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Data Logging

Basic Concepts

Using the LI-6400

9-3

What does it look like?

A sample file with logged data is shown in Figure 9-1, in very small print.

At the start of the file is the header. The header consists of a series of lines
identifying some configurations associated with the data. The data consist of
a line of labels identifying each column, and rows of observations. The delim-
iter in these files can be commas, as in Figure 9-1, or tabs, or spaced into jus-
tified columns. 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.

OPEN 3.01"
"Thr Sep 18 1997 11:35:08"
"ComputeList=","/User/Configs/Comps/Default"
"BLCTable=","/Sys/Lib/StdBLCTable"
"LightSource=","Sun+Sky",1,0.19
"LogFormat=","/User/Configs/LogFormats/Std Outputx"
“PromptList=”,”Default (none)”
"11:35:09 unidentified grass"
"Obs","Time","Photo","Cond","Ci","Trmmol","VpdL","Area","StmRat","BLCond","Tair","Tleaf","TBlk","CO2R","CO2S","H2OR",…

…"H2OS","RH_R","RH_S","Flow","PARi","PARo","Press","CsMch","HsMch","Status"

1,419.21,15.4,0.216,238,3.49,1.62,3.5,1,3.94,24.98,28.25,23.17,399.7,365.9,15.79,22.70,48.74,70.09,172.8,1026,1311,98.07,-2.2,0.04,111115
2,643.72,11.3,0.202,180,3.33,1.65,3.5,1,3.94,24.80,28.25,22.97,299.4,279.6,17.15,22.44,53.53,70.03,215.7,1070,1354,98.07,-1.2,0.03,111115
3,803.47,7.2,0.213,127,3.48,1.64,3.5,1,3.94,24.84,28.21,23.02,199.7,187.9,17.37,22.47,54.07,69.97,233.3,1062,1337,98.07,-0.8,0.02,111115
4,1093.22,2.16,0.215,76.8,3.81,1.77,3.5,1,3.94,25.20,28.59,23.43,100.7,96.2,15.42,21.96,46.98,66.92,199.4,1164,1450,98.07,-0.6,0.01,111115
5,1283.28-0.39,0.213,51.4,3.81,1.79,3.5,1,3.94,25.17,28.71,23.35,49.5,49.9,15.52,22.04,47.41,67.31,200.2,1160,1440,98.07,-0.5,-0.01,111115
6,1393.97,-2.97,0.219,27.1,3.85,1.76,3.5,1,3.94,25.15,28.65,23.34-0.3,4.9,15.60,22.20,47.69,67.86,199.7,1113,1374,98.06,-0.6,0.00,111105
"11:58:30 Turned coolers off"
7,1585.53,21.4,0.207,759,3.64,1.76,3.5,1,3.94,25.12,28.76,23.29,1000.6,956.9,16.29,22.52,49.86,68.95,199.5,1262,1533,98.06,-7.5,0.10,111115
8,1747.03,23.7,0.203,442,3.6,1.77,3.5,1,3.94,25.22,28.84,23.39,699.4,653.5,16.43,22.61,50.02,68.85,199.1,1214,1467,98.06,-4.1,0.07,111115
9,1909.28,14.2,0.17,225,3.11,1.81,3.5,1,3.94,25.23,29.11,23.40,399.5,372.5,17.51,22.84,53.26,69.46,199.6,1228,1497,98.05,-1.9,0.03,111115

Figure 9-1. Sample data file, in comma delimited format.

Header

Label-
Line

Obser-
vations

Remark

«
...
245
246
247
248
249
...
»

Summary of Contents for LI-6400

Page 1: ...Using the LI 6400 Portable Photosynthesis System ...

Page 2: ...8 1999 LI COR Inc Publication Number 9806 122 Printing History 1st Printing July 1998 OPEN Software version 3 2 2nd Printing May 1999 OPEN Software version 3 3 Macintosh is a registered trademark of Apple Computer Inc Printing History New editions of this manual will incorporate all material since the previous editions Update packages may be used between editions which contain replacement and addi...

Page 3: ...n Summary 1 7 The System Components 1 12 2 Assembling the LI 6400 Putting it all together Preparations 2 2 Using a Tripod 2 6 6400 01 CO2 Injector Installation 2 7 External Quantum Sensor Installation 2 14 6400 02B LED Light Source Installation 2 15 Powering the LI 6400 2 18 Installing System Software 2 19 3 Guided Tours Learning how to make it work Before You Start 3 2 Tour 1 OPEN Overview 3 4 To...

Page 4: ...esponse Curves 4 24 CO2 Response Curves 4 30 Matching the Analyzers 4 34 Stability Considerations 4 41 Leaks 4 42 Operational Hints 4 47 Answers to Questions 4 53 Part II Useful Details 5 Standard Tools Menus Editors and File Dialogs Standard Menu 5 2 Standard Line Editor 5 5 Standard File Dialog 5 9 Standard Edit 5 13 Hot Keys 5 16 Low Battery Warning 5 17 The Boot Screen 5 18 The LPL Screen 5 20...

Page 5: ...ources 8 6 Gallium Arsenide Phosphide GaAsP Sensor 8 7 9 Data Logging Storing what you want where you want when you want Basic Concepts 9 2 Getting Started 9 4 Determining What is Logged 9 7 Prompts and Remarks 9 12 AutoPrograms 9 18 AutoProgram Descriptions 9 21 Making Your Own AutoPrograms 9 33 Part III Working With Files 10 The LPL File System Managing your data storage space Files Directories ...

Page 6: ...phIt 12 2 Data File Format 12 4 Defining Plots 12 6 Selecting Observations 12 10 Curve Fitting 12 14 Viewing Data 12 17 PlotDef File Format 12 19 Storing and Retrieving Graphics Images 12 19 13 Recomputing Data Files How to recompute data files Reasons to Recompute 13 2 A Step By Step Example 13 2 The Details 13 7 Hints 13 14 Part IV Configuration Issues 14 OPENÕs System Variables Quantities provi...

Page 7: ... Default ComputeList 15 16 Old Style vs New Style 15 17 16 Configuration Basics What you need to know to get by A Definition of Terms 16 2 Making Configuration Files 16 4 Installation Menu Behind the Scenes 16 10 Modifying Config Files 16 12 The Reset Menu 16 16 Configuration Command Summary 16 18 17 Using an Energy Balance Computing what you canÕt measure The Theory 17 2 Using Energy Balance in O...

Page 8: ...re Thermocouple 19 18 Leaf Chambers 19 20 LED Source Maintenance 19 22 Match Valve Maintenance 19 23 IRGA Maintenance 19 26 Servicing the External CO2 Source Assembly 19 32 Shipping The LI 6400 19 35 Useful Part Numbers 19 36 20 Troubleshooting When things go wrong Power On Start up Problems 20 2 Real Time Clock Problems 20 6 New Measurements Mode Warning Messages 20 7 Unreasonable Results 20 9 Pu...

Page 9: ...lic and Static 22 22 Compiler Directives 22 25 23 LPL Topics Programming with LPL Stack Control 23 2 Conditionals and Loops 23 4 Array Operations 23 6 Math Functions 23 18 Display Control 23 23 Keyboard Control 23 29 Clock 23 31 Event Handling 23 33 The Function Keys 23 37 I O Programming 23 39 File System 23 46 Menus and Editors 23 51 Graphics 23 56 RS 232 Communications 23 64 Analog Measurements...

Page 10: ...t you what them to do Autoprogram Format 25 2 Some AutoProgram Listings 25 4 Useful AutoProgram Commands 25 12 AutoPrograms and the Control Manager 25 19 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 ...

Page 11: ...umber of customers and potential customers were looking to answer deep er questions The deeper answers could be found in response curves and that meant using a system that could control the environmental quantities impor tant to photosynthesis CO2 light humidity and temperature Several inno vators attempted to do various response curves with the LI 6200 with varying degrees of success Meanwhile we...

Page 12: ...ight in the leaf chamber but suitable IRGAs did not exist Secondly chamber CO2 could in principle be controlled by mixing scrubbed air and pure CO2 available in very portable 12 gram cylinders but again a suitable mixing device did not exist So we set about inventing them Five years and one name change1 later we shipped the first LI 6400 And many more since then We trust that this instrument will ...

Page 13: ... New to the LI 6400 new to gas exchange methodical and thorough Work through Chapters 1 2 3 and 4 YouÕll understand the LI 6400 and the fundamentals of making measurements fairly well by the end New to the LI 6400 experienced at gas exchange measurements Skim Chapter 1 Chapter 2 Assembling the system Chapter 3 Tours 1 through 5 Chapter 4 The check lists are important pick and choose after that Exp...

Page 14: ...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 Acrobat Reader is required You can download this software for no charge from www adobe com ...

Page 15: ...Part I The Basics ...

Page 16: ......

Page 17: ... 1 3 Leaks 1 3 THE FLOW SCHEMATIC 1 4 Matching the IRGAs 1 6 EQUATION SUMMARY 1 7 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 THE SYSTEM COMPONENTS 1 12 The Standard Parts 1 13 The Optional Accessories 1 14 ...

Page 18: ...rences in CO2 and H2O in an air stream that is flowing through the leaf cuvette Figure 1 1 Sample IRGA Reference IRGA Flow x DCO2 Area Photo Trans Flow x DH2O Area Figure 1 1 In an open system photosynthesis and transpiration are computed from the differences in CO2 and H2O between in chamber conditions and pre chamber conditions The equations are given in Equation Summary on page 1 7 Sample IRGA ...

Page 19: ...ength of an open system is that the incoming air stream can be condi tioned That is its humidity CO2 concentration temperature etc can be es tablished by some means prior to entering the system Regardless of what is done to the incoming air however one thing is crucial This is especially true for CO2 where the potential for fluctuations is huge your breath for example is probably about 50 000 µmol...

Page 20: ...ortion desired CO2 however is best controlled by scrubbing all of it from the incoming air and using the 6400 01 CO2 mixer to inject just enough CO2 to provide a stable concentration at the desired value If the 6400 01 is not part of your system you will need to use a buffer volume For a more complete discussion of buffer volumes see Air Supply Considerations on page 4 47 Humidity control in the l...

Page 21: ...Reference Air In Pump 25 75 25 CO2 Flow Control Air Flow Control Pump CO2 Flow Flow Meter Vent Bypass Valve Bypass Valve Liquid CO2 Vent Restrictors Desiccant CO2 Scrubber Pure CO 2 Sample Reference Air In Figure 1 2 LI 6400 flow schematic with and without a 6400 01 CO2 mixer Schematic with a 6400 01 CO2 Mixer Schematic without a 6400 01 CO2 Mixer ...

Page 22: ... 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 Match mode is something that you do at least once at the start of the day and periodically throughout the day Matching is important when the DCO2 or DH2O value is small low rates small leaf areas For example a 1 µmol mol 1 offse...

Page 23: ...n by 1 1 where s is leaf area m 2 E is transpiration rate mol m 2 s 1 ui and uo are incoming and outgoing flow rates mol s 1 from the chamber and wi and wo are incoming and outgoing water mole fractions mol H2O mol air 1 Since 1 2 we can write 1 3 1 S von Caemmerer and G D Farquhar 1981 Some relationships between the biochemistry of photosynthesis and the gas exchange of leaves Planta 153 376 387 ...

Page 24: ...at the LI 6400 uses for transpiration is thus 1 6 Total Conductance to Water Vapor The total includes stomatal and boundary layer conductance of the leaf gtw mol H2O m 2 s 1 is given by 1 7 where Wl is the molar concentration of water vapor within the leaf mmol H2O mol air 1 which is computed from the leaf temperature Tl C and the total atmospheric pressure P kPa 1 8 E ui wo wi Ð s 1 wo Ð ui F 10 ...

Page 25: ...on ductances of one side of the leaf to the other termed stomatal ratio through out this manual 1 10 and gbw is the boundary layer conductance to water vapor mol H2O m 2 s 1 from one side of the leaf The boundary layer conductance correction thus de pends on whether the leaf has stomata on one or both sides of the leaf Net Photosynthesis The mass balance of CO2 in an open system is given by 1 11 w...

