannot open /. Error The root directory "/" cannot be opened as a file. Cannot open device manager. Error The file "/dev" cannot be opened. Cannot remove /. Error The root directory "/" cannot be removed.
  • Page 168 There is a problem with the hardware and/or software. Restart the system. If the error reoccurs, record sequence of events that caused error, if possible, and contact LI-COR. IRGAs not ready Warning Flashes in New Measurements screen if either IRGA is not functioning properly.
  • Page 169 Section 7 Displayed Message Error/Warning Explanation Out of disk space on Error "/<diskname>" does not have any /<diskname> space available for writing. This can occur while writing to a file or while the operating system is updating the file's directory entry. Access the FILER and defragment as soon as possilble.
  • Page 170 Troubleshooting Displayed Message Error/Warning Explanation Unlinked fragments : Warning Can occur at startup if some data was Scanning disk... found without a corresponding directory entry. The file system will scan the disk for the last stable root directory entry. Version number not allowed. Error Occurs when attempting to remove a file with a semicolon in the filename.
  • Page 171 Configuration List Area = value Default = 6.0. This is the area of the leaf chamber cuvette, in cm . When measuring narrow leaves, you may want to enter a smaller leaf area value. The area can also be changed in New Measurements mode. StomRat = value Default = 1.
  • Page 172 The LightSource = command contains three pieces of information: Whether or not the 6400-02 is being used. This determines which calibration constant is applied to the light sensor signal from the chamber, either the CalParGaAs = value or the CalParLED = value. The actinity correction (the value immediately following the label) to be automatically applied to the light sensor calibration value.
  • Page 173 BLCond = file Displays the file containing the boundary layer conductance table. If you want to use a fixed value for the boundary layer conductance, enter the number after the = (equals) sign and before the file name. If you choose to enter your own value, it should represent one side of the leaf;...
  • Page 174 Specifications Temperature Range: 0 °C to 50 °C. Operating temperature: Optical housing air temperature Range: -10 to 50 °C. 3-wire thermistor Accuracy: Maximum error < ± 0.5 °C. Typical error < ± 0.25 °C. Optical housing block temperature Range: -10 to 50 °C. 3-wire thermistor Accuracy: Maximum error <...
  • Page 175 Air Flow Range: 0 to 600 µmol s Flow rate (with 6400-01 CO injector): Range: 150 to 750 µmol s (without CO injector): Resolution: < 1 µmol s Flow meter: Accuracy: < ± 5% of reading, with flow > 30 µmol s and flowmeter zeroed.
  • Page 176 Analyzer Type Absolute, open path, non-dispersive infrared gas analyzer. Range 0-3000 ppm. Bandwidth 10 Hz. ≤ 0.1 ppm. Resolution of readout Signal noise (at 350 ppm) With 1 second signal averaging: < 1 ppm peak-to-peak. 0.4 ppm typical. With 4 second signal averaging: <...
  • Page 177 System Console Memory 512K bytes nonvolatile flash memory for programs; 512K bytes RAM for operation; 1.5M bytes nonvolatile flash memory for data storage. 40 character × 8 line (240 × 64 dot) LCD graphic display. Display Keyboard Full ASCII keypad, sealed from dust and moisture with membrane overlay.
  • Page 178 Connector Descriptions 9-Pin RS-232C Port The RS-232C connector on the LI-6400 console is a 9-pin AT type male "D" connector. The pin assignments are as follows: Pin # Name No Connect Received Data (input) Transmitted Data (output) Data Terminal Ready (output)
  • Page 179 Pin # Name LPL Assignment Digital Output 1 (open drain) 0x0401 Digital Output 3 (open drain) 0x0403 Digital Output 5 (open drain) 0x0405 Digital Output 7 (open drain) 0x0407 0 to + 5V D/A (8-bit analog output) 0 to + 5V D/A (8-bit analog output) - 5V to + 5V D/A (8-bit analog output) - 5V to + 5V D/A (12-bit analog output) Analog Ground...
  • Page 180 5. No-charge repair parts may be sent at LI-COR, inc.'s sole discretion to the purchaser for installation by purchaser. 6. LI-COR, inc.'s liability is limited to repair or replace any part of the instrument without charge if LI-COR, inc.'s examination disclosed that part to have been defective in material or workmanship.
  • Page 181 LI-COR, inc.'s authorized distributor, whichever is earlier. This warranty supersedes all warranties for products purchased prior to June 1, 1984, unless this warranty is later superseded.

Table of Contents