Download Print this page

LI-COR LI-6400 Manual

LI-COR LI-6400 Manual

Portable photosynthesis system

Hide thumbs Also See for LI-6400:

Installation instructions (2 pages)

,

Installation and operational instructions (2 pages)

,

Primer (181 pages)

Table Of Contents

Table of Contents

Advertisement

Quick Links

Download this manual

Using the LI-6400

Portable

Photosynthesis

System

¨-

Table of Contents

Advertisement

Table of Contents

Troubleshooting

Need help?

Need help?

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

Questions and answers

Summary of Contents for LI-COR LI-6400

Page 1 Using the 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 consequen- tial damages in connection with the furnishing, performance, or use of this material.
Page 3: Table Of Contents
Contents 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...
Page 4: Table Of Contents
Hot Keys 5-16 Low Battery Warning 5-17 The Boot Screen 5-18 The LPL Screen 5-20 Power ON Hooks 5-23 6 Real Time Data Viewing real time data using text and graphics Text Display 6-2 Real Time Graphics 6-8 Using the LI-6400...
Page 5: Table Of Contents
Part III: Working With Files 10 The LPL File System Managing your data storage space Files, Directories, and Disks 10-2 Defragmentation 10-5 The Filer 10-6 FilerÕs Directory Operations 10-9 FilerÕs File Operations 10-11 FilerÕs Disk Operations 10-18 Troubleshooting 10-21 Using the LI-6400...
Page 6: Table Of Contents
Contents 11 Downloading Files Retrieving your data Connecting the LI-6400 to a Computer 11-3 File Exchange Mode 11-4 Using WinFX 11-4 Using FX for DOS 11-8 Using FX on Macintosh 11-10 Using EW 11-12 Odds and Ends 11-21 Using a Data Capture Program 11-23...
Page 7: Table Of Contents
Using Energy Balance in OPEN 17-6 Energy Balance And Boundary Layer 17-9 Further Reading 17-11 Part V: Maintenance & Troubleshooting 18 Calibration Issues How much is good data worth? CO2 and H2O Analyzers 18-3 Flow meter 18-17 Using the LI-6400...
Page 8: Table Of Contents
Leaf Chambers 19-20 LED Source Maintenance 19-22 Match Valve Maintenance 19-23 IRGA Maintenance 19-26 Servicing the External CO2 Source Assembly 19-32 Shipping The LI-6400 19-35 Useful Part Numbers 19-36 20 Troubleshooting When things go wrong Power On / Start-up Problems 20-2...
Page 9: Table Of Contents
21 Diagnostics and Utilities Useful programs Diagnostics & Tests Menu 21-2 /Sys/Utility Programs 21-10 Part VI: Programming 22 Programming with LPL An introduction to the LI-6400Õs programming language Overview of LPL 22-2 Making Objects 22-7 Functions 22-12 Pointers 22-17 Public and Static 22-22...
Page 10: Table Of Contents
Low Level Control Tools 25-19 26 Customizing Open ÒCry ÔHavocÕ - and let slip the dogs of warÓ Using PATCH= 26-2 Useful Variables 26-4 OpenÕs Hooks 26-7 New Style ComputeList Files 26-16 Using Spare Channels 26-22 INDEX Using the LI-6400...
Page 11: Welcome To The
Welcome to the LI-6400 A Bit of History The LI-6400 is LI-CORÕs third generation gas exchange system. In the begin- ning was the LI-6000; it used a third party CO analyzer having the novel (for 1983) features of small size, light weight, and low power. Photosynthesis was...
Page 12 So, we set about inventing them. Five years and one name change later, we shipped the first LI-6400. And many more since then. We trust that this instrument will serve you well, and stand ready with support and help as you put it to work.
Page 13: Assembling The
Finally, a Troubleshooting Guide (Chapter 20) is now available. The Old Manuals If you are not a new LI-6400 user, you may be wondering how Using the LI-6400 relates to the original documentation, The LI-6400 Primer and The LI-6400 Technical Reference. If you have these original manuals, you can safely get rid of them, because Using the LI-6400 includes the relevant prior material, and adds much new material.
Page 14 Welcome to the LI-6400 About this Manual Electronic version This manual is also available as an Adobe¨ Acrobat¨ file, on CD and from our web site (www.licor.com). All cross references in the text, table of con- tents, and index are hyper-linked, allowing one-click access. (Version 3.0 of Adobe¨...
Page 15 Part I The Basics...
Page 17 Transpiration 1-7 Total Conductance to Water Vapor 1-8 Stomatal Conductance to Water Vapor 1-9 Net Photosynthesis 1-9 Intercellular CO2 1-10 Everything Else 1-11 Summary of Symbols 1-11 1-12 YSTEM OMPONENTS The Standard Parts 1-13 The Optional Accessories 1-14 Using the LI-6400...
Page 18: An Open System
This chapter acquaints you with the LI-6400Õs operating principle, major components, and equations. An Open System Measuring Differentials The LI-6400 is an open system, which means that measurements of photosyn- thesis and transpiration are based on the differences in CO and H O in an air stream that is flowing through the leaf cuvette (Figure 1-1).
Page 19 The black neoprene gaskets that we use on the LI-6400 (except for the light source) have the low- est diffusivity to CO of all the gasket material we have tested, but itÕs not...
Page 20: The Flow Schematic
See Diffusion Leaks on page 4-43 for more details. The Flow Schematic The LI-6400 provides mechanisms for modifying the incoming airÕs CO O concentrations (Figure 1-2 on page 1-5). There are chemical tubes for scrubbing CO...
Page 21 Schematic with a 6400-01 CO2 Mixer Desiccant Vent Flow Control Pump Bypass Valve Vent Liquid CO Flow Control Scrubber Flow Meter Flow Sample Restrictors Reference Air In Bypass Valve Figure 1-2. LI-6400 flow schematic, with and without a 6400-01 CO mixer. Using the LI-6400...
Page 22 Matching in this manner is a problem, however, because you donÕt want to remove the leaf from the chamber in the middle of an experiment. The LI-6400 provides a mechanism to match the IRGAs without disturbing the leaf: it is called match mode, and it is illustrated in Figure 1-3.
Page 23: Equation Summary
System Description Equation Summary Equation Summary If you are not interested in the details of the LI-6400Õs gas exchange calcula- tions, you can safely skip this section. The equations for net photosynthesis, transpiration, etc. are essentially those derived by von Caemmerer and Farquhar .
Page 24 System Description Equation Summary which rearranges to Ð --------------------------- (1-4) s 1 w Ð The relationships between the terms in (1-4) and what the LI-6400 measures ¤ F 10 ¤ (1-5) ¤ ¤ S 10 where F is flow rate (µmol s-1), W...
Page 25 System Description Equation Summary The function e(T) is saturation vapor pressure (kPa) at temperature T (C). The formula used by the LI-6400 is (14-21) on page 14-10. Stomatal Conductance to Water Vapor The stomatal conductance g to water vapor (mol H...
Page 26 System Description Equation Summary Ð ------------------------ - Ec Ð (1-13) To write (1-13) in terms of what the LI-6400 measures, we use (1-5) and ¤ ¤ (1-14) ¤ A 10 where C and C are sample and reference CO concentrations (µmol CO...
Page 27 1.37 is the same ratio in the boundary layer. Everything Else There are many other relationships that the LI-6400 uses (calibration equa- tions for sensors, dew point temperatures, relative humidity, etc.), which are documented in Chapter 14.
Page 28: The System Components
The System Components The System Components If you have just taken delivery of your LI-6400 check the packing list to ver- ify that you have received everything that you ordered. Or, if youÕve just in- herited an LI-6400 from someone else, check to see that you have everything.
Page 29 Spare Parts Kit This box contains replacement parts for your LI-6400. As you become famil- iar with the system you will learn which items to keep close at hand and which items can be safely stored away.
Page 30 The Optional Accessories There are several optional accessories that you may have ordered with your LI-6400. Any of them can also be purchased later, and (with the exception of the 6400-01 CO Mixer), they do not require factory installation:...
Page 31 A 2x3 cm chamber bottom with a Propafilm¨ window. Leaf temperature is computed using an energy balance. Can be used with any 2x3 cm chamber top (such as the fluorometer adapters) or 6400-02 or -02B LED source. Using the LI-6400 1-15...
Page 32 6400-20 / 6400-21 File Exchange Software The 6400-20 (for DOS) and 6400-21 (for Macintosh) file exchange (FX) soft- ware is used for rapid file transfer between the LI-6400 and a computer. Your computer communicates with the LI-6400 (which is in file exchange mode), allowing you to do file transfers and other file management operations right from your computerÕs keyboard.
Page 33 Assembling the LI-6400 Putting it all together REPARATIONS The CO2 Scrub and Desiccant Tubes 2-2 Cables And Hoses 2-3 Connecting the Chamber / IRGA 2-5 SING A RIPOD 6400-01 CO2 I NJECTOR NSTALLATION Using 12 gram CO2 Cartridges 2-8 External CO2 Tanks 2-10...
Page 34: Preparations
Assembling the LI-6400 This chapter guides you through the assembly and preparations necessary to operate the LI-6400. Preparations This section explains how to prepare the console and sensor head for opera- tion. The CO Scrub and Desiccant Tubes The CO scrub and desiccant tubes can remain attached to the console at all times, except when changing chemicals.
Page 35 Assembling the LI-6400 Preparations Air Passage Holes Scrub Tube Desiccant Tube O-Rings Figure 2-1. Desiccant and CO scrubber tubes. Cables And Hoses Air inlet and outlet ports and electrical connectors are located on the right side (end) of the console (Figure 2-2).
Page 36 Assembling the LI-6400 Preparations Air Outlets The two sections of Bev-a-line tubing attached to the sensor head must be connected to the console air outlet ports. One of the tubes has a black band near the end of the hose. Attach this hose to the port of the console.
Page 37 IRGA/chambers? The simple answer is probably no; they are not de- signed to do it. Each LI-6400 console is adjusted at the factory for a par- ticular head. If you mismatch them, you may not able to zero the IRGAs.
Page 38: Using A Tripod
Assembling the LI-6400 Using a Tripod Using a Tripod A mounting bracket is included in the spare parts kit for mounting the sensor head on a tripod. A tripod is a virtual requirement when making long-term measurements in the absence of cooperative graduate students.
Page 39: Co2 Injector Installation
Injector Installation The optional 6400-01 CO Injector consists of a controller that is factory installed within the LI-6400 console, and an external part that attaches between the chemical tubes on the end of the console. This external part can be either ¥...
Page 40 Assembling the LI-6400 6400-01 CO2 Injector Installation Using 12 gram CO Cartridges mixer regula- tor attaches here. Check for O-rings in these two locations Cylinder Cover Oil Filter 12 gram cylinder Figure 2-6. Location of external CO source assembly. To install the 9964-026 Source Assembly Attach the assembly block.
Page 41 If the filter is getting discolored, change the filter. See Servicing the External CO2 Source Assembly on page 19-32 for more details. (With LI-COR cylinders, the filter should last for 25 cylinders. We have encountered other cylinders, however, that contain much more oil, notably Copperheadª...
Page 42 Assembling the LI-6400 6400-01 CO2 Injector Installation Screw the cylinder cover onto the piercing block. You may feel some resistance as the piercing pin contacts the cylinder. A short burst of venting CO may occur as the cylinder is pierced; the leak is minimal if you continue to quickly tighten the cylinder cover.
Page 43 If you are unable to obtain 1/8Ó copper tubing, you can connect the Tank Con- nector Block to a CO source using 4mm tubing and the compression fitting (LI-COR part #300-04439) included with the Tank Connector Block. Install the Tank Connector Block and copper tubing This is described in steps 1-4 above.
Page 44 Assembling the LI-6400 6400-01 CO2 Injector Installation Connect the 1/8Ó and 4mm tubing Use the 1/8Ó to 4mm compression fitting to connect the two pieces of tubing (Figure 2-9). Be sure to orient the ferrules correctly; the narrow tapered end of each ferrule must be oriented toward the compression fitting.
Page 45 Assembling the LI-6400 6400-01 CO2 Injector Installation 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 2-9. Use the compression fitting to connect 1/8Ó and 4mm tubing.
Page 46: External Quantum Sensor Installation
Connector Figure 2-10. The external quantum sensor installed. If the LI-6400 was shipped from the factory with an external quantum sensor, itÕs calibration factor will have already been entered into the instrument. Oth- erwise, you will have to do this. See The Installation Menu on page 16-4.
Page 47: B Led Light Source Installation
Assembling the LI-6400 6400-02B LED Light Source Installation 6400-02B LED Light Source Installation The optional 6400-02 or -02B 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 48 Assembling the LI-6400 6400-02B LED Light Source Installation Remove the top leaf chamber Use the 3/32Ó hex key provided in the spare parts kit to remove the two long screws that hold the chamber top in place (Figure 2-12). Top View...
Page 49 Connector Figure 2-13. Attach the lamp and PAR sensor connectors. If the LED source was purchased with the LI-6400, its calibration factor will have been installed in the console. Otherwise, you will have to do this. See Example: 6400-02B LED Source on page 16-5 for how to do this using the Installation Menu.
Page 50: Powering The Li-6400
LI-6020 Battery Charger and a single 6400-03 Recharge- able Battery. To use the LI-6020, plug a fully charged 6400-03 battery into one of the LI-6400 battery jacks, and plug the LI-6020 into the other jack us- ing the 9960-062 cable (in spares kit).
Page 51: Installing System Software
ItÕs easy to do (I speak from experience), and it quickly brings your measurements to an abrupt halt. Note that you can also power the LI-6400 using any 12 volt battery with suf- ficient capacity; a car battery, for example, will run the system for 24 to 48 hours before recharging is necessary.
Page 52 Two pieces of software are installed: LPL and the /Sys disk. LPL is the oper- ating system that supports the programs that run on the LI-6400, and the /Sys disk contains those programs. The installation should not affect any other disk, other than updating the factory default files (listed in Table 16-3 on page 16-17) on the /User disk.
Page 53: Text Display
Dynamic Response of Humidity Control 3-27 CO2 Control - Without a 6400-01 3-32 CO2 Control - With a 6400-01 3-33 Temperature Control 3-36 Lamp Control 3-39 Control Summary 3-40 #4: L 3-41 OGGING Logging Data Manually 3-41 Using the LI-6400...
Page 54: Before You Start
Guided Tours The purposes of this chapter are to teach you a) how to operate the LI-6400, and b) how the LI-6400 accomplishes its tasks. We do this with a series of guided tours. We recommend that you follow along on your instrument. You wonÕt need plant material for these tours.
Page 55 Function keys & escape " enter ctrl enter Õ space < > shift shift escape key Figure 3-1. The LI-6400 keypad. The cursor control keys, labels, and enter are paired to facilitate access with either hand. Using the LI-6400...
Page 56: Tour #1: Open Overview
Loading OPEN 3.3... Figure 3-2. OPENÕs bar chart is displayed while loading. If your LI-6400 doesnÕt behave as described here, refer to Power On / Start- up Problems on page 20-2. The only reason for answering No is if you are about to connect the sensor head in the next minute.
Page 57 OPENÕs Main Screen After some more messages, OPENÕs main screen appears (Figure 3-4). This screen represents the home base of operations for OPEN, and also shows some status information. The function keys (f1 through f5) have 2-line labels Using the LI-6400...
Page 58 PSC-401 has been changed, and above). but is not stored. Software version Space remain- LI-6400 Photosynthesis System ing for file stor- OPEN 3.3 age on the disk named /User FUSE CONFIG /User 10% full 12.03V...
Page 59 (saveAs). For details, see Config Status on page 16-14. Clock Stopped This message will appear instead of the time and date if the real time clock is not operating. See Real Time Clock Problems on page 20-6. Using the LI-6400...
Page 60: Diagnostics & Tests Menu
LPL version: 3.0.007 OPEN version: 3.01 Available memory: 58205 bytes Only appears if 6400-12 installed Coprocessor Installed Fuse Aware Only appears if the LI-6400 Press Any Key can detect blown fuses Diagnostics & Tests Menu "CO2 Mixer Test" "DAC Status"...
Page 61 OPEN (if you havenÕt turned the power off), all control settings (lamp, flow, etc.) will remain the same. There is normally no need to do either of these, however; when you have finished using the LI-6400, you can just power down from OPENÕs main screen.
Page 62 ÒLI-610 Fct Key ControlÓ ÒReset to Factory DefaultsÓ ÒSurvey MeasurementsÓ ÒReset to User ConfigurationÓ Figure 3-6. The Config Menu Press f2 and explore in the Config Menu if you like. Otherwise, weÕll move on to the Calibration Menu. 3-10 Using the LI-6400...
Page 63 WeÕre done, so press escape or f5 (Done). Plot the mixer calibration Whether or not your LI-6400 is equipped with a CO mixer, it will have a cal- ibration curve for one. This curve relates the control signal used to provide mixer set points to the resulting CO concentration.
Page 64 (This shortcut works for any plot done by GraphIt, the built in plotting pack- age. GraphIt is introduced in Tour #4.) The data values are shown in a list that you can scroll. Return to Calib Menu When you are done viewing the data values, press escape. 3-12 Using the LI-6400...
Page 65 You can also do this er with this. "Graph stored data" from the Filer. "New File (Editor)" When the LI-6400 is in file "Recompute stored data" exchange mode, it can Discussed in "Set the Time and Date" serve as a file server for a Chapter 13 "Sleep mode"...
Page 66: Tour #2: New Measurements Mode Basics
Tour #2: New Measurements Mode Basics New Measurements mode is entered by pressing f4 (New Msmnts) while in OPENÕs main screen. When using the LI-6400, you will likely spend most of your time here, coming out only to do configuration changes, calibrations, download data, and other ancillary operations.
Page 67 Available for user use. Figure 3-12. Summary of New MeasurementÕs default function key labels.* - keys f4 and f5 of level 3 only shows these labels when user constants are defined (described in Prompt Control on page 9-12). Using the LI-6400 3-15...
Page 68 Press O (the letter), and the fan will stop. If you are listening, you should here a drop in the noise level. Turn the fan back on (fast) Press f3, then f, and the fan will resume running. 3-16 Using the LI-6400...
Page 69 Note that these display definitions can be modified (what variables are shown, and where) to suit nearly any taste. ItÕs all explained in Chapter 6. This concludes our basic tour of New Measurement mode. Using the LI-6400 3-17...
Page 70 Coefficient of variation of Flow_µml (%) RH_R_% Relative humidity in the reference cell (%) RH_S_% Relative humidity in the sample cell (%) Td_R_% Dew point temp in the reference cell (C) Td_S_% Dew point temp in the sample cell (C) 3-18 Using the LI-6400...
Page 71 Numerical summary of the four stability flags totalCV% See totalCV% under E above CRagc_mv Reference CO AGC (automatic gain control) sig- nal, in mV CSagc_mv Sample CO AGC signal HRagc_mv Reference H O AGC signal HSagc_mv Sample H O AGC signal Using the LI-6400 3-19...
Page 72: Tour #3: Controlling Chamber Conditions
Clamp your ÒleafÓ into the leaf chamber ThereÕs actually a fifth control: wind speed, via the fan. The fan control is on level 3, but we usually keep the fan speed on fast. 3-20 Using the LI-6400...
Page 73 ItÕs far enough. Use a high flow rate: 700 µmol s Press 2 (if necessary, to bring up the level 2 function keys). Then press f2, F (for fixed flow), 700, then enter (Figure 3-17). Using the LI-6400 3-21...
Page 74 Observe what happens when you change the desiccant from full scrub to full bypass. The reference (H2OR_mml) will increase to whatever the ambient humidity is, since we are now not drying the incoming airstream at all. The 3-22 Using the LI-6400...
Page 75 (For a picture of this, see Figure 3-39 on page 3-47.) Fixed Humidity Operation One of the powerful features of the LI-6400 is itÕs ability to operate in a fixed humidity mode. It does this by actively regulating the flow rate to maintain a If you have a CO mixer, the reference value will decrease rapidly, because Òex-...
Page 76 F) Flow Rate 400 µmol/s ¨ H2O_sample (20 mmol) R) RH_sample 50% V) VPD ( Tleaf¡C) 1.00 kPa Figure 3-18. Constant H2O mode can be set by pressing H, or by highlighting the H line and pressing enter. 3-24 Using the LI-6400...
Page 77 If the humidity wonÕt go low enough, the only recourse to raise the target value. Hence the message. Using the LI-6400 3-25...
Page 78 Z to turn it off (hold the ctrl key down and press Z). Note that this is a toggle: if you press ctrl Z again, the message will re-appear. Also, note that each time you re-enter New Measurements mode, OPEN resets this flag, so that warnings will again be displayed. 3-26 Using the LI-6400...
Page 79: Real Time Graphics
Press 4 to view the Real Time Graphics control keys, then press f4 (Graph Setup). You will eventually see something like Figure 3-21. Our task is to make this look like Figure 3-22 on page 3-29. Using the LI-6400 3-27...
Page 80 Y axis will adjust as needed to keep the curve on scale.) To see the structure of this menu, refer to Figure 6-6 on page 6-6. 3-28 Using the LI-6400...
Page 81 WeÕll now change the input humidity from dry to ambient and back, and watch how the flow rate adjusts. Your hint to do this is the + just to the left of the labels. A + or a number there always means Òmore keys definedÓ. Using the LI-6400 3-29...
Page 82 Change to medium response, and repeat Steps 4 and 5. Press escape to stop viewing the graph. Press 2, then f1 to drop the response from fast to medium. Resume watching the graph by pressing 4, then f3. 3-30 Using the LI-6400...
Page 83 (For details and suggestions, see the dis- cussion under The RSPNS Key on page 7-12.) ¥ Typically, you will be best served by operating with RSPNS=fast for the ÒtightestÓ humidity control. Using the LI-6400 3-31...
Page 84 Tour #3: Controlling Chamber Conditions Control - Without a 6400-01 In the absence of a 6400-01 CO Mixer, the LI-6400Õs means of controlling is limited to the soda lime adjustment knob. The following experiment illustrates how this works. Experiment #4 Adjusting the Soda Lime For this experiment, the chamber should be empty and closed.
Page 85 Low for much of this time. When CO2R_µml finally does reach 2000 µmol mol , it should be fairly stable. Change to 400 µmol mol Press f3 400 enter. CO2R_µml should drop to 400 µmol mol much faster than it rose to 2000 µmol mol Using the LI-6400 3-33...
Page 86 Press 4 then f1 to start the graph you should have defined in Figure 3-25. After 1 minute, change reference target to 900 µmol mol When the CO2S curve flattens out, press escape 2 f3 900 enter. 3-34 Using the LI-6400...
Page 87 ¥ Controlling on reference concentration is faster than controlling on sample concentration, for 3 reasons: 1. The larger volume of the sample cell / leaf chamber. 2. Flow changes when controlling constant humidity. 3. Possible photosynthetic rate changes Using the LI-6400 3-35...
Page 88 ¥ Controlling on block temperature is slow but steady. ¥ Limit of control is generally within 7 degrees of ambient. ¥ The further Tblock is from ambient, the larger the temperature gradient through the leaf chamber and IRGA. 3-36 Using the LI-6400...
Page 89 (Figure 3-28b). There will typically be a large increase in block temperature to get the leaf temperature to begin to rise, followed by a step-wise decline in block temperature as it approaches the target value. Using the LI-6400 3-37...
Page 90 ¥ Block temperature will warm or cool as needed in its efforts to control leaf temperature. ¥ Leaf temperature control is not as fast a block temperature control, since the mechanism is to control the air temperature that is blowing by the leaf. 3-38 Using the LI-6400...
Page 91 If there are none, then follow the instructions on page 16-5. Leaf reflectance plays a big role, but it is stable while the leaf is in the chamber, so we donÕt worry about it. Using the LI-6400 3-39...
Page 92 Chapter 7 provides a more thorough discussion of these controls, their options and limitations. At some point in your experience with the LI-6400, you should take time to read this material, and acquaint yourself more fully with these tools.
Page 93: Tour #4: Logging Data
See how much space is left A note appears informing of the approximate number of observations that can be stored before you run out of space. Press enter or escape to clear the mes- sage. Using the LI-6400 3-41...
Page 94 Figure 3-31. Level 1 function key labels when logging to a file. Graph the data Earlier we showed how to view strip charts of data in real time. Now weÕll show how to graph data youÕve recorded, before closing the data file. 3-42 Using the LI-6400...
Page 95 More keys avail- able - press labels, or 1 or 2 Pick from some pre-deter- View the data Define graph mined graph parameters file text parameters Figure 3-32. The first time GraphIt is entered from New Measurements mode. Using the LI-6400 3-43...
Page 96 Figure 3-34. Viewing a file Òas storedÓ. a) This is the header information at the top of the file. b) After pressing pgdn, the rest of the file is shown. An ex- planation of the top line banner in each figure is given in Figure 5-1 on page 5-3. 3-44 Using the LI-6400...
Page 97 Figure 3-36. Viewing the data set in column format. Only the data is shown. Use shift and shift ® ¬ to page left and right, and ctrl and ctrl to move one column at a time. Using the LI-6400 3-45...
Page 98 * for either the min or the max to let that value be adjusted according to the data being plotted. When you are done, if the display does not return to the menu shown in Figure 3-37, youÕll have to press escape. 3-46 Using the LI-6400...
Page 99 Press escape to stop viewing the graph, and return to GraphItÕs main screen. Press f5 (Config SaveAs), and name the file Ò Ó. (Storing this file uses RH & Flow the Standard File Dialog again, just as you saw when you opened a log file.) Using the LI-6400 3-47...
Page 100 Press escape until you get back to New Measurements Mode, then press f3 (Close File). ThatÕs the quick introduction to GraphIt, the tool for viewing logged data. It is accessible from New Measurements mode for a file that is open for logging, 3-48 Using the LI-6400...
Page 101 Auto match every __ obs (0 == none): To which you should answer 15, 10, and 0 respectively (pressing enter after each reply). This will log every 15 seconds, add 10 observations to the data file, and do no matching. Using the LI-6400 3-49...
Page 102 However, if you launch an AutoProgram with- out having a log file open, you will be asked to open one. A complete discus- sion of AutoPrograms is in Chapter 9. This concludes our tour of logging data. 3-50 Using the LI-6400...
Page 103: Tour #5: Configuration Adventures
Tour #5: Configuration Adventures This tour will acquaint you with the Configuration Menu. While Chapter 16 describes the LI-6400 configuration scheme in detail, this tour serves as a hands-on introduction to the topic. WeÕll take you through three fairly common tasks for which you need the Config Menu: building a configuration, checking to see what accessoriesÕ...