Page 26: ...ar in the equation for photosynthesis Asking this question means you didnÕt follow the derivationÉ The short answer is that it serves as a dilution correction as the leaf adds water vapor to the cham ber it dilutes all other gasses including CO2 Intercellular CO2 The intercellular CO2 concentration Ci µmol CO2 mol air 1 is given by 1 16 where gtc is the total conductance to CO2 and is given by 1 1...

Page 27: ...C i intercellular CO2 concentration µmol CO2 mol air 1 E transpiration mol H2O m 2 s 1 F molar flow rate of air entering the leaf chamber µmol s 1 gbw boundary layer conductance to water vapor mol H2O m 2 s 1 gsw stomatal conductance to water vapor mol H2O m 2 s 1 gtc total conductance to CO2 mol CO2 m 2 s 1 gtw total conductance to water vapor mol H2O m 2 s 1 kf K2 1 K 1 2 K stomatal ratio dimens...

Page 28: ...u 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 HereÕs a brief description of what should be there Figure 1 5 The LI 6400 Portable Photosynthesis System Console Sensor Head IRGA Quantum Sensor Optional Chemical Tubes Cable Assembly CO2 Cartridge Holder and Regulator Optional 2x3 Chamber ...

Page 29: ... Two Sensors on page 8 2 Leaf temperature is measured with a thermocouple held in the bottom of the 2x3 and 2x6 cm leaf chambers other chambers use energy balance to compute leaf temperature Cable Assembly The cable assembly has two electrical cables and two air flow hoses and con nects the console to the sensor head IRGA These are held together with a flexible outer wrapping Spare Parts Kit This ...

Page 30: ...sole It normally remains there and you can attach or detach the legs as needed Store the legs in the narrow front slot of the carrying case 6400 50 System Software The System Software disk contains the system software in your LI 6400 Keep this disk in a safe place Note New versions of this software are re leased periodically You can get the most recent version by contacting LI COR or by downloadin...

Page 31: ...tral Considerations on page 8 6 for a comparison of the 6400 02 and 6400 02B 6400 05 Conifer Chamber A cylindrical chamber suitable for short needled shoots Leaf temperature is obtained by energy balance for which an external PAR sensor reading is re quired External PAR sensor not included with this option 6400 06 PAM 2000 Adaptor This chamber top is designed for 8 mm fluorometer probes such as is...

Page 32: ...installable if obtained later To determine the presence of a coprocessor visit the Welcome Menu described on page 3 8 If a coprocessor is installed the item Coprocessor Installed will appear in the list of information displayed by the ÒAbout this unitÓ entry 6400 13 Thermocouple Adapter Allows a type E thermocouple to be connected to the 37 pin connector on the LI 6400 console This adapter is incl...

Page 33: ...necting the Chamber IRGA 2 5 USING A TRIPOD 2 6 6400 01 CO2 INJECTOR INSTALLATION 2 7 Using 12 gram CO2 Cartridges 2 8 External CO2 Tanks 2 10 EXTERNAL QUANTUM SENSOR INSTALLATION 2 14 6400 02B LED LIGHT SOURCE INSTALLATION 2 15 POWERING THE LI 6400 2 18 Mains Power 2 18 Batteries 2 18 INSTALLING SYSTEM SOFTWARE 2 19 What To Do 2 19 What Happens 2 20 ...

Page 34: ... full of chemicals To change the chemical grasp the tube barrel not the top cap and unscrew the bottom cap If the top cap is unscrewed with chemical inside damage to the air mufflers will occur Remove the bottom cap of the CO2 scrub tube and fill the tube with soda lime in the spares kit to within 1 cm of the tubeÕs end Replace the bottom cap and attach the tube to the console using the lower of t...

Page 35: ...e screws can break off if tight ened too much See Replacing Connector Screws on page 19 12 Air Inlet There are three air flow ports located to the right of the ON OFF switch The port labeled INLET is the intake port where the pump draws in the air that flows through the system If your system does not have a CO2 injector attach tubing from a buffer vol ume to the INLET port The buffer volume can be...

Page 36: ...ched 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 SAMPLE port of the console Attach the other hose to the REF port Figure 2 2 Console tubing and cable connections RS 232 Air Inlet Sample Reference Power Switch ...

Page 37: ...l the red dots meet and there is a click Figure 2 3 Electrical connectors air hoses and tripod bracket mounting holes on the sensor head IRGA Red Dots To Sample To Reference IRGA Connector Chamber Connector Tripod Bracket Mounting Holes Interchanging IRGAs If you have more than one LI 6400 at your disposal can you interchange the IRGA chambers The simple answer is probably no they are not de signe...

Page 38: ...ive graduate students The three screws included with the mounting bracket are threaded into holes on the right side of the analyzer housing on the sensor head Figure 2 4 using the 3 32Ó hex key in the spare parts kit The tripod mounting bracket is thread ed for use with standard 3 8 16 and 1 4 20 tripod heads Figure 2 4 Mounting holes for the tripod bracket are found on the right side of the senso...

Page 39: ... Tank Connector Block for using a tank of pure CO2 with a regulator described on page 2 10 Warning CO2 cylinders contain 12 grams of high pres sure liquefied CO2 Follow the handling precautions on the cylinder and cylinder cover carefully Note 12 gram CO2 cartridges last about 8 hours from the time they are pierced regardless of whether the system is in use or not However every once in a while say...

Page 40: ...e mounting block to secure the assembly to the console 2 Unscrew the CO2 cylinder cover 3 Install a new O ring in the groove around the piercing block Use your finger to press the O ring into the groove Figure 2 7 If the O ring is not in place when the CO2 cartridge is pierced gas will rapidly vent out a hole on the underside of the mounting block Figure 2 6 Location of external CO2 source assembl...

Page 41: ...rce assembly Figure 2 6 ItÕs a good idea to unscrew the cap before you install the cylinder and look down in at the end of the filter to check for any oil accumulating on the white filter material 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 e...

Page 42: ...ale NPT to 1 8Ó tubing fitting This fitting has a flow restrictor installed 10 cm3 min 1 Do not remove this fitting A 1 8Ó to 4mm compression union is also provided for users who may be unable to obtain 1 8Ó copper tubing Directions for installing the Tank Connector Block to a CO2 source using 4mm copper tubing are given in In stallation Using 4mm Copper Tubing on page 2 11 To install the 9964 033...

Page 43: ... unable to obtain 1 8Ó copper tubing you can connect the Tank Con nector Block to a CO2 source using 4mm tubing and the compression fitting LI COR part 300 04439 included with the Tank Connector Block 1 Install the Tank Connector Block and copper tubing This is described in steps 1 4 above Figure 2 8 Insert tubing through nut and ferrule Note proper orienta tion of ferrule 250 PSIG Pressure Relief...

Page 44: ...ing 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 Tighten the nuts on the compression fitting until snug plus 1 1 4 turn 3 Connect the 4mm tubing to your CO2 source Adjust the regulatorÕs pressure to between 180 and 220 PSIG ...

Page 45: ...ation Using the LI 6400 2 13 Figure 2 9 Use the compression fitting to connect 1 8Ó and 4mm tubing 1 8 Nut Ferrule 1 8 Copper Tubing Connector 1 8 Copper Tubing 4mm Copper Tubing To CO2 Tank Ferrule Ferrule 1 8 to 4mm Compression Fitting 1 8 Nut 4mm Nut ...

Page 46: ...urned with a 0 050Ó hex key provided in the spares kit The BNC connector plugs in at the rear of the chamber 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 Figure 2 10 The external quantum sensor installed BNC Connector S...

Page 47: ...ing it with the lamp assembly Follow these steps to install the lamp 1 Remove the tripod mounting bracket This is necessary to access the connector for the in chamber PAR sensor 2 Disconnect the light sensor Pull the connector straight out donÕt wiggle side to side with a pair of long nose pliers or your fingernails gripping the connector Figure 2 11 Figure 2 11 Disconnecting the in chamber PAR se...

Page 48: ...kit to remove the two long screws that hold the chamber top in place Figure 2 12 4 Install the o rings Ensure that there are o rings in the air passage holes Figure 2 12 The top and bottom chamber lips are held on with two hex head bolts Use the 3 32 inch hex key to loosen and tighten them Gasket GaAsP PAR sensor Connector O rings Upper leaf chamber cuvette Top View ...

Page 49: ...og switch connector 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 Figure 2 13 Attach the lamp and PAR sensor connectors Lamp Connector PAR Sensor Connector External Quantum Sensor BNC Connector Log Switch Co...

Page 50: ...duces about 1 5A The LI 6400 on average draws 1 5A therefore if the LI 6400 is drawing 1 5A the LI 6020 used with a 6400 03 will power the LI 6400 indefinitely At maximum draw with LED light source on running the coolers etc the LI 6400 will use about 3A Without the light source it will draw about 2A Table 2 2 shows the approx imate battery life when the LI 6400 is used with two 6400 03 batteries ...

Page 51: ...to the LI 6400 To see what version of software you have in stalled select ÒAbout this unitÓ in the Welcome Menu see Figure 3 5 on page 3 8 You can see what the latest available system software is and download it by checking our web site www licor com What To Do To install new system software requires a computer with a Windows DOS or Macintosh operating system Here is a general step by step 1 Obtai...

Page 52: ...d on our web site that explains how to use this pro gram Macintosh Double click the installer icon then click the INSTALL button What Happens 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 facto...

Page 53: ...isplay 3 17 TOUR 3 CONTROLLING CHAMBER CONDITIONS 3 20 Fixed Flow Operation 3 20 Fixed Humidity Operation 3 23 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 TOUR 4 LOGGING DATA 3 41 Logging Data Manually 3 41 Viewing Stored Data 3 43 Automatically Logging Data 3 49 TOUR 5 ...

Page 54: ...nt panel The left group does the same thing as the right group and it doesnÕt matter which you use Similarly there are two enter keys and two labels keys Function Keys Keys labeled f1 through f5 below the display are called function keys and of ten have labels associated with them on the bottom line s of the display When there are multiple definitions for these keys the labels key can be used to c...

Page 55: ... Cursor control keys escape key Function keys A S D F G H J K L Z ctrl X C V B N M P Q W E R T Y U I O Õ space _ shift escape shift 1 2 3 4 5 6 7 8 9 0 enter enter pgdn end pgup home pgdn end pgup home labels labels f1 f1 f1 f1 f1 LI 6400 Photosynthesis System OPEN 3 3 User 10 full Wed Jun 301999 09 46 55 12 01V Welcome Menu Config Menu Calib Menu New Msmnts Utility Menu ...

Page 56: ...N is assumed If you pressed Y the IRGA will be powered on so it can warm up while OPEN loads The LI 6400 then scans the file system Scanning file system adding a dot to the screen for each directory it finds Following this OPEN is loaded This takes a couple of minutes and a bar graph is displayed for your entertainment Figure 3 2 1 If your LI 6400 doesnÕt behave as described here refer to Power On...

Page 57: ... 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 Connecting and Disconnecting the chamber IRGA While the bar graph is displayed you can safely connect the chamber if you answered No at the ÒIs the chamber IRGA connected Ó prompt Once t...

Page 58: ...e OPEN main screen Software version Current time System info Help screens Test Menu Terminate program Configuration status and related utilities FLow meter zero IRGA zero span Mixer Lamp calibration Make New Measurements Filer File exchange recompu tations set clock sleep mode and date LI 6400 Photosynthesis System OPEN 3 3 User 10 full Wed Apr 14 1999 14 50 44 12 03V PAD FUSE CAL CONFIG Appears w...

Page 59: ...in the Welcome Menu as shown in Figure 3 5 CAL This message appears if you have changed the IRGA zero and or span setting or else the flow meter zero and have not stored the new setting s To store them press f3 Calib Menu select ÒView Store Zeros SpansÓ then press f1 Store For details see View Store Zeros Spans on page 18 18 Config The instrumentÕs configuration has been changed but is not stored ...