Page 104 LED light source for Step 6.) Press E for Energy Balance When prompted Leaf Temperature: Measured or Energy Balance? (M/E) press E. Press N for Needles When prompted Enter leaf type Needles or Broadleaves (N/B)? press N. 3-52 Using the LI-6400...
Page 105 2x3 Opaque Needles EB Modify the name if you like (press labels to access the line editing function keys), then press enter. No more configurations Press N when asked if you wish to build another configuration. Using the LI-6400 3-53...
Page 106 Tair_C, since that is air temperature in the sam- ple cell of the IRGA, not the leaf chamber.) If you wish now to reset to the default configuration, do so by going to the Reset Menu, and selecting ÒReset to Factory DefaultÓ. 3-54 Using the LI-6400...
Page 107 What Calibrations Are Installed? A number of the LI-6400Õs optional chambers and accessories have calibra- tions associated with them. If they were purchased along with your LI-6400, then their calibrations will likely have already been entered into the console at the factory. Otherwise, youÕll have to do it yourself, using the Installation Menu.
Page 108 When your file looks like Figure 3-48, press escape to view the exit menu, then press S to store this under a new name. The Standard File Dialog will appear with the current name in the edit box. Append the word TOUR to the name, and press enter. 3-56 Using the LI-6400...
Page 109 Figure 3-49. Display editor after having added a new line (ÒmÓ) that con- tains two items: P_gdd and Photo. Press f5 (OK) to leave the editor, and press N when asked if you wish to store your changes. Using the LI-6400 3-57...
Page 110 Menu (in the Config Menu), and select either ÒReset to Factory DefaultÓ, or ÒReset to User ConfigurationÓ. If you do the latter, then select ÒFactory De- faultÓ from the list of configurations, itÕs equivalent to doing the former. 3-58 Using the LI-6400...
Page 111: Tour #6: Boot Screen And Lpl
Boot Figure 3-51. A depiction of software layers in the LI-6400. There are three main ones: 1) Boot code, 2) LPL operating system, and 3) LPL programs. LPL programs can run other programs, so multiple layers of them can build up.
Page 112 Accessing the Boot Screen escape + power on, or else ctrl shift escape. If the LI-6400 is off, hold the escape key down, and turn on the power switch. If power is on, then you can simultaneously press ctrl + shift + escape.
Page 113 You should now be viewing the LPL Screen (Figure 3-53), our second stop on the tour. The LPL Screen LPL stands for LI-COR Programming Language, and its description starts in Chapter 22. The application that we ran back in Step 3 is the LPL Operating System.
Page 114 This editor is described in Standard Edit on page 5-13. No file name YouÕll be asked Edit What File: /SYS/AUTOST Press f1 (DelLn) to clear the file name, and press enter. YouÕll be editing a new (empty) file. 3-62 Using the LI-6400...
Page 115 Press escape to view the exit menu, followed by X, to run the file you just typed. Hello there will be printed, and the LI-6400 will wait for you to press a key. Press enter and youÕll return to Standard EditÕs exit menu. Save the program...
Page 116: Sys/Utility Programs
Press f1 if necessary to clear the line, and type /sys/open/open and press enter. YouÕll see the familiar bar chart displayed, as OPEN loads. Interrupt it Press escape to stop OPEN from loading, and press escape again to return to the LPL Screen. 3-64 Using the LI-6400...
Page 117 ScanDirs function) before launching /sys/open/open Return to LPL Screen Press escape, then Q. WeÕre done. If you would like to pursue programming in LPL, youÕll find a tutorial and reference in this manual, starting in Chapter 22. Using the LI-6400 3-65...
Page 118 1 0x0302 DIOSET THEN HALT ScanDirs 1000 OPEN_BUFF IF RETURN THEN Open a buffer :PTR buff buff DIRALL Get the list of directories Close the buffer buff CLOSE CLEAR Figure 3-55. Listing of /sys/open/start, which ultimately launches /sys/open/open. 3-66 Using the LI-6400...
Page 119 Operational Considerations 4-30 Step-By-Step 4-32 4-34 ATCHING THE NALYZERS How to Match 4-35 What Happens in Match Mode 4-36 Messages in Match Mode 4-37 When To Match 4-39 Logging Match Adjustments 4-39 Modifying the Match Display 4-40 Using the LI-6400...
Page 120: Preparation Check Lists
Making Measurements The presentation in this chapter presumes that you have assembled the LI-6400, learned how to operate the software - especially the chamber control functions - and are ready to make measurements on plants. Preparation Check Lists We present a checklist of things that should be done prior to making measure- ments.
Page 121 (see Chapter 20). Leave the fan on when you are done. Is Flow Control OK? Use the flow control key (f2 level 2) to set up fixed flow at 1000 µmol s Watch the Flow_µms (display group b) to determine the actual maximum Using the LI-6400...
Page 122 Why turn off the chamber fan? If itÕs on when the pump is off, it will actually push a bit of air (1 or 2 µmol s ) back through the flow meter, throwing off your zero reading. Using the LI-6400...
Page 123 This isnÕt critical however, but the chamber should at least be closed. Check T zero leaf Unplug the leaf temperature thermocouple connector (itÕs purple colored), and compare the leaf and block temperatures. If they differ by more than 0.1¡, Using the LI-6400...
Page 124 Light If using the LED source, set the light to the desired value (ambient is a good value to start with - it wonÕt be an abrupt change for the leaf). If you arenÕt Using the LI-6400...
Page 125 From this point on, what you do is going to depend on your experiment, or what it is you wish to accomplish. For example, you might wish to measure a response curve (light, for example, is discussed on page 4-24), or make sur- Using the LI-6400...
Page 126: Some Simple Experiments
100 if you need to. (Leaks are a bigger problem at low flow rates - see Leaks on page 4-42.) You are now ready to do some or all of the following elementary experiments. Using the LI-6400...
Page 127 DH2O? If you didnÕt, why not? (Answer on page 4-53.) Find the lower humidity limit Now set the desiccant on full scrub, and increase the flow to 800 µmol s probably wonÕt achieve that value). Give it a minute or so to stabilize, and ob- Using the LI-6400...
Page 128 (If flow jumps to either extreme, and you start seeing flashing messages about targets being too dry or too wet, make sure you selected the H option, and entered a reasonable value in mmol mol Note the CO2S_µml value. 4-10 Using the LI-6400...
Page 129 Note the current value of VpdA (display line d), the vapor pressure deficit based on air temperature. Then change to controlling to a constant VPD, based on Tair, and target that value. (See V) Constant VPD on page 7-10.) Using the LI-6400 4-11...
Page 130 Start with the conditions described by Do this first on page 4-8. Make sure the desiccant knob is mid-range. Set flow control for constant water mole fraction Target the current value of H2OS_mml (Step 1 on page 4-10). 4-12 Using the LI-6400...
Page 131 CO change? (Answer on page 4-54.) Watch the response Photosynthesis will immediately start to drop, and (if you wait 10 or 15 min- utes), conductance will eventually decrease as well. Using the LI-6400 4-13...
Page 132 If you arenÕt, turn the soda lime knob a bit toward scrub, so that the reference drops to more or less what you want. Use these targets for reference con- DonÕt despair. Just buy one. ItÕs worth it. 4-14 Using the LI-6400...
Page 133 Hint: If your low CO point had negative photosynthesis (respira- tion), you may want to change the default A-Ci plotting to automatically scale the axis minimum for photosynthesis. Otherwise, it wonÕt show that point. Using the LI-6400 4-15...
Page 134 Clamp onto the leaf Use Real Time Graphics Implement strip charts for viewing photosynthesis, conductance, and C . Use a time scale of 180 seconds for each plot, and plot Photo from 0 to 20, Cond 4-16 Using the LI-6400...
Page 135 Change from controlling on reference CO , to controlling on the sample cell . Target the current value of CO2S_µml. Repeat Steps 4 and 5. How does the photosynthesis response differ from the first time you tried it? Using the LI-6400 4-17...
Page 136 Experiment #6 Sun And Shade Leaf Survey This experiment uses the LI-6400 in a survey mode in which a succession of leaves is measured, and each measurement lasts a minute or less. Should you use the LED light source for this experiment? If you have this choice, here are some things to consider.
Page 137 Measure 5 shaded leaves Now measure 5 leaves that have been well shaded for some time. If you are using a light source, be sure to remember to lower itÕs value to match the typ- ical shade leafÕs environment. Using the LI-6400 4-19...
Page 138 This section has introduced you to survey. light response, and CO response measurements that you can do with the LI-6400. The next sections describe these measurements in more detail, providing physiological and operational considerations to help guide you as you determine measurement protocols for your experiments.
Page 139: Making Survey Measurements
With more abun- dant clouds, the most a light source can offer is the chance to let each leaf equilibrate for 10 or 15 minutes in constant light, and that makes for very slow survey work. Using the LI-6400 4-21...
Page 140 The other says you should use the coolers to maintain ambient temperature, so that the chamber doesnÕt get hot being in the sun. You decide. Make sure its inside diameter is larger than 1/8 inch, to avoid pressure drops and reduced pump performance. 4-22 Using the LI-6400...
Page 141 (Config Menu ® Installation Menu ® Examples Menu), and modify that to suit your needs. Also, if leaf area and/or stomatal ratio is changing from leaf to leaf, they can be automatically prompted for them as well. Using the LI-6400 4-23...
Page 142: Light Response Curves
Survey A third approach is to generate a light curve using multiple leaves that are equilibrated at a range of light values. Experiment #6 on page 4-18 uses this 4-24 Using the LI-6400...
Page 143 It is important to maintain the chamber CO concentrations as constant as possible while measuring a light response curve. Otherwise, the effects of on photosynthesis will be confounded with the effects of light. If you Using the LI-6400 4-25...
Page 144 (shows logged data), and has a strip chart for totalCV. The second re- places the conductance plot with a plot of humidity vs. flow rate. This lets you monitor the flow/humidity status during the measurement, without having to leave the graphics display. (Figure 4-7). 4-26 Using the LI-6400...
Page 145 : Constant reference CO , about 400 µmol mol , or your choice. (This is temporary - weÕll switch to constant sample in a few minutes.) Flow: Constant flow, 500 µmol s Clamp onto the leaf Using the LI-6400 4-27...
Page 146 200. That gives it 80 seconds after the initial 120 second delay for photosyn- thesis to stabilize. For the stability, enter 1% Ó) press N. Open 3.01 and below: When asked Ò Match before each obs? 4-28 Using the LI-6400...
Page 147 What does a graph of photosyn- thesis vs. conductance look like? Exit GraphIt, and close the file Press escape until you get back to New Measurements mode, then press CLOSE_FILE (f3 level 1) to close the file. Using the LI-6400 4-29...
Page 148: Co2 Response Curves
See, for example, G.D. Farquhar and T.D. Sharkey (1982) Stomatal conduc- tance and photosynthesis. Annual Review of Plant Physiology 33,317-45. Also G.D.Farquhar, S. von Caemmerer, J.A.Berry (1980) A biochemical model of photosynthetic (CO ) assimilation in leaves of C species. Planta 149,78-90. 4-30 Using the LI-6400...
Page 149 Two useful pre-defined real time graphics configurations are "A-Ci, RH_Flow, totalCV" "A-Ci, totalCV, CO2S" The first one is recommended, since it shows photosynthesis as a function of intercellular CO . It also contains the RH-Flow plot that lets you monitor the Using the LI-6400 4-31...
Page 150 Match the IRGAs Be sure CO2S_µml is stable before you do this. Launch the ÒA-CiCurveÓ Autoprogram Press 5 then f1. Pick ÒA-CiCurveÓ from the list. When asked Ò Ó Press Y Append to current data file? 4-32 Using the LI-6400...
Page 151 Answer these questions by plotting the appropriate data. Did the sample cell humidity stay constant? Did leaf temperature stay constant? Exit GraphIt, and close the file Press escape until you get back to New Measurements mode, then press CLOSE_FILE (f3 level 1) to close the file. Using the LI-6400 4-33...
Page 152: Matching The Analyzers
O and CO (page 14-5 and page 14-6) contain adjust- ment terms (W and C ), and it is these that are changed when matching. Thus, the sample, not the reference, CO and H O values are adjusted. 4-34 Using the LI-6400...
Page 153 H O IRGA. After a change in incoming air, water will take longer to come to a new equilibrium than CO , because of sorption effects. During this period, the display will Using the LI-6400 4-35...
Page 154 Pressing f5 (MATCH IRGAs) will cause C and W to be adjusted so that the sample and reference values become the same. You can do this as often as you like while 4-36 Using the LI-6400...
Page 155 Reasons for this would be a match valve that is stick- ing, or the air flow tube connecting the chamber to the match valve not being in place, or some other flow related problem. Using the LI-6400 4-37...
Page 156 If MATCH is pressed, and the difference between sample and reference IR- GAs exceeds 10 µmol mol for CO or 1 mmol mol for H O, a warning will be displayed: WARNING Excessive Deltas! -Chamber closed? -Match valve working? Still want to match? Press (Y/N) 4-38 Using the LI-6400...
Page 157 -0.5 -0.01 111115 199.7 1113 1374 98.06 -0.6 0.00 111105 Figure 4-8. The default log file format includes the adjustment factors that are set when the IRGAs are matched. This provides a record of what happened. Using the LI-6400 4-39...
Page 158 (f3), and use an editor (described in The Display Editor on page 6-4) to pick the variables you wish to view. Changes will stay in effect until power off. To make the changes permanent, store (when exiting the editor) the configura- tion in the file “/user/configs/MatchDisplays” 4-40 Using the LI-6400...
Page 159: Stability Considerations
Stability Considerations Stability Considerations In New Measurements mode, the LI-6400 measures and computes continual- ly, regardless of the state of equilibrium of the leaf in the chamber. It can also log data with the same disregard for stability. The question is, how do you...
Page 160: Leaks
(neoprene) can recover if left uncompressed overnight. When the chamber is not being used, you can preserve your gaskets by adjusting the thumb nut so that the gaskets are not compressed when the chamber is latched. 4-42 Using the LI-6400...
Page 161 Mylar, and Propafilm (polypropylene coated with Saran). Diffusion of CO into or out of the LI-6400 leaf chamber is proportional to the difference between the inside and outside CO concentrations. It is useful to think of this diffusion leak as a flux of CO .
Page 162 IRGA using the match valve. This eliminated any potential errors due to IRGA drift, since the same IRGA Simple in hindsight - it took a couple of weeks to get it right. 4-44 Using the LI-6400...
Page 163 = 400 µmol mol 2066 Flow Rate (µmol s Figure 4-10. CO diffusion into a closed, empty LI-6400 chamber with black neo- prene gaskets as a function of flow rate, for various reference concentrations C (ambient CO ) was 400 µmol mol .
Page 164 Note that there are now two Òcorrection termsÓ: one for transpiration, and one for diffusion. The diffusion correction term is insignificant for measurements with near-ambient CO concentrations in the chamber (Table 4-2). Near the compensation point itÕs a different matter; diffusion becomes signifi- 4-46 Using the LI-6400...
Page 165: Operational Hints
Implement the correction in the Compute List. Operational Hints Air Supply Considerations An open system, such as the LI-6400, is only as good as the incoming air stream is stable, especially with respect to CO concentration. When the in- coming air is fluctuating in CO...
Page 166 Acceptable volumes depend on the magnitude of the fluctuations that need to be damped, but several liters is a good starting volume. A plastic five gallon enclosed bucket is a good buffer volume, or - if nothing else - use the LI-6400 carrying case as a buffer volume.
Page 167 Air Supply Source LI-6400 Figure 4-13. When supplying air to the LI-6400 from a supply with itÕs own flow control, make sure the supplied air flow exceeds that required by the LI-6400, and that there is excess flow coming out the T.
Page 168 As the differentials become small, the effect of any offset error is magnified. Using Closed Mode We have experimented with using a closed system technique in the LI-6400 to handle low rates. This is accomplished by turning off the pump for 10 or...
Page 169 When it is used in dry environments (such as in a closed loop with a desiccant - not a normal con- figuration for the LI-6400), the scrubbing capacity of soda lime can be greatly diminished.
Page 170 IRGA at these low rates. Replace ÒYÓ with straight union To Reference divider To Sample flow meter Figure 4-16. To achieve flow control down to zero, replace the T downstream of the diverter with a straight union. 4-52 Using the LI-6400...
Page 171: Answers To Questions
Answer 8: Warming the air will not directly change the vapor pressure of the air, but it has a profound effect on the saturation vapor pressure of the air. Therefore, warming will increase the vapor pressure deficit and lower the rel- Using the LI-6400 4-53...
Page 172 ÒbelongsÓ. Answer 15: Operate in fixed flow mode with as high a flow rate as you can, and set the mixer to control on reference CO . High flow rates will do three 4-54 Using the LI-6400...
Page 173 2) minimize the time necessary to flush out the leaf chamber, which gives you the best dynamic response; 3) make the humidity in the chamber low. This last feature can be overcome by moistening the incoming air stream. See Hu- midifying Incoming Air on page 4-50, for example. Using the LI-6400 4-55...
Page 174 Making Measurements Answers to Questions 4-56 Using the LI-6400...
Page 175 Part II Useful Details...
Page 177 Cursor Control Keys 5-15 Tabs 5-15 The Exit Menu 5-15 5-16 5-17 ATTERY ARNING 5-18 CREEN How To Access 5-18 Boot Screen Functions 5-18 LPL S 5-20 CREEN Editing a File 5-21 Running a File 5-21 The Shell Program 5-21 Using the LI-6400...
Page 178: Standard Menu
Standard Tools As you use the LI-6400, you will encounter the same few interface tools over and over. The three most common are 1) a dialog for selecting a file, 2) a menu for selecting one of several choices, and 3) a single line editor for en- tering a remark or numeric value.
Page 179 A subsequent keystroke (such as an arrow key, or a function key) will make the labels disappear again. Whether or not the labels are displayed, the function keys themselves are al- ways active in Standard Menu. Using the LI-6400...
Page 180 Action - ¯ Moves cursor up or down one line. ¬ ® Moves cursor back or ahead one character. Moving back will Òline-wrapÓ, but not moving ahead. home Jump to upper left (first byte of the data). Using the LI-6400...
Page 181: Standard Line Editor
Figure 5-3. The prompt for a remark for logged data is an example of the Stan- dard Line Editor The cursor may or may not be in a window with a border containing prompts or default values (Figure 5-4). Using the LI-6400...
Page 182 Deletes the character at the cursor location, but does not move the cursor. Caplock Toggles caps lock on and off. This applies only letter keys, not number keys. AnyChar Access the AnyChar routine, for generating any key code or character. Using the LI-6400...
Page 183 This menu (Figure 5-5) allows you to view all the characters in the character set, and select the one you want (Figure 5-5). The character codes are view- able in decimal or hex. Pressing D and H toggle between decimal and hex modes. Using the LI-6400...
Page 184 One example is entering units or a label in which you want the symbol µ (as in µmol, for instance). You can generate a µ by pressing AnyChar, followed by 2 3 0. Or press AnyChar, then enter, then pick µ from the menu. Using the LI-6400...
Page 185: Standard File Dialog
¨ ¨ ¨ ¨ Help CANCEL SELECT ¨ ¨ ¨ ¨ DelLn ClrEnd DelChar CapLock AnyChar Figure 5-6. The Standard File Dialog for selecting a file name. a) for existing files. b) for new or existing files. Using the LI-6400...
Page 186 Note that the file list is scrollable with the - ¯ pgup pgdn; even though you are not using that list like a menu, you are still able to view all of the file names in that directory. 5-10 Using the LI-6400...
Page 187 To change directories and get a new list of files, press Dir (f1). This will bring up a Standard Menu of all the directories presently in the file system, as illustrated in Figure 5-10. Using the LI-6400 5-11...
Page 188 Dir (f1), and then use - or ¯ keys to highlight a different di- rectory. Press Enter or Select (f5) to select the directory; a new list of files in that directory is displayed. (The file system, with itÕs directories, disks, and its terminology, is described in Chapter 10.) 5-12 Using the LI-6400...
Page 189: Standard Edit
The reason for this behavior is to maximize the view area of the edit window, and not lose a line to key labels. Using the LI-6400 5-13...
Page 190 Find Search for a target string, which you enter. The search starts at the current cursor location, and goes to the end of the file. ReFind Find the next location of the current target. 5-14 Using the LI-6400...
Page 191 Menu, whose options are listed in Table 5-6. Current file name shown here Exit Menu <esc> - Resume editing U - Update file /User/MyData S - Store as new file Q - Quit editor X - eXecute Figure 5-13. Standard EditÕs exit menu. Using the LI-6400 5-15...
Page 192: Hot Keys
Abort the current application. ctrl shift escape Reboot, and display the boot screen. a.Adjustments to display contrast made this way will be lost at power off. To adjust the contrast permanently, see The Boot Screen on page 5-18. 5-16 Using the LI-6400...
Page 193: Low Battery Warning
OFF. If the batteries are not replaced, or you do not turn off some of the power draining devices (i.e., LED light source, thermo- electric coolers, etc.), the LI-6400 will turn itself OFF when the count reaches zero.
Page 194: The Boot Screen
How To Access You can prevent the boot program from launching the LPL operating system by powering on with escape held down. If you do this, the display will show the Boot Screen Welcome to LI-6400 (R)un (V)oltages (U)pload (S)save parms...
Page 195 Table 5-8. (Continued)Useful items in the Boot Screen. Press... To Do... Upload a new application into the LI-6400. This feature is used by installation programs, such as is found on the 6400-50 System Software diskette. Computes a 32bit value that verifies if the application was in- stalled correctly.
Page 196: The Lpl Screen
Access the Filer, the file system utility program whose de- scription begins on page 10-6 Run an LPL program. Launch the shell program Enter file exchange mode (for use with the FX/DOS, FX/Mac- intosh, or FX/Windows applications) running on an external 5-20 Using the LI-6400...
Page 197 Pressing escape quits the program. A Calculator You can use StdShell as a calculator, by typing in the expression to be eval- uated, then pressing enter. Use postfix notation, or else begin with a $. For example Using the LI-6400 5-21...
Page 198 Step 4: Press enter to recall the line. Go to Step 2. 3055 ok:getms getkey drop getms swap - print ¨ ¨ ¨ ¨ + DelLn ClrEnd DelChar CapLock AnyChar Figure 5-17. A stop watch example using StdShell. 5-22 Using the LI-6400...
Page 199: Power On Hooks
File Exchange Mode Prior to the LPL Copyright screen appearing, if the LI-6400 detects a partic- ular sort of incoming data on the Comm Port, file exchange mode will be en- tered automatically. The particular sort of incoming data that will do this is the sort that comes from a computer that is running FX (either FX/Dos, or FX/Macintosh) and trying to establish communications with the instrument.
Page 200 Standard Tools Power ON Hooks 5-24 Using the LI-6400...
Page 201 Viewing real time data using text and graphics ISPLAY Display Update Frequency 6-3 Display Function Keys 6-3 Display Files 6-7 RAPHICS RTG Control Keys 6-8 RTG Editor 6-9 RTG Limitations 6-12 RTG Configuration Files 6-13 Track ParOut 7-19 Using the LI-6400...
Page 202 Select a display View each label and configuration itÕs description from a file Modify this display Show all label configuration lines in a menu Figure 6-1. New MeasurementÕs text display, showing the Display Function keys (level 6) Using the LI-6400...
Page 203 Ci/Ca VpdL VpdA e: totalCV% ÆCO2CV_% ÆH2OCV_% FlowCV_% RH_R_% RH_S_% Td_R_¡C Td_S_¡C g: Prss_kPa ParIn_µm ParOutµm BLC_mol h: Tblock¡C Tair¡C Tleaf¡C Figure 6-2. The current list of display labels is shown by the Display List function., f2. Using the LI-6400...
Page 204 It functions as a dialog, so nothing that you do affects the current display con- figuration if you quit by pressing cancel. OK, however, implements your changes. Using the LI-6400...
Page 205 ¨ + Print Find Refind CANCEL SELECT Figure 6-5. When Editing or Adding a display format line, you are prompt- ed for each item in turn, selecting it from a menu of user and system vari- ables. Using the LI-6400...
Page 206 Compute List (Defining User Variables on page 15-1). 10:(U/S) 20:Trans 21:Trmmol 23:Cond User Variables 30:Photo 42:C2Sfc 43:AHs/Cs -1:CO2R_µml -2:CO2S_µml System Variables -107:AuxS1 -108:AuxS2 -109:AuxS3 Figure 6-6. The variable menu consists of user variables at the top, followed by the system variables. Using the LI-6400...
Page 207 Figure 6-7. Display format files have a marker (DISPLAYMAP=), followed by the number of display lines to be defined. Following this are the ID values of each item. System variables have ID values <0, while user items have positive ID values. Using the LI-6400...
Page 208 , and the logged data by +. RTG Control Keys The Real Time Graphics control keys are located in New Measurements mode, level 4 (Figure 6-9). These keys allow you to start and stop plotting, Using the LI-6400...
Page 209 In the editor, the arrow keys are used to move the cursor (inverse video box) around from field to field. The field thatÕs highlighted may be modified by pressing enter or Edit. The number of graphs to be plotted (1, 2, or 3) is set by pressing the function key #Curvs. Using the LI-6400...
Page 210 Figure 6-10. The Strip Chart Editor allows the parameters for up to three curves to be set. Parameters can be stored or retrieved from the file system using the function keys available on the 2nd level. 6-10 Using the LI-6400...
Page 211 (at the top of the selection menu). Selecting any other variable for the Time" X axis will make it an XY plot. This isnÕt really a system variable; itÕs just an entry in the menu when youÕre selecting an X axis variable. Using the LI-6400 6-11...
Page 212 RTG ÒactiveÓ in New Measure- ments mode, it has the effect of turning RTG off. Prior to OPEN 3.2, using GraphIt (Chapter 12) would erase the RTG display. 6-12 Using the LI-6400...
Page 213 Figure 6-10 on page 6-10. The X and Y scroll flags are 1 (no scroll) or 0 (au- toscroll). The final 5 values can be left off of the plot information line; that was the format used prior to OPEN 3.0, and it is still recognized. Using the LI-6400 6-13...
Page 214 Real Time Data Real Time Graphics 6-14 Using the LI-6400...
Page 215 Constant Sample Option 7-14 Interaction with Humidity Control 7-15 Constant Control Signal Option 7-15 CO2 Mixer Calibration 7-15 7-16 EMPERATURE ONTROL Constant Block Temperature 7-16 Constant Leaf Temperature 7-16 Condensation? 7-17 7-18 IGHT ONTROL Quantum Flux 7-18 Control signal 7-19 Using the LI-6400...
Page 216: Openõs Control Manager
Environmental Control One of the things that makes the LI-6400 a powerful system is itÕs ability to control conditions in the leaf chamber. A clear understanding of how this hap- pens is vital to proper use of the system. This chapter discusses the mecha-...
Page 217 Current (default) value Variable Target Allowed Figure 7-3. Once a control option is selected, you are prompted for a target value. A blank entry (just press enter) will retain the current value. Variable targets are discussed on page 7-5. Using the LI-6400...
Page 218 A trivial example is turning off the light source; once itÕs off, thereÕs no further adjustment necessary. A not-so-trivial example is fixed flow mode, which main- tains itself independent of software because of the hardware circuitry controlling Using the LI-6400...
Page 219 RH_sample #1001 50 % # Figure 7-4. Instead of entering a fixed target value, you can specify a vari- able, system or user. The target value comes from this variable, and is up- dated every 30 seconds. Using the LI-6400...
Page 220 (Figure 7-7). RH_sample #1001 (xtrnRH) Figure 7-7. When a control has a variable target, the default value reflects the variables ID value, and label. Using the LI-6400...
Page 221: Humidity Control
AutoPrograms. See AutoPrograms and the Control Man- ager on page 25-19. Humidity Control Humidity control in the LI-6400 is done by a combination of two mecha- nisms: Incoming humidity The mechanism for controlling incoming humidity is manual: the amount of...
Page 222 Table 7-1. Flow/Humidity control menu options Option Description N) None Turns off the pump. Not normally used, except for diag- nostics, or to save the battery or motor when not taking measurements. Or, to provide some peace and quiet. Using the LI-6400...
Page 223 / leaf chamber. Note: For constant humidity options to work well, the leaf must be supplying a reasonable source of humidity. Thus, small leaf areas and/or low transpiration rates, or an emp- ty leaf chamber, can make these problematic. Using the LI-6400...
Page 224 Where is there? Well, you have at least two options: the sample cell IRGA, or the sub- stomatal cavity of the leaf. In the case of the former, Ð (7-1) and in the case of the latter, 7-10 Using the LI-6400...
Page 225 Figure 7-11. When asked to select a temperature for the VPD calculation, be sure what you select is a temperature. DonÕt select a VPD! The system does its own VPD computation based on the value of the (temperature) variable you select. Using the LI-6400 7-11...
Page 226 The RSPNS key applies ONLY to the constant humidity control circuit. 7-12 Using the LI-6400...
Page 227: Co2 Control
S) Sample CO2 Maintains a constant CO concentration in the sam- ple cell and chamber. C) Control signal The mixer control signal is set and held a target val- ue. This is a diagnostic tool. Using the LI-6400 7-13...
Page 228 Opening the chamber might seem to be a way to really mess up the constant sample CO option, but usually the subsequent sample cell CO fluctuations are sufficient to keep the controller from even trying to control it. 7-14 Using the LI-6400...
Page 229 If you find (when op- erating in constant reference concentration mode) that the first guesses donÕt seem very good, you can generate a new set of calibration points for it to use, described in 6400-01 CO2 Mixer on page 18-20. Using the LI-6400 7-15...
Page 230: Temperature Control
The constant leaf temperature option is not a tight control loop, for two rea- sons: 1) the control of leaf temperature is indirect, via air temperature, and 2) there are factors beyond the reach of the controller that affect leaf tempera- ture, including leaf transpiration rate and incident radiation. 7-16 Using the LI-6400...
Page 231 IRGA and leaf chamber, and if it gets above 95%, will display a blinking warning >> High Humidity Alert << For example, using the leaf temperature thermocouple to measuring air temper- ature and calculating leaf temperature from an energy balance. Using the LI-6400 7-17...
Page 232: Light Control
Af- ter a few seconds, that guess is adjusted based on what the light sensor is actually reading. If you notice that the first guess is not very close, you can 7-18 Using the LI-6400...
Page 233 This is an example of variable tracking, a feature that all of the control sys- tems have (for flow/humidity, CO , temperature, as well as light). See Vari- able Targets on page 7-5 for more details. Using the LI-6400 7-19...
Page 234 Environmental Control Light Control 7-20 Using the LI-6400...
Page 235 ENSORS PECIFYING THE OURCE AND ENSOR Calibration Equations 8-3 The Light Source Control Utility 8-4 6400-02 -02B L IGHT OURCES Spectral Considerations 8-6 Temperature Effects 8-7 Aging 8-7 ALLIUM RSENIDE HOSPHIDE ENSOR Temperature 8-8 View Angle 8-8 Using the LI-6400...
Page 236: Why Two Sensors?
10 lower than the actual irradiance on the leaf. In more typical conditions, there will easily be differences of 10%. To address this problem, the standard light sensor in the LI-6400 is an unfil- tered gallium arsenide phosphide (GaAsP) device that is small enough to be placed in the chamber very near the leaf plane.
Page 237: Specifying The Source And Sensor
Light Sensor Considerations Specifying the Source and Sensor There is a third type of light sensor that is used in the LI-6400. It is a silicon diode that monitors and controls the optional 6400-02 or -02B LED Light Source. The silicon diode light sensor has a wide response that covers the red and blue LED emission range.
Page 238 Chapter 17.) When the light source is something other than a 6400-02 or -02B, the related items are alphaK, CalParGaAs (the calibration of the light sensor in the chamber top being used), and actinity (a correction factor for spectral variations from solar). Using the LI-6400...
Page 239 Note that this is NOT the method of modifying the LED source entries. They are added via the Installation Menu. Revert StdFile The revert file option changes the file back to itÕs de- /User/Configs/LightSources fault state. The default version of this file is stored in /Sys/Lib/LightSources Using the LI-6400...
Page 240: And -02B Light Sources
Figure 8-3. Typical output of a 6400-02B LED source at 25¡C. (A 6400-02 source has the same red peak, but no blue peak.) Tennessen D.J., D.L. Singsaas, T.D. Sharkey, 1994. Light-emitting diodes as a light source for photosynthesis research. Photosynthesis Research 39: 85-92. Using the LI-6400...
Page 241: Gallium Arsenide Phosphide (Gaasp) Sensor
Mixed light sources will cause complications, but if one light source predom- inates, the appropriate value for that source can be used, or the GaAsP sensor can be calibrated to the specific lighting conditions using a LI-COR quantum sensor (Generating a Calibration Correction on page 18-28).
Page 242 +0.2% C View Angle The GaAsp sensor, especially as mounted in the LI-6400 leaf chamber, is sub- ject to serious errors when measuring irradiance at non-normal incidence an- gles. There primary reason for this is reflections from the chamber walls. For example, at angles when the sun reflects off the wall nearest the sensor, the sensorÕs readings can be boosted by 25%.
Page 243 A stronger reason to be careful of non-normal incidence radiation is the po- tential for the chamber walls to shade the leaf. Uniform lighting is critical to good gas exchange measurements. If sunlit and shaded leaf areas are mea- sured together, it becomes very difficult to interpret the results. Using the LI-6400...
Page 244 Light Sensor Considerations Gallium Arsenide Phosphide (GaAsP) Sensor 8-10 Using the LI-6400...
Page 245 Prompt List Files 9-17 9-18 ROGRAMS What are AutoPrograms? 9-18 Launching AutoPrograms 9-19 While an AutoProgram is Active 9-19 Controlling an AutoProgram 9-20 9-21 ROGRAM ESCRIPTIONS ÒA-CiCurveÓ 9-21 ÒAutoLogÓ 9-22 ÒAveraging AutoLogÓ 9-23 ÒBuffered AutoLogÓ 9-23 ÒLightCurveÓ 9-27 Using the LI-6400...
Page 246: Basic Concepts
Basic Concepts The LI-6400, in its default configuration, is an open system. As such, it shows a continuous stream of measurements and calculations. You can monitor light levels and photosynthetic rates, for example, while changing those light lev- els.
Page 247 This latter option makes the file more readable for humans, but at the price of using more memory for storage. Note that regardless of how the file is stored, GraphIt (described in Chapter 12) allows the data to be viewed in columns. Using the LI-6400...
Page 248: Getting Started
If you wish to log to memory or the Comm port, just press CANCEL or es- cape. If you do not want to log to a file, press escape to get the alternate destination prompt (Figure 9-4). Using the LI-6400...
Page 249 Remarks can also be entered at any time the file is open, by pressing Add_Remark (F4 level 1), and will take the form of a quoted string on itÕs own line in the file. The start of a remarks line contains the time (HH:MM:SS) the remark was entered (Figure 9-6). Using the LI-6400...
Page 250 Press and hold the log button until an audible tone sounds (within 1 second), indicating an observation has been logged. The log button does not function unless logging is active. The log button can be disabled by unplugging it (Figure 2-13 on page 2-17). Using the LI-6400...
Page 251: Determining What Is Logged
Format List. Append the Log List items to the information in the window. Figure 9-8. The Logging Control program. Status information can include: Écontains <n> items The number of items in the Log Format list. Using the LI-6400...
Page 252 Also, as an aid to building log lists, the master list (the menu of possibilities from which you choose when Changing or Inserting) indicates whether or not an item is already in the Log List. Using the LI-6400...
Page 253 Figure 9-9. The LogList Editor. Any of the entries in the list may be removed or changed. The ÒUser defined itemsÓ in the Group Add menu are any user defined (Compute List) items that arenÕt already in the Log List. Using the LI-6400...
Page 254 Description Example HH:MM:SS Clock time string, 24 hour. Ò12:02:54Ó Time Number of seconds since file opened. 1234.56 StartHR Decimal hour when file was opened. 15.0237 Day of the year (1É366) YYYYMMDD Year, month, and day 19970811 9-10 Using the LI-6400...
Page 255 ¥ Will you want to plot data as a function of time? If you are plotting data on the LI-6400 using GraphIt (Chapter 12), then you can use HH:MM:SS as the time variable, because GraphIt will convert the string to decimal hours automatically when plotting. Thus, for example, Ò10:40:17Ó...
Page 256: Prompts And Remarks
(Prompt Quikpik). The prompts are used when f5 level 3 is pressed in New Measurements mode, or when f3 is pressed here (Ask Prompts). The prompt configuration shown in Figure 9-11 will prompt for ÒPlot#Ó (an integer), ÒCommentsÓ (a 16 character maximum length string), and ÒAreaÓ (a 9-12 Using the LI-6400...
Page 257 With OPEN 3.01 and below, the graphs DO NOT go away, and itÕs not clear what is happening. You can press ctrl shift ¬¬ to turn off graphics mode, and turn on text mode, so you can see Using the LI-6400 9-13...
Page 258 Read another Prompt List Specify the file version of the list stant (-101 to -109), you may re- into the Editor. name and save label it. this list. Figure 9-12. The Prompt List Editor, and associated function keys. 9-14 Using the LI-6400...
Page 259 There is a slight exception to this. The AutoProgram, ÒAveraging AutoLogÓ, uses auxN3 (-106). See page 9-23. It does this to provide a value (the # of sam- ples averaged) that you might wish to log in the file. Using the LI-6400 9-15...
Page 260 To trigger the prompt list from an AutoProgram, use the command UcnAskAll Chapter 25 discusses AutoProgram programming. If you are making an Au- toProgram using the AutoProgram Builder (described on page 9-33), the menu selection will accomplish this task. ÒG) Prompt for user constantsÓ 9-16 Using the LI-6400...
Page 261 Figure 9-13. Listing of the PromptList file ÒPlot#, Comments, AreaÓ. The list contains the IDÕs of values to be prompted for, and the label list contains the names of all 10 system variables that can be renamed. Using the LI-6400 9-17...
Page 262: Autoprograms
Data Logging AutoPrograms AutoPrograms One mechanism by which the LI-6400 can operate automatically is the Auto- Program. What are AutoPrograms? AutoPrograms are small LPL application programs designed to run on top OPEN. While there is practically no limit to the scope of what an AutoPro-...
Page 263 While an AutoProgram is active, an asterisk is on the display (Figure 9-14). VIEW CLOSE Match File FILE REMARK Figure 9-14. An asterisk appears to the left of the function keys while an Auto- Program is active. Using the LI-6400 9-19...
Page 264 To do either, press escape to access the AutoProgram Exit screen (Figure 9-15 on page 9-20), and press A or T. 9-20 Using the LI-6400...
Page 265: Autoprogram Descriptions
During the maximum wait time period, if the stability parameter TotalCV% falls below this value, logging will occur. Matching OPEN version 3.01 and below will prompt: Match before each obs (Y/N)? With OPEN 3.2, this changed to Match if |ÆCO2| < Using the LI-6400 9-21...
Page 266 Log every __ secs: Enter the desired period between logged observations. Add __ observations: This determines how many observations AutoLog should record. If you man- ually log data while AutoLog is running, it does not affect when AutoLog quits. 9-22 Using the LI-6400...
Page 267 ¥ Buffering A/D readings so no measurements are lost This introduces a time restriction, since the buffer is limited (64K, or avail- able memory). For example, if raw mV readings are being generated at 5 Hz, Using the LI-6400 9-23...
Page 268 The slower the logging rate, the more often it can update the display. Keyboard response remains fairly fast, however, and there should never be worse than about a one second delay. Note that pressing a key forces a screen update. 9-24 Using the LI-6400...
Page 269 (s ), and f is the rate at which observations are com- puted and stored in the log file (s ). After logging, the time W (s) that it takes to process the buffered observations is Using the LI-6400 9-25...
Page 270 Ð Table 9-5 contains typical values for f , D and T for an LI-6400 with and without a coprocessor . Thus, for example, if logging at 5 Hz for 30 sec- onds, there will be about a 2 minute wait (3.9 x 30 secs) after the logging pe- riod without a coprocessor, and a 1 minute (1.9 x 30 secs) wait with a...
Page 271 Maximum wait time (secs) The time period (following the minimum wait time) during which logging could occur, if stability is reached. If stability is never reached, logging will occur at the end of this time. Using the LI-6400 9-27...
Page 272 Enter the period of time you wish logging to occur, in minutes. For example, if you enter a 7.3 second logging interval, and a period of 5 minutes, 41 ob- servations will be logged, each 7.3 seconds apart. In addition, while the pro- 9-28 Using the LI-6400...
Page 273 If you send it valid LPL commands and functions defined by OPEN, they will be executed by the LI-6400, just like they would be if they were commands in an AutoProgram running on the instrument. Useful Auto- Program Commands on page 25-12 and Low Level Control Tools on page 25-19 list some of the commands that will work for Remote Control.
Page 274 You are asked to select a file from those in the directory Ò /User/Configs/Auto- Ó. Progs/TimedLamp Defaults DIR: /User/Configs/AutoProgs/TimedLamp Def Select TimedLamp Specs "Dflts" "JoeÕs test" "Sunfleck 4" "Sunfleck 2" ¨ ¨ ¨ ¨ CANCEL SELECT 9-30 Using the LI-6400...
Page 275 Once you leave the editing window, you are presented with some options: Options <esc> - abort S - store this, then run R - run E - resume editing Press A Key Figure 9-19. TimedLampÕs options screen is presented after the edit screen. Using the LI-6400 9-31...
Page 276 DIR: /User/Configs/AutoProgs/TimedLamp/Default File: Data Store TimedLamp parameters ÒDfltsÓ ÒJoeÕs testÓ ÒSunfleck 4Ó ÒSunfleck 2Ó ¨ ¨ ¨ ¨ CANCEL SELECT Figure 9-20. TimedLampÕs set points can be stored for use next time. 9-32 Using the LI-6400...
Page 277: Making Your Own Autoprograms
This guarantees that the AutoProgram will generate the widest range of humidity, regardless of what ambient conditions are, or what the leaf is doing. Thus the program would have the following structure: Using the LI-6400 9-33...
Page 278 G) Prompt for user constants Make it a Control Loop Press 1 to select a control loop. Loop Options Loop N times, where 1) N = # of settings for a control 2) N = user entered (1/2) 9-34 Using the LI-6400...
Page 279 The first action is the wait, so highlight Ò Ó and press C) Wait: Fixed Time enter, or press C. Main Event #1 Loop (Flow: Flow) Event #1 A) End Loop B) Begin Loop... C) Wait... D) Match... E) Log F) Set a control... Using the LI-6400 9-35...
Page 280 The second action is logging, so highlight Ò Ó and press enter, or simply F) Log press F. Main Event #1 Loop (Flow: Flow) Event #2 A) End Loop B) Begin Loop... C) Wait... D) Match... E) Log F) Set a control... 9-36 Using the LI-6400...
Page 281 2) You can be prompted each time, with the values entered the last time used as the default.Press 0, 1, or 2. Enter prompting preferences: 0) Never prompt 1) Prompt with fixed defaults 2) Prompt with last time defaults Enter (0/1/2) Using the LI-6400 9-37...
Page 282 The program will have this structure: Prompt for inputs LOOP over light level Set light level Wait fixed time LOOP over reference CO2 Set reference CO2 Wait for stability Match if deltas are small END LOOP END LOOP 9-38 Using the LI-6400...
Page 283 Set Prompt Preferences, and Store. Press 2 for the prompt preference (use last time defaults), then Y to store the program. The default name will be Ò Ó, but you can change it BjCaBeCbaDdEAAA to something like ÒA-Ci Multi LightÓ. Using the LI-6400 9-39...
Page 284 There are two types of loops: Type 1 sets a control, and the number of loops is determined by the number of control settings. The possible controls are shown in ÒControl ListÓ in Figure 9-21, and they essentially correspond to the 9-40 Using the LI-6400...
Page 285 A) Wait: Fixed Time: The A option will generate a prompt for the wait time (it can be in minutes or seconds), and a prompt for the default value to be used. Using the LI-6400 9-41...
Page 286 You select the control from the list shown in Figure 9-21 on page 9-40. For example, if you were building an light curve AutoProgram, and wanted to set the CO controller for controlling on sample 9-42 Using the LI-6400...
Page 287 H) Add a remarks record This option does the same thing as pressing F4 level 1 (Log Remark) in New Measurements mode: it adds a remark record to the data file. (Note: This sus- pends operation until the user responds.) Using the LI-6400 9-43...
Page 288 Data Logging Making Your Own AutoPrograms 9-44 Using the LI-6400...
Page 289 Part III Working With Files...
Page 291 Tagging One File 10-13 Tagging Groups of Files 10-14 Removing Files 10-15 Copying and Moving Files 10-15 Duplicating Files 10-16 Renaming Files 10-16 Printing Files 10-16 Executing Programs 10-17 Õ 10-18 ILER PERATIONS Space Available 10-18 Using the LI-6400 10-1...
Page 292: Files, Directories, And Disks
The LPL File System This chapter describes the LI-6400Õs file system, and a very useful tool for its management: the Filer. Files, Directories, and Disks The LI-6400Õs file system contains the programming that makes the instru- ment work, as well as the data files that result from that work. To efficiently manage all of this information, the storage space is partitioned into groupings of disks, directories, and files.
Page 293 LI-6400, while other files are your own creation, con- taining data youÕve collected. Naming Convention File names on the LI-6400 can be as long as youÕd care to make them, and can consist of any combination of numbers, letters, spaces, and punctuation, ex- cept the following five characters: / \ * ? ;...
Page 294 Disks The Root Figure 10-2. Illustration of disks, directories, and files as structured in the LI-6400Õs file system. Disks are like directories in terms of naming a file, but they differ from direc- tories in that the user cannot create or destroy them. The system provides a fixed number of disks for you to work with.
Page 295: Defragmentation
Figure 10-3. Illustration of defragmentation. a) Before defragmentation, there are 3 files and 1 directory, along with a deleted file and old directory information. b) After defragmentation, the deleted files and directories are gone, and their space is reclaimed. Also, fragmented files (such as File3) are consolidated. Using the LI-6400 10-5...
Page 296: The Filer
The Hidden Disk For defragmentation to work, there needs to be some destination memory for the files to be copied to. This is achieved in the LI-6400 by keeping one of the flash disks hidden. Normally, only the and the...
Page 297 This shortcut key is al- ways the capitalized key in the function keyÕs label. (Note: This is only true for the Filer, and is not generally true for other screens in the LI-6400). Table 10-1. The FilerÕs main function key labels and short cuts.
Page 298 Quit Return to the main level of function keys escape (Table 10-1). Table 10-3. Disk key labels. Label Short Description Space Find out how much space is available on a select- ed disk. 10-8 Using the LI-6400...
Page 299: Filerõs Directory Operations
Figure 10-5. The ÒSelect DirectoryÓ screen is accessed by pressing D (or the Dir function key) from the main menu. The function keys are described in Table 10-4. Table 10-4. The Directory function key labels Label Short Description Add a new directory Using the LI-6400 10-9...
Page 300 NOTE: You cannot remove disks. Thus, /SYS /USER can't be removed. You can, however, take a disk off-line. See Using the Hidden Disk on page 10-19 10-10 Using the LI-6400...
Page 301: Filerõs File Operations
Tagged: 0 Data (Jason) 11:10:10 Bytes: 0 MixerTestResults 13:08:50 ¬ ® ¨ ¨ ¨ ¨ + Dir Filter Sort purGe ¬ ® Figure 10-6. Use the keys to display file sizes, modification dates, and modification times. Using the LI-6400 10-11...
Page 302 Table 10-5. Examples of Filters, and the files they would include and exclude. Filter Includes Files Excludes Files (all) (none) *123* 123.dat 12.3 Data123 data.1 data Data.? data.x data.123 *.??? junk.dat junk.12 this is long.123 junk.1234 10-12 Using the LI-6400...
Page 303 When a file is tagged, press the keys again to remove the tag. Additional function keys asso- Space Enter ciated with the Tag function (below) are accessed by pressing Using the LI-6400 10-13...
Page 304 Tag all files that are currently not tagged, and re- move the tag from those files that are tagged. tag One Tag the currently highlighted file. (A faster way to tag one file is to press enter or space from FilerÕs main screen.) 10-14 Using the LI-6400...
Page 305 File Copy Overwrite duplicate files ? (Yes, No, Ask when it happens) (Y/N/A) Figure 10-10. When moving or copying, you are given options on what to do if there is a duplicate file in the destination directory. Using the LI-6400 10-15...
Page 306 ¥ Print headers? (Y/N) If you press Y, a banner will be output before each file. The banner will in- clude the file name, modification date, and current date. 10-16 Using the LI-6400...
Page 307 FILER. As an example, you can set the communications pa- rameters from the FILER by executing the program file. /Sys/Utility/Setcomm Utility programs in the directory are described in /Sys/Utility /Sys/Utilities Programs on page 21-10. Using the LI-6400 10-17...
Page 308: Filerõs Disk Operations
As an example, a disk containing one large file takes only about half a minute to defragment, whereas a disk that contains a lot of smaller files and directories can take several minutes. 10-18 Using the LI-6400...
Page 309 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. To format a disk: Access the disk keys In the FILER, press the Disk function key (or K).
Page 310 Select a disk to hide Highlight the entry, and press enter. Read the warning. You are then prompted to continue. Press Proceed to hide the disk (and loose all data stored on it). 10-20 Using the LI-6400...
Page 311: Troubleshooting
Take the temp disk back off line From the Filer, press K, then f3, and select the temp disk to take off line. Tak- ing the disk off line will format it, and make it available for use with defrag- menting again. Using the LI-6400 10-21...
Page 312 The LPL File System Troubleshooting 10-22 Using the LI-6400...
Page 313 Installation 11-10 Example 11-11 Program Comments 11-12 EW 11-12 SING Installation 11-12 Examples 11-13 EWÕs Switches 11-17 11-21 DDS AND Text vs. Binary Files 11-21 File Name Considerations 11-21 Non-standard Serial Port Configuration (DOS only) 11-23 Using the LI-6400 11-1...
Page 314 Downloading Files Eventually youÕll want to move files from the LI-6400 to your computer, or even load files back onto the LI-6400. When you do, you have three options: Use FX software FX is available for DOS or Windows or Macintosh. These programs are found on the LI-6400 CD (ÒUsing the LI-6400Ó, Edition 2), and can also be...
Page 315: Connecting The Li-6400 To A Computer
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. Since the LI-6400 is a 9-pin AT device, youÕll need a null modem cable to communicate with your computer.
Page 316: File Exchange Mode
Downloading Files File Exchange Mode File Exchange Mode To use EW or any of the FX programs, the LI-6400 must be in File Exchange Mode. There are three methods of accomplishing this: From the LPL Copyright Screen Press X. While OPEN is running Access the Utility Menu, and select ÒFile Exchange ModeÓ...
Page 317 Select in Figure 11-2. WinFXÕs Tree Views WinFX provides a graphical view of the contents of the LI-6400, and the Lo- cal System. You can expand or contract the view by clicking on the node box- es that have a + or - in them (Figure 11-3).
Page 318 Downloading Files Using WinFX Open the Destination Directory Click on the directory you wish to receive the files. In Figure 11-4, for exam- ple, weÕll be putting LI-6400 files into the directory on the C drive. MyData The active directories are shown here Figure 11-4.
Page 319 Select the file or files to be deleted, then click on the Delete button for that view. Copying Directories This is allowed. Click on the directory to be copied, and either drag it to the destination directory, or use the arrow button. Using the LI-6400 11-7...
Page 320: Using Fx For Dos
Being a lowly DOS program, it dealt with long file names by maintaining a special file that mapped legal DOS names to any LI-6400 files with illegal names that were sent to the PC (File Name Considerations on page 11-21).
Page 321 Figure 11-8. FX/DOS screen. The double border window indicates the active window. The FX/DOS display shows the PCÕs directory and files on the left, and the LI-6400Õs on the right. The double window indicates the active window, and Using the LI-6400...
Page 322: Using Fx On Macintosh
The installation program will create a directory on your hard disk named , in contains the application. If you have a 680x0 processor, FX 1.4 this application is named . On a PowerPC, it is named FX 1.4 FX 1.4 PowerPC 11-10 Using the LI-6400...
Page 323 Figure 11-9. FX/Macintosh shows files and directories on both the LI-6400 and the Macintosh. Di- rection of file transfer is set by the arrow direction. Using the LI-6400...
Page 324: Using Ew
Unless a file is fragmented, you will find them intact. Using EW EW is a tool for copying files and/or directories from the LI-6400 to a PC (or PC to LI-6400). It is a command line version of FX .
Page 325 DOS prompt. <dos> is the starting DOS directory to be involved in the transfer, and <lpl> is the starting LI-6400 directory to be involved. The op- tional switches are described below. Both <dos> and <lpl> must exist when EW is run;...
Page 326 Once all of these things are set, proceed. Important Hint: If you ever plan on sending files BACK to the LI-6400, make sure you donÕt have EW.EXE sitting in a directory that is going to be sent. This is why in the...
Page 327 The -r switch specifies EW 1.3 Copyright (c) LI_COR, inc 1995, 1996 LI-6400 to PC. Receive mode No subdirs Establishing contact with the LI-6400 LI-6400 must be in file exchange mode... The -n switch suppresses ...Go....subdirectories from also aci..being transferred.
Page 328 -u switch, which means Òcopy only if it isnÕt there, or is there but with an older dateÓ. Variation #1 How to restore the data? If the LI-6400Õs /user disk has been recently format- ted, do this: ew data /user...
Page 329 -i(irq) The interrupt vector for the comm port (only needed for non-standard comm ports). Send files from the LI-6400 to the computer (default: files go to the LI-6400) Skip files that haven't changed. (Default: do all files) Send only this directory (Default: does all subdirectories...
Page 330 LI-6400 and executed before any files are copied. The following exam- ew data /user -b115200 -fprep.lpl will send the file prep.lpl to the LI-6400, which will compile and run it, prior to doing the prescribed data transfer. If the file prep.lpl looked like this: :fct main { "/user"...
Page 331 The wild cards ? and * can be used together. The command The INSTALL program uses the -s to launch LPL (by sending an R), since the LI-6400 is still sitting in the boot screen after downloading LPL. Using the LI-6400 11-19...
Page 332 <filename> is now the name of the DOS file to be used for the binary image (the destination, if switches include -r, or else the source file - that is, a previ- ously downloaded disk image). <lpldisk> is the name of the LI-6400Õs disk to used. For example ew user.bin /user -d -r -b115200...
Page 333: Odds And Ends
Text vs. Binary Files Most of the data and LPL program files that you will ever encounter on the LI-6400 are text files. The only exception (as of this writing) are files that are created by the program , which stores graphics imag- /Sys/Utility/Graphics Capture es.
Page 334 If you look at the contents of _MAPFILE.FX_ you will see two entries: "MYTESA.AAA" "MyTestDataFile" "12345A.AAA" "123.456.789.test" If you transfer files to the LI-6400 using FX or EW, they will have their orig- inal names. Macintosh When using FX/Macintosh, you wonÕt have to worry about file name incom- patibilities if you avoid these characters : ;...
Page 335: Using A Data Capture Program
3 Using a Data Capture Program Any generic serial communications program can be used to capture LI-6400 data files. The examples below use the programs available from LI-COR. Whatever program you use, however, you must explicitly set its and the LI-6400Õs communications parameters to match.
Page 336 To copy files from the LI-6400 to a PC with COMM. The steps below will put multiple LI-6400 data files into one PC file. If you wish a one-to-one correspondence, then repeat Steps 6 through 9 for each file.
Page 337 (For how to do this, see page 10-13.) Open a capture file On the PC, press F6 and type in the file name in which the LI-6400 data will be captured. Press Enter. If the file already exists, you will be asked if you wish to overwrite or append, and the left and right cursor keys will toggle be- tween those choices.
Page 338 Simple Terminal terminal programs running on both the LI-6400 and the Mac, so what you type on the LI-6400 should appear on the MacÕs screen, and what you type on the MacÕs keyboard, should appear on the LI-6400Õs display. Verify this.
Page 339 On the Macintosh, open a capture file by selecting ÒCapture DataÓ from the File Menu. Run the print program On the LI-6400, run the print program by pressing P (discussed in Printing Files on page 10-16). The tagged file(s) are then sent to the RS-232C port. Close the capture file Once the data has been sent, press close the capture file by selecting ÒStop...
Page 340 Downloading Files Using a Data Capture Program 11-28 Using the LI-6400...
Page 341 Picking the First and Last Observation 12-10 Using Every nth Observation 12-11 Logic Based Inclusion 12-11 Dealing With Strings 12-13 12-14 URVE ITTING Configuring for Curves 12-14 Viewing Curve Fit Results 12-15 12-17 IEWING 12-19 ORMAT TORING AND ETRIEVING RAPHICS 12-19 MAGES Using the LI-6400 12-1...
Page 342: Accessing Graphit
GraphIt GraphIt is a utility included with the LI-6400 programming that allows you to view data in labelled columns, plot selected variables, do polynomial curve fitting. Accessing GraphIt There are several ways to access GraphIt: From the Filer ¥ Highlight the file to be viewed, and press H (or press the function key labelled grapH).
Page 343 Figure 12-1. GraphItÕs main screen shows the name of the data file being used, and the current plot definition (if any). There are 2 levels of function keys defined, and one can toggle between them by pressing labels or 1 or 2. Descriptions of GraphItÕs functionality begin with Defining Plots on page 12-6 Using the LI-6400 12-3...
Page 344: Data File Format
Figure 12-2. Illustration of the data file format expected by Graphit. The data set labelled "Problem" is just that because the first thing that appears in the data line is a double quote. (OPEN 3.2 and above handles this.) 12-4 Using the LI-6400...
Page 345 NOTE (OPEN 3.01 and below): If you include the system variable "HH:MM:SS" in your data files, be sure it is not in the first column. OPEN 3.2 removed this restriction. Once the label line is identified and read, GraphItÕs main screen appears (Figure 12-1). Using the LI-6400 12-5...
Page 346: Defining Plots
/User/Configs/PlotDefs and you can select from the definitions stored there. Select ÒA-Ci CurveÓ from the menu Figure 12-4 illustrates the resulting plot definition and plot (provided, of course, that the data were actually an A-Ci measurement!). 12-6 Using the LI-6400...
Page 347 L - Logic for including observations C - Curves Press choice or <esc> Figure 12-5. GraphItÕs configuration editorÕs main window. Note: you can by-pass this window by typing X, Y, Z, L, or C directly from GraphItÕs main screen. Using the LI-6400 12-7...
Page 348 (0 through 5). 0 will cause the points to be connected by straight line segments, and 1 through 5 specifies a polynomial of that power. 12-8 Using the LI-6400...
Page 349 Enter MIN (* to autoscale) Enter MAX ¨ ¨ ¨ ¨ + DelLn ClrEnd DelChar CapLock AnyChar Figure 12-8. An axisÕs min and max are prompted for in sequence, with the default value or response displayed. Using the LI-6400 12-9...
Page 350: Selecting Observations
The starting and ending data lines can be manually selected. Press ÒData Set PickÓ (f1 level 2), then P. You will be prompted to select three lines in suc- cession using Standard Menu: the label line, the first data line, and the ending data line (Figure 12-9). 12-10 Using the LI-6400...
Page 351 Inclusion logic is defined by pressing ÒEdit ConfigÓ (f4 level 1) then L from GraphItÕs main screen (short cut: just press L from the main screen). The logic screen (Figure 12-10) appears, and you can type in or edit the logical state- ment to be used. Using the LI-6400 12-11...
Page 352 Less than, greater than, <= >= Less than or equal, greater than or equal <> == Not equal, is equal AND OR Logical and, logical or For this logical expression, spaces donÕt matter, so, for example 12-12 Using the LI-6400...
Page 353 The value is 0 if there are no numbers in it. If the string is quoted time, such as Ò14:22:45Ó, the value will be decimal hours. Using the LI-6400 12-13...
Page 354: Curve Fitting
0:Dot-to-Dot 1:StaightLine 2:2ndOrderPoly 3:3rdOrderPoly 4:4thOrderPoly 5:5thOrderPoly Figure 12-11. Selecting a curve option when only 1 Y or Z variable. If multiple Y and/or Z variables are defined, then it is a two part process (Figure 12-12). 12-14 Using the LI-6400...
Page 355 Select a straight line curve Press Edit Config, then C, and select a straight line as the curve type. Ignore the higher Ci values While in the config editor, press L to select observation logic. Use an expres- sion like Using the LI-6400 12-15...
Page 356 Press View Data, then C. The display will look similar to Figure 12-13. Offset Slope CurveFit Information Photo vs Ci coeffs: -5.22275 0.0939082 RMS= 0.7112 Figure 12-13. Polynomial coefficients are presented in ascending order of power. 12-16 Using the LI-6400...
Page 357: Viewing Data
G - Graphed vars and obs only This options shows the data plotted in the last plot. You can also see this after viewing a plot by pressing V instead of escape. Using the LI-6400 12-17...
Page 358 RMS = 0.7112 Figure 12-16. The E view option for the Initial Slope example (page 12-15). As with the C option, you are given the option of storing the information to disk when you exit from viewing it. 12-18 Using the LI-6400...
Page 359: Plotdef File Format
If you wish to use these binary files on another computer (that is how the plot images were done for this manual, for example), then you will have to write a program to handle the data, and will need to know the ÒencodingÓ scheme (Figure 12-18). Using the LI-6400 12-19...
Page 360 Figure 12-18. If the image border is not divisible by 8, then there will be unused portions of some of the bytes. Note that the image length and width must be preserved, or else the image will be shuffled. 12-20 Using the LI-6400...
Page 361 How to recompute data files 13-2 EASONS TO ECOMPUTE 13-2 XAMPLE 13-7 ETAILS RecomputeÕs Main Screen 13-7 Source File Considerations 13-8 Destination File Considerations 13-11 Customizing the Recompute 13-12 13-14 INTS Suppressing a VariableÕs Recomputation 13-14 Multiple (Appended) Files 13-14 Using the LI-6400 13-1...
Page 362: Reasons To Recompute
(you used 6.0, and it should have been 4.4) and stomatal ratio (you used 0 and it should have been 0.5). This example shows how to make a new file named Ò Ó with those values corrected. /user/MyData Corrected 13-2 Using the LI-6400...
Page 363 BLCond: -- ComputeList= /User/Configs/Comps/Defau Change the high- Edit Custom quit lighted entry ¯ Figure 13-2. The recompute programÕs main screen. Use to move the highlight bar up and down, and press edit to change the highlighted entry. Using the LI-6400 13-3...
Page 364 . If you wish to be prompted as the file recomputes for each new leaf value" area, then select "Prompt for new values" For our example, weÕll highlight and press enter. We "One global value" are then immediately asked for that value, and weÕll enter 4.4. 13-4 Using the LI-6400...
Page 365 ComputeList= /User/Configs/Comps/Defau Edit ViewSrc quit RECOMP Figure 13-5. Ready to recompute. WeÕll be setting a new leaf area, and a new stomatal ratio. The recomputed data will be writen to an as yet un- named file. Using the LI-6400 13-5...
Page 366 As the file recomputes, the display will show a dot for every observation pro- cessed: Recomputing..View the results After the file is generated, GraphIt (Chapter 12) is called to allow you to view the new file either graphically or textually. 13-6 Using the LI-6400...
Page 367: The Details
ParIn value to absorbed W/m2. This is relevant only to energy balance computa- tions. AlphaK= If none of the light source entries has the AlphaK you need, then you can enter it here explicitly. Using the LI-6400 13-7...
Page 368 Is it different from the one currently in effect? to be done. one currently in effect? Figure 13-7. When a source file is opened, the program scans the header for configuration information. 13-8 Using the LI-6400...
Page 369 The address list is the programÕs list of items to be written to the file when recomputing. The program uses two pieces of information to build this list: The original log format file This is the list of ID values, in order, that were stored. Using the LI-6400 13-9...
Page 370 (Figure 13-11). Note: In OPEN 3.01, there is a bug that can cause misalign- ment of data columns with data headers, if there is an ÒunknownÓ column la- bel. This is fixed in OPEN 3.2. 13-10 Using the LI-6400...
Page 371 OPEN version 3.2, the recompute program would use the recomputed time stamp, rather than the original time stamp, as the ÒbaseÓ time for the file. If you changed time formats as part of the recompute (changing Time in sec- Using the LI-6400 13-11...
Page 372 Figure 13-13. The list is of the variables that will be written to the recomputed file. In general, system variables are left un- changed, and user defined variables will be recomputed, but you can override individual cases, if you choose. 13-12 Using the LI-6400...
Page 373 -65 CsMch :No Change -66 HsMch :No Change -23 Status :No Change Figure 13-13. The CUSTOM function key allows you to edit the entire list of variables, selecting what happens to each (with some limitations, of course). Using the LI-6400 13-13...
Page 374: Hints
It probably means if found a remark after 5 observations, and then after an- other three observations, if found another data set appended on, with 4 obser- vations. Or, someone logged nine remarks one after the other. 13-14 Using the LI-6400...
Page 375 Part IV Configuration Issues...
Page 377 External PAR 14-8 14-9 OMPUTED ARIABLES Humidity Variables 14-9 Stability Variables 14-10 14-11 IME AND OGGING ARIABLES 14-12 TATUS ARIABLES 14-17 OUNDARY AYER ARIABLES 14-19 IST OF YSTEM ARIABLES ROADENING ORRECTION FOR 14-23 APOR Literature Cited 14-26 Using the LI-6400 14-1...
Page 378: Background Information
Formats dictate how much space to take up when displaying the variableÕs value, how many significant digits to show, right or left justified, etc. Typi- cally, display formats take up 8 spaces, while logging formats are more com- pressed. 14-2 Using the LI-6400...
Page 379 Layer Variables on page 14-17. Status variables ThereÕs a group of system variables that convey some system status informa- tion. These are updated every 10 seconds, and are described in Status Vari- ables on page 14-12. Using the LI-6400 14-3...
Page 380: Measured Variables
OPENÕs System Variables Measured Variables Measured Variables These system variables are measured signals or computed quantities associ- ated with the various analog sensors of the LI-6400. This section discusses analog measurements and computations, presenting equations for each sensor used. Pressure Atmospheric pressure P (kPa) is measured with a transducer located in the console of the LI-6400.
Page 381 GAÕs background temperature now (T ) and the temperature when the IR- GAÕs water channel was last zeroed ( T¢ )S w T¢ xw Ð (14-7) is the zero shift calibration term for water. It, and the corresponding value Using the LI-6400 14-5...
Page 382 ÒIRGA SpanÓ routine set in the Calib Menu of OPEN (Setting the CO2 Span on page 18-11). The zero drift correction term z for CO is analogous to that for water (14-7). T ¢ xc )S c Ð (14-10) 14-6 Using the LI-6400...
Page 383 The flow meter is located in the console, and itÕs signal V (mV) relates to flow rate F (µmol s ) by ID: -7 a f V f (14-13) The calibration factor a is specified by the configuration command CalFlow= < > Using the LI-6400 14-7...
Page 384 For further details about the LightSource= configuration command, refer to LightSource= on page 16-21. External PAR The optional external quantum sensor is a LI-COR LI-190 Quantum Sensor, whose signal V relates to reading Q (µmol m...
Page 385: Computed Variables
T a Saturation Vapor Pressure The saturation vapor pressure function e() used by OPEN is from Buck (1981) Buck, A.L. (1981) New equations for computing vapor pressure and enhance- ment factor. J. Appl. Meteor. 20:1527-1532. Using the LI-6400 14-9...
Page 386 FlowCV_%), and the sum of the three (T labelled Total- CV%). These values are computed based on the last n measurements (by de- fault, n = 30) using a stability function c c v DC ID: -18 C cv (14-25) 14-10 Using the LI-6400...
Page 387: Time And Logging Variables
ÒObsTimeÓ ID: -36 The number of seconds (floating point) since a log destination has been opened. If no log destination is active, this number is meaningless. Using the LI-6400 14-11...
Page 388: Status Variables
0x0201 is port 2, pin1, etc. The error condition is triggered by too much light blockage in the cell, or by the IRGAs not being connected. See ÒIRGAs Not ReadyÓ on page 20-7 for details. 14-12 Using the LI-6400...
Page 389 A spent cartridge will always cause this. The ÒHighÓ value will briefly appear when lowering the concentration, or when asking for too low a value (see the related troubleshooting discussion starting on page 20-26). Using the LI-6400 14-13...
Page 390 Fan at the High voltage. The fan is controlled by setting a DAC (channel 7) between 0 (off) and 5 (high) Volts. The setting for ÒLowÓ is defined by the configuration command FanSlow=, and defaults to 4 volts. 14-14 Using the LI-6400...
Page 391 Figure 14-1 illustrates a piece of LPL code that does one thing if the IR- GAs are OK, and another if they are not. StatusCO2 StatusH2O OR IF /* Not ok */ ELSE /* both ok */ THEN Figure 14-1. Using status information from an LPL program. Using the LI-6400 14-15...
Page 392 Chapter 7.) CO2 Mixer Cooler Lamp Flow Control FwMxCrLp 1 0 1 1 Flow *CO2S= Temp Lamp <range> 500µms 350µml Off Figure 14-2. The control manager status variable indicates if a control is on target and stable. 14-16 Using the LI-6400...
Page 393: Boundary Layer Variables
BLCond= <file name> The file specified is data for a lookup table, that accounts for the leaf area and the fan speed in computing the boundary layer conductance of broadleaves. Using the LI-6400 14-17...
Page 394 (0 to 5). is then g' bw computed from (14-31). The Table() function is a linear interpolation based on leaf area, using the lookup table boundary layer values for the appropriate fan voltage. 14-18 Using the LI-6400...
Page 395: List Of System Variables
P Eqn (14-1), pg 14-4 Press ParIn_µm In-chamber PAR Eqn (14-14), pg 14-8 parIn_um PARi µmol m ParOutµm Eqn (14-16), pg 14-8 parOut_um External PAR µmol m PARo RH_R_% Eqn (14-19), pg 14-9 Reference RH% rhIn RH_R Using the LI-6400 14-19...
Page 396 The status line statLineVar page 14-12 BLC_mol Total Boundary Layer Con- gÕ Eqn (14-31), condBL_mol BLCond 14-17 ductance (mol m AREA_cm2 area_cm2 page 16-18 In-chamber leaf area cm Area STMRATIO Stomatal ratio estimate stom_rat page 16-22 StmRat 14-20 Using the LI-6400...
Page 397 Eqn (14-18), pg 14-9 Sample vapor press kPa eAir_2_kPa BLC1_mol 1-sided Boundary Layer Eqn (14-31), pg 14-17 condBL_one Conductance (mol m ProgPrgs AutoProgram Progress lpProgress page 14-16 FwMxCrLp Control Panel Stability: cpStable page 14-16 Flow Mixer Cooler Lamp Using the LI-6400 14-21...
Page 398 -107 AuxS1 User defined, string (8) auxS1 -108 AuxS2 User defined, string (18) auxS2 -109 AuxS3 User defined, string (38) auxS3 a.Same as Display Label, if none shown b.Default. -101 thu -109 have user defined labels. 14-22 Using the LI-6400...
Page 399: Band Broadening Correction For Water Vapor
CO mole fraction over the short pathlengths found in LI-COR infrared gas analyzers (Wolfe and Zissis, 1978). This leads to a Òscaling lawÓ that allows absorption measured under one set of condi- tions to be scaled to other conditions (Jamieson, et al., 1963), g u P ¤...
Page 400 Band Broadening Correction for Water Vapor In principle, (14-36) can be solved for mole fraction, giving 1 Ð A --- ( )T (14-37) Since LI-COR gas analyzers produce an output voltage that is proportional to absorptance, (14-38) substituting (14-38) into (14-37) yields ------...
Page 401 ( ) for gas exchange measurement condi- X CO tions and is neglected. LI-COR analyzers are calibrated with CO in dry air, not nitrogen. If dry air is taken as reference instead of nitrogen, then (14-41) becomes a w 1 Ð...
Page 402 (14-43) forms the basis of the pressure broadening correction for water vapor in LI-COR gas analyzers. We use a value of 1.5 for the LI-6400 IRGA. Thus, Equation (14-11) comes from c w ( ) 1.5 1 Ð...
Page 403 Compilation Errors 15-10 EFINED ONSTANTS AND 15-12 EMARKS User Constants 15-12 User Remarks 15-12 Using Constants and Remarks 15-12 15-13 XAMPLES Water Use Efficiency 15-13 SEFUL ARIABLES AND 15-15 UNCTIONS 15-16 EFAULT OMPUTE 15-17 TYLE VS TYLE Using the LI-6400 15-1...
Page 404: The Computelist File
ComputeList files can be specified as part of a configuration by using the ComputeList= configuration command (Chapter 16). 15-2 Using the LI-6400...
Page 405: Computelist File Format
The file containing the list of user computations must adhere to a particular format. We illustrate by showing the first few variables of the default Com- puteList (Figure 15-2). The complete listing is in The Default ComputeList on page 15-16. Using the LI-6400 15-3...
Page 406 3 signifi- cant digits, resulting in values such as 1.23 0.0123 -1.23E+7 You can specify other formats by appending a format specifier to the ID 15-4 Using the LI-6400...
Page 407 The first of the three quoted strings following the ID/Format sequence is the label, which must be 8 characters or less. The variableÕs label is used to iden- tify the variable in text, graphics, and file output. Using the LI-6400 15-5...
Page 408 Suppress the automatic assignment with IF (#25 > 0) NOASSIGN in the first row, then write the desired u1953 = 10.23 / #25 ELSE code in subsequent lines, and do the variable assign- u1953 = 0 ment yourself. THEN " 15-6 Using the LI-6400...
Page 409: Writing And Modifying Computelist Files
Therefore, if #448 uses #633 in its definition, make sure #633 comes first in the ComputeList. What can I put in the equation? Equations can include: ¥ Numerical System Variables See Table 14-8 on page 14-19 for a list of variable names. Using the LI-6400 15-7...
Page 410 ##102 "Flag" "1 if photo, 0 if resp" " NOASSIGN if (#30 > 0) u102 = 1 ELSE u102 = 0 THEN " The word NOASSIGN in the first line of the equation string will prevent the 15-8 Using the LI-6400...
Page 411 What good is that? Well, you can log TxAir by itself, and not have to log chan21_mv. If you recompute, TxAir will not get recomputed (unless you ask it to be), so itÕs value wonÕt be changed. And you probably wouldnÕt want its Using the LI-6400 15-9...
Page 412 " #20 * xyz" The symbol xyz will not be found, so when Trmmol is compiled, an error will be reported (Figure 15-6). This doesnÕt happen when using :include (OpenÕs Hooks on page 26-7) or NOASSIGN. 15-10 Using the LI-6400...
Page 413 Module: "/UserConfigs/Comps/MyComputeList" ¨ ¨ ¨ ¨ View Debug quit Figure 15-7. When a module generated from a ComputeList fails to link to open, a message such as this is shown. No user defined variables will be available. Using the LI-6400 15-11...
Page 414: User Defined Constants And Remarks
Using Constants and Remarks To include user defined prompts and remarks in the prompt list, use the Prompt List Editor, and add them, once they are defined (see Prompts and 15-12 Using the LI-6400...
Page 415: Examples
" -#10 * co2_diff_um - co2_2_um * #20" Put cursor here ##35 "CndCO2" "Total Conductance to CO2" " 1.0 / (1.6 / #23 + 1.37 / condBL_mol)" Figure 15-9. Implementing Equation 15-1 in a Compute List. Using the LI-6400 15-13...
Page 416 Display List under a new name. Update or Make a New Config File Go to Config Status in the Config Menu, and Update or saveAs to store all of these changes for the next power on. 15-14 Using the LI-6400...
Page 417: Useful Variables And Functions
EB_DeltaT(Rn, Tw, Ta, Blc, E) Returns Tleaf - Tair from energy balance. E - transpiration (mol m Blc - boundary layer cond (mol m Ta - Air temp (C) Tw - Chamber wall temp (C) Rn - Net radiation (W/m2) Using the LI-6400 15-15...
Page 418: The Default Computelist
##39 "Ci/Ca" "Intercellular CO2 / Ambient CO2" " #36 / co2_2_um " ##25 "VpdL" "Leaf VPD (es(Tleaf) - eair)" " SatVap(Tleaf_c) - eAir_2_kPa" ##27 "VpdA" "Air VPD (es(tair) - eair)" " satVapTair_kPa - eAir_2_kPa" Figure 15-11. Listing of file /User/Configs/Comps/Default 15-16 Using the LI-6400...
Page 419: Old Style Vs. New Style
ÒNew StyleÓ. Essentially, the new style ComputeList is one that is directly written in LPL, the LI-6400Õs programming language (see Chapter 22). When an old style ComputeList is used, OPEN converts it into a new style, then links it. If you use a new style to start with, this step is eliminated.
Page 420 Defining User Variables Old Style vs. New Style 15-18 Using the LI-6400...
Page 421 Using Energy Balance 16-11 Boundary Layer Conductance 16-12 16-12 ODIFYING ONFIG ILES Config Status 16-14 Config Editor 16-15 16-16 ESET ÒConfig File (Re-)InstallÓ 16-16 ÒReset to Factory DefaultsÓ 16-18 ÒReset to User Configuration 16-18 ONFIGURATION OMMAND 16-18 UMMARY Using the LI-6400 16-1...
Page 422: A Definition Of Terms
Configuration Basics In the early days of the LI-6400, there was but one way to do any configura- tion change: go to the Config Editor. While this tool is still available as a last resort, more recent versions of software have introduced various configura- tion ÒhelpersÓ, such as Logging Control (page 9-7), Prompt Control (page...
Page 423 . Whenever OPEN im- plements a configuration, this master file is first read and implemented. In case youÕre interested, this master ÒfileÓ is actually two files: Ò/Sys/Open/Con- fig Items 1", and Ò/dev/parm0Ó. Using the LI-6400 16-3...
Page 424: Making Configuration Files
Note: In OPEN 3.01, there is a potential problem with using the Installation Menu for installing external quantum sensors, or LED light sources, if it is the first one being installed. The problem is that the calibration file can become corrupted. See ÒUnknown config commandÓ on page 20-5. 16-4 Using the LI-6400...
Page 425 Suppose, for example, you were going to use a clear bottomed 2x6 chamber, and wanted to configure the LI-6400 accordingly. If you were some sort of a LI-6400 guru, you might be able to go to the Config Editor and build one from scratch , keeping in mind the following issues: leaf temperature is no longer measured, so you need an energy balance computation;...
Page 426 YouÕll need the calibration sheet (Figure 16-6) for the next three questions: 6400-02B LED Light Source Calibration Certificate Serial Number SI-505 Date: 6 June 1997 Technician CalParLED= -.59 Figure 16-6. The required calibration information is available from the light sourceÕs calibration sheet. 16-6 Using the LI-6400...
Page 427 Ò6400-02 Red LED #SI-183Ó Ò6400-02B RedBlue #SI-505Ó ÒSun+SkyÓ 1.0 0.19 ÒQuartz HalogenÓ 1.11 0.26 ÒFluorescentÓ 0.88 0.18 ÒMetal HalideÓ 0.87 0.17 Figure 16-7. The light source menu includes standard sources, plus whatever 6400-02 and -02B sources have been installed. Using the LI-6400 16-7...
Page 428 LightSource= Ò6400-02B RedBlue #505 ComputeList= ÒDefault using EBÓ Displays= ÒStd+EBTleafÓ LogFormat= ÒStd+EBÓ Figure 16-8. After building a configuration, you are given a chance to view it before storing or discarding it. Press escape when done viewing the file. 16-8 Using the LI-6400...
Page 429 None of the configurations that can be generated by the Installation Menu ac- tually take effect until you select them after a) power on, or b) you select , found in , in the Config "Reset To User Configuration" "_Reset Menu" Menu. Using the LI-6400 16-9...
Page 430: Installation Menu: Behind The Scenes
(the last one will take precedence). The Installation Menu entry scans “/dev/parm0” "View Installed Cal Items" for the following entries (commented or not): CalParGaAs= CalParLED= CalParOut= and presents the results in a list such as shown by Figure 16-11. 16-10 Using the LI-6400...
Page 431 The configuration builder sets the ComputeList= configuration command to the appropriate file, based on what chamber you are using, and/or how you answered the energy balance question. The 6400-05 Conifer chamber, and the clear bottom chambers, always use an energy balance. Using the LI-6400 16-11...
Page 432: Modifying Config Files
LogList QuikPik (F2) in Prompt Control PromptList= SaveAs (F5 level 2) in PromptList Editor ÒChoose a Compute ListÓ in ComputeList Menu ComputeList= GRAPH QuikPik (F2 level 4) New Msmnts Mode StripDefs= SaveAs or OK in Config Editor Any command 16-12 Using the LI-6400...
Page 433 Config Sta- tus, described on page 16-14. Indicates a modi- fied and unstored configuration LI-6400 Photosynthesis System OPEN 3.2 CONFIG /User 66% full Tue Jun 16 1998 12:29:36 12.25V...
Page 434 Config File File under a new name. Ôas storedÕ version Figure 16-13. The Config Status screen shows the user config file, and (if it has been modified and is un- stored), what the changes are to it. 16-14 Using the LI-6400...
Page 435 Dialog box, and if a file is selected, the file is read in to be edited, replacing the current config file. Cancel Abandon the config editor, and make no configuration changes. Implement the current contents of the config editor, and up- date the file. Using the LI-6400 16-15...
Page 436: The Reset Menu
After the program opening message, you are asked to choose a destination. Choose a destination ÒSysÓ ÒUserÓ Typically this would be User. The disk selected will then have a directory cre- 16-16 Using the LI-6400...
Page 437 Clear Bottom EB Conifer Chamber EB Display Formats Configs/Displays Std Display Std+EBTleaf Diagnostic Log File Formats Configs/LogFormats Std Output Std+EB QuikPlot Definitions Configs/PlotDefs Photo, Cond vs Obs Light Curve A Ci Curve Prompt Lists Configs/Prompts Default (none) Using the LI-6400 16-17...
Page 438: Configuration Command Summary
Config Files Configs/UserPrefs Factory Default ÒReset to Factory DefaultsÓ This program is designed to put the LI-6400 into a ÒknownÓ state quickly. It simply implements the master list without any user list. It is functionally equivalent to , and selecting (provid- “Factory Default”...
Page 439 (If you are thinking about interchanging IRGA/sensor heads, donÕt.) CalH2O= H2O IRGA cal coefficients for Equations (14-5) and (14-6) on page 14-5. These are coefficients for a 3rd order polynomial with no 0-order term. Using the LI-6400 16-19...
Page 440 Is the CO2 mixer installed? This is also a Yes/No toggle, and should be set to reflect whether the mixer is installed or not; it has nothing to do with whether you are actually using the mixer. 16-20 Using the LI-6400...
Page 441 Ò Ó is assumed. /User/Configs/LogFormat PATCH= This is a catch-all tool. Whatever comes after the = is compiled (using LPLÕs COMPILE keyword) and run. The usual use for this is to set variables from Using the LI-6400 16-21...
Page 442 Input Channels on page 26-22. This marks a comment. Any line starting with // is ignored. Note that the En- able and Disable function keys in the Config Editor comment and uncom- ment lines in this manner. 16-22 Using the LI-6400...
Page 443 Using an Energy Balance Computing what you canÕt measure 17-2 HEORY OPEN 17-6 SING NERGY ALANCE IN How To Do It 17-6 The Details 17-6 Recomputation Considerations 17-9 NERGY ALANCE OUNDARY 17-9 AYER 17-11 URTHER EADING Using the LI-6400 17-1...
Page 444: The Theory
This chapter explains the the- ory and the practice of using energy balance. The Theory The energy balance of a leaf in the LI-6400 cuvette has three major compo- nents: net radiation R (W m ), sensible heat flux Q (W m...
Page 445 , and c = 28 J 5.67 10 . While a and k can vary widely for different light sources (Figure 17-2 on page 17-5), their product is fairly conservative (Table 17-1). Using the LI-6400 17-3...
Page 446 LI-1800 spectroradiometer. Leaf spectral measurements were made on a green ash leaf using an 1800-12 In- tegrating Sphere. 900 1000 1100 Wavelength Figure 17-1. Leaf absortance spectrum used in the computations of Table 17-1. 17-4 Using the LI-6400...
Page 447 Wavelength (nm) Mercury Vapor Tungsten 0.25 0.15 0.05 1000 1100 1000 1100 Wavelength (nm) Wavelength (nm) Figure 17-2. Spectra used to compute results in Table 17-1 on page 17-4. Vertical scales have units of in all cases. Using the LI-6400 17-5...
Page 448: Using Energy Balance In Open
(Chapter 15). There are three factory-provided compute lists that use energy balance. When you use the Installation Menu to build a configuration, it will use one of these compute lists. One of them, , is shown in “Default using EB” Figure 17-3 on page 17-7. 17-6 Using the LI-6400...
Page 449 ##25 "VpdL" "Leaf VPD (es(Tleaf) - eair)" " SatVap(#101) - eAir_2_kPa" ##27 "VpdA" "Air VPD (es(tair) - eair)" " satVapTair_kPa - eAir_2_kPa" Figure 17-3. Listing of ÒDefault using EBÓ. The energy balance leaf temperature is used in Cond and VpdL. Using the LI-6400 17-7...
Page 450 Wall Temperature The second parameter needed for the EB_DeltaT function is wall tempera- ture. The LI-6400 doesnÕt have such a sensor per se, but the air temperature thermistor is located in the IRGA beneath the air circulation fan. Between this location and the leaf chamber, the air comes in contact with a lot of metal wall material, so this sensorÕs signal is not a bad first guess for wall temperature.
Page 451: Energy Balance And Boundary Layer
Energy Balance And Boundary Layer Air Temperature The third parameter is the air temperature next to the leaf. The LI-6400 has sensors for this only in the 6400-05, -07, and -08 chambers, so in the rest of the chambers we use the leaf thermocouple to do this job (variable tLeaf_C), by pulling it down a bit so that the junction is not in contact with any leaf ma- terial.
Page 452 (17-10). An LPL program is provided with OPEN that does im- plements this solution, and it is described in ÒENERGYBALÓ on page 21-12. Its primary use is for doing boundary layer conductance determina- tions. 17-10 Using the LI-6400...
Page 453: Further Reading
Press, San Diego, London. Ehleringer, J.R. 1989. Temperature and energy budgets. in Plant Physiologi- cal Ecology: Field Methods and Instrumentation. R.W. Pearcy, J. Ehleringer, H.A. Mooney, P.W. Rundel, eds. Chapman and Hall, London, New York. Using the LI-6400 17-11...
Page 454 Using an Energy Balance Further Reading 17-12 Using the LI-6400...
Page 455 Part V Maintenance & Troubleshooting...
Page 457 Calibrating the CO2 Mixer 18-20 6400-02(B) LED S 18-24 OURCE Light Source Calibration 18-24 18-28 IGHT ENSORS Factory Calibration 18-28 Generating a Calibration Correction 18-28 ALIBRATION AND ONFIGURATION 18-30 UMMARY /dev Files 18-30 The Configs directory 18-31 Using the LI-6400 18-1...
Page 458 Calibration Issues This section describes the calibration issues for the various sensors in the LI-6400. While some sensors require no such attention, others require period- ic user or factory service (Table 18-1). Table 18-1. Sensors and accessories, and their calibration requirements...
Page 459: Co2 And H2O Analyzers
0 to about 3000 µmol mol . Water concentrations are generated using a LI-COR LI-610 Dew Point Generator. These measurements are made at a series of temperatures (typically 30, 40, and 50C), with the entire instrument in a temperature controlled chamber.
Page 460 Just because you changed the chemicals in the tubes recently does not necessarily mean that they are good. Ò/dev/parm1Ó, if you are curious. 18-4 Using the LI-6400...
Page 461 Figure 18-2 illustrates the IRGA zero screen. WeÕll do CO first, because itÕs quickest. Put the desiccant on full bypass, because (if itÕs Drierite) it will buff- er CO , resulting in a longer time to reach zero as it flushes out. Using the LI-6400 18-5...
Page 462 Now we do the water zero. Since water sticks to everything, it can take many minutes to come to a reasonably stable ÒdryÓ reading, since the chamber and Note that the zero only affects absolute concentrations; the relative readings (differentials) are taken care of by matching, described on page 4-34. 18-6 Using the LI-6400...
Page 463 ÒYÓ connection and flow air to both sample and ThereÕs a trick to doing this faster. See Manually Zeroing the IRGAs on page 18-10. Using the LI-6400 18-7...
Page 464 To shorten the dry down time, block the upper half of the chamber, as ex- plained under step 5 on page 18-6. When stable, press AutoAll Since the air source is dry and CO free, you can zero both IRGAs simulta- neously. 18-8 Using the LI-6400...
Page 465 (Figure 18-10 on page 18-18). ¥ Not Zero Air The most common problem results from zeroing the IRGAs with air thatÕs not really CO -free, or not really dry. Using the LI-6400 18-9...
Page 466 When one of the manual zeroing function keys is pressed, the value of the D/A channel that controls that IRGAÕs zero is displayed to the right of the Match Status. This is also the value displayed in the ÒView,Store Zeros&SpansÓ program in the Zero column (Figure 18-10 on page 18-18). 18-10 Using the LI-6400...
Page 467 The sample IRGA is CO2Sµml. The span values should be close to 1.0, as described in What Can Go Wrong Setting the Span on page 18-15). At the factory, we use our 1500 µmol mol tank for setting spans. Using the LI-6400 18-11...
Page 468 IRGA by a factor ¯ of 0.001. To change the span factor by 0.010, hold shift down while you press . To change the active ¬ ® IRGA, press the F1 through F4, or else use 18-12 Using the LI-6400...
Page 469 To check the span of the H O analyzer, youÕll need a known concentration of O. The best choice for this is the LI-COR Dew Point Generator (LI-610). If you do not have an LI-610, or some device of similar accuracy, do not adjust the IRGA span values for water.
Page 470 This allows us to measure the sample cell dewpoint. We then use this value as a momentary target for setting the sample IRGA.) 18-14 Using the LI-6400...
Page 471 ¥ Leak in the chamber The chamber has to be well sealed for this to work. Starting in version 3.2, you are not allowed to adjust the span outside of the range 0.9 to 1.1. Using the LI-6400 18-15...
Page 472 This will check the flow meter zero, the IRGA zeros, and the IRGA spans to see if they are different that what is stored. You will be prompted "Store (Y/N)" for each item if there is a difference. 18-16 Using the LI-6400...
Page 473: Flow Meter
Calibration Issues Flow meter Flow meter Flow in the LI-6400 is measured with an electronic mass flow meter in the console. Factory Calibration The flow meter is calibrated at three temperatures using a series of mass flow controllers. (The flow controllers are, in turn, periodically calibrated with a precision device that operates on a volumetric displacement principle.) The...
Page 474: View, Store Zeros & Spans
Set Flow Zero to 0. Select a key Figure 18-10. The ÒView,Store Zero&SpansÓ screen. The zero and span data for factory defaults and power on defaults is stored in the file "/dev/parm1", along with a number of other settings. 18-18 Using the LI-6400...
Page 475: Zeroing The Leaf Temperature Thermocouple
30 minutes to warm up, use the small flat head screwdriver in the spares kit to turn the adjustment screw until the displayed leaf temper- ature and block temperature match. Zero Adjust Figure 18-11. Location of the leaf temperature zero adjustment screw. Reconnect the thermocouple connector. Using the LI-6400 18-19...
Page 476: Co2 Mixer
(Figure 18-12). ÒStableÓ means the Rangeµml value drops below 1.0 while the Status indicates ÒOKÓ. The func- tion key earlyOK will override these conditions and force the software to pro- ceed to the next step. 18-20 Using the LI-6400...
Page 477 The pump speed is adjusted based on the ratio of what the upper limit of CO was measured to be, and what you want it to be. Type in some value, such as 2500, and press enter. Using the LI-6400 18-21...
Page 478 CO to stabilize, then re- adjust the pump speed, etc. Allow several seconds for the CO concentration to equilibrate after a pump speed change. Pressing OK takes you back to step 18-22 Using the LI-6400...
Page 479 Figure 18-15. Typical plot of a CO2 mixers calibration curve. The range of CO concentrations is typically 40 to 2200 µmol mol If the user accepts the calibration, it is stored in , along with /User/Configs/Mixer Using the LI-6400 18-23...
Page 480: B) Led Source
Calibration data relating the LED SourceÕs command signal with light output can be generated by running the program in the "LED Source - Calibrate" Calib Menu. This program is fairly automatic, once you get past the opening screen (Figure 18-17). 18-24 Using the LI-6400...
Page 481 1 minute, then proceed anyway. The program then goes through a series of command voltages (50, 100, 1000, 3000, and 5000 mV), at each waiting for 10 seconds then recording the QNTM value (PAR in µmol m ) (Figure 18-19). Using the LI-6400 18-25...
Page 482 Plot this? (Y/N) Figure 18-20. The LED source calibration data is displayed, and you are given a chance to plot the graph. To actually implement this calibration data, you must respond by pressing Y when asked (Figure 18-21). 18-26 Using the LI-6400...
Page 483 100 1000 3000 5000 20.097 45.639 507.48 1493.4 2358 PPFD (µmol m Figure 18-22. Typical Ò/User/Configs/LampÓ file. The lowest set point is 10 mV in OPEN 3.01 and below. With OPEN 3.2, it changed to 50 mV. Using the LI-6400 18-27...
Page 484: Gaasp Light Sensors
GaAsP Light Sensors Gallium Arsenide Phosphide light sensors are used in the standard 2x3 LI-6400 chamber top, as well as many of the optional chamber tops. Standard chambers have serial numbers GA- nnn , while accessory chambers with GaAsP sensors have GB- nnn serial numbers.
Page 485 Note: We do not recommend using an LI-190 quantum sensor to calibrate, or even accurately measure, the LED light source output because the drop off in quantum sensor sensitivity near 700nm (Figure 8-4 on page 8-8) is similar to Using the LI-6400 18-29...
Page 486: Calibration And Configuration File Summary
Calibration and Configuration File Summary /dev Files The LI-6400Õs file system includes items not shown in the Filer. These items reside in a directory named . Two of these are 8K (maximum size) blocks /dev...
Page 487 This file contains the latest LED source calibration, generated by executing in the Calib Menu. It is illustrated in "_LED Source - Calibrate" Figure 18-22 on page 18-27. The Configs directory can be installed on any disk. See ÒConfig File (Re-)In- stallÓ on page 16-16. Using the LI-6400 18-31...
Page 488 Calibration Issues Calibration and Configuration File Summary ÒConfigs/mixerÓ This file contains the latest CO2 mixer calibration, generated by executing in the Calib Menu. It is illustrated in "_CO2 Mixer - Calibrate" Figure 18-16 on page 18-24. 18-32 Using the LI-6400...
Page 489 Getting To Know Your Mixer 19-33 Replacing Connector Screws 19-12 If the Flow Restrictor Becomes Clogged 19-33 19-14 LI-6400 19-35 HAMBER ANDLE HIPPING Handle Maintenance 19-14 Latch Maintenance 19-14 19-36 SEFUL UMBERS Latch Return Spring 19-16 Handle Removal 19-16 Using the LI-6400 19-1...
Page 490: Chemical Tubes
Maintenance & Service This chapter describes the maintenance and service tasks that may be required in the normal course of operating the LI-6400. Chemical Tubes The chemical tubes can be left in place on the console until itÕs time to replace the chemicals, or to service a tubeÕs flow control assembly.
Page 491 Do not overtighten the mufflers, as they can break at the threads very easily. There are air mufflers in the spare parts kit. Open Muffler Figure 19-2. Air mufflers in soda lime and desiccant tubes. Using the LI-6400 19-3...
Page 492 The Desiccant Tube: Use Drierite To regenerate Drierite LI-COR recommends indicating Drierite (W.A. Hammond Drierite Compa- ny, P.O. Box 460, Xenia, OH 45385) for use with the LI-6400. Drierite is an- hydrous 97% calcium sulfate (CaSO ) and 3% cobalt chloride. Calcium sulfate is safe, chemically inert except toward water, economical, and can be regenerated.
Page 493 O-rings a bit. ThereÕs no need to tighten any more than that, and if you do, youÕll have a problem getting the tube back off again later. Air Passage Holes O-rings Figure 19-3. Each chemical tube has two air passage holes protected by O-rings. Using the LI-6400 19-5...
Page 494 (opposite the side where the nut was) of the assembly. Leave these 2 2 on top 3 this side 3 this side Figure 19-5. Removing 8 screws from the flow adjust as- sembly. 19-6 Using the LI-6400...
Page 495 How do you tell? There is a set screw threaded into the knob; the back of the set screw accepts a 3/32 hex key (donÕt turn it!), and this is the side that should face away from the flow control assembly. Using the LI-6400 19-7...
Page 496: Batteries
(To test, plug the battery by itself into the LI-6400 console, and power it on. If nothing happens, then itÕs the fuse, or the battery is dead.) A fully discharged 6400-03 battery requires about 3 hours to recharge.
Page 497: System Console
Internal Air Filter Replacement The air filter should be replaced annually; more frequently in dirty environ- ments. The filter is located inside the LI-6400 (Figure 19-8 on page 19-11). Disas- semble the console as described above NOTE: Console serial numbers PSC101-160 that do...
Page 498 (See Figure 20-9 on page 20-36 or Figure 20-14 on page 20-44 for flow schematics.) Spare filters can be ordered from LI-COR under part number 300-01961 (one each). Replacing the Fuses Remove the card cage as described above.
Page 499 F2 (Flow board) 3A Air Filter Figure 19-8. Location of console fuses. The back plane board fuses protect the analyzer board, flow board, and digital boards. The flow board fuses protect the thermoelectric coolers and fan. Using the LI-6400 19-11...
Page 500: Real Time Clock
When the console is powered off, the clock is run from a 3V lithi- um battery. The battery should operate for many years. When the voltage on the battery drops to 2.7V, the battery (LI-COR part num- ber 442-03791) should be replaced. See Real Time Clock Problems on page 20-6 for instructions about measuring and replacing the battery.
Page 501 Maintenance & Service Cables Part Number 314-04913 Figure 19-9. A connector screw can be removed by firmly pulling it straight out. It is held in place by friction. Using the LI-6400 19-13...
Page 502: The Chamber Handle
Chamber doesnÕt latch reliably This rod must have a 90 degree bend at the top, or the chamber will not latch correctly. If it becomes straightened, reach in with a pair of needle nosed pli- ers and re-bend it. 19-14 Using the LI-6400...
Page 503 Figure 19-11. The chamber catch rod should have a 90 degree bend at the top. If it doesnÕt, the chamber will not latch correctly. The catch rod can be re-bent with a pair of needle nosed pliers, if necessary. Should the wire break, you can replace it (6564-057) or replace the entire assembly (6400-903). Using the LI-6400 19-15...
Page 504 Handle Removal The handle must be removed for certain service operations, and for installing certain chambers (e.g. the 6400-09 Soil Chamber and the 6400-05 Conifer Chamber). 19-16 Using the LI-6400...
Page 505 Rear View Handle Quantum sensor holder Remove these 2 (or 3) screws Figure 19-14. Remove the 3 screws shown. (More recent models have only two screws). Using the LI-6400 19-17...
Page 506: Leaf Temperature Thermocouple
Male Thermocouple Connector Figure 19-15. Leaf temperature thermocouple and connector. To replace the 6400-04 leaf temperature thermocouple: Unplug the connector Remove the male thermocouple connector by pulling straight out. Provided the leaf temperature is properly zeroed. 19-18 Using the LI-6400...
Page 507 Leaf Chamber Leaf Temperature Gasket Thermocouple Lower Leaf Chamber Male Thermocouple Connector Thermocouple Retainer Ring Thermocouple Holder Figure 19-16. Position thermocouple bead just above foam gasket. Using the LI-6400 19-19...
Page 508: Leaf Chambers
Several chambers use Propafilm (ICI Americas, Inc., Wilmington, DE), such as the standard 2x3 chamber top, the 6400-07 top and bottom, the 6400-08 bottom, and the 6400-11 top. You will need to replace the film if it 19-20 Using the LI-6400...
Page 509 Maintenance & Service Leaf Chambers becomes torn or punctured, or excessively dirty. Replacement film (LI-COR part #250-01885) and double-sided tape (part #212-04341) can be found in the spare parts kit. To replace the Propafilm: Detach the affected chamber part Use the 3/32Ó hex key provided in the spare parts kit to remove the two long screws.
Page 510: Led Source Maintenance
There is a layer of silicone cement underneath the chamber top, but it wonÕt stick to the top because of its Teflon lining. Self adhesive Teflon is available from LI-COR as part number 212-02314. LED Source Maintenance The most important maintenance item for the LED source is the foam gaskets, concerning which there is one thing to remember: Use white polyethylene gaskets on the LED source.
Page 511: Match Valve Maintenance
Match mode is OFF Quit Toggle Figure 19-18. The Match Valve manual control program. The status line indicates where the valve should be, not necessarily where it ac- tually is. Using the LI-6400 19-23...
Page 512 Disassemble Remove the 4 screws that hold the black cover in place, and lift off the cover. Lift the match valve housing up from the paddle end, exposing the pads. Do not remove the plastic cover. 19-24 Using the LI-6400...
Page 513 Do this by sliding the cover back and forth a bit to see if you can feel the wires between the cover and the block. Available from Dow Corning under the trade name MolyKote Z, part number 88050-21, or (on request) from LI-COR. Using the LI-6400 19-25...
Page 514: Irga Maintenance
(Figure 19-23). Pull up on the bottle covers to ex- pose the bottles; the O-rings can expand to form a very tight seal, so you may have to pull hard. Housing Cover Bottle Cover Figure 19-21. Remove the two screws that secure the housing cover. 19-26 Using the LI-6400...
Page 515 Several grades of magnesium perchlorate are available from com- Bottle Cover/O-Ring Soda Lime/Desiccant Bottles Cover Analyzer Housing Soda Lime Mg(ClO Figure 19-23. Insert the new bottles lid first, followed by the bottle cover/O-ring and housing cover. Using the LI-6400 19-27...
Page 516 Consult the container label. Cleaning the Optical Bench Because the LI-6400 contains open path analyzers, it is possible for air-borne debris to enter the system and contaminate the sample optical path. When the analyzers become too dirty, the ÒIRGA(s) not readyÓ message will be displayed in New Measurements mode.
Page 517 Figure 19-24. Remove the 2 screws shown. Remove the optical bench cover. Pull off the air hose from the underside of the leaf chamber. Remove the male end of the thermocouple connector by pulling straight out. Using the LI-6400 19-29...
Page 518 Figure 19-25. Remove the optical bench cover (leave the chamber bottom attached) by removing the 8 screws in the manifold. Clean the windows Moisten a cotton swab and swab the two optical windows for the sample cell (Figure 19-26). 19-30 Using the LI-6400...
Page 519 This gasket is reusable; it should adhere to the optical bench. If it becomes detached, be sure to reposition it before reassembly. Tighten (but not overly so - theyÕre small and can break) the 8 screws evenly. Using the LI-6400 19-31...
Page 520: Servicing The External Co2 Source Assembly
(notably CopperHeadª) contain considerable oil, requiring a filter change every cartridge. It is therefore good policy to check the filter (remove cap and look for discoloration on the filter end) every time you replace a cylinder when using non-LI-COR cylinders. Cylinder To install the filter:...
Page 521 (Figure 19-28), and can not be removed; you must replace the entire fitting. A spare fitting with the restrictor in place (part number 9964-042) can be found in the 6400-01 spare parts kit. Using the LI-6400 19-33...
Page 522 Replace the flow restrictor Remove and discard the fitting containing the flow restrictor. Install the new fitting/restrictor (LI-COR part #9964-042). Note that the fitting is wrapped at one end with Teflon tape (Figure 19-28). Insert this end into the mounting block and tighten securely.
Page 523: Shipping The Li-6400
Shipping The LI-6400 Install the copper supply tube Tighten the two nuts. Shipping The LI-6400 If you need to transport the LI-6400 in its shipping case, we recommend that you observe the following tips: Tie the chamber handle closed. ¥...
Page 524: Useful Part Numbers
Part Number 10 Amp fuse 438-03142 Battery 6400-03 Male connector (as on the battery) 318-02031 Female connector (as on the console) 318-02030 Cable between charger and console 9960-062 Clock battery (keeps time while power off) 442-03791 19-36 Using the LI-6400...
Page 525 Upper half of 2x6 chambers 9964-052 Lower half of clear bottom, 2x6 needle chamber 9964-051 Lower half of 2x6 narrow chamber 9964-050 O-ring (smaller) for outer air passage 192-04357 O-ring (larger) for inner air passage 192-04356 Using the LI-6400 19-37...
Page 526 Chamber catch rod (wire only) 6564-057 Chamber tension adjustment assembly 6400-908 Log switch replacement kit 6400-904 Fan motor (field installation version) 6400-902 Vinyl gasket (top of sample cell) 6564-022 Vinyl gasket (mirrors) 6564-021 Connector screws for chamber/IRGA cables 314-04913 19-38 Using the LI-6400...
Page 527 SEFUL NFORMATION The Diagnostic Display 20-42 20-21 ATCH ALVE ROBLEMS System Flow Schematic 20-44 ÒCO2 has ChangedÓ Message 20-21 Chamber Connectors 20-45 ÒExcessive DeltasÓ Message 20-21 ÒCO2R DidnÕt ChangeÓ Message 20-22 Match Valve DoesnÕt Move 20-22 Using the LI-6400 20-1...
Page 528: Power On / Start-Up Problems
Power On / Start-up Problems Usually, when you turn on the LI-6400, there is about a two minute wait be- fore OPEN is ready to use. If there are multiple configurations, youÕll be asked to pick one, but other than that, no user intervention is required. This section describes some of the unusual things that might happen during these two minutes.
Page 529 (Figure 19-8 on page 19-11) is plugged in. Otherwise, contact LI-COR for further assistance. Console Continually Restarts The LI-6020 battery charger does not have enough power to run the LI-6400 when the IRGAs turn on, so the usual cause of continual power on recycling is the following configuration: ¥...
Page 530 Power On / Start-up Problems Messages ÒFlash disk not foundÓ Message Serious problems with the memory board. Contact LI-COR. ÒUnlinked fragmentsÓ Message Data was found at the end of a disk that ÒdoesnÕt belongÓ anywhere. Likely cause: turning the instrument off while in New Measurements mode when a log file was open.
Page 531 ÒVerify CalibrationÓ to fix the file. Look especially for missing cali- bration items, such as CO2Cal=. Examples of ÒproperÓ calibration files are given in Figure 16-10 on page 16-10, and on page 21-20. ÒnewÓ means there wasnÕt one installed before. Using the LI-6400 20-5...
Page 532: Real Time Clock Problems
Figure 20-1. Location of the clock battery, Test Point 10, and capacitor C3. The battery (LI-COR part number 442-03791) is a ÒcoinÓ type, and is held in place in a holder on the corner of the board. It is easily removed, but be sure the instrument is powered off, lest you short the test points right in front of the battery holder and blow a fuse.
Page 533: New Measurements Mode Warning Messages
95%, the ÒHigh Humidity AlertÓ message appears. The usual remedy is some combination of the following: ¥ Give the coolers a warmer target. Perhaps youÕre asking for a block or leaf temperature that is too cold. Using the LI-6400 20-7...
Page 534 CO injec- tor. ÒFLOW: Need -SCRUB or wetter targetÓ The Ò- refers to the desiccant tube adjustment label, and the direction SCRUBÓ you may wish to turn the knob. Specifically, this message means that the tar- 20-8 Using the LI-6400...
Page 535: Unreasonable Results
(that being the abominable nature of computers); crazy numbers come from crazy inputs. You need to look behind the compu- tations and determine which input is crazy and why. Using the LI-6400 20-9...
Page 536 If the photosynthetic rate is low, try operating at a low fixed flow rate (such as 100 µmol s ); this will a) keep the flow rate stable, and b) make the CO differential as large as possible. See Dealing With Low Rates on page 4-49 for other suggestions. 20-10 Using the LI-6400...
Page 537 If itÕs much more than that, you may have problems. An OPEN system such as the LI-6400 depends upon stable inputs. Because air flows through the sample and reference cells at different flow rates, and because there are differing vol- umes involved, any fluctuation in the input will show up in the sample and reference at different times, causing the differential value to oscillate.
Page 538 Conductance is generally the culprit, but here are three things to check: Transient condition? Very low C Õs can be real, especially for short time periods. Example: take a low light leaf into bright light. The plantÕs photosynthetic biochemistry re- 20-12 Using the LI-6400...
Page 539: Pump/Flow Problems
CO concentration. Refer to Calibrating the CO2 Mixer on page 18-20. Remove the soda lime tube If the flow does not increase substantially, go to Step 3. Using the LI-6400 20-13...
Page 540: Irga Problems
(see discussion under ÒCO2Ó and ÒH2OÓ on page 14-12). What triggers this message is Òtoo muchÓ light attenuation in the non-absorbing reference wave bands for CO and H O. Causes: 20-14 Using the LI-6400...
Page 541 >5000, then clean out the sample cell (page 19-28). Contact LI-COR If youÕve gotten to this point (the chopper motor is running, and the chamber and optics are clean, but ÒIRGAs Not ReadyÓ persists), then contact LI-COR. Using the LI-6400 20-15...
Page 542 Typically, they are numbers in the hundreds. Try resetting to factory settings to see if that makes a difference. Unstable CO and/or H The noise of the LI-6400 analyzers is typically 0.2 µmol mol for CO , and 0.04 mmol mol for H .
Page 543 If the IRGA mV values are stable, but the molar concentrations arenÕt, then look for instability in pressure (display line g), IRGA temperature, chamber temperature, and block temperature (display line h). Pressure is used for both sample and reference concentration computations. Block temperature is used Using the LI-6400 20-17...
Page 544 LI-COR. There is a stop-gap work-around, however, that could keep you going, and thatÕs to use a constant value instead of a measured one for the offending sensor.
Page 545 In New Measurements mode, turn off the pump (2 F2 N) and chamber fan (3 F3 O [the letter, not the number]), so you can hear the chopper motor. Put the LI-6400 to sleep Go to the Utility Menu, and select ÒSleep ModeÓ. Listen for a motor in the sensor head (NOT the console) to wind down once you press Y indicating itÕs...
Page 546 Troubleshooting IRGA Problems Wake the LI-6400 up Exit the Utility Menu. The fan in the console will begin running immediately, but listen for the chopper motor to begin running after that (press your ear to the IRGA); it should start anywhere from 10 seconds to 1 minute later.
Page 547: Match Valve Problems
Figure 4-4 on page 4-35 shows how the match valve should be positioned in and out of match mode. ¥ Is the return flow tubing in place? Check to be sure there is a piece of tubing connecting the chamber bottom with the match valve (Figure 20-3). Using the LI-6400 20-21...
Page 548 Match Valve DoesnÕt Move Stuck match valves are discussed in Match Valve Maintenance on page 19-23. Chamber exhaust tube Figure 20-3. The exhaust from the leaf chamber is sent to the match valve. 20-22 Using the LI-6400...
Page 549: Co2 Mixer Problems
Alternatively, put a drop of liquid (soapy water or saliva) on the hole, and look for bubbles. Lack of flow from the regulator can be due to a clogged filter or flow restric- tor. See Servicing the External CO2 Source Assembly on page 19-32. Using the LI-6400 20-23...
Page 550 (especially if you were also in constant humidity mode, in which the flow can fluctuate) or leaf photosynthetic changes. Try running in R mode in- stead. If C mode doesnÕt help, then continue on: 20-24 Using the LI-6400...
Page 551 Step 4, Check the regulator for flow on page 20-23. If the problem is er- ratic closure on the target value (overshooting, undershooting, etc.), then try See the important hint in Getting To Know Your Mixer on page 19-33. Using the LI-6400 20-25...
Page 552 See Step 4, Check the regulator for flow on page 20-23. Calibration problem? Change to C mode (constant control signal), and set a 5000 mV target. If that fixes the problem, then re-do the mixer calibration. 20-26 Using the LI-6400...
Page 553 It is shown in Figure 20-4 on page 20-24. ¥ Examine the pierced hole in the top of the cartridge If it is not round, but oblong, then a bent piercing pin on the source may be the culprit. Using the LI-6400 20-27...
Page 554 6400-01 CO2 Mixer Problems The Bad Valve Saga If your LI-6400 has serial number 437 or above, then this discussion does not apply to you. In 1997, we discovered that a number of mixers were failing in the field. The...
Page 555 Figure 20-5. A solenoid valve with yellow tape on the winding. The original (good) valves had white tape. The faulty valves as well as the good replacement valves have yellow tape. Using the LI-6400 20-29...
Page 556: Light Source / Sensor Problems
(Figure 20-6). Make sure it is not pushed too far in, as it can get into the fan and prevent the blades from turning. Thermistor Figure 20-6. The temperature sensor in 6400-02BÕs. 20-30 Using the LI-6400...
Page 557 Contact LI-COR. If the voltage is over 100V: (Normal)The problem may be a broken connec- tion within the light source itself. Contact LI-COR. Check the 26 pin D connector Make sure none of the pins have been pushed in or broken (Table 20-1 on page 20-45).
Page 558 PSC-388 or below. These units operate the light source with a lower power limit than do later units, and this can be changed by a simple factory modification. Contact LI-COR for details. 20-32...
Page 559: Chamber Problems
It should be about 63 Ohms. If it is 0 Ohms, you need a new motor. An alternate way to check this is to use the program Control Panel (see ÒCon- trol PanelÓ on page 21-10). Power the LI-6400 on, press escape to prevent OPEN from loading, access the Filer, select the...
Page 560 Erroneous Leaf Temperature Leaf temperature is referenced to block temperature. Therefore, if leaf tem- perature is reading a strange number, the first thing to check is the block tem- perature - maybe it is the problem. Otherwise... 20-34 Using the LI-6400...
Page 561: Finding Leaks
CO a few seconds later in both IRGAs. (This test is best done with the CO scrub ON, so that any of your breath that makes it into the normal air inlet will be scrubbed) Using the LI-6400 20-35...
Page 562 Orientation ¥ If the console sitting on its side, rather than sitting upright, a gap can occur along the length of the chemical tube at the top, creating a channel with re- duced CO removal. 20-36 Using the LI-6400...
Page 563 The clamp ring leaves a mark on the end of the hose; if this mark is 1/4Ó from the end, the hose was inserted correctly. Actually, if it does rotate freely, it could be leaking. Using the LI-6400 20-37...
Page 564 Check the divider assembly screws for tightness. Be careful, as they are small (2-56 thread) and can break. If you dis- assemble the divider to check the 8 internal O-rings (2 for each flow restric- 20-38 Using the LI-6400...
Page 565: Soil Chamber Problems
Figure 20-11. Schematic representation of the LI-6400Õs flow divider, that partitions flow to the sample and reference cells of the IRGA.
Page 566 If this fixes the problem, then look for a flow blockage, probably in the narrow how barb (#9 in Figure 20-12) inside the soil chamber. (In late June 1998, we changed from a narrow hose barb to a normal one, to prevent this from happening.) 20-40 Using the LI-6400...
Page 567 Troubleshooting Soil Chamber Problems Figure 20-12. Exploded view of the 6400-09 Soil Flux Chamber. Using the LI-6400 20-41...
Page 568: Useful Information
Figure 20-13. The diagnostic display map for New Measurements mode. The quantities in levels a, c, d, f, and j are common system variables, also found in the standard display list. Levels b, e, and g contain the raw signals (mV) for the sensors. 20-42 Using the LI-6400...
Page 569 OK). User Channel Voltages The spare analog input channels are shown in level i. These will show 0 mV if they have not been enabled via the ÔUserChan=Õ configuration command. Using the LI-6400 20-43...
Page 570 Troubleshooting Useful Information System Flow Schematic Figure 20-14 provides a schematic of the flow components of the LI-6400. 20-44 Using the LI-6400...
Page 571 Circ fan - Tleaf +10V Signal Gnd Power Gnd PAROut PARIn 4, 5 10, 23 TEC- 2, 3 9, 22 +12V TEC Fan Lamp+ Warning: voltages can exceed 100V Lamp- Lamp Fan a.TEC stands for thermoelectric cooler. Using the LI-6400 20-45...
Page 572 Troubleshooting Useful Information 20-46 Using the LI-6400...
Page 573 TILITY ROGRAMS ÒBoardsOffÓ 21-10 ÒBoardsOnÓ 21-10 ÒControl PanelÓ 21-10 ÒENERGYBALÓ 21-12 ÒGeopotentialÓ 21-16 ÒGraphics CaptureÓ 21-16 ÒGraphics RestoreÓ 21-17 ÒGraphit UtilityÓ 21-17 ÒNested Directory CopyÓ 21-18 ÒSETCLOCKÓ 21-18 ÒSETCOMMÓ 21-19 ÒSimple TerminalÓ 21-19 ÒVerify CalibrationÓ 21-20 Using the LI-6400 21-1...
Page 574 Diagnostics and Utilities This chapter documents the diagnostics and utility programs that are available on the LI-6400. Diagnostics & Tests Menu These programs are found in the Diagnostics and Tests Menu, accessed via OPENÕs Welcome Menu. OPEN need not be running for these to work, un- less otherwise stated.
Page 575 Any file that has pairs of numbers that can be interpreted as set point and wait time can be used, and the file is selected using the Standard File dialog. Once the input data is established, you are prompted to prepare the chemical tubes. Using the LI-6400 21-3...
Page 576 When the test is over, the results are shown. After viewing the results, press Mixer Test Results SetPt time ppm range status ===== ==== ==== ===== ===== 1000 47 310 0.15 5000 90 1920 10.2 escape. You are given the option of storing the results. 21-4 Using the LI-6400...
Page 577 ÒDAC StatusÓ The DAC Status program presents the state of the 20 D/A convertors on the LI-6400. Most of the channels are controlled by OPEN, but a 6 are available for the user. See Analog Output Channels on page 26-23.
Page 578 Diagnostics and Utilities Diagnostics & Tests Menu ÒDigital StatusÓ The Digital Status program presents the state of the LI-6400Õs digital I/O ports. P:01234567 status direction 0:10110011 [in OUT] 1:10111111 out] 2:1111 out] 3:1110 [in OUT] 4:00000000 [OUT] The display is live, so a change in one of the digital inputs will show up on the screen within a second or two.
Page 579 Figure 21-2. The Match Valve manual control program. The status line indicates where the valve should be, not necessarily where it ac- tually is. ÒPressure SensorÓ The pressure sensor test program merely runs the program ÒGeopotentialÓ on page 21-16. Using the LI-6400 21-7...
Page 580 Figure 21-3). You will be given an opportunity to store the list in a file. Store this ? (Y/N) Pressing Y will bring up the standard file dialog. The default name is Ò /us- Ó. er/SnapShot Data 21-8 Using the LI-6400...
Page 581 -107 Remark8 " " -32 BLC_mol 2.84 -108 Remark18 " " -33 AREA_cm2 6 -109 Remark38 " " -34 STMRATIO 1 Figure 21-3. Sample data from the ÒSys & User Variable SnapshotÓ program, shown in two columns. Using the LI-6400 21-9...
Page 582 IRGA board. OK ? (Y/N) ÒControl PanelÓ This program allows direct access to most of the analog and digital outputs of the LI-6400 (Figure 21-4). The complete list is presented in Table 21-3. ÒonÓ ÒoffÓ Digital Change all...
Page 583 Analog outputs available on the 37 pin connector. LPL ad- Analog Output: Pin 9 (10) dress shown in (). See Analog Output Channels on page Analog Output: Pin 29 (17) 26-23. Analog Output: Pin 11 (18) Analog Output: Pin 30 (19) Using the LI-6400 21-11...
Page 584 2 (this assumes that the leaf area used in the transpira- tion rate was a one-sided value). For more information on how the LI-6400 uses boundary layer conductances, see Boundary Layer Variables on page 14-17. Enter: P_kPa vap_kPa Trans_mmol Tair 90.73 1.45 13.7 24.97...
Page 585 = EBIterate(&EBEnergyBal, tleaf) blc_mol = /* 0.5 * */ _EBtrans_mol * _EBp_kPa / (EBSatVap(tleaf) - _EBvap_kPa) RETURN(tleaf, blc_mol) EBIterate /* &fct, FirstGuessT */ /* final T */ :FLOAT t1 :PTR fct 0 :FLOAT x 0 :FLOAT t2 Using the LI-6400 21-13...
Page 586 $ RETURN(0.61365 * EXP(17.502 * t / (240.97 + t))) EBLambdaFn /* t (C) */ /* latent heat af vapor, W/m2 */ 42.91 * 45060.0 + EBQDenom /* t (C) */ :FLOAT t RETURN (EBLambdaFn(t) + EBCpStuff(t) / EBVpd(t)) 21-14 Using the LI-6400...
Page 587 Diagnostics and Utilities /Sys/Utility Programs EBVpd /* t (C) */ /* guess */ EBSatVap _EBvap_kPa - Using the LI-6400 21-15...
Page 588 (see Storing and Retrieving Graphics Images on page 12-19). DIR: /User/images File: a-ci curve 3 Store Graphics to... "a-ci curve 1" "a-ci curve 2" ¨ ¨ ¨ ¨ Help CANCEL SELECT 21-16 Using the LI-6400...
Page 589 This program uses the Standard File Dialog (page 5-9) to select a file to be graphed. GraphIt (Chapter 12) is run for the selected file. DIR: /User Plot what file? "ivy data" "HalÕs experiment" "light curve" "light curve 2" ¨ ¨ ¨ ¨ Help CANCEL SELECT Using the LI-6400 21-17...
Page 590 - and ¯. Press Set (f5) to implement your changes, or Cancel (f4) to abandon them. Set Date & Time Sat Mar 14 1998 10:31:34 Use Arrow Keys Cancel 21-18 Using the LI-6400...
Page 591 In file capture mode, the destination file is selected using the Standard File Dialog. While data is being captured, the display will show only a byte count of captured data, not the actual data. Bytes Captured ¨ ¨ ¨ ¨ Config StopCpt Quit Using the LI-6400 21-19...
Page 592 CalCO2= 0.21732 2.1807E-05 1.9303E-08 -3.2863E-12 3.272E-16 CalH2O= 0.0063802 1.9083E-06 -2.4303E-11 CalZero= -4.0 -2.3 CalFlow= 0.35307 CalPress= 88.522 0.005458 CalParGaAs= 0.77 // GA-103 20 Jan 1995 CalParOut= 5.78 // Q13436 27 Aug 1990 ThisUnit= "PSC-0103" Serviced= "9 Jan 1995" 21-20 Using the LI-6400...
Page 593 Part VI Programming...
Page 595 Programming with LPL An introduction to the LI-6400Õs programming language LPL 22-2 VERVIEW OF A Simple Example 22-3 The View From the Stack 22-4 22-7 AKING BJECTS Syntax 22-7 Legal Names 22-8 Naming Convention 22-8 Numerical Objects 22-8 Numerical Arrays 22-9...
Page 596: Overview Of Lpl
LPL Operating system has been ported. LPL itself is platform independent, which means that LPL programs can be developed and tested on a DOS computer, and run on the LI-6400 or a Macintosh without modification. LPL provides control over a range of hardware, from keyboards and displays, to A/D converters and digital I/O lines.
Page 597 This creates two floating point variables for storing the numbers to be aver- aged. These variables are given the names x and y, with initial values of zero. Following that is a function declaration (:FCT), used to declare a series of ex- ecutable steps. Using the LI-6400 22-3...
Page 598 First, the prompting stringÕs address is pushed onto the stack, and the PRINT pops it back off. The Stack Operation 1. Stack is empty: 2. "Enter 2 ..." Address of "Enter 2..." 3. PRINT 22-4 Using the LI-6400...
Page 599 ENTER to see if the user in fact entered any values, or enough values, (or even too many values), but we didnÕt. At the very least we should have dis- posed of this 2 with a DROP, which drops the top entry from the stack. Using the LI-6400 22-5...
Page 600 This is easy. First, we pop up the standard ÒPress Any KeyÓ message: The Stack Operation 17. "Press Any Key" Address of ÒPress...Ó 18. PRINT Then we wait until the user presses something (weÕll assume the user presses 22-6 Using the LI-6400...
Page 601: Making Objects
Syntax To declare any of the objects listed in Table 22-1, use a colon followed by the object type. For example, the following segment of an LPL program :LONG secs 0 thisTime 0 Using the LI-6400 22-7...
Page 602 Numerical Objects Numeric objects (CHAR, INT, LONG, FLOAT, and DOUBLE) are initial- ized by following the objectÕs name with the initial value. In the case of inte- 22-8 Using the LI-6400...
Page 603 (as in def[] above), the size comes from the number of items in the initialization string. The initializing sequence for arrays can have fewer items than the declared size. If there are more initializing items than the declared Using the LI-6400 22-9...
Page 604 Character arrays can also be initialized with a combination of characters and numeric values by using escape sequences. For example, suppose you wish to include double quotes within the string. Knowing that the decimal equiva- lent of the double quote character is 34, one can write 22-10 Using the LI-6400...
Page 605 Three digits making a number in the range 0É255 (e.g. \10 \255). ¥ A hex value An x or X, followed by up to two hexidecimal digits (0ÉF) (e.g. \x0d \xff) another back slash \ ¥ (e.g. \\) Using the LI-6400 22-11...
Page 606: Functions
The stack can be thought of as a list of objects, and as new items are added to the list, they are added to the top, pushing all other items down. As items are removed from the list, they are also removed from the top. Many of the built- 22-12 Using the LI-6400...
Page 607 Pictori- ally, the stack operations might look like this: The Stack Operation Stack is empty: Push 17.83 17.83 Push 2.5 17.83 Do the + 20.33 Push address 20.33 9057:0018 Do the = Using the LI-6400 22-13...
Page 608 (spaces, tabs, or end of line characters). With in-fix, this is not necessary. Pa- renthesis, square brackets, and math operators (+,-,/,*,^) can serve as delim- iters between items. Thus, the post-fix sequence 1.23 x + &y = can be written with no spaces as y=x*1.23 22-14 Using the LI-6400...
Page 609 The 0 is popped from the stack. DonÕt confuse normal LPL declarations with local declarations. The :INT that appears inside a :FCT definition serves a slightly different purpose, and has a different syntax, than an :INT that appears outside. Using the LI-6400 22-15...
Page 610 The sequence :CHAR {10 13 32} :PTR whiteSpace illustrates a method of ÒnamingÓ an unnamed local array. In this case, a 3 el- ement CHAR array is created by the first declaration, and itÕs address is put 22-16 Using the LI-6400...
Page 611: Pointers
0 for the destination variable name. We have seen pointers used already in Figure 22-6 on page 22-17. But point- ers arenÕt restricted to being local objects. They can be declared out of func- Using the LI-6400 22-17...
Page 612 Pointer array declarations can also be nested. For example, theList[] { :PTR :PTR { :INT[5] labelOne } :PTR { :INT[5] labelTwo } The PTR array has two elements, each one of which is an (unnamed) theList 22-18 Using the LI-6400...
Page 613 PTRs and PTR arrays have many uses in LPL programs. Figure 22-9 illus- trates the use of PTRs to handle function parameters. In this program, the function named expects to find three items on the stack waiting for it. Using the LI-6400 22-19...
Page 614 Another use of PTRs is for handling LPL objects that are not declarable. For example, when a file is opened, a path to the file is created and put on the stack. Since there is no declarable object in LPL to handle the path, we assign 22-20 Using the LI-6400...
Page 615 3 elements. Main goes through the array calling with each receives 1 parameter, which it assumes is a PTR element found in array with 3 elements: 1) the label, 2) the symbol, and 3) the function to exe- cute. Using the LI-6400 22-21...
Page 616: Public And Static
To declare that an object is public instead of private, precede the object name by the keyword PUB (or pub). Figure 22-13 illustrates the use of a public variable. 22-22 Using the LI-6400...
Page 617 All of the functions and variables that GenPlot might use are STATIC, to pre- vent name conflicts with any application that might use this file. Using the LI-6400 22-23...
Page 618 , because the latter was defined as stat- /sys/lib/plotter There is also a :STATIC directive. This saves having to include numerous STATIC keywords. We could rewrite the library file described above as shown in Figure 22-15. 22-24 Using the LI-6400...
Page 619: Compiler Directives
When on, all subsequently defined objects in the current file are STATIC. :IFNDEF name If the name is not defined, ok. Otherwise, skip to the ENDIF :IFDEF name If the name is defined, ok. Otherwise, skip to the ENDIF :ENDIF Used with :IFNDEF and :IFDEF Using the LI-6400 22-25...
Page 620 , which is de- “/sys/utility/geopotential” signed to run either by itself, or on top of the application OPEN on the LI-6400 (see ÒGeopotentialÓ on page 21-16). This is accomplished by use of the :INCLUDE directive, as illustrated in Figure 22-16. Geopotential Heights...
Page 621 FlowBdOn main :FCT CLEAR "This program will power OFF the flow board and the IRGA board. OK ? (Y/N)" PRINT GETKEY UPC == IF 0 0x0301 DIOSET 0 0x0302 DIOSET THEN :ENDIF Figure 22-17. BoardsOff listing Using the LI-6400 22-27...
Page 622 Programming with LPL Compiler Directives 22-28 Using the LI-6400...
Page 623 23-46 TACK ONTROL YSTEM Basic Stack Manipulation 23-3 Hierarchical Structure 23-47 Stack Size, Status, Errors 23-3 Working With Files 23-48 The Trash Directory 23-49 The LI-6400 File System 23-49 23-4 ONDITIONALS AND OOPS 23-51 ENUS AND DITORS 23-6 RRAY PERATIONS...
Page 624: Stack Control
STKREADY Returns number of items on the stack STKRESIZE Change the stack size STKSHARE Controls stack sharing between a parent and child applications STKSIZE Returns stack size SWAP Exchange the top two items on the stack 23-2 Using the LI-6400...
Page 625 (such as divide by zero), and stack errors (such as pushing too many items onto the stack). The LPL operating system can be made to report either of these types of errors, or ignore them, by use of the keywords MATHERR and STKCHECK. Using the LI-6400 23-3...
Page 626: Conditionals And Loops
Exit the current function. LPL provides two basic flow control tools for program execution within a function: the IFÉELSEÉTHEN structure and the LOOPÉENDLOOP structure. Either of these structures can be nested up to 20 deep. Figure 23-1 23-4 Using the LI-6400...
Page 627 '\f' == "<ctrl+l>" BREAK THEN k "Ascii '%c' " ENDLOOP ELSE k "NonAscii, code = %04x" THEN PRINT CLREOL /* Increment the counter. */ &counter 1 + DROP ENDLOOP Figure 23-1. IFÉELSEÉTHEN and LOOPÉENDLOOP illustrated. Using the LI-6400 23-5...
Page 628: Array Operations
Also, all of the mathematical transform keywords (listed in Math Functions on page 23-18) can also be applied to arrays. Array SIZE and READY values All arrays share a common feature - they maintain header information that tells the following: 23-6 Using the LI-6400...
Page 629 Ò 1234567890 Ó, but the sequence line '"ABC" line = changes the first three characters to and sets the ready length to 3. Run- ning the program illustrated in Figure 23-2 will produce the following output: Using the LI-6400 23-7...
Page 630 Some I/O tools (I/O Programming on page 23-39) can be used on arrays: ENTER will append data onto any array, while arrays of type CHAR can be made into Paths, allowing PRINT to be used to append data to them. 23-8 Using the LI-6400...
Page 631 VAL pops that address off the stack, looks up the numeric value of that INT, and pushes that value onto the stack. In Figure 23-4, the functions are functionally PrintArray1 PrintArray2 equivalent - they both print out the contents of an integer array whose address Using the LI-6400 23-9...
Page 632 That is, create it when you need it, then dispose of it when youÕre done, and recover that memory. Such arrays are created by the application (MAKE), used, then disposed of (FREE). Figure 23-5 contains some snip- 23-10 Using the LI-6400...
Page 633 (using FREE) before the function is done. If we wanted to use the new array after the creating function terminates, we would want to be sure to assign a global PTR to the arrayÕs address. Figure 23-6 illustrates how to do this. Using the LI-6400 23-11...
Page 634 The applicationÕs data segment. e.g. :INT x[5] {1 2 3 } Local The local stack. (ItÕs size is set by the :LO- e.g. :FCT x { "hello" } CAL directive) Allocated with MAKE or Free memory. MAKE4 23-12 Using the LI-6400...
Page 635 It turns out that VAL has the 2nd meaning. But how can meaning 1) be achieved, namely getting the address of x on the stack, to change itÕs value, for example? For that we use PVAL. Figure 23-7 illustrates. Using the LI-6400 23-13...
Page 636 Note that intermediate pointers, if any, are hidden. If we change the declara- tions in Figure 23-7 to be x 50 :INT y 100 :PTR /* Add a pointer -> x */ z[2] {p y} /* 1st element is p */ 23-14 Using the LI-6400...
Page 637 Table 23-5. Explanations of the FIND and PFIND in Figure 23-8. Statement Meaning p3 p2 FIND Does {&a &p1 &b} contain {&p1 &b}? Yes, at 2 p3 p1 FIND Does {&a &p1 &b} contain {&c &a}? Using the LI-6400 23-15...
Page 638 3, since this string is contained in the second element of an array pointed at by the 3rd element of If this is not complicated enough, further subscripting is supported by FIND, allowing statements such as pArray 1 4 3 target FIND 23-16 Using the LI-6400...
Page 639 3rd element of arrays pointed at by the 4th element of ar- rays pointed at by the 1st element of the arrays pointed at by the elements con- tained in . Up to 10 (no kidding!) subscripts may thus be specified. pArray Using the LI-6400 23-17...
Page 640: Math Functions
ASIN Arcsine ATAN Arctangent (result -90 to +90) ATAN2 Arctangent (result -180 to +180) BINAND Binary and BINCMP Binary complement BINEOR Binary exclusive or BINIOR Binary inclusive or BSHIFT Binary shift left or right Change sign 23-18 Using the LI-6400...
Page 641 Use radians for trig functions RANDOMIZE Randomizes the seed for the random generator REGRESS Compute coefficients for a polynomial Random float between 0 and 1 Sine SQRT Square root Sum a vector Tangent Convert to upper case <> not equal? Using the LI-6400 23-19...
Page 642 Single Object Transform executes. We illustrate the pos- sible before and after stack status by the following shorthand: 23-20 Using the LI-6400...
Page 643 The target of a Two Object Transform is the 2nd item on the stack, not the top item on the stack. The target can be a ÒNumÓ, ÒNAddrÓ, or an ÒArrayÓ, just like with Single Object Transforms. The object Using the LI-6400 23-21...
Page 644 Table 23-7 summarizes the combinations Table 23-7. Two Object Transform combinations Target Top-of-Stack Object Object NAddr Array Resulting value left on stack Transform performed multiple times, once for each array item. Resulting value left on stack. 23-22 Using the LI-6400...
Page 645: Display Control
Gets display text, attribute, and window info GETTEXT Gets text from a rectangle, (display coords). GETWINDOW Get current window info (rectangle, cursor, etc.) MOVETEXT Move a rectangle to a new location (lcd coords) POSXY Positions the cursor (window coords). Using the LI-6400 23-23...
Page 646 Figure 23-11. Illustration of DISPHEIGHT and DISPWIDTH. Text Windows LPL supports windowing the display. A text window is simply a rectangle on the display in which text operations are confined. There are two types of units 23-24 Using the LI-6400...
Page 647 The WINDOW keyword creates a window on the display; the window can be framed by a single or double line border with up to two labels on it, or no bor- der at all. Figure 23-13 illustrates. Using the LI-6400 23-25...
Page 648 ItÕs counterpart, PUTWIN- DOW, will immediately implement a windowÕs scaling, attribute, and cursor location. Figure 23-15 creates two windows with differing attributes, then switches between them as it prints what you type. 23-26 Using the LI-6400...
Page 649 If you run the program illustrated in Figure 23-14 and type Òabcdefghijklm- nopÓ, it will appear as shown above, with every character going into alternat- ing windows. (The inverted square in the left hand window is the full cell cursor for that window.) Using the LI-6400 23-27...
Page 650 _TEXT functions, while GETDISP allocates space, and PUTDISP disposes of it. Therefore, GET- DISP and PUTDISP should always occur in pairs, with GETDISP first, and you cannot PUTDISP twice using the same allocated space. 23-28 Using the LI-6400...
Page 651: Keyboard Control
Put back a keystroke Keyboard Behavior When you press a key on the LI-6400, there may or may not be a beep (con- trolled by KBDCLICK - default is no beep). If you hold the key down, there will be a slight delay (controlled by KBDDELAY - default 500 ms) followed by regular repetition (time interval controlled by KBDREPEAT - default 50 ms).
Page 652 0x63 pgdn _PgDn 0x22 0x64 _UpArrow 0x26 0x65 ¯ _DnArrow 0x28 0x66 ¬ _LeftArrow 0x25 0x67 ® _RightArrow 0x27 0x68 ¬ _Back 0x08 0x69 escape _Esc 0x1b 0x6a enter _Enter 0x0d 0x6b 0x2d 0x6c 0x2e 0x6d 23-30 Using the LI-6400...
Page 653: Clock
Get current date and time in seconds SECS2TD Convert seconds to time and date info SETTDS Set current date and time using seconds TD2SECS Convert time and date info to seconds TIME Convert seconds to hour, minute, second Using the LI-6400 23-31...
Page 654 Real Time Time in LPL is measured from some base time that is platform specific. In the LI-6400, the base time is 1 Jan 1989. A quick way to find the time base for any particular platform is the LPL se-...
Page 655: Event Handling
These events are not in general predictable - exactly when is the user going to press a key, for example - so we need a method to Òcontin- ually testÓ for the desired event, and if it has occurred, handle it. Using the LI-6400 23-33...
Page 656 &HandleKeys ONKBD &HandleClock ONTIC &HandleA/D 1 ONA2D IDLE HandleKeys { GETKEY ... } HandleClock {...} HandleA/D {...} Figure 23-16. Programming for events in LPL. We register the functions to be called using the ON... LPL keywords. 23-34 Using the LI-6400...
Page 657 1 second intervals ONTIC User defined intervals ONCYCLE A/D Readings are ready ONA2D A certain characterÕs arrival in the Comm port ONCOMM To illustrate, consider the AutoProgram , whose listing is “Remote Control” shown in Figure 23-17. Using the LI-6400 23-35...
Page 658 (LPMeasure), and incoming data from the comm port is collected in a buffer (COMM buff XFER). Ev- ery time a line feed is received, however, that data is compiled and executed (FCT GotIt). This allows a re- mote device to control the LI-6400. The sequence 10 &GotIt ONCOMM sets this up. 23-36...
Page 659: The Function Keys
Even though the specific platform on which LPL is installed has a fixed num- ber of physical function keys (the LI-6400 has 5, for example), you can define any number of function keys in LPL; the user can only see them in groups of 5 (or whatever) at a time, but the labels key on the keyboard (or the equiva- lent) will change the displayed group.
Page 660 If another IDLE is encountered, do the old key definitions stay active? When the IDLE is done, do the old key defi- nitions get restored? All of this is controlled by one flag set with the keyword GLOBALKEYS. 23-38 Using the LI-6400...
Page 661: I/O Programming
Get a byte from a path GETCONVERTIN Get current incoming filters GETCONVERTOUT Get current outgoing filters GETDFCIN Get current default file convertin GETDFCOUT Get current default file convertout IOCLEAR Clear path error IOERR Get latest path error Using the LI-6400 23-39...
Page 662 Set default file convertout SETEMPTY Set empty (reading) pointer for a path SETFILL Set fill (writing) pointer for a path UNGETCH Character put back function for a path XFER Send data from one path to another 23-40 Using the LI-6400...
Page 663 OPEN_FILE OPEN_FILE_ASK A simple example of using Paths is shown in Figure 23-19, which writes a line of text to a file. Files are treated more thoroughly in the section File Sys- tem on page 23-46. Using the LI-6400 23-41...
Page 664 A very powerful feature of paths is the character filtering capability that they have. Filters can be independently enabled for reading data from a path, and for writing data to a path. Table 23-20 indicates the filters available for LPL paths. 23-42 Using the LI-6400...
Page 665 Note that filters can be chained together in any sequence. The keywords CONVERTIN and CONVERTOUT define the filtering (if any) for data in- flow and outflow for any path. GETCONVERTIN and GETCON- VERTOUT will return the current filter sequence for any path. Using the LI-6400 23-43...
Page 666 LPL program execution. For example, with an over- lapped XFER, a file can be sent out the comm port at the same time that mea- surements are being taken. As an example of data transfers, consider Figure 23-21, a simple terminal emulator program. 23-44 Using the LI-6400...
Page 667 IOCLEAR resets the error number for a path to 0 (no error). Table 23-21. I/O Error codes Error Number Condition No error Attempting to write to a full path Attempting to read from an empty path Attempting to move a pointer outside of a pathÕs limits Using the LI-6400 23-45...
Page 668: File System
Get write protect status of a file or directory FLIST Get a list of files and/or directories FMERGE Merge path and file names into file specifier FMOVE Move a file FPARSE Parse file specifier into path and file names FRENAME Rename a file 23-46 Using the LI-6400...
Page 669 Within each directory there may be files and/or more directories. An illustration of a file system containing three disks, named Dir A, Dir B, and Dir C is shown in Figure 23-22. Using the LI-6400 23-47...
Page 670 (I/O Pro- gramming on page 23-39). Files can be opened with various combinations of attributes: write access, read access, and write-append. Am example program is shown in Figure 23-23. 23-48 Using the LI-6400...
Page 671 DUP FTRASH FMOVE The LI-6400 File System On the LI-6400 platform, the file system uses flash memory, and is part of a general file system structure that includes all hardware devices (the keyboard, comm port, A/D converter, digital ports, etc.). In general, you neednÕt be con-...
Page 672 These underlying hardware names are the reason that on the LI-6400, one can have multiple disks with the same name. This is not a good thing to do inten- tionally, of course, but it can be done.
Page 673: Menus And Editors
Options available for STDMENU in- clude a menu bar (highlighted band that moves up and down with the cursor), what ascii keys cause exit, what non-ascii keys cause exit, and if/how to ad- just the cursor on exit. Using the LI-6400 23-51...
Page 674 We fix this prob- lem in Figure 23-25 by making a Path to the menu items, then after STD- MENU is finished (if the user pressed enter) we read in the selected line. 23-52 Using the LI-6400...
Page 675 The keyword STDLINE creates a borderless window from the current cursor position to the right edge of the current window, displays in this window the Text object to be edited, and lets the user edit the object. escape or enter ter- minate STDLINE. Using the LI-6400 23-53...
Page 676 This routine shows the makeup of OPENÕs display lines, and al- lows the user to edit them. An abbreviated listing of this routine is shown in Figure 23-27. Note the inclusion of the file , which contains “/Sys/Lib/CEDefs” useful tools for these operations. 23-54 Using the LI-6400...
Page 677 EDCLOSE menu CLOSE /* Write the initial contents of the menu to the path passed to this function. */ Figure 23-27. Partial listing of OPENÕs Display Editor, which uses a custom editor based on EDOPEN. Using the LI-6400 23-55...
Page 678: Graphics
Graphics pen absolute move (user units) GPGET Get a pixel (user units) GPLOT Executes move/draw data stored in a structure. GPPUT Put a pixel (user units) GRAPH Show / hide graphics display GRDRAW Graphics pen relative draw (user units) 23-56 Using the LI-6400...
Page 679 On the LI-6400, the graphics and text displays use the same LCD display, but this device has two separate modes of operation; text and graphics can be shown separately, or together.
Page 680 GWIGET. To scale a graphics window to user coordinates, use GSCALE. Its counterpart, GSCGET returns the current scaling parameters. Figure 23-28 illustrates the use of some of these graphics key words for scal- ing. 23-58 Using the LI-6400...
Page 681 GMOVE (go to a certain location without drawing) and GDRAW (draw from the present location to the given location). There are also a relative move and Using the LI-6400 23-59...
Page 682 GLSIZE returns the height and width of a label in pixels, which can be an aid to positioning it. Graphics Label Figure 23-29. GLORG locations for a graphics label relative to pen location. 23-60 Using the LI-6400...
Page 683 /* Make the arrays look full */ 100 4 n angle GMOVE SETREADY "DEGREES" GLABEL n cosine SETREADY Figure 23-30. Labelling in graphics mode. The program in Figure 23-30 produces a labelled cosine curve (Figure 23-31). Using the LI-6400 23-61...
Page 684 The possibilities are listed in Table 23-25. Table 23-25. Graphics Drawing Modes Mode Name Action default Draw or erase without checking existing graphics state. Invert, then Mode 0 The effects of the graphics drawing mode is illustrated in Figure 23-32. 23-62 Using the LI-6400...
Page 685 Example 2: The open rectangles and the lower labels are drawn first, using mode 0. The mode is changed to the indicated values, and the solid rectangles and upper labels are drawn. Figure 23-32. Illustration of drawing modes Using the LI-6400 23-63...
Page 686: Rs-232 Communications
Enter file exchange mode ONCOMM Incoming comm port interrupt (when a specified charac- ter arrives) The utility program (described on page 21-19) illus- “/Sys/Utility/SETCOMM” trates the use of . Its listing is shown in COMMSTATUS COMMCONFIG Figure 23-33. 23-64 Using the LI-6400...
Page 687 GETDISP :PTR hold commRect 2 1 "Baud Data Stop Parity" WINDOW cline COMMSTATUS cline STDLINE cline COMMCONFIG 1 "Bad Configuration!" MESSBOX THEN ELSE 1 "Config unchanged" MESSBOX THEN hold PUTDISP Figure 23-33. Listing of the program SETCOMM. Using the LI-6400 23-65...
Page 688: Analog Measurements
0, and the number of channels available is one of the three values obtained via AINUM. Thus, if there are 24 channels, they are addressed as 0 thru 23. A group, on the other hand, has no physical manifestation. A group is simply 23-66 Using the LI-6400...
Page 689 5) is also obtained via AINUM. To illustrate groups and channels, consider the main LI-6400 application, OPEN. The LI-6400 has a four gas analyzer signals (two CO and two H and about 12 other sensors, such a light sensors, thermistors, etc. We want readings for all of these sensors every, say, 1 second, and we want those read- ings to be an average over the prior 1 second.
Page 690 It turns out that the ÒwhenÓ is just as controlled as the ÒwhereÓ. Timing, which is what weÕre talking about here, is controlled by the groups. When a group is defined (AIGDEF), the following information is passed: 23-68 Using the LI-6400...
Page 691 A more elegant approach, however, rather than sitting around in a tight loop testing AIREADY, is to use ONA2D. This event command (see Event Handling on page 23-33) allows you to specify a function to call whenever readings become available. Using the LI-6400 23-69...
Page 692 An Example (At last, a complete example!) Figure 23-34 is not particularly useful, beyond illustrating proper technique. The program measures both light sensors on the LI-6400 at 1 second intervals, showing the values on the screen. Illustrate Analog Measurements Setup /* Open a structure.*/...
Page 693 4 channels are actually defined. In addition to channels 15 and 16, channels 0 and 1 also got defined. WhatÕs going on here? The A/D converter in the LI-6400 needs some reference measurements for ac- curacy. It must look at a true 0V signal now and again, and also a true 5.0 volt signal.
Page 694 LPL Topics Analog Measurements Table 23-28. LI-6400 Analog Input Channels Channel Channel Descriptions Variable Name In-chamber PAR sensor. aParInChan External PAR sensor aParOutChan Pressure sensor aPressChan aLostChan ÒLostÓ spare channel Sample cell air temp aTairChan Spare channel 1 aUser1Chan Spare channel 2...
Page 695: Analog Output Control (D/A)
The number of digital to analog converters is found from AONUM, and is 20 on the LI-6400. They are addressed starting at 0, so number 0 to 19. The range of each, and itÕs resolution is found using the AOMIN, AOMAX, and AORES functions.
Page 696 (analog output port number 2) is changed by 200 mV, either up or down. AOVAL is used to read the current value, and the change is added to it, and the new value set with AOSET. 23-74 Using the LI-6400...
Page 697: Digital I/O
Thus, port 2 pin 3 can be most conveniently referenced in hex as 0x0302. The sequence 0x0005 1 DIOSET would turn the lamp on, since that is port 0, pin 5 (Table 23-32). Using the LI-6400 23-75...
Page 698 PORT and DIOSETPORT. Thus, to set all pins on port 4 high, you could use the following sequence: 0xff 0xff 4 DIOSETPORT The first 0xff specifies the desired pattern of the 8 pins, and the second is a mask pattern. Table 23-32. LI-6400 digital port and pin assignments Pins Port Status Match Cham-...
Page 699 Digital I/O Digital Errors The LI-6400 runs a watch dog program that looks for problems in the digital output ports, and restores them to the way they should be if any are found. If this sort of thing happens (usually due to static electricity, for example), a counter is incremented.
Page 700: Application Tools
Strips token information from an application. SYSID Get the ID of the current application UNLINK Remove one or more modules from an application USES List cross reference information for an object XREF Outputs a cross reference for an application. 23-78 Using the LI-6400...
Page 701 LINK adds modules. In OPEN 3.0 and above, user defined equations are appended using this method. When changing ComputeLists, the old user de- fined module(s) are unlinked, and the new ones linked. Prior to OPEN 3.0, it was all done with COMPILE. Using the LI-6400 23-79...
Page 702 /sys/lib/stdshell main screen. <esc> quits 4 - /sys/lib/stdshell 3 - /sys/open/open 2 - /sys/open/start 1 - /sys/autost Figure 23-37. Picking the target application. Select /sys/open/start , whose listing is shown on Figure 3-55 on page 3-66. 23-80 Using the LI-6400...
Page 703 Id Space Space for names of objects :NAMES Data Segment Data segment information :DATA Code Segment Code segment information :CODE Total Wasted. Wasted space total. View the list of LPL keywords Press Z for the entire list. Using the LI-6400 23-81...
Page 704: Battery And Power
7V. returns the battery state (0, 1, or GETBATT 2 for ok, low, and critical). does what youÕd think it does, and POWEROFF is the equivalent of power off then back on. START 23-82 Using the LI-6400...
Page 705 LPL Reference Keyword Summary 24-2 YNTAX UMMARIES LPL Type Declarations 24-2 Compiler Declarations 24-8 24-11 EFINITIONS Single Value Transforms 24-13 Two Value Transforms 24-13 Two Value Logical Transforms 24-15 24-16 EFERENCE Using the LI-6400 24-1...
Page 706: Syntax Summaries
Õ Õ Item Description Range name valid LPL name size integer 1É32767 decimal Any combination of the chars 0É9 hexidecimal Any combination of 0É9 plus AÉF character Any character string Delimiter char is first encountered 24-2 Using the LI-6400...
Page 707 LPL Reference Syntax Summaries High precision floating point declaration :DOUBLE :DOUBLE name value value name STATIC name size value I t e m Description Range name valid LPL name size integer 1É32767 value integer or floating point Using the LI-6400 24-3...
Page 708 Note 1 This operation consumes an item from the stack. Note 2 This operation consumes nothing from the stack, and leaves the address (of the unnamed array on the stack. 24-4 Using the LI-6400...
Page 709 Short integer declaration :INT :INT name value value name STATIC name size value Value: decimal 0x hexidecimal character Õ Õ Item Description Range name valid LPL name size integer 1É32767 decimal hexidecimal Using the LI-6400 24-5...
Page 710 Description Range character Long integer declaration :LONG :LONG name value value name STATIC name size value Value: decimal 0x hexidecimal character Õ Õ Item Description Range name valid LPL name size integer 1É32767 decimal hexidecimal character 24-6 Using the LI-6400...
Page 711 " string " array :CHAR initialization :INT :LONG :FLOAT function definition :DOUBLE :FCT :PTR initialization Item Description Range name, object name valid LPL name size integer 1É32767 array initialization specify each array element function definition Using the LI-6400 24-7...
Page 712 Declares data space for this application :DATA :DATA Bytes Item Description Range Bytes Creates a data segment. 1 to 64000 :IFDEF Compiler logic :IFNDEF :IFDEF Directive :ENDIF :IFNDEF Item Description Range Directive LPL compiler directive or decla- ration 24-8 Using the LI-6400...
Page 713 The number of bytes to make a name segment. 1 to 64000 Multiple segments are allowed. Print a message to the display :PRINT :PRINT String Item Description Range String The first non-whitespace character following the :PRINT is used as the string delimiter. Using the LI-6400 24-9...
Page 714 Declare number of private objects :STATCOUNT :STATCOUNT count Item Description Range count The number of static objects that this 1 to 4096 module defines. 24-10 Using the LI-6400...
Page 715: Definitions
0 :PTR tempHdr /* Create the ptr */ $ tempHdr = SUBSET(array, first, last) /* Do SUBSET */ To describe what each stack item is, we use the conventions and symbols shown in Table 24-1. Using the LI-6400 24-11...
Page 716 ÕnameÕ is arbitrary, and represents how the parameter is used by the keyword. b.Note that window must have a size of at least 4, since elements 1 through 4 are taken to be left, top, right, and bottom respectively. 24-12 Using the LI-6400...
Page 717 NObj targetVal ,<Num b | NObj c | Array d > Final: NObj targetVal -or- Initial: Array targetArray , <Num b | NObj c | Array d > Final: Array targetArray Figure 24-2. Two value transform stack requirements Using the LI-6400 24-13...
Page 718 If xArray = (1 2 3 4), and yArray = (10 20 30), then xArray = (11 22 33 4). If yArray = (10 20 30 40 50), then xArray = (11 22 33 44). Address of xArray always left on stack. 24-14 Using the LI-6400...
Page 719 5.5, otherwise it sets it to 0. 0 arr1 == Puts 0 on stack if no element of arr1 is 0, otherwise 1. 1 arr1 == Puts 1 on stack if every element of arr1 is 1, otherwise 0. Using the LI-6400 24-15...
Page 720: The Reference
Logical negative compare <> Initial / Final: (see T w o V a l u e L o g i c a l T r a n s f o r m s on page 24-15) 24-16 Using the LI-6400...
Page 721 The ground channel (0ÉNg) group The group to which this measurement belongs. This group must have previously been defined with AIGDEF. chan The signal channel (0ÉNs) The A/D structure returned by a prior call to AIOPEN. Using the LI-6400 24-17...
Page 722 The A/D structure returned by a prior call to AIOPEN. numRead The actual number sets of readings read. Free A/D space AIFREE Initial: Final: Deallocates internal memory structures used for A/D measurements. See Analog Measurements on page 23-66. 24-18 Using the LI-6400...
Page 723 Pause the A/D operation AISTOP Initial: Final: This is a good idea during times that the user will obviously not be interested in getting new numbers, as it frees up the processor for more important things.To restart, use AISTART Using the LI-6400 24-19...
Page 724 Initial / Final: (see Two Value Logical Transforms on page 24-15) Related Keywords: Returns max signal that can be put on a D/A channel AOMAX Initial: Num chanNum (0..AONUM-1) Final: Double mV Related Keywords: AOSET AORES AOMIN 24-20 Using the LI-6400...
Page 725 Provides a path to arguments (if any) for that application. ARGS Initial: Final: Addr path This path is used by the Filer for itÕs launched applications, such as file copy, file move, etc. Related Keywords: COMM Using the LI-6400 24-21...
Page 726 Initial / Final: (See T w o V a l u e L o g i c a l T r a n s f o r m s on page 24-15.) Table 24-10. BINAND Truth Table Related Keywords: BINCMP BINEOR BINIOR BSHIFT 24-22 Using the LI-6400...
Page 727 BSHIFT Binary inclusive or BINIOR Computes an inclusive or for two LONGs. If a value is not LONG, an internal con- version is done first. Table 24-13. BINIOR Truth Table Related Keywords: BINAND BINCMP BINEOR BSHIFT Using the LI-6400 24-23...
Page 728 The address can get there via , or the & operator, or ing from a PTR array. COMPILE PICK Returns the code value for type CHAR. CHAR Initial: Final: LONG typeVal Related Keywords: LONG FLOAT DOUBLE MAKE, MAKE4 24-24 Using the LI-6400...
Page 729 RS-232 Communications COMM_ Set a break condition on the Comm port transmit line. COMMBREAK Initial: Final: Configure the Comm port COMMCONFIG Initial: Text config Final: Long errCode (0=ok, 1=failed) The string config should contain Using the LI-6400 24-25...
Page 730 Array arr1 , Array arr2 Final: LONG result (1=same, 0=different) Arrays are the same if 1) they are the same type, 2) they have the same ready value, 3) their contents (elements 1ÉREADY) are the same. 24-26 Using the LI-6400...
Page 731 Converts seconds since base time to a time and date string. CTIME Initial: [Text dest (default is LCD)], Num tdSecs Final: The format used is Fri Apr 7 1995 11:22:33. See Real Time on page 23-32. Related Keywords: GETTDS DATE TIME Using the LI-6400 24-27...
Page 732 /dev/flashdisk1. This name is needed when reading or writing disk images. on page 23-75 For a discussion of the keywords, see Digital I/O DIO_ Counts since the last inquiry DIOCOUNT Initial: Num portPin (e.g. 0x0301) Final: Long counts to define a counter. DIODEFCOUNT 24-28 Using the LI-6400...
Page 733 Initial: Num port Final: Long pins How many ports are available DIONPORTS Initial: Final: Long numPorts Set a portPin high or low DIOSET Initial: Num state (1=high, 0=low), Num portPin (e.g. 0x0302) Final: Related Keywords: DIOGET Using the LI-6400 24-29...
Page 734 Initial: Text newName Final: Long error (0=ok, -1=failed) Note that you cannot create a directory in the root on the LI-6400, since items in the root are determined by hardware. Force an update of the flash file system DIRSAVE Initial: Final: This function is generally not required.
Page 735 Note: All files and directories on the disk taken off-line are erased! Related Keywords: DSKONLINE DSKPACK Bring the off-line disk on-line, and name it DSKONLINE Initial: Text name Final: Long error ( 0=ok, 1=failed) Related Keywords: DSKOFFLINE DSKISSWAP Using the LI-6400 24-31...
Page 736 Delete the character at the cursor 0x11 Split line insert 0x14 Delete the current line 0x12 Delete the char behind the cursor 0x15 Clear to the end of the line 0x20 Insert mode on 0x24 Caps lock off 24-32 Using the LI-6400...
Page 737 Initial: Path text , EditInfoPtr edInfo Final: interprets nonascii key codes; doesnÕt. EDKEY EDWRITE Create a custom edit structure. EDOPEN Initial: Text objectText Final: [EditInfo edInfo ], Long 0 -or- Final: Long 1 Related Keywords: EDCLOSE Using the LI-6400 24-33...
Page 738 ..., Addr var1 , CArray format , [PATH source ] Final: LONG numRead Default source is KBD. format is explained below. The number of addresses on the stack should correspond to elements in the format string. numRead is the count of ob- 24-34 Using the LI-6400...
Page 739 Table 24-19. Repeat Format Codes Rep Code Append items until..n are appended ...until a newline (Õ\nÕ) character is reached..until the array is full. Table 24-20. Format Type Codes for ENTER Type Description d or D Integer Using the LI-6400 24-35...
Page 740 3 hex and 1 binary value, and store them as 4 in- teger variables (a, b, c, and d), we would write &d &c &b &a "%rf %rf %rf %r1" file ENTER 24-36 Using the LI-6400...
Page 741 Related Keywords: DIRERASE Return the last-modified date for a file or directory FGETTDS Initial: Text filename Final: Long secsSinceBaseTime To interpret secsSinceBaseTime, see Real Time on page 23-32. Related Keywords: FSETTDS FTYPE TIME DATE CTIME SECS2TD Using the LI-6400 24-37...
Page 742 Final: If sysID is 0, it specifies the current application. The tokens address can be an LPL pointer, or else a LONG. ownerDest will contain the name of the module in which the token is defined. 24-38 Using the LI-6400...
Page 743 Break a file specifier into path and file name FPARSE Initial: Text pathDest , Text nameDest , Text fullSpecifier Final: If fullSpecifier doesnÕt start with a / or \, the current working directory is taken into Using the LI-6400 24-39...
Page 744 If dest is not specified, is assumed. Update a text file FUPDATE Initial: Path contents , Text filename Final: Long error (1=OK, -1=failed) LI-6400 Note: If contents matches the actual current contents of the file, nothing is 24-40 Using the LI-6400...
Page 745 Related Keywords: GWINDOW Draws to a location GDRAW Initial: Point userUnits Final: Related Keywords: GSCALE GMOVE GRDRAW Returns state of the alpha display GETALPHA Initial: Final: Long 1 (visible) or 0 (off) Related Keywords: ALPHA GRAPH GETGRAPH Using the LI-6400 24-41...
Page 746 Returns the next key code from the keyboard queue GETKEY Initial: Final: LONG keyCode See Keyboard Codes on page 23-29 for interpreting keyCode. Key codes can be placed in the queue by any of the following means: by either the user typing on the 24-42 Using the LI-6400...
Page 747 Rect area , Text dest , [Num attr (ignored)] Final: area is in absolute display coordinates. dest should be large enough to allow for 1 byte per area element. If not, excess characters are ignored. Related Keywords: . To save text+attribute, use PUTTEXT GETDISP Using the LI-6400 24-43...
Page 748 Figure 24-4. Relation between location in the 5x5 image and bits in the source Long. In the example on the left, the value 0x8A88A880 results in a 5x5 X image. Related Keywords: GSCALE GMODE GPLOT GLABEL 24-44 Using the LI-6400...
Page 749 Specify the origin position of a graphics label GLORG Initial: Num value (1 through 9) Final: The labelÕs location will be relative to the current pen location, as shown by Graphics Label Related Keywords: GLABEL GLSIZE Using the LI-6400 24-45...
Page 750 GPGET, GICON Turns on/off the graphics display. GRAPH Initial: Logic onOff (1=on, 0=off) Final: Related Keywords: ALPHA GETALPHA GETGRAPH Draws relative to the current pen location GRDRAW Initial: Point userUnits Final: Related Keywords: GSCALE GRMOVE GDRAW 24-46 Using the LI-6400...
Page 751 GTMODE Set the graphics-text drawing mode GTMODE Initial: Num newMode (1=or, 2=eor, 3=and) Final: This affects what is seen when both graphics and text are visible on the same display device. Related Keywords: ALPHA GRAPH GTMDGET Using the LI-6400 24-47...
Page 752 Initial: Final: Related Keywords: SHOWSOFT High speed counter HSCOUNTS Initial: Final: Long counts Returns the number of counts from the high speed counter since the previous call to . See Pulse Counting on page 26-27. HSCOUNTS 24-48 Using the LI-6400...
Page 753 Long logic (1 = yes, 0 = no) Modules can be referenced by their file specifier (name), or else by their number. If sysID is 0, the current application is used. Related Keywords: LINK UNLINK SYSID SETMODNUM GETMODNUM Using the LI-6400 24-49...
Page 754 [Num sysID , Addr messPath , Num code ], Text fileName , Num anything Final: Long error (0=ok, non-zero = failed) To link a file, have any numeric value on the top of the stack. Otherwise, have a path 24-50 Using the LI-6400...
Page 755 LOWWARN Initial: Num onOff (0=off, 1=on) Final: Related Keywords: GETBATT Return the LPL version number Initial: [Text dest (default = LCD)] Final: Lower case Initial / Final: (See Single Value Transforms on page 24-13.) Related Keywords: Using the LI-6400 24-51...
Page 756 Related Keywords: FREESOFT ONSOFT Enable / disable math error corrections MATHERR Initial: Num onOff (0 = report errors, 1=overlook errors) Final: The following math errors normally generate fatal errors, but they can be overlooked 24-52 Using the LI-6400...
Page 757 Returns min value Initial / Final: (See T w o V a l u e T r a n s f o r m s on page 24-13.) Related Keywords: Using the LI-6400 24-53...
Page 758 Related Keywords: LOOP ENDLOOP, BREAK, BREAKIF Logical NOT Initial / Final: (See Single Value Transforms on page 24-13.) Disable an ONA2D condition OFFA2D Initial: Final: Related Keywords: ONA2D Disable ONCOMM condition OFFCOMM Initial: Final: Related Keywords: ONCOMM 24-54 Using the LI-6400...
Page 759 The timers are global to any (T)IDLE within an application, however. Thus, any function called from within a (T)IDLE can modify any timerÕs parameters (period and function address), and the changes remain in effect until another is encountered. ONCYCLE OFFCYCLE Using the LI-6400 24-55...
Page 760 Define a function to be executed once when a certain time is reached. If this time oc- curs when there is no in effect, then the function will not be executed until the (T)IDLE next (T)IDLE Related Keywords: IDLE TIDLE, OFFTIME 24-56 Using the LI-6400...
Page 761 Text opts , Text name Final: Addr path , Long 0 -or- Final: Long 1 The opts string is made up of one or more of the items in Table 24-26. For example, ÒwaÓ is write-append. Using the LI-6400 24-57...
Page 762 Long 1 Every application has available to it the standard path . One reason to open another path to the keyboard would be to implement different filtering without changing the standard filters associated with Related Keywords: CLOSE 24-58 Using the LI-6400...
Page 763 LONG type , LONG size , LONG fill , LONG empty code and type are given in Table 24-28, and Table 24-29. Table 24-28. PATHSTAT Code Values value code Path type: See Table 24-29 Path size Path fill Path empty Using the LI-6400 24-59...
Page 764 The power of the polynomial is determined from the number of values in the coeffi- cient array coeffs. 2 values = 1st order, 3 values = 2nd order, etc. Position the cursor within the current text window POSXY Initial: Num column , Num row Final: Related Keywords: GETWINDOW 24-60 Using the LI-6400...
Page 765 Flag Meaning Left justifies the result, pads on the right with blanks. If not given, right-justifies the result, pads on the left with zeros or blanks. Numeric values always begin with a + or - sign. Using the LI-6400 24-61...
Page 766 LL is the low byte in hex. Table 24-33. PRINT Format Examples Item on Stack Format Result 12 (LONG) " 12" "abcdefg" %5.5s "abcde" 1.2345 %7.2f " 1.23" 1.2345 %-7.1f" "1.23 " "ABC" "(*,)d" "65,66,67" 24-62 Using the LI-6400...
Page 767 LONG result (theChar if ok, or -1 on error) Related Keywords: GETCH Redisplay text and attribute information PUTDISP Initial: DispInfo old Final: This disposes the structure pointed at by old, so donÕt use it again! Related Keywords: GETDISP Using the LI-6400 24-63...
Page 768 Num power , DArray xArray , DArray yArray , DArray coeffs , Num forceZero Final: Double determinant Size of coeffs should be at least as large as 1 + power. If forceZero is true (not 0), the first coefficient will always be 0. Related Keywords: POLY 24-64 Using the LI-6400...
Page 769 Obj a , Obj b , Obj c Final: Obj c , Obj b , Obj a Related Keywords: SWAP DROP Launch an LPL application Initial: Path sourceCode -or- Initial: CArray fileName Final: Related Keywords: STKSHARE COMPILE, LINK Using the LI-6400 24-65...
Page 770 Convert seconds since base time to the time and date (numerical) Related Keywords: TD2SECS TIME DATE CTIME Set text attribute for subsequent printing SETATTR Initial: Num newValue Final: Attributes (value of newValue) are given in Table 24-37. 24-66 Using the LI-6400...
Page 771 Num offsetBytes , Num Ref (from: 0=start, 1=current, 2=end), Addr Path Final: Related Keywords: PATHSTAT SETEMPTY Change the owner of on allocated item or A/D structure SETID Initial: Num newID, Addr object Final: Related Keywords: MAKE MAKE4 SYSID Using the LI-6400 24-67...
Page 772 SHOWSOFT Initial: Final: Related Keywords: HIDESOFT Computes sine Initial / Final: (See Single Value Transforms on page 24-13.) Related Keywords: Returns maximum size of an array SIZE Initial: Array arr Final: Long size Related Keywords: READY 24-68 Using the LI-6400...
Page 773 SOFTGETM SHOWSOFT Returns the number of function keys that can be displayed SOFTWIDE Initial: Final: LONG nKeys (5 for the LI-6400) Square root SQRT Initial / Final: (See Single Value Transforms on page 24-13.) Related Keywords: MATHERR Invokes the system editor using the current text window...
Page 774 Num newSize (number of items) Final: This also flushes the stack. Related Keywords: STKSIZE Enable/disable stack sharing STKSHARE Initial: Num yesNo (0=no sharing, non-zero=stack sharing) Final: Stack sharing applies to subsequent child applications launched by the current appli- 24-70 Using the LI-6400...
Page 775 ..., Obj b , Obj a Related Keywords: DROP Returns the system ID number for the current application SYSID Initial: Final: LONG sysID Related Keywords: SETID Tangent Initial / Final: (See Single Value Transforms on page 24-13.) Related Keywords: Using the LI-6400 24-71...
Page 776 The module to be removed can be refereed to by name or number. If all is non-zero, all modules having a number greater than or equal to the targetÕs number are removed. Related Keywords: LINK ISLINK Uppercase function Initial / Final: (See Single Value Transforms on page 24-13.) Related Keywords:LWC 24-72 Using the LI-6400...
Page 777 Figure 24-5. Window label position codes The right border and/or the bottom border can be suppressed by specifying the right (or bottom) boundary to be any value larger than the value. DISPWIDTH DISPHEIGHT Related Keywords: CLEAR SCRLOCK CLREOL Using the LI-6400 24-73...
Page 778 Queue Keyboard Error Overlapped Overlapped Display Error Error Overlapped Overlapped Comm Port Overlapped Overlapped Error Overlapped File, Buffer, Overlapped or Queue Generate a cross reference for an application XREF Initial: Text filename , Path dest Final: 24-74 Using the LI-6400...
Page 779 ONTROL OOLS General Control Functions 25-19 Flow Control Functions 25-20 Mixer Control Functions 25-21 Cooler Control Functions 25-22 Lamp Control Functions 25-22 IRGA Control Functions 25-23 Chamber Fan Control Functions 25-24 Example: Using the Library 25-24 Using the LI-6400 25-1...
Page 780: Autoprogram Format
LetÕs look at a simple but fully functional LPL program that can serve as an Autoprogram. This task is very simple: log five observations spaced one minute apart to the log file. That is, they will not run successfully unless OPEN is also running. 25-2 Using the LI-6400...
Page 781 (if lpAbort is non-zero), we just jump out of the loop. lpAbort BREAKIF Data recording is done by LPLog which causes a record to be written to the open log file (or RAM file or comm Using the LI-6400 25-3...
Page 782: Some Autoprogram Listings
:PTR { matchEvery ÒAuto match every __ obs (0=none) Ò} :FCT main progName LPSetName progName Ò\f%sÓ PRINT defaultFile user LPPrompts2 IF RETURN THEN 0 :INT actual 1 :INT i LPPrep matchEvery :INT count quitAfter NLOOP logInterval &actual = matchEvery IF 25-4 Using the LI-6400...
Page 783 :PTR { maxWaitTime ÒMaximum wait time (secs) Ò} :PTR { stable ÒStability (total CV %) Ò} :PTR { matchIf ÒMatch if |ÆFCO2| less than (ppm) Ò } :FCT main /* Set program name ÒLight CurveÓ DUP LPSetName Ò\f%s\nÓ PRINT Using the LI-6400 25-5...
Page 784 970502 - remembers last time defaults 980309 - delta-based matching :CHAR defaultFile[] ÒA-CiCurve DfltsÓ :FLOAT co2Vals[20] {400 300 200 100 50 400 400 600} stable 1.0 matchIf 20 :INT minWaitTime 60 maxWaitTime 300 pmWait 10 :PTR user[] 25-6 Using the LI-6400...
Page 785 READY LPRegLoop NLOOP LPLoopStat co2Vals i PICK VAL DUP IF If asking for a zero value, turn the mixer off. theTarget ELSE THEN MixerSetNewTarget stable minWaitTime maxWaitTime LPMeasureTilStable lpAbort BREAKIF MatchFct LPLog &i 1 + DROP ENDLOOP LPDeregLoop LPCleanup Using the LI-6400 25-7...
Page 786 ÒAutoProgs/TimedLamp Defaults/Ó fullSpec[80] ÒÒ myName[] ÒTimedLampÓ :FCT main FLUSH CLEAR myName LPSetName 15 1 POSXY myName PRINT 500 OPEN_BUFF IF RETURN THEN :PTR buff buff PickParams IF buff CLOSE RETURN THEN 0 0 buff SETEMPTY 25-8 Using the LI-6400...
Page 787 _Esc key == IF 1 &rtn = BREAK THEN ÔSÕ key == IF buff StoreDefaults BREAK THEN ÔRÕ key == BREAKIF ENDLOOP 1 1 DISPWIDTH DISPHEIGHT 0 WINDOW CLEAR rtn RETURN FromFile Parameters come from a file. :PTR buff Using the LI-6400 25-9...
Page 788 THEN k ÔFÕ == IF buff FromFile RETURN THEN Does the default directory CheckDir exist? theConfigDir fullSpec = Ò/Ó fullSpec APP defaultDir fullSpec APP fullSpec FTYPE 0 == IF fullSpec DIRMAKE DROP THEN defaults fullSpec APP 25-10 Using the LI-6400...
Page 789 Table 26-3 on page 26-5. ResetComp { 2 &compEvery = } :FCT SetUpdate { 1 &hiResUpdateTime = A2dProgram 1 LPMeasure} hiResUpdateTime is described in Table 26-2 on ResetUpdate { .75 &hiresupdatetime = A2dProgram } page 26-4. Using the LI-6400 25-11...
Page 790: Useful Autoprogram Commands
1 minute for the CO sample analyzer to stabilize. If it does, the sample water and CO IRGAs are adjusted to read the reference IRGAs. Otherwise, a warning message is logged. 25-12 Using the LI-6400...
Page 791 Each item in the pointer array should have two elements: 1) variable name, 2) prompt (Figure 25-3). Related Keywords: LPPrompts2 :PTR myList[] { :PTR { lampVals "Desired lamp values\n" } :PTR { delayTime "Wait time (s)" } Figure 25-3. Example pointer array suitable for LPPrompts LPPrompt2. Using the LI-6400 25-13...
Page 792 Òthis/maxÓ that is displayed as the ProgPrgs system variable (ID #-56). Prompt for all user constants UcnAskAll Initial: Final: Same as pressing User Consts (f5 level 3) in New Measurements mode. 25-14 Using the LI-6400...
Page 793 Us this to determine the current control method and target value. typeCodes are given in Table 25-1. Sets the current target value without changing control type. LampSetTargetVal Initial: Num value Final: Control type remains the same. Only the target changes. Using the LI-6400 25-15...
Page 794 Use this function to get the current control type and target value. typeCodes are given in Table 25-2. Sets the target value independent of control mode. MixerSetTargetVal Initial: Num value Final: Sets a new target without changing the control type. 25-16 Using the LI-6400...
Page 795 Double value , Long typeCode Use this to determine the current set point and control type. typeCode values are given in Table 25-3. Set new target value independent of control mode FlowSetTargetVal Initial: Num value Final: Using the LI-6400 25-17...
Page 796 Intermediate values (4.38) will work here, as well. Set fan speed (Off Slow Fast) LPSetFanOSF Initial: Num selection (0, 1 or 2 for off, slow, fast) Final: 2 is the highest speed, 1 uses the current definition of ÒslowÓ (default is 4 volts). 25-18 Using the LI-6400...
Page 797: Autoprograms And The Control Manager
AbdOn Initial: Final: This board must be on to control any of the analog or digital inputs or outputs. Uses digital output dio_flowbd (0x0302). Turns off the flow control board. AbdOff Initial: Final: Counterpart of AbdOn Using the LI-6400 25-19...
Page 798 Digital output dio_null is set, and D/A channel da_null_set is set to the target value. Are we controlling on water (as opposed to flow)? IsRHNull Initial: Final: Long logic (1=humidity control, 0=flow control) Returns the state of digital output dio_null. 25-20 Using the LI-6400...
Page 799 Returns the state of the digital output dio_co2. Set the CO mixer control voltage (0 to 5000 mV) SetCo2MixerMv Initial: Num setPoint (mV) Final: Converting µmol mol to mV takes place at a higher level. Sets D/A channel da_co2_set (1). Using the LI-6400 25-21...
Page 800 D/A channel da_lamp (2) is set to the target val- Returns the current lamp control value (mV). GetLamp_mv Initial: Final: Double setPoint (mV) Returns the state of D/A channel da_lamp. 25-22 Using the LI-6400...
Page 801 This information comes from 2 digital inputs: dio_co21 and dio_co22 (0x0202 and 0x0203). Turn on the IRGA matching valve. IrgaMatchOn Initial: Final: Unsets digital output dio_match (0x0007). Turn off the IRGA matching valve. IrgaMatchOff Initial: Final: Sets digital output dio_match (0x0007). Using the LI-6400 25-23...
Page 802 Ò\nEnter command signal (0-5000):Ó PRINT &x Ò%fÓ KBD ENTER NOT BREAKIF &x 0 MAX 5000 MIN DROP /* range check */ x SetLamp_mv ENDLOOP Figure 25-4. Listing of a stand alone program to run the lamp. 25-24 Using the LI-6400...
Page 803 The userList Pointer Array 26-18 Soil Flux Example 26-20 26-22 SING PARE HANNELS Analog Input Channels 26-22 Analog Output Channels 26-23 Digital Output 26-25 Digital Input 26-26 Pulse Counting 26-27 Summary of the ConsoleÕs 37 Pin Connector 26-27 Using the LI-6400 26-1...
Page 804: Using Patch=
For example, if you wish to set the digital output on pin 7 (0x0405) high, type Patch= 1 0x0405 DIOSET Press enter to end the editing. 26-2 Using the LI-6400...
Page 805 There are limits to what you can do with this method, however. You can only change a variable that is already defined (and PUB), and it only happens when the configuration file is actually processed. The section OpenÕs Hooks on page 26-7 describes more powerful method for modifying OPEN. Using the LI-6400 26-3...
Page 806: Useful Variables
Customizing Open Useful Variables Useful Variables A/D Measurements Table 26-2 lists some variables that pertain to how the LI-6400 makes analog measurements in New Measurements mode. Table 26-2. Variables defined in /sys/open/open.a2d that are useful for modifying the A/D behavior.
Page 807 2 = every 3rd time, etc. matchStableLimit FLOAT range limit (ppm) for de- termining ÒstabilityÓ when auto-matching (during an Au- toProgram). matchAutoTimeLimit How long (secs) to wait for stability during auto-matching. a.DonÕt change it if itÕs shaded! Using the LI-6400 26-5...
Page 808 Duration of beep when log- ging, in milliseconds. obsInPad Number of observations logged since destination opened. (System variable, #-35) obsOneTime Long Time and date (seconds) des- tination was opened. a.DonÕt change it if itÕs shaded! 26-6 Using the LI-6400...
Page 809: Openõs Hooks
OpenÕs Hooks OPEN provides extended control to users via a series of hooks. What is a hook? Suppose that you want the LI-6400 to print a CO value to the RS-232 port (or any other task) every 1 second while in New Measurements mode.
Page 810 Called in OpenÕs main screen to put the :FCT StdMainDisplay UserMainDisplay top three lines on the display. HookCalibMenu Called from OpenÕs main screen in re- :FCT StdCalibMenu UserCalibMenu sponse to pressing the Calib Menu FCT key. 26-8 Using the LI-6400...
Page 811 Figure 26-1. The file Ò/User/Configs/Modules/LI-610 Fct KeyÓ. It uses two hooks by defining the functions DefUserKeys, and UserNMStartUp. Discussion We accomplish this task by using two hooks: DefUserKeys is the most impor- tant, since that is how weÕll get our key defined. The other hook, UserNM- Using the LI-6400 26-9...
Page 812 In our example, the ComputeList that is active for the LI-610 configuration has a line near the top of it that says The soil flux configuration, on the other hand, uses this hook and purposefully skips StdNewMeasureStartup. 26-10 Using the LI-6400...
Page 813 ComputeList you wish. A useful addition to this module would be a function key for turning this transmission on and off. We leave that as an exercise for the reader, as math texts are prone to say. Using the LI-6400 26-11...
Page 814 { -35 -36 } :LONG stopTime 0 :CHAR progName[] "AvgAutoLog" defaultFile[] "AvgAutoLog Dflts" :PTR user[] :PTR { logInterval "Log (and average) interval (sec)="} :PTR { totalDuration "Quit after (minutes)="} :PTR { matchAfter "MATCH every Nth Log (0 = never)="} 26-12 Using the LI-6400...
Page 815 &matchCount 1 - VAL 0 <= IF LPMatch matchAfter &matchCount = THEN THEN ENDLOOP /* Restore A2d behavior oldUpdate &hiResUpdateTime = This is important! If you don’t do it, no one else will. oldComp &compEvery = A2dProgram Using the LI-6400 26-13...
Page 816 PICK VAL actionList i PICK = &i 1 + DROP ENDLOOP numAdded &auxN3 = LPLog 0 &auxN3 = 0 &numAdded = 0 totals = &numLogged 1 + DROP BuildActionList 1 :INT i "xx" TYPE SWAP DROP :INT stringType userLogList READY NLOOP 26-14 Using the LI-6400...
Page 817 A/D (with a call to A2DProgram). Again, the original values are preserved, and the A/D reprogrammed at the end of the AutoProgram. See Table 26-2 on page 26-4, and Table 26-3 on page 26-5. Using the LI-6400 26-15...
Page 818: New Style Computelist Files
##27 "VpdA" "Air VPD (es(tair) - eair)" " -#10 * co2_diff_um - co2_2_um * #20" " satVapTair_kPa - eAir_2_kPa" ##35 "CndCO2" "Total Conductance to CO2" " 1.0 / (1.6 / #23 + 1.37 / condBL_mol)" Figure 26-3. Listing of file /User/Configs/Comps/Default 26-16 Using the LI-6400...
Page 819 = ((u35 - u20/2) * co2_2_um - u30) / (u35 + u20/2) u38 = u36 * press_kPa * 1E-3 u39 = u36 / co2_2_um u25 = SatVap(Tleaf_c) - eAir_2_kPa u27 = satVapTair_kPa - eAir_2_kPa Figure 26-4. The ComputeList ÒDefaultÓ, converted to New Style. Using the LI-6400 26-17...
Page 820 For New Measurements mode. Typically something like Ò%8sÓ. This is String the mechanism by which a short label is made to take up the requisite number of spaces. The Variable The variable name. Must be defined somewhere, as a :FLOAT, or :INT, etc. 26-18 Using the LI-6400...
Page 821 Old Style Display Format Used Logging Format Used Format Code Variable String Variable String Name Name Ò%8.0fÓ Ò%1.0fÓ Ò%8.5fÓ Ò%1.5fÓ Ò%8.1fÓ Ò%1.1GÓ Ò%8.6fÓ Ò%1.6GÓ a. Not all are shown, but enough to give you the idea. Using the LI-6400 26-19...
Page 822 :PTR { 324 ÒTsch_CÓ s8 tLeaf_c df2f ÒSoil Chamber Air Temp CÓ sad lf2f } :PTR { 330 ÒR(C)mÓ s8 dcdtSlope df3g ÒSlope of dcÕ/dt vs CO2Ó sad lf5g } :PTR { 331 ÒR(C)bÓ s8 dcdtOffset df3g ÒOffset of dcÕ/dt vs CO2Ó sad lf5g } 26-20 Using the LI-6400...
Page 823 = press_kPa * 1.2028 / (tleaf_c + 273) dcdt = density * (co2Slope - co2Mean * h2oSlope / (1000.0 - h2oMean)) THEN IF (opMode == 4) dcdt = dcdtSlope * co2Mean + dcdtOffset THEN soilEfflux = dcdt * va Using the LI-6400 26-21...
Page 824: Using Spare Channels
Chamber signals Pressure sensor Measurements are referenced to a ground signal that is software selectable (Table 26-9). All of the LI-6400Õs analog inputs are over voltage protected to ±35V, with or without power. Connections To wire an analog input, select a signal pin (Table 26-8) and a ground pin (Table 26-9).
Page 825 Only when the user presses a function key and enters a new value This technique involves defining function keys in New Measurements mode. An example of doing this can be seen by installing the "LI-610 Fct Key Using the LI-6400 26-23...
Page 826 The control can be set at the start of the AutoProgram, or, if frequent updates are necessary, the control can be up- dated once each second during the AutoProgram. See Example #3: Hooks in AutoPrograms on page 26-12. 26-24 Using the LI-6400...
Page 827 Use the DIOSET command. (This and related commands are discussed in Digital I/O on page 23-75.) For example, 1 0x0402 DIOSET 0 0x0401 DIOSET will set 0x0402 high (0V), and 0x0401 low (5V, if using pin 1 for voltage sup- ply). Using the LI-6400 26-25...
Page 828 The question of where one does the programming arises: it depends on how often you need to check the digital input. You might want to include this in a ComputeList, or an AutoProgram, or do it every second in New Measure- 26-26 Using the LI-6400...
Page 829 Using Spare Channels ments mode. Pulse Counting The LI-6400 has one pulse counting channel, that can count pulses up to about 4 KHz. Connections Use pin 20 for the digital ground, and pin 3 for the pulsed signal. A pulse is counted each time the signal drops from >5V to 0.
Page 830 Analog Input Ground 5 Analog Input Channels on page 26-22 Sample CO2 raw analog output Reference H2O analog output Reference CO2 raw analog output Analog Input 20, ±5V Analog Input Channels on page 26-22 Analog Input 23, ±5V 26-28 Using the LI-6400...
Page 831 13-14 "Adjust -¯" fct key 18-17 6400-21 FX/Macintosh 11-10 "AutoCO2" fct key 18-5 adjusting the latch 4-4 6400-50 System Software 1-14 "AutoH2O" fct key 18-5 agc signals 20-15 installing 2-19 "AutoAll" fct key 18-5 monitoring 20-43 Using the LI-6400...
Page 832 "_CO2 Mixer - Calibrate" equation 14-4 18-20 ref for leaf temp 18-19 "_LED Source - Calibrate" viewing 3-19 back plane board 18-24 "BLOWN FUSE" 20-7 location 19-11 "_LED Source - Plot boot screen 5-18 backing up data Curve" 18-26 Using the LI-6400...
Page 833 "CO2R_mv" label 14-21 CalParOut= 14-8 16-20 "Close Logging" fct key 9-7 "CO2_R/S" fct keys CalPress= 14-4 16-20 "Clr all" fct key (Filer) 10-14 18-14 CalZero= 14-6 16-20 "ClrAll" fct key (LogList edi- "CO2S=" fct key 7-14 CO2Mixer= 16-20 Using the LI-6400...
Page 834 18-23 console description 1-13 "DAC Status" menu item 21-5 Comps" directory 15-2 control manager 7-2 data bits 11-24 history" 18-31 controls "Data Set Pick" fct key 12-10 lamp" 18-27 chamber fan date. See time and date Using the LI-6400...
Page 835 10-10 parm1" 18-30 definition of 10-3 "earlyOK" fct key Dew Point Generator (LI-610) Filer functions 10-9 LED Calib 18-25 controlling from LI-6400 removing 10-10 Mixer Calib 18-21 26-9 renaming 10-10 EB_Deltat() function 17-8 H2O span gas 18-13 root 10-4 "Edit Config"...
Page 836 18-24 "eXecute" fct key 10-17 Standard Menu 5-4 PlotDefs 12-19 exit menu "flash disk not found" 20-4 PromptList config 9-17 AutoPrograms 9-20 flow RTG config 6-13 Standard Edit 5-15 controlling low rates 4-52 typical data file 9-3 Using the LI-6400...
Page 837 "LogBeep ON/Off" 9-7 "Add" "Display QuikPik" 6-3 "LogList Editor" 9-8 Config Editor 16-15 "dUplct" 10-16 "LogList QuikPik" 9-7 Filer 10-9 "earlyOK" "MATCH IRGAs" 4-36 "AddGrp" 9-9 LED Calib 18-25 "MATCH" 4-35 "Adjust -¯" 18-17 Mixer Calib 18-21 "Move" 10-15 Using the LI-6400...
Page 838 "H2O_R/S" fct keys 18-14 "H2O R/S -¯" fct keys 18-10 "Retag" 10-14 in the Filer 10-7 "Revert StdFile" 8-4 RTG control 6-8 "H2OR" label 14-19 "Revert" "FUSE" message 3-7 "H2OR_mml" label 14-19 Config Status 16-14 fuses "H2OR_mv" label 14-21 Using the LI-6400...
Page 839 PromptList editor 9-14 "FwMxCrLp" 14-16 Installation Menu 16-4 label line "H2O" 14-12 "Configuration Examples in GraphIt 12-5 "H2OR" 14-19 Menu" 3-10 in log file 9-3 "H2OR_mml" 14-19 "View InstalledÉ" 16-5 manually selecting 12-10 "H2OR_mv" 14-21 examples 16-5 Using the LI-6400...
Page 840 LED source (6400-02 / -02B) observations 9-6 "TdR" 14-20 calibration 18-24 prompts 9-12 "TdS" 14-20 installation example 16-5 setup 9-7 "Time" 14-11 installing 2-15 time and date 9-10 "Tirga" 14-22 introduction to using 3-39 "Logging Control" menu item I-10 Using the LI-6400...
Page 841 "IRGAs Not Ready" when to 4-39 20-7 20-7 McFee, R.H. 14-26 NOASSIGN command 15-8 "NeedÉdrier target" "Measured or Energy Bal- "NoAuto" fct key 18-17 20-9 ance?" 16-8 Nobel, P. 17-11 "NeedÉwetter target" memory board null balance 7-7 Using the LI-6400 I-11...
Page 842 "Plot" fct key 18-6 20-39 PromptList editor 9-14 polyurethane tubing 19-7 "Pump is Off" 20-8 RTG editor 6-10 powering the LI-6400 2-18 "PUMP" label 14-13 "Open LogFile" fct key 9-4 preparation check lists 4-2 "Pump+/-" fct keys 18-22 open system "Press"...
Page 843 LogList editor 9-9 files 10-16 Standard File Dialog 5-9 PromptList editor 9-14 "REPLOT GRAPH" fct key "StartHR" label 9-11 14-12 RTG editor 6-10 12-3 "Status" label 18-21 scaling "Reset" fct key 18-18 Stefan-Boltzmann constant in GraphIt 12-9 Using the LI-6400 I-13...
Page 844 "Tair" label 14-19 Open.lmp" 25-15 trash directory 10-15 23-49 "Tair_mv" label 14-21 Open.lp" 25-12 tripod mount 2-6 tape, double sided 19-21 Open.mxr" 25-16 troubleshooting 20-1 "Tblk" label 14-19 Open.msr" 26-5 "Tblk_mv" label 14-21 Start" 3-66 "Tblock" label 14-19 I-14 Using the LI-6400...
Page 845 5-17 "File Exchange Mode" 11-4 New Measurements 20-7 "Graph Stored Data" 12-2 water corrections "New File (Editor)" 5-13 band broadening 14-23 "Recompute stored data" dilution 1-10 13-3 water use efficiency example "Set the time and date" Using the LI-6400 I-15...
Page 846 Index I-16 Using the LI-6400...

Save PDF