Page 60: ... Diagnostics Tests Menu Help Menu _Quit OPEN IRGAs left ON _Quit OPEN IRGAs OFF Serial Number PSC 0103 Last Serviced 9 Jan 1995 LPL version 3 0 007 OPEN version 3 01 Available memory 58205 bytes Coprocessor Installed Fuse Aware Press Any Key CO2 Mixer Test DAC Status Digital Status Log Button Tester Match Valve Tester Pressure Sensor Sys User Variable SnapShot Figure 3 5 The welcome menu is a gate...

Page 61: ...and press enter The Help Menu contains one or more files that you can read by highlighting and pressing en ter Prior to OPEN 3 2 there were a number of files stored here that would also be called up in response to ÒHelpÓ keys in various parts of the program With version 3 2 most of these have gone away 9 A word about exiting OPEN The bottom two entries in the Welcome Menu will terminate OPEN If yo...

Page 62: ...ControlÓ ÒPrompt ControlÓ Ò_ComputeList MenuÓ Ò_Reset MenuÓ Ò6400 02 or 02B LED SourceÓ Ò6400 05 Conifer ChamberÓ Ò6400 06 PAM InterfaceÓ Ò6400 07 or 11 2x6 ChamberÓ Ò6400 08 Clear 2x3 BottomÓ Ò6400 09 Soil ChamberÓ Ò6400 10 MiniPAM InterfaceÓ Ò6400 13 TC AdapterÓ Ò6400 14 OptisciencesÓ ÒExternal Quantum SensorÓ ÒStd 2x3 Chamber TopÓ ÒView Installed Cal ItemsÓ _Configuration Examples Menu Installa...

Page 63: ...urned off thereby eliminating all sourc es of air movement through the flow meter The display will show a count down for 10 seconds along with the flow meterÕs signal mV At the end of 10 seconds an internal adjustment is made so that the flow meterÕs signal is zero or very close to it Figure 18 9 on page 18 17 3 Return to the Calib Menu WeÕre done so press escape or f5 Done Plot the mixer calibrat...

Page 64: ...pe If you would like to see the values of the plotted data however press V for View instead 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 3 Return to Calib Menu When you are done viewing the data values press escape Figure 3 8 A typical CO2 mixer calibration curve relating set ...

Page 65: ... opera tions like deleting copying and editing files It is described in Chapter 10 Set the baud rate data bits stop bits etc of the COMM port See ÒSET COMMÓ on page 21 19 If you use File Exchange mode you need not both er with this When the LI 6400 is in file exchange mode it can serve as a file server for a PC See Chapter 11 Runs GraphIt Chapter 12 to plot data from any data file You can also do ...

Page 66: ...ons if you press labels seven times youÕll see them all Here is a shortcut press the number keys 1 through 7 on the keypad and youÕll jump directly to that function key level The current function key level number is displayed in the bottom left hand corner of the display Figure 3 11 To change function key levels 1 Press 1 through 7É This directly accesses the selected level 2 Éor press labels or s...

Page 67: ...d Match rspns Flow Mixer Temp Lamp 500µms OFF OFF OFF AREA STOMRT LeafFan Prompts User 6 00 1 00 Fast off Consts Graph GRAPH view GRAPH XYPlot is OFF QuikPik graph Editor LOG AUTO LOG LogList PROG Help QuikPik Display Display WhatÕs Display Display QuikPik List What Editor Help Logging control IRGA matching Environmental control manager keys CO2 humidity temp light Chamber fan speed system and use...

Page 68: ...er and the fan will stop If you are listening you should here a drop in the noise level 4 Turn the fan back on fast Press f3 then f and the fan will resume running AREA STOMRT LeafFan 6 00 1 00 Fast 3 399 7 365 9 15 79 22 70 33 8 6 91 172 8 70 09 ÆCO2_µml ÆH2O_mml Flow_µml RH_S CO2R_µml CO2S_µml H2OR_mml H2OS_mml a b 399 7 365 9 15 79 22 70 CO2R_µml CO2S_µml H2OR_mml H2OS_mml a current fast Leaf F...

Page 69: ...y press or Pressing the horizontal arrow keys will scroll the change line through all the possible displays But itÕs a lot faster to use the letter shortcuts 4 Go exploring Table 3 1 lists the default displays and their variables Use the arrow keys and letter keys to view them yourself Note that these display definitions can be modified what variables are shown and where to suit nearly any taste I...

Page 70: ...Flow rate to the sample cell µmol s 1 RH_S_ Relative humidity in the sample cell C Photo Photosynthetic rate µmol CO2 m 2 s 1 Cond Conductance to H2O mol H2O m 2 s 1 Ci Intercellular CO2 concentration µmol CO2 mol 1 Trmmol Transpiration rate mmol H2O m 2 s 1 D Ci Ca Intercellular CO2 Ambient CO2 VpdL Vapor pressure deficit based on Leaf temp kPa VpdA Vapor pressure deficit based on Air temp kPa E ...

Page 71: ...e J Battery Battery voltage V J CO2 Status of CO2 IRGAs H2O Status of H2O IRGAs Pump Status of pump Flow Status of Flow controller Mixr Status of CO2 mixer Fan Speed of chamber fan K Program Shows AutoProgram status ProgPrgs AutoProgram step counter FwMxCrLp Numerical summary of the four stability flags totalCV See totalCV under E above L CRagc_mv Reference CO2 AGC automatic gain control sig nal i...

Page 72: ...y vs Flow Rate This experiment illustrates the relationship between chamber humidity and flow rate 1 Simulate a leaf with filter paper Use Whatman 1 filter paper or even towel paper folded a couple of times and moist but not dripping Clamp your ÒleafÓ into the leaf chamber 3 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 f...

Page 73: ...ube roll the knob away from you for scrub ThereÕs no need for strong fingers here when the knob gets resistive at the end of itÕs travel quit ItÕs far enough 3 Use a high flow rate 700 µmol s 1 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 Figure 3 16 Set the adjustment knob so that the chamber gaskets are slightly compressed w...

Page 74: ...n key label f2 level 2 The fourth item RH_S_ is relative humidity in the sample cell in percent 6 Change the desiccant to full bypass 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 N None Pump OFF Humidity Control Options Targets ...

Page 75: ... reference and sample humidities fall and note that a the sample value comes down slowly because of the slow flow rate4 and b the reference goes back to near zero but c the sample doesnÕt return to the value you had in Step 4 because now the flow is slower 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 active...

Page 76: ... achievable 1 Set flow to 400 Press 2 f2 then 400 enter 2 Put desiccant mid range Set the knob midway between scrub and bypass ItÕs about one complete knob turn from either extreme but you donÕt have to look you can feel the mid point because this is the region where the knob is the loosest 3 Note the sample water mole fraction The H2OS_mml value is probably about 20 mmol mol 1 4 Switch to humidit...

Page 77: ...arget e g 18 mmol mol 1 The flow rate will eventually settle on a higher value that maintains this lower humidity 9 Enter a target thatÕs too dry Now change the target to a much lower value like 5 mmol mol 1 below the original target value e g 15 mmol mol 1 The flow rate will go as high as it can but if itÕs not high enough eventually the message FLOW Need SCRUB or wetter target will begin flashin...

Page 78: ... you to possible problems Experiment 2 illus trated two The complete list of possible causes is in New Measurements Mode Warning Messages on page 20 7 When such a situation occurs a warning message is displayed on the middle label line on the display as illustrated in Figure 3 20 If you wish to disregard the displayed message and get it out of the way press ctrl Z to turn it off hold the ctrl key ...

Page 79: ... in Real Time Graphics on page 6 8 But for now just follow along and youÕll get the job done 1 Use the Real Time Graphics Editor 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 Photo Cond Ci Trmmol 399 7 365 9 15 79 22 70 33 8 6 91 172 8 70 09 15 4 0 216 238 ...

Page 80: ..._ Ó from the menu of possibilities5 and press enter When asked to enter scaling information press f1 DelLn then type 5 then enter By entering one value we are specifying the range of the plot the actual max and min of the Y axis will adjust as needed to keep the curve on scale Figure 3 21 The Real Time Graphics Editor allows the parameters for up to three curves to be set Parameters can be stored ...

Page 81: ...a dialog box for naming files Standard File Dialog on page 5 9 Press labels then f1 DelLn to clear the entry line then type in a file name such as ÒFlow and RHÓ without the quotes and press enter 8 Exit the Editor Press labels to return to the first level of key definitions then press f5 OK Part B Do the Test WeÕll now change the input humidity from dry to ambient and back and watch how the flow r...

Page 82: ... seconds continue on with the next step 4 Turn the desiccant to full bypass Moister air will enter the chamber so flow must increase to maintain the tar get humidity 5 Wait about 15 or 20 seconds turn to full scrub The flow drops to a new value but humidity stays the same 6 Change to medium response and repeat Steps 4 and 5 Press escape to stop viewing the graph Press 2 then f1 to drop the respons...

Page 83: ...se the humidity is the most stable and the flow rate the most unstable On slow re sponse the flow rate is most stable but the humidity is least stable reacting slow ly to the changing incoming humidity Note the downward trend in flow rate at full scrub indicating that the paper is drying out Fast Med Slow Fast Med Slow Points to Remember You have control over a trade off stable humidity and unstab...

Page 84: ...le and reference IR GAs arenÕt reading the same thing Matching discussed on page 4 34 will take care of that but weÕll ignore it for now 4 Desiccant full scrub Notice the burst of CO2 that you get ThatÕs because the desiccant buffers CO2 chemically as well as volumetrically 5 Soda lime full bypass desiccant full bypass Now weÕll let ambient air into the chamber Watch how unstable photosyn thesis b...

Page 85: ...the CO2R_µml val ue line a should be close to 400 the target 4 Once CO2R_µml is stable change target to 200 µmol mol 1 Press f3 200 enter Notice how much faster CO2R_µml drops than rises It may overshoot or undershoot the target value but will correct itself eventual ly Calibrating the mixer page 18 20 can improve this performance 5 Once CO2R_µml is stable change to 20 µmol mol 1 Press f3 20 enter...

Page 86: ...mixer for a 400 µmol mol 1 reference target Press f3 R 400 enter 4 Turn on Real Time Graphics Press 4 then f1 to start the graph you should have defined in Figure 3 25 5 After 1 minute change reference target to 900 µmol mol 1 When the CO2S curve flattens out press escape 2 f3 900 enter Points to Remember Soda lime must remain on full scrub when using the mixer The lowest stable value is typically...

Page 87: ...d the faster response of the reference cell Your results should be similar to Figure 3 26 Figure 3 26 Controlling on reference CO2 concentration with a closed empty chamber Note the slower response of the sample cell due to its larger volume is aggravated at lower flow rates Note also the faster response when lowering CO2 than when raising it b Flow 100 µmol s 1 a Flow 500 µmol s 1 Points to Remem...

Page 88: ...k temperature 2 Set block target to 3 cooler than current value Press 2 f4 B value 3 enter where value is the block temperature from Step 1 The external fans on either side of the chamber should start to run Watch the block temperature slowly drop to this new target value 3 Note the temperature gradient You should see that Tblock Tair Tleaf 4 Now make the target 3 degrees warmer than ambient Press...

Page 89: ... temperature will drop in discrete increments as the control algorithm works to get the leaf tem perature down to where it belongs 4 Now add 1 degree to the target leaf temperature Press escape to get back to text mode then 2 f4 value 1 enter Then 4 f3 to view the strip charts Figure 3 28b There will typically be a large increase in block temperature to get the leaf temperature to begin to rise fo...

Page 90: ...af temperature a Cooling by 1 degree and b warming by 1 degree a Cooling b Warming Points to Remember 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 ...

Page 91: ...n screen then f3 New Msmnts The lamp control is the most straight forward of all the control algorithms The feedback is immediate since there is a sensor right in the light source measuring its output and there is no other mechanism such as flow rate or leaf response that will interfere with the light value9 Experiment 9 Simple Lamp Control 1 Close the chamber no leaf 2 Monitor in chamber PAR on t...

Page 92: ...ump and or proportioning valve for humidity control LEDs for light control etc they have common interfaces and logic In fact this control software offers some powerful features that our tour did not touch upon 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...

Page 93: ...he Standard File Dialog This screen will appear anytime you need to enter a file name and is fully described on page 5 9 Press labels to access the editing keys then f1 DelLn to clear the default name then type Experiment 1 and press enter If you enter the name of a file that already exists you will be given the choices of overwriting that file appending to it or entering a different name 4 See ho...

Page 94: ...f1 7 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 Figure 3 30 The prompt for entering remarks into a log file The details of this type of dialog box are described in Standard Line Editor on page 5 5 Enter Edit Remarks DelLn ClrEnd DelChar CapLock AnyChar LOG VIEW CLOSE ADD Match 2 File F...

Page 95: ... that appears in several contexts and is explained thoroughly in Chapter 12 But for now just follow along and weÕll make some graphs LOG VIEW CLOSE ADD Match 4 File FILE REMARK 1 OPENÕs Graphics Packages OPEN uses two graphics packages Real Time Graphics is used to plot measurements as they happen providing you with strip charts GraphIt on the other hand is only used on data that is stored in a fi...

Page 96: ... Appears only if curves are defined OPEN 3 01 Tue Nov 4 1997 15 40 30 ComputeList User Configs Comps Defa BLCTable Sys Lib StdBLCTable LightSource Sun Sky 1 0 19 LogFormat User Configs LogFormats S PromptList User Configs Prompts Def Experiment 1 0 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 e...

Page 97: ...12 7 0 529 6 1 2 84 26 40 20 44 26 51 1316 1 1293 4 8 678 19 358 24 42 54 48 700 2 0 10 97 21 0 0 111105 3 206 3 1 85 1 44 1 27E 03 2 92 0 289 6 1 2 84 26 49 22 81 26 58 1316 5 1283 1 8 745 25 716 24 48 71 98 100 4 0 11 97 2 0 0 111105 4 261 0 2 09 2 49 1 28E 03 4 61 0 328 6 1 2 84 26 52 23 62 26 61 1333 0 1284 9 0 226 26 737 0 63 74 69 99 9 0 11 97 2 0 0 111105 Figure 3 35 Experiment 1 as stored ...

Page 98: ...imum and then the maximum of the axis Figure 3 38 If you had to press V to change the variable youÕll have to press R now to set the range When you are done if the display does not return to the menu shown in Figure 3 37 youÕll have to press escape Edit which item X X horizontal axis Y Y left vertical axis Z Z right vertical axis L Logic for including observations C Curves Press choice or esc Figu...

Page 99: ...tically upon leaving the configuration editor then press f2 to plot the graph Figure 3 39 These data illustrate the concept of an operating envelope for humidity con trol if we draw a line around these data we draw the envelope Figure 3 40 8 Save this definition for future use Press escape to stop viewing the graph and return to GraphItÕs main screen Press f5 Config SaveAs and name the file ÒRH Fl...

Page 100: ... to redraw to our first plot 11 Éand view the plotted data Instead of pressing escape to stop viewing the graph you can press V and a scrollable menu of the data points plotted will appear Figure 3 42 Press escape to exit from this 12 Return to New Measurements mode and close the file Press escape until you get back to New Measurements Mode then press f3 Close File ThatÕs the quick introduction to...

Page 101: ... that logs data at regular intervals Logging data at regular intervals 1 Open a data file Press 1 if necessary then f1 to name and open a data file 2 Pick the AutoProgram ÒAutoLogÓ Press 5 then f1 A menu of AutoPrograms will appear Select the one named AutoLog and press enter Figure 3 43 3 Answer the questions YouÕll be asked the following three questions in succession Log every __ secs Add __ obs...

Page 102: ...escape then A Try that now 7 Close the data file Press 1 then f3 to do this Notice that AutoPrograms donÕt automatically close data files You can open a file for logging then run several AutoPrograms accumulating data in that file 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 ...

Page 103: ...eaf Area You probably wonÕt be using 6 cm2 for leaf area so at the very least youÕll have to remember to set the area to your best estimate of what the needle area really is ItÕs easy to enter a value thereÕs a function key in New Measure ments mode for that 10 Boundary Layer Conductance The default configuration uses a lookup table based on leaf area and fan speed but that table is appropriate fo...

Page 104: ...iguration file and of course we do so press Y again 5 Select a chamber bottom YouÕll get a menu of the two chamber bottoms that fit the 2x3 chamber the clear bottom and the opaque bottom Highlight the ÒStd 2x3 Opaque Bot tomÓ entry and press enter 6 Pick the light source Highlight the ÒSun SkyÓ entry and press enter 7 Pick the chamber top if more than one If you have more than one chamber top that...

Page 105: ...other configuration CalParGaAs 0 77 GA_103 20 Jan 1995 BLCond 5 AREA 2 LightSource Sun Sky 1 0 0 19 ComputeList Default using EB Displays Std EBTleaf LogFormat Std EB Which chamber top and light sensor Use a fixed boundary layer conductance instead of a lookup table Default leaf area Proper light source is im portant for the energy bal ance computation The standard equation set for photo cond etc ...

Page 106: ...4 View the new variable EBTlf Press escape until you get to OPENÕs Main Screen then go to New Measure ments mode and press H The computed leaf temperature will be labelled EBTlf and the variable Tleaf C will be chamber air temperature When using this configuration be sure to pull the thermocouple down a bit so it does not contact the leaf but measures air temperature in the chamber instead This wi...

Page 107: ...re 3 47 It will include the three classes of light sensor calibrations 4 Return to the Config Menu Press escape until you get there A step by step example of how to install a 6400 02B Light Source starts on page 16 5 User Defined Equations The final stop on our configuration tour will be to view the user defined equa tions Chapter 15 covers this topic in detail 6400 02 02B LED s CalParLED 55 SI 50...

Page 108: ...press en ter to insert a new line and type the new definition Figure 3 48 5 Store the file under a new name 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 30 Photo Photosynthesis umol m2 s 10 co2_diff_um co...

Page 109: ... Add A menu of variables will appear Scroll down through the list until you find Ò31 P_gddÓ Highlight it and press enter Then highlight Ò30 PhotoÓ and press enter Then press escape to signal that weÕre adding no more variables to this line Note the line label for this new line it will probably be m if youÕve started with the default display list When youÕre done the display should look like Figure...

Page 110: ... factory configuration or to a configuration of your choice Access the Reset 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 Photo Cond Ci Trmmol 1 95 1 23 0 233 0 101 499 5 40 09 1 23 0 0141 438 0 119 ÆCO2_µml ÆH2O_mml Flow_µ...

Page 111: ...eside in the file system When it starts up however LPL looks for a specific file sys autost to run if it exists The default sys autost runs sys open start which scans the file system and asks if the chamber IRGA is connected then runs sys open open OPEN launches many applications such as AutoPrograms calibration pro grams and various editors Figure 3 51 A depiction of software layers in the LI 640...

Page 112: ...omputer and run the 6400 50 instal lation program INSTALL EXE you must be in the Boot Screen and the program will make use of the Upload option More details are provided in The Boot Screen on page 5 18 2 Make sure Debug is OFF If Debug is ON press D to toggle it to OFF then press S to save the configu rations Debug is used for testing and having it on will slow some operations noticeable especiall...

Page 113: ...the LPL Operating System The user interface to LPL is the LPL Screen Figure 3 53 which allows you to edit files access the Filer enter File Exchange Mode run LPL programs or execute LPL commands from the keyboard For details see The LPL Screen on page 5 20 For this tour weÕll perform a series of tasks to demonstrate what can be done from this level View Data Files from LPL 1 Access the Filer Press...

Page 114: ...and press H again This time GraphIt is accessed im mediately because its libraries remain loaded and will until you leave the Filer 7 Return to the LPL Screen Press escape until you get there Write and Run an LPL Program The LPL program youÕll see the most is OPEN The file system contains a number of other programs however that donÕt require OPEN What weÕll do now is have you write a simple progra...

Page 115: ...menu press S and use the Standard File Dialog to name the file Hello and put it in the directory User To specify the directory user if itÕs not already selected press f1 Dir and pick it 6 Return to the LPL Screen From the exit menu press Q 7 Run your program again Press R and enter user hello Your program should run again Press enter to end it Run another program LetÕs run a slightly more useful p...

Page 116: ...atmosphere change 4 Quit Press escape to exit the program and return to the LPL Screen Launch OPEN from LPL Now letÕs run a familiar program from the LPL Screen OPEN 1 Press R YouÕll be asked for a file name 2 Enter OPENÕs name and directory 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 3 Interrupt it Press ...

Page 117: ...pe sys autost and press enter You will see FCT main sys open startÓ RUN which means the only thing this program does is run another program named sys open start 2 View sys open start Press escape then Q to stop viewing sys autost and press E then f1 DelLn change the name to sys open start and press enter This is the program Figure 3 55 on page 3 66 that prompts you for Is the chamber IRGA connecte...

Page 118: ...IF 1 0x0301 DIOSET 1 0x0302 DIOSET THEN HALT ScanDirs 1000 OPEN_BUFF IF RETURN THEN PTR buff buff DIRALL buff CLOSE CLEAR Figure 3 55 Listing of sys open start which ultimately launches sys open open Get flow and analyzer board status If either are off ask if they can be turned on Scan the file system get directory list Set current working directory Run OPEN This function called when user presses ...

Page 119: ...ight Curve Step By Step 4 27 CO2 RESPONSE CURVES 4 30 Why Measure CO2 Response 4 30 Operational Considerations 4 30 Step By Step 4 32 MATCHING THE ANALYZERS 4 34 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 STABILITY CONSIDERATIONS 4 41 Stability Variables 4 41 Real Time Graphics 4 4...

Page 120: ...g Warm Up 1 Air Supply Prepare CO2 Mixer or Buffer Volume 2 Temperatures Values OK Tleaf responding 3 Light Source Sensors Responding Values OK 4 Pressure Sensor Value OK Stable 5 Leaf Fan Running 6 Flow Control Max flow OK Chemical tube restrictions B After Warm up 1 Check the flow zero 2 Adjust latch close chamber 3 Check CO2 zero 4 Check H2O zero 5 Mixer Calibration optional 6 Lamp Calibration ...

Page 121: ...ee Specifying the Source and Sensor on page 8 3 The light sensors ParIn_µm and ParOut_µm are both in default display group g See that they respond as expected when the light sensors are illumi nated and darkened If you get negative ParIn_µm values there is probably a mismatch between the real light source and the one OPEN thinks it has A trip to LightSource Control page 8 4 will fix that 4 Check t...

Page 122: ...ow meter Ze roing the Flow meter on page 18 17 Turn the fan back on when done 2 Adjust the latch and close the chamber 1 Adjust the latch so that the chamber lips are slightly apart when the cham ber is closed 2 With the chamber closed close the adjustment knob until it starts to become snug 3 Open the chamber and turn the knob one or two more half turns Now the chamber is adjusted properly for se...

Page 123: ...RGAs 5 Mixer Calibration If you are using the 6400 01 CO2 Mixer run the calibration program de scribed in 6400 01 CO2 Mixer on page 18 20 The chamber can be open for this Make sure that the soda lime is on full scrub 6 Lamp Calibration If you are using the 6400 02 or 02B LED Source run itÕs calibration which is described in 6400 02 B LED Source on page 18 24 You will do the best calibration by hav...

Page 124: ... any fluctuations in the sample cell CO2 concentration CO2S_µml display group a If there are no leaks the CO2S_µml value should not increase by more than 1 µmol mol 1 10 Match the IRGAs Matching the IRGAs is easily accomplished whether the chamber is empty or not but itÕs good policy to do this once right before starting a measurement Refer to Matching the Analyzers on page 4 34 for how to do this...

Page 125: ...ful with the chamberÕs orientation avoid shading part of the leaf with the walls of the chamber 6 Set Area and Stomatal Ratio In New Measurements mode press 3 and set the leaf area and stomatal ratio for this leaf Leaf area is simply the area exposed inside the chamber If you are using a 2x3 chamber and filling it the area is 6 cm2 Stomatal ratio is an estimate of the ratio of stomata on one side ...

Page 126: ...is will take you through getting the leaf into the chamber 3 Observe the CO2 concentrations Note CO2S_µml Is it below CO2R_µml If so thatÕs good because it means photosynthesis is occurring Photosynthetic rate will be on display line c un der Photo Is CO2S_µml stable within 0 2 or 0 3 µmol mol 1 It should sta bilize after 30 seconds or so of clamping onto the leaf If itÕs not stable check CO2R_µml...

Page 127: ...to photosynthesis CO2R_µml CO2S_µml DCO2 and Photo and the values that pertain to conductance H2OR_mml H2OS_mml RH_S_ and Cond 4 Find the upper humidity limit Set the desiccant on full bypass and the flow rate to 100 µmol s 1 Wait about one minute then observe the water numbers The value of H2OS_mml will be about as high as youÕll be able to achieve with this leaf at this stomatal con ductance Que...

Page 128: ...duct an experiment at a consistent chamber humidity This experiment lets you see the automatic hu midity control in action 1 Pick a humidity target Start out in fixed flow mode at 400 µmol s 1 with the desiccant adjustment knob midway between scrub and bypass When H2OS_mml is stable change to constant humidity control use the H option constant H2O mole fraction and target that current value of H2O...

Page 129: ...hanged in the previous step not to give the answer to Question 6 awayÉ 4 Change to constant RH Return the desiccant knob to midway and after the flow rate stabilizes note the value of RH_S_ Now change to constant RH control and target that value of RH_S_ 5 Turn on the coolers Turn on the temperature controllers f4 level 2 and set the block temperature for a target about 5 C below itÕs present valu...

Page 130: ...ormal You can turn the temperature control off if you like Controlling CO2 The next two experiments are best done with a 6400 01 CO2 mixer If you donÕt have one installed you can still do approximate CO2 control between ambient and zero by adjusting the soda lime tube flow adjust knob Experiment 3 CO2 and Humidity Control Interactions Start with the conditions described by Do this first on page 4 ...

Page 131: ... much less rapidly so the sample cell CO2 control option isnÕt faced with large swings in flow rate The next two steps will illustrate a more typical sequence of events 4 Return the desiccant knob to mid range Watch the sequence reverse itself Also note the order in which things hap pen Once Flow_µml stabilizes then CO2S_µml can stabilize 5 Shade the leaf If you are using a light source cut the li...

Page 132: ...ol 1 If you donÕt set the soda lime knob on full bypass Temperature Control Constant leaf temperature and target the current value Light Use 1000 µmol m 2 s 1 If you donÕt have a light source beware this experiment is meaningless without steady light 2 Open Log File Name it ÒSample CO2 curveÓ or whatever you like f1 level 1 3 Wait for stability and log the first point When the CO2 and humidity con...

Page 133: ...5 points between your starting value and ending points Go down to 30 µmol mol 1 or so for C3 plants and 0 for C4Õs Hint If you are using the CO2 mixer you get 0 µmol mol 1 by turning the mixer off At any point along the way you can view a graph of your logged data by do ing Step 8 7 Finish the curve back at the starting point Repeat the starting point See how long it takes for the photosynthetic r...

Page 134: ...ht ItÕs low tech but effec tive We start once again with the conditions that Do this first on page 4 8 de scribes 1 Set the controls Flow Constant mole fraction target the current value Step 1 on page 4 10 CO2 If you have a CO2 mixer set it to control reference CO2 to a bit above ambient such as 400 µmol mol 1 If you donÕt set the soda lime knob on full bypass Temperature Control Constant leaf tem...

Page 135: ...t really happened 5 Simulate longer shade slow cloud Now try decreasing the light by 80 for 2 minutes then returning it to its starting value Was this long enough to get the stomata to start to respond If you are patient you might find out how long it takes for the stomata to stop responding when the light drops That is how long before they stabilize in the new conditions It might be 10 or 15 minu...

Page 136: ...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 This experiment will measure sun and shade leaves that are adapted to their radiative environment If you donÕt use the light source you wonÕt ...

Page 137: ...vel 1 or else press the button on the chamber handle for about 1 second After logging move on to the next leaf If you arenÕt using a light source be careful about shading these sunlit leaves If a leaf is tipped very much away from the sun prior to measurement the chamber walls will cast a shadow on the leaf when you place it in the cham ber Changing the orientation to avoid this shading will cause...

Page 138: ...e 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 The remaining sections in this chapter describe some op erational hints and considerations with which you should be familiar Points to Remember Measurements c...

Page 139: ...he leaf If you are measuring sunlit leaves donÕt select one that just happens to be in a small sunfleck or one that just became sunlit when you moved some stems out of the way When you put a leaf into a clear topped chamber the light incident on the leaf will be reduced by about 10 Photosynthesis will respond fairly quickly to that reduction and should equilibrate in a few seconds Stomatal respons...

Page 140: ...t right On the other hand if you can afford 2 or 3 minutes per measurement and want consistent sample CO2 concentrations try the S op tion f3 level 2 Flow Humidity Use a fixed flow rate medium or high with little or no desiccant scrubbing HereÕs the rationale Fixed flow rate minimizes the time for system equilibra tion once a leaf is installed Minimal scrubbing along with a high flow rate means th...

Page 141: ...eaf area as you log data Extra Data Are there extra data you wish recorded such as numbers or remarks the op erator is to enter to help identify the data later How Many Log Files Are all the measurements destined for one file or should there be several If several whatÕs the rationale for the grouping Does it matter in which order the measurements are done The simplest approach is log all the data ...

Page 142: ...nd fairly rapidly decrease the light spending perhaps 1 or 2 minutes at each light value and dropping in steps of 200 µmol mol 1 or less When you do this youÕll find that the stomata have not had time to adjust and tend to be more open at the low light values than they normally would This manifests itself as a steadily rising Ci throughout the measurement ThereÕs nothing wrong with this but be car...

Page 143: ...te each new light level with the starting light value with time to equilibrate That is use a sequence such as 1800 1000 1800 500 1800 300 1800 µmol m 2 s 1 The starting point neednÕt be high you could work the other direction with shade leaves Data collected in this manner might be most appropriate for addressing questions of light dynamics in canopies Operational Considerations Once you decide on...

Page 144: ...ing to be changing much dur ing a light curve thereÕs no real reason to match after every measurement Match once before starting If you are doing a slow curve however matching wonÕt hurt anything since youÕll have time to burn With OPEN version 3 2 and above you are asked for a matching threshold the absolute value of the DCO2 value Thus you donÕt have to decide whether to match before each observ...

Page 145: ...vents throughout the experiment letting you record how the leaf responded with time as well as with light Rapid Light Curve Step By Step HereÕs how to make an automatic light response curve It uses ÒLightCurveÓ and does a rapid response curve 1 Prepare the chamber Light Typically 1500 µmol s 1 for C3 plants or 2000 for C4 plants CO2 Constant reference CO2 about 400 µmol mol 1 or your choice This i...

Page 146: ...sh to adjust the scale of the Photo PAR plot 9 Match the IRGAs Be sure CO2S_µml is stable before you do this 10 Launch the ÒLightCurveÓ Autoprogram Press 5 then f1 Pick ÒLight CurveÓ from the list When asked ÒAppend to current data file Ó Press Y When asked ÒEnter the desired light values Ó edit the list as needed and press enter When asked ÒEnter min timeÓ enter the desired value 120 seconds is u...

Page 147: ...chamber if you are done with it 14 After the fact analysis Before you close the data file you may want to access GraphIt press View File f2 level 1 in New Measurements mode If the axes are not defined for a light curve press QuikPik Config f1 and select ÒLight CurveÓ Press REPLOT GRAPH f2 and draw it Answer these questions by plotting the appropriate data Did sample cell CO2 stay constant Did the ...

Page 148: ...ns Operational Considerations Some things to consider when doing a CO2 response curve Light Either the 6400 02 or the 02B LED source will work just fine for CO2 re sponse curve since the goal is to maintain constant light during the measure ment Stomatal behavior which the blue light controls is not so important for this measurement as long as the stomata stay reasonably open Differential closing ...

Page 149: ...e coolers for a constant leaf temperature Humidity Control Operate the flow control for constant water mole fraction Expect higher con ductances and transpiration rates at the low CO2 values so leave room for the flow rate to increase Matching Since the concentrations of CO2 are covering a large range match before each reading With OPEN version 3 2 and above you are asked for a matching threshold ...

Page 150: ...n change the flow control to constant mole fraction and target this value The flow should be 300 µmol s 1 or so WeÕll need room for it to increase because the conductance will likely increase dur ing the measurement as the chamber CO2 decreases 4 Set the temperature Set the temperature control for constant leaf temperature 5 Open a log file Make sure you have the computations prompts log list etc ...

Page 151: ...take For the stability enter 1 Open 3 01 and below When asked ÒMatch before each obs Ó press Y Open 3 2 and above When asked ÒMatch if ÆCO2 ppmÓ enter 15 The experiment will then start automatically 10 Watch the curve develop Press 4 then f3 and watch the curve develop 11 When itÕs done Once the curve is done you may want to set the CO2 back to the starting val ue to let the leaf recover Or just t...

Page 152: ...r by 1 30 or 3 3 If however the differential is small for example Cr 360 and Cs 355 then the error in photosynthetic rate due to a 1 µmol mol 1 offset is 1 5 or 20 Clearly the smaller the differentials the more important matching becomes The first step to matching is making the IRGAs see the same air This is a me chanical exercise accomplished by a small valve on the bottom of the cham ber IRGA Fi...

Page 153: ...RGA After a change in incoming air water will take longer to come to a new equilibrium than CO2 because of sorption effects During this period the display will Reference Sample Leaf Chamber Reference Sample Leaf Chamber Normal Match Mode LI 6400 PSH 0001 PORTABLE PHOTOSYNTHESIS SYSTEM MODEL SR NO LI 6400 PSH 0001 PORTABLE PHOTOSYNTHESIS SYSTEM MODEL SR NO Match Position Normal Position Figure 4 4 ...

Page 154: ...ens in Match Mode Once in match mode Figure 4 6 your choices are provided by the function keys f5 MATCH IRGAs matches the IRGAs computes a new Cms and Wms or f1 exit quits The display indicates the values of sample CO2 and H2O when last matched and the elapsed time since the last match Pressing f5 MATCH IRGAs will cause Cms and Wms to be adjusted so that the sample and reference values become the ...

Page 155: ... 1 after the match valve closed and the expected change was much larger than that 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 IRGA Match Mode ÒCONFIG JoeÓ CO2R_µml CO2S_µml H2OR_mml H2OS_mml 330 1 329 2 18 24 18 55 Prev 00 22 01 CO2 402 H2O 18 8 exit MATCH Elapsed time...

Page 156: ... leak in the chamber exhaust tube or else a problem with the match valve itself See page 20 21 for troubleshooting help The best way to prevent this message is to not enter match mode when the sample cell concentrations are unstable ÒExcessive DeltasÓ If MATCH is pressed and the difference between sample and reference IR GAs exceeds 10 µmol mol 1 for CO2 or 1 mmol mol 1 for H2O a warning will be d...

Page 157: ...ver the IR GAs may not be so well zeroed and spanned so matching will be a function of concentration Periodically How often That depends most on temperature changes so itÕs hard to pre scribe a definite time Start with 30 minutes or so and adjust as needed Use of the coolers to stabilize temperatures will help to minimize zero drift and thus reduce the need for matching Logging Match Adjustments T...

Page 158: ...oesnÕt change enough when match mode is entered and the second message means that the sample CO2 value never stabilized sufficiently in 1 minute to do a match Modifying the Match Display OPEN 3 2 and above While in match mode press labels then Edit Display 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...

Page 159: ...ystem When the sum of these totalCV is sufficiently small say less than 1 or 0 5 then you can be assured that the system is stable Also if you include this information in your logged data6 you can tell after the fact how stable the system was for any given observation Real Time Graphics A useful visual indicator of stability can be had with judicious use of New MeasurementÕs strip chart mode Real ...

Page 160: ...leaks bulk flow and diffu sion Bulk flow leaks occur when there is a hole apart from the system inlet and outlet that allows air to move into or out of the system Diffusion occurs when a particular gas such as CO2 moves through the walls of the system in response to a concentration gradient Bulk Flow Leaks The pressure inside the leaf chamber is slightly positive so that bulk flow leaks tend not t...

Page 161: ...ned with ethylene vinyl acetate through gasket material ethylene and neoprene and through O rings butyl rubber It goes through just about everything thatÕs not glass or metal There are some thin film materials that have very low per meabilities to CO2 however such as Teflon Saran polyvinylidene chlo ride Mylar and Propafilm polypropylene coated with Saran Diffusion of CO2 into or out of the LI 640...

Page 162: ...t was set up in a vacant well mixed greenhouse 3 an external fan continually ventilated the chamber 4 the ambient CO2 concentration was monitored with a second gas analyzer Sample cell CO2 concentrations were measured by the reference IRGA using the match valve This eliminated any potential errors due to IRGA drift since the same IRGA 7 Simple in hindsight it took a couple of weeks to get it right...

Page 163: ...er than Flow k is then the slope of the line Note that the outliers tend to be the data collected with the smallest gradient so uncertainties in what the true gradient was are largest Figure 4 10 CO2 diffusion into a closed empty LI 6400 chamber with black neo prene gaskets as a function of flow rate for various reference concentrations Cr Ca ambient CO2 was 400 µmol mol 1 Diffusion effects are hi...

Page 164: ...sÓ one for transpiration and one for diffusion The diffusion correction term is insignificant for measurements with near ambient CO2 concentrations in the chamber Table 4 2 Near the CO2 compensation point itÕs a different matter diffusion becomes signifi Figure 4 11 Data from Figure 4 10 normalized by the CO2 gradient Ca Cr 2 2 2 2 2 2 I I I I I I 0 0 005 0 01 0 100 200 300 400 500 600 C s C r C a...

Page 165: ...s the incoming air stream is stable especially with respect to CO2 concentration When the in coming air is fluctuating in CO2 concentration there will be phase differences as those fluctuations pass through the reference IRGA and the sample IRGA resulting in fluctuations in the CO2 differential even with no leaf in the chamber There are essentially three options for making the incoming air stable ...

Page 166: ...ough a large mixed volume fluctuations in incoming CO2 are greatly damped and can be stable enough to use for gas exchange purposes Figure 4 12 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 vo...

Page 167: ...bration See Light Sensor Considerations on page 8 1 for more details Dealing With Low Rates Measuring very low rates of photosynthesis or transpiration becomes prob lematic in an open system Eventually the CO2 or H2O differential becomes so small that it is in the noise level of the analyzers Some things to try Use as much leaf area as possible The more leaf area you can get in the chamber the lar...

Page 168: ...af area and or low transpiration rate when it is desired to have high humidity in the chamber Another source of water besides the leaf is needed One solution to this problem if you are using the 6400 01 CO2 Mixer is to add a small amount of water 10 ml to the soda lime tube Figure 4 14 After about an hour of subsequent use the water output becomes quite stable and remains so for many hours thereaf...

Page 169: ...desiccant tube with this humidifying material The former method adds a tube to the system but maintains a wide humidity control while the later method adds no hardware but sacrifices the ability to dry incoming air Figure 4 14 Reference H2O concentration plotted against time At hour 0 the des iccant and soda lime tubes were fully bypassed and ambient humidity was mea sured After 30 minutes the sod...

Page 170: ...s about 20 or 30 µmol s 1 If low flows are needed for some special experiment this behavior can be pre vented quite simply by replacing the ÒYÓ connector with a straight union Figure 4 16 and letting the flow from the flow controller vent to the atmo sphere This will allow precise flow control down to 0 but at the expense of horrendously slow response times in the reference IRGA at these low rates...

Page 171: ...at the higher humidity a drop in humidity will cause water to come off the walls and be added to the air stream This would make the DH2O too big and the conductance high Answer 4 Both leaf conductance and water sorption affect the water vapor in the chamber but they have different time scales Water sorption effects will be most pronounced in the first minute or two after a change in chamber humidi...

Page 172: ...1 The sample cell and reference cell have different volumes and different flow rates through those volumes Thus any change in incoming concentration will wash through the two cells at different rates creating os cillations in the differential The wildly fluctuating photosynthetic rate isnÕt real itÕs just reflecting this phase difference After a minute or two it should stabilize however Answer 12 ...

Page 173: ...ce in the sample cell CO2 concentration as the photosynthetic rate changes 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 ...

Page 174: ...Making Measurements Answers to Questions 4 56 Using the LI 6400 4 ...

Page 175: ...Part II Useful Details ...

Page 176: ......

Page 177: ...Files Reading 5 10 For New or Existing Files Writing 5 10 Changing Directories 5 11 STANDARD EDIT 5 13 Function Key Definitions 5 13 Cursor Control Keys 5 15 Tabs 5 15 The Exit Menu 5 15 HOT KEYS 5 16 LOW BATTERY WARNING 5 17 THE BOOT SCREEN 5 18 How To Access 5 18 Boot Screen Functions 5 18 THE LPL SCREEN 5 20 Editing a File 5 21 Running a File 5 21 The Shell Program 5 21 POWER ON HOOKS 5 23 File...

Page 178: ...see so often Standard Menu Menus have two basic uses Figure 5 1 1 Picking one of a number of possibilities OPENÕs Welcome Menu is as example You are presented with a list of op tions and you scroll the highlighted bar up or down to select the desired one 2 Viewing uneditable text This doesnÕt look like a menu because there is no highlighted bar that runs across the display that follows the cursor ...

Page 179: ...active in Standard Menu About this unit Help Menu Welcome Menu Diagnostics Tests Menu _Quit OPEN IRGAs left ON _Quit OPEN IRGAs OFF _ maxWaitTime 300 pmWait 10 PTR user PTR co2Vals Ò nDesired Ca values µm PTR minWaitTime ÒMinimum wait time 237 A CiCurve Figure 5 1 Two examples of Standard Menu in action a a list of selections with a highlighted bar that the user can move up or down with the arrow ...

Page 180: ...sent replaces the CANCEL key Jump to some byte offset specified by you in the file CANCEL Exit the menu without making a selection Same as press ing escape SELECT Select the currently highlighted item Same as pressing en ter Table 5 2 Standard Menu cursor key definitions Key Action Moves cursor up or down one line Moves cursor back or ahead one character Moving back will Òline wrapÓ but not moving...

Page 181: ...ine shift end Jump to end of current line pgup Page up if text rows outnumber window height pgdn Page down if text rows outnumber window height shift Scroll display left or right regardless of line length of data so itÕs possible to scroll the window blank ctrl Jump to start of previous or next word This is useful for moving left and right by columns if data is space delimited Table 5 2 Continued ...

Page 182: ... Standard Line Editor Table 5 3 Standard Line Edit function key definitions Label Action DelLn Clears the line ClrEnd Clears from the cursor to the end of the line DelChar 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 chara...

Page 183: ...enu 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 Table 5 4 Standard Line Edit cursor key definitions Key Action Moves cursor back or ahead one character home Jump to start of the line end Jump to the end of the line shif...

Page 184: ...s 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 The cursor is a highlight ed box that you can move with the arrow keys The decimal code of the current charac ter To view hex press x x and d toggle between decimal and hex modes Figure 5 5 The AnyChar routine lets you ...

Page 185: ... and for selecting new or existing files usually for writing Figure 5 6 The Standard File Dialog for selecting a file name a for existing files b for new or existing files DIR User Configs UserPref Conifer Chamber AbeÕs config Select a Configuration File Config dat Default Energy Balance DIR User Log File esc none Data File Data Data2 Response curve StanÕs test a For reading b For writing The prom...

Page 186: ...ble with the sec ond level being that of the Standard Line Editor which is used here 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 Print Find Refind CANCEL SELECT Dir Help CANCEL SELECT Change directories Help message Optional DonÕt Select a FIle Select This File same a...

Page 187: ...Standard File Dialog are the files in the current directory 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 File ÕDataÕ exists Overwrite Append or Cancel O A C File ÕDataÕ exists Replace it Y N Figure 5 9 When an existing file is specified that is different from the d...

Page 188: ...hown To change directories press 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 User Configs User Configs AutoProgs User Configs Comps User Configs Displays Select a Directory User Print Find ...

Page 189: ...ts on page 10 13 From OPENÕs Utility Menu Select ÒNew File Editor Óentry in the Utility Menu of OPEN You are given an empty buffer to type into and can name it and store it on exit from the ed itor When the editor runs the name of the file is displayed on the top line of the display Figure 5 11 Function Key Definitions In Standard Edit there are four levels of function keys defined even though no ...

Page 190: ...ock BlkPRNT Copy the selected text block to the RS 232 port BlkWRT Store the selected text block as a file whose name you are asked to enter using Standard File Dialog BlkREAD Insert a file at the current cursor location You are asked to name the file using Standard File Dialog PRINT Print the current contents of the buffer being edited to the comm port Find Search for a target string which you en...

Page 191: ...e case for most of the LPL program files you may observe lines that begin with small squares rather than spaces such as this This line starts with 3 tabs The little squares are tab characters and Standard Menu and Standard Edit treat tabs like spaces so ignore them If you feel the need to generate a tab character in Standard Edit press ctrl i The Exit Menu When you are done editing press escape to...

Page 192: ... have not done Update or Store you will be asked if you wish to abandon the changes X Execute the contents of the edit buffer as an LPL program This makes sense only if the edit buffer is an LPL program of course Table 5 7 Hot key combinations Press To Do ctrl shift Darken display contrast a a Adjustments to display contrast made this way will be lost at power off To adjust the contrast permanentl...

Page 193: ...ou ever need to extend operation a few more minutes and are facing an immanent shutdown due to a low battery here is a way to buy some time From OPENÕs main screen press K and type the following at the ok prompt 0 lowwarn and press enter Then press escape to get back to the main screen This com mand disables the software low battery warning behavior The instrument will now operate to about 7 or 8 ...

Page 194: ...d to inputs typed on the keyboard and from inputs from the Comm Port In fact all messages printed on the display are also echoed to the Comm Port Boot Screen Functions Although some of the items in the Boot Screen are for factory technician use there are items that you may find useful Table 5 8 Useful items in the Boot Screen Press To Do R Launch the application That application is the LPL operati...

Page 195: ...yped on the key board are sent out the Comm Port This is useful for verifying communications between the LI 6400 and a terminal or com puter V Set the values for the 5 and 5 reference voltages and the ref erence values for the various D A outputs For factory tech nician use S Save any changes you make such as baud rate or contrast for the next power on or Adjust the display contrast D Toggles Debu...

Page 196: ...s options Table 5 9 Tools available in the LPL Copyright screen Press To Do E Edit an existing file or to create a new empty file See be low F Access the Filer the file system utility program whose de scription begins on page 10 6 R Run an LPL program S Launch the shell program X Enter file exchange mode for use with the FX DOS FX Mac intosh or FX Windows applications running on an external PC Edi...

Page 197: ... program files can be run from the LPL Copyright screen by pressing R The prompt for the file name is similar to that of the Editor described above so use of a wildcard will allow file selection from a menu of matches The Shell Program Pressing S launches the file Sys Lib StdShellÓ When run this program will ap pear as in Figure 5 16 The rules are pretty simple your one line entry must be a valid ...

Page 198: ...7 illustrates a method to use StdShell to make a stop watch DelLn ClrEnd DelChar CapLock AnyChar ok getms getkey drop getms swap print Figure 5 17 A stop watch example using StdShell Step 1 Type this in Step 2 Press enter to start Step 3 Press enter to stop The elapsed time mS is printed DelLn ClrEnd DelChar CapLock AnyChar ok getms getkey drop getms swap print Step 4 Press enter to recall the lin...

Page 199: ...change 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 Specifically a certain character is looked for a hex 04 This is the mechanism that allows you to connect to the computer run FX or indeed EW and then turn ...

Page 200: ...Standard Tools Power ON Hooks 5 24 Using the LI 6400 5 ...

Page 201: ...l time data using text and graphics TEXT DISPLAY 6 2 Display Update Frequency 6 3 Display Function Keys 6 3 Display Files 6 7 REAL TIME GRAPHICS 6 8 RTG Control Keys 6 8 RTG Editor 6 9 RTG Limitations 6 12 RTG Configuration Files 6 13 Track ParOut 7 19 ...

Page 202: ... line marker and pressing the desired group code letter Alternatively pressing or will cycle through the available choices Photo Cond Ci Trmmol 399 7 365 9 15 79 22 70 33 8 6 91 172 8 70 09 15 4 0 216 238 3 49 ÆCO2_µml ÆH2O_mml Flow_µml RH_S CO2R_µml CO2S_µml H2OR_mml H2OS_mml Display Display WhatÕs Display QuikPik List What Editor a b c 6 Figure 6 1 New MeasurementÕs text display showing the Disp...

Page 203: ...is can be modified See Useful Variables on page 26 4 The reason for this split behavior is to allow some measured variables to be viewed as fast as they are measured but without giving the processor so much to do that it canÕt keep up Display Function Keys New Measurements function key level 6 contains the control keys pertaining to the text display Figure 6 1 The function keys are Display QuikPik...

Page 204: ...ditor The Display Editor Figure 6 4 allows you to modify the current display con figuration store it as a file and or retrieve a previously stored configuration 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 CO2R_µml Ref CO2 µmol mol CO2S_µml Chmbr CO2 µmol mol H2OR_mml Ref H2O mmol mol H2...

Page 205: ...RH_S_ Td_R_ C Td_S_ a CO2R_µml CO2S_µml H2OR_mml H2OS_m Remove Open SaveAs Display Editor Edit Add Help cancel OK 2nd level definitions press labels Cursor line Modify current line Add a display line to the end of the list Read display definition list from a file Delete the current line renumber the list Store this display definition list to a file Implement this display definition list Figure 6 4...

Page 206: ... OPENÕs System Variables on page 14 1 while the user variables are determined by the cur rent Compute List Defining User Variables on page 15 1 10 U S 20 Trans 21 Trmmol 23 Cond 30 Photo 42 C2Sfc 43 AHs Cs 1 CO2R_µml 2 CO2S_µml 107 AuxS1 108 AuxS2 109 AuxS3 É É User Variables System Variables Figure 6 6 The variable menu consists of user variables at the top followed by the system variables ...

Page 207: ...15 30 23 36 21 25 41 42 52 18 19 20 14 15 16 17 11 12 13 32 8 9 10 21 22 23 24 31 22 56 57 52 Marker label number of display lines defined ID values for line B ID values for line A ID values for line K 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 u...

Page 208: ...s 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 Figure 6 8 Illustration of real time graphics using the 6400 09 Soil Chamber The right plot is a strip chart showing how sample cell CO2 is changing with time The left plot is an XY Plot of soil CO2 efflux as a func tion of average chamber CO2 concentration ...

Page 209: ... 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 Figure 6 9 New Measurement modeÕs strip chart control key labels Graph GRAPH VIEW GRAPH XYPlot is off QuikPik GRAPH Setup LOG If any XY plots are de fined mark the plots with a at the current curso...

Page 210: ...S___________ 1 PARi 0 to 2000 Photo 0 to 20 2 PARi 0 to 2000 Cond 0 to 1 Edit Curvs Cancel OK 3 Æt 120 3 totalCV 0 to 5 Determines the number of plots 1 2 or 3 Open SaveAs Highlight box is a cursor that is moved by Edit the high lighted field Read in an existing defini tion from disk Save definition to disk in a named file Stripcharts have Dt for the x axis label XY Plots donÕt have Dt for the x a...

Page 211: ...___ __Y_AXIS___________ 1 PARi 0 to 2000 Photo 0 to 20 2 PARi 0 to 2000 Cond 0 to 1 Æt 120 3 totalCV 0 to 5 10 U S 20 Trans 21 Trmmol 23 Cond 30 Photo 35 CndCO2 Pick X Variable 0 Strip Chart Time RealTime Graphics __X_AXIS_________ __Y_AXIS___________ 1 PARi 0 to 2000 Photo 0 to 20 2 PARi 0 to 2000 Cond 0 to 1 100 400_ 3 totalCV 0 to 5 Enter Scaling Info for Flow 1 val Æ or 2 vals min max DelLn Cl...

Page 212: ...n data is plotted Scrolling does not take place in re sponse to current values That is the graphics cursor can drift off the plot but scrolling wonÕt occur until a point is actually plotted Exiting the Editor If you exit the RTG Editor by pressing escape or Cancel you will abandon any changes you may have made and the active RTG configuration will re vert back to what it was before you entered the...

Page 213: ... RTG Configuration Files are generally stored in the User Configs StripDefs di rectory The format of these files is illustrated in Figure 6 7 StripDef 3 30 20 2000 12 1 0 1 0 23 1 2000 12 1 0 1 0 52 5 120 0 1 0 0 0 Figure 6 12 RTG Configuration file format This configuration is shown in 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 lef...

Page 214: ...Real Time Data Real Time Graphics 6 14 Using the LI 6400 6 ...

Page 215: ...tional Envelope 7 7 Control Options 7 8 Constant Humidity Operation 7 9 CO2 CONTROL 7 13 Constant Reference Option 7 14 Constant Sample Option 7 14 Interaction with Humidity Control 7 15 Constant Control Signal Option 7 15 CO2 Mixer Calibration 7 15 TEMPERATURE CONTROL 7 16 Constant Block Temperature 7 16 Constant Leaf Temperature 7 16 Condensation 7 17 LIGHT CONTROL 7 18 Quantum Flux 7 18 Control...

Page 216: ...trols OpenÕs Control Manager In OPENÕs New Measurements mode the environmental control function keys Figure 7 1 provide a means of controlling humidity using flow rate CO2 with optional 6400 01 CO2 Mixer temperature and light with option al 6400 02 or 02B LED Source Each of the four control areas represented by the key labels above share a common control manager The control manager is simply the s...

Page 217: ...p the target value entry box which al lows the user to change the target value Figure 7 3 A blank entry just press enter will retain the current value Variable targets are discussed on page 7 5 N None Pump Off F Flow rate 500 µmol s H H2O_sample 20 0 mml R RH_sample 50 V VPD Tleaf C 1 0 kPa Humidity Control Options Targets Target value Short Cut key Current Option Figure 7 2 The elements of a typi...

Page 218: ...while the 10 and 30 second ISRs do nothing Control ling leaf temperature however is a much slower process so the 10 and 30 second ISRs are needed Active vs Inactive Control Manger An inactive control manager means that the fine tuning necessary for active target tracking is not being done The consequences of this depend on the con trol Some controls are fully implemented in hardware leaving nothin...

Page 219: ...r the target enter a pound sign and press enter You will be shown a list of system and user defined variables from which you can pick the quantity that is to be tracked Alternatively if you know the ID number for the system variable or user vari able you can enter it directly and bypass the menu selection 13 Variable number 13 is the external quantum sensor for example When a variable target is sp...

Page 220: ...u will show the variable name and target value Figure 7 6 and if we select it again the target default will indicate the variable target Figure 7 7 RH CO2S Temp Lamp range 63 350µml Off Off 2 Latest value of xtrnRH Figure 7 5 When a control has a variable target the value is updated every 30 seconds This value is shown on the control key label N None Pump Off F Flow rate 500 µmol s H H2O_sample 20...

Page 221: ...through desiccant is set by the adjust valve on the top of the desiccant tube allowing incoming humidities to range from ambi ent to dry You could also moisten the air see Humidifying Incoming Air on page 4 50 2 The flow rate of air through the chamber The flow of air through the chamber is controlled by the software either by controlling pump speed CO2 mixer not installed or diverting excess flow...

Page 222: ...e some peace and quiet Dry Wet Chamber Humidity Figure 7 8 The operating envelope is determined by the transpiration from the leaf To maintain any given humidity a combination of flow rate and desiccant knob settings might achieve it Typically the knob remains fixed and the flow is adjusted automatically Flow Rate Low High Full Bypass Full Scrub N None Pump Off F Flow rate 500 µmol s H H2O_sample ...

Page 223: ...O2 mixer installed or 50 µmol s 1 with a mixer installed Constant Humidity Operation The H R and V options actively regulate the flow rate to maintain a constant humidity either vapor mole fraction or relative humidity or vapor pressure deficit in the sample cell leaf chamber F Flow rate Maintains a fixed flow rate through the chamber This is a good default option H H2O_sample Maintains a constant...

Page 224: ...A will be putting out when the mole fraction is at the target value this is communicated to the con trol circuit via an analog output signal Since this signal is also a function of pressure temperature and how the IRGA is zeroed and matched then there needs to be periodic updates of this target signal even when the target mole fraction doesnÕt change R Constant RH The constant RH control is a simp...

Page 225: ...iration rate etc When you select the V option for vapor pressure deficit control you are asked for a target value followed by a temperature Figure 7 10 If you press N to change the temperature you are shown a menu of all user defined variables and two system variables Tleaf C and Tair C Figure 7 11 VPD e Tl es Ð VPD based on Tleaf C Y N Currently selected temperature Figure 7 10 The VPD control ne...

Page 226: ...e you tight humidity con trol but at the expense of ÒjumpyÓ flow readings This is best for survey mea surements when you are doing humidity control and want the lock in rapidly on the target humidity as you go from leaf to leaf The med setting will drop the variability of the flow in half and still do a reasonable job of maintaining humidity on target This is best for response curves and AutoProgr...

Page 227: ... the mixer ItÕs actually not turned off but its output is switched out of the air stream and has no effect on the systemÕs CO2 concentration R Ref CO2 Maintains a constant CO2 concentration in the refer ence cell That is the incoming chamber CO2 con centration is held constant at a target value This is a good default option S Sample CO2 Maintains a constant CO2 concentration in the sam ple cell an...

Page 228: ...lly in the domain of the humidity controller All the CO2 controller can do is regulate CO2 concentration coming into the chamber once those other things are stable For best results with the S option 1 Start out with the R option Specify a target 20 or 30 µmol mol 1 above what you want in the chamber and wait for the system to stabilize 2 Switch to the S option Once things are stable the controller...

Page 229: ...CO2 concentration and makes no further adjustment Thus when you specify a target you may not know exactly what the final concentration will be but youÕll be assured the controller will be making no changes so any change or fluctuation you see in reference CO2 concentration will be coming from something else leaks bad soda lime flow rate changes long term drift of the controller etc CO2 Mixer Calib...

Page 230: ...are within 7 de grees of ambient larger if warming since warming is more efficient than cooling Constant Leaf Temperature 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 inc...

Page 231: ...rdless of whether that signal is actually being used for leaf temperature or not4 Condensation It is possible and certainly not advisable to specify a target temperature that will cause the coolers to bring the IRGA below the dewpoint temperature While in New Measurements mode OPEN keeps track of the humidity in the IRGA and leaf chamber and if it gets above 95 will display a blinking warning High...

Page 232: ...control system will adjust the lamp to bring the light back to the target When you specify a target value the software makes a first guess of the re quired control signal it will take to achieve that light level in the chamber 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 Table 7 4 Light c...

Page 233: ...o the lamp is set directly in mV not µmol m 2 s 1 The range is 0 to 5000 mV Track ParOut The tracking option works just like the Quantum Flux option except the tar get value potentially changes every 3 seconds and the target value comes from the external quantum sensor This is an example of variable tracking a feature that all of the control sys tems have for flow humidity CO2 temperature as well ...

Page 234: ...Environmental Control Light Control 7 20 Using the LI 6400 7 ...

Page 235: ... measure WHY TWO SENSORS 8 2 SPECIFYING THE SOURCE AND SENSOR 8 3 Calibration Equations 8 3 The Light Source Control Utility 8 4 6400 02 AND 02B LIGHT SOURCES 8 6 Spectral Considerations 8 6 Temperature Effects 8 7 Aging 8 7 GALLIUM ARSENIDE PHOSPHIDE GAASP SENSOR 8 7 Temperature 8 8 View Angle 8 8 ...

Page 236: ...m sensor does not have the same field of view as the leaf element in the chamber nor is it subject to similar shading conditions angular responses or attenuation by the chamber window In an extreme case when the quantum sensor is shaded and the leaf isnÕt the quantum sensor could be measuring a factor of 10 lower than the actual irradiance on the leaf In more typical conditions there will easily b...

Page 237: ...s a light source installed The answer to this question determines whether or not the lamp control key in New Measurements mode is active It also tells the software what type of in chamber light sensor is connected Calibration Issues Whatever the type of light sensor being used it has a calibration factor which converts raw mV to µmol m 2 s 1 photon flux This conversion factor depends on the spectr...

Page 238: ...ed in 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 Figure 8 1 The Light Source Select screen Press F1 to choose a different light source Pick Source Done Edit Revert StdFile StdFile LightSource 640...

Page 239: ...rt file option changes the file User Configs LightSources back to itÕs de fault state The default version of this file is stored in Sys Lib LightSources 6400 02 Red LED SI 120 1 0 0 16 0 69 6400 02B RedBlue SI 501 1 0 0 16 0 61 Sun Sky 1 0 0 19 Quartz Halogen 1 11 0 26 Fluorescent 0 88 0 18 Metal Halide 0 87 0 17 Select Light Source Standard Light sources 6400 02 and 02B Light Sources that have be...

Page 240: ...942 the addition of the blue LEDs in the 6400 02 enlarges the scope of suitable applications to include stomatal kinet ics In chamber light is measured with an unfiltered silicon photodiode that is part of the LED source See Light Source Calibration on page 18 24 2 Tennessen D J D L Singsaas T D Sharkey 1994 Light emitting diodes as a light source for photosynthesis research Photosynthesis Researc...

Page 241: ...12 months If you find that your light source cannot achieve high enough light levels and you suspect itÕs simply due to the age of the source then there is a possible remedy See Source IsnÕt Bright Enough on page 20 32 Gallium Arsenide Phosphide GaAsP Sensor The spectral response of a GaAsP sensor is shown in Figure 8 4 on page 8 8 along with the spectral response of an ideal quantum sensor for co...

Page 242: ...ing 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 For this reason you should not trust this sensor very much at non normal incidence angles Figure 8 4 Spectral response of GaAsP sensor and ideal quantum response 0 10...

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 ...

Page 244: ...Light Sensor Considerations Gallium Arsenide Phosphide GaAsP Sensor 8 10 Using the LI 6400 8 ...

Page 245: ...pts 9 15 Prompts and AutoPrograms 9 16 Prompt List Files 9 17 AUTOPROGRAMS 9 18 What are AutoPrograms 9 18 Launching AutoPrograms 9 19 While an AutoProgram is Active 9 19 Controlling an AutoProgram 9 20 AUTOPROGRAM DESCRIPTIONS 9 21 ÒA CiCurveÓ 9 21 ÒAutoLogÓ 9 22 ÒAveraging AutoLogÓ 9 23 ÒBuffered AutoLogÓ 9 23 ÒLightCurveÓ 9 27 ÒPrecision AutoLogÓ 9 28 ÒRemote ControlÓ 9 29 ÒTimedLampÓ 9 30 MAKI...

Page 246: ...ght be studying the dynamics of the change from X to Y and want to record data as frequently as possible over that 5 minutes Where does it go When the LI 6400 records data it generally does so in its file system which is described in Chapter 10 It can also record data in memory or send it out of the RS 232 port in real time Files can be named allowing you to go back and retrieve your prized data t...

Page 247: ... 94 24 98 28 25 23 17 399 7 365 9 15 79 22 70 48 74 70 09 172 8 1026 1311 98 07 2 2 0 04 111115 2 643 72 11 3 0 202 180 3 33 1 65 3 5 1 3 94 24 80 28 25 22 97 299 4 279 6 17 15 22 44 53 53 70 03 215 7 1070 1354 98 07 1 2 0 03 111115 3 803 47 7 2 0 213 127 3 48 1 64 3 5 1 3 94 24 84 28 21 23 02 199 7 187 9 17 37 22 47 54 07 69 97 233 3 1062 1337 98 07 0 8 0 02 111115 4 1093 22 2 16 0 215 76 8 3 81 ...

Page 248: ... log to a file press escape to get the alternate destination prompt Figure 9 4 Open view close add Match LogFile file file remark Pick a destination for logged data file memory or comm port 1 Figure 9 2 Logging is initiated and controlled from New MeasurementsÕ function key level 1 DIR User Log File esc none Data File Data Data2 Response curve StanÕs test Dir Help CANCEL SELECT Figure 9 3 Specifyi...

Page 249: ... 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 Log to Memory room for 335 obs Comm port unlimited obs M C Figure 9 4 The alternate destination prompt Press M for memory or C for Comm port or escape to not log anywhere Estimate based on the available memory and the current log format file Figure 9 5 The prompt f...

Page 250: ... sensor head handle 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 6 1393 97 2 97 0 219 27 1 3 85 1 76 3 5 13É 11 58 30 Turned coolers off 7 1585 53 21 4 0 207 759 3 64 1 76 3 5 1 3 É Figure 9 6 Rema...

Page 251: ...t Figure 9 8 The Logging Control program LogList LogList Show WhatÕs Editor QuikPik Items Missing Quit LogBeep Close ON Logging Log Destination inactive LogFormat ÒReneeÕs FormatÓ contains 26 items lacks 1 item for RECOMPUTING contains 2 undefined items Logging Control These messages only appear as needed The LogFormat file and number of items Only appears if logging is active Toggles on off the b...

Page 252: ...insert them into the log list or else use the LogList Editor Or QuikPik another Log List Écontains n undefined items These will be labelled as Ò Ó To take care of undefined items either switch to the appropriate ComputeList that defines these items or else use the LogList Editor to remove the items LogList Editor The LogList Editor Figure 9 9 on page 9 9 allows you to edit the entire list but item...

Page 253: ...the list Read another Log Format List into the Editor Specify the file name and save this list Remove all items from this list Choose up to three groups of missing items to insert above the selected item The groups are selected using the box below Items required for Recompute 0 User defined items 6 Prompt items 2 Mark Groups to Add Toggle CANCEL OK Figure 9 9 The LogList Editor Any of the entries ...

Page 254: ...re not particularly convenient to look at There are alternatives available Table 9 1 lists the system variables that contain time and date information To include any of these in your log file simply access the Log Editor and insert them where you want them to be LogFormat 35 36 30 23 36 21 25 33 34 32 9 10 8 1 2 4 5 14 15 7 12 13 11 65 66 23 Marker Figure 9 10 Listing of the default LogList file Ò...

Page 255: ...ped by testing the first character If the first character is a quote the line is skipped Therefore you do not want to have HH MM SS or any other string as the first data column This is not a problem for OPEN 3 2 and above however Using StartHR 64 StartHR exists for historical reasons from the time before GraphIt could con vert HH MM SS to decimal hours If you wish to have a column of numeric data ...

Page 256: ... screen lists the currently defined prompts You can edit them Prompt Editor or select a new list Prompt Quikpik The prompts are used when f5 level 3 is pressed in New Measurements mode or when f3 is pressed here Ask Prompts Prompt Prompt Ask Update Editor QuikPik Prompts LogList Quit Show Prompts Names off 104 Plot 0 108 Comments Ò Ò 33 Area 6 Plot Comments Area The Prompt List file name Try them ...

Page 257: ...re 9 11 on page 9 12 The Prompt Control screen will indicate which if any prompts are missing from the active Log List To add missing items to the Log List you can press Update Loglist F4 or else go to the Logging Control screen and update from there The Prompt List Editor is illustrated in Figure 9 12 This editor functions in a similar manner to the Log List editor but with some small differences...

Page 258: ...e com putations done for the logged data will use the latest values that you have en tered 108 Comments 18 char remark 33 AREA_cm2 Entered In chmbr leaf Plot Comments Area 104 Plot User defined integer Change Insert Remove cancel OK 1 Revert Relabel Open SaveAs 2 Replace the selected item with another from the master list Insert a new item above the selected item Remove the selected item from the ...

Page 259: ...ystem constants to use Table 9 2 System Variables that can be used as prompts ID Label Description LPL Variable Namea a Necessary if you wish to use the value in a computation such as in a Com pute List where you need to refer to the item by itÕs name not its label 33 AREA Leaf area cm2 area_cm2 34 STMRAT Stomatal Ratio stom_rat 101 AuxF1b b Items 101 through 109 have user defined labels WhatÕs sh...

Page 260: ...t data records for plotting based on the value of these con stants then use the numeric ones The logical selection criterion of GraphIt described in Chapter 12 works for numeric fields not string fields ÒWhat If I Need More Ó You can add as many constants as you like by modifying your Compute List See Chapter 15 Remarks strings can also be defined in Compute List Files Prompts and AutoPrograms To ...

Page 261: ...own in Figure 9 13 PromptList 104 108 33 Relabels 101 AuxF1 102 AuxF2 103 AuxF3 104 Plot 105 AuxN2 106 AuxN3 107 Remark8 108 Comments 109 Remark32 List Marker 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 Relabel Marker The List Labels ...

Page 262: ...See Chapter 25 2 That is they cannot be launched unless OPEN is running Table 9 3 Standard AutoPrograms Name Description A CiCurve Controls CO2 mixer logs data based on stability AutoLog Logs instantaneous data at regular intervals Averaging AutoLog Logs averaged data at regular intervals Buffered AutoLog Logs instantaneous data at high frequency for a short time interval LightCurve Controls LED s...

Page 263: ...ination 3 Select the AutoProgram The user is then prompted to pick an AutoProgram This list of programs shown uses Standard Menu consists of all files in the directory User Con figs AutoProgs 4 Answer the questions Most AutoPrograms will prompt you for some input data The default values will be the values that you entered the last time that AutoProgram was launched While an AutoProgram is Active O...

Page 264: ...nd change any control setting F1 through F5 level 2 enter match mode F5 level 1 etc Controlling an AutoProgram Once it is launched thereÕs not much one can do to an AutoProgramÕs course of action other than terminate it early or trigger the next step before it would otherwise occur To do either press escape to access the AutoProgram Exit screen Figure 9 15 on page 9 20 and press A or T Prog Name i...

Page 265: ...er control only the value Usually for A Ci curves it is best to operate in constant reference mode R or constant command signal mode C 2 Minimum wait time secs The time between a change in the mixerÕs target and when the program will begin to check stability to see if an observation can be logged No logging will occur during this period 3 Maximum wait time secs The time period following the minimu...

Page 266: ...o Styles for ÒProgramÓ The Program field Figure 9 16 on page 9 20 has two styles with the A Ci Curve AutoProgram and also LightCurve The delimiter used is a semico lon or asterisk as explained in Table 9 4 ÒAutoLogÓ AutoLog is designed to log instantaneous data at regular intervals If you need data faster than every 2 or 3 seconds then you should use Buffered AutoLog instead AutoLog prompts for th...

Page 267: ... will quit after this time period 3 MATCH every Nth Log 0 never Enter 0 for no matching 1 to match every observation 2 for every other one etc Uses AuxN3 Averaging AutoLog uses AuxN3 for the number of samples in each observa tion Therefore to get this information included with your logged data in clude system ID 106 in your log list Note Bug in Version 3 01 In OPEN 3 01 the final log period or par...

Page 268: ...Obs sec 0 2 10 How many readings per second do you want to record 2 Logging duration secs If you have selected a frequency greater than the instrument can keep up with causing data to accumulate in the buffer and a time period that is longer than the buffer can cover you are warned and given the option of shortening the logging period to that time For example Readings may start to be skipped after...

Page 269: ...nce of Buffered AutoLog is largely dependent on how fast OPEN can do the user computations The following results are based on the standard equation set ÒComputeList DefaultÓ and log file formats ÒLog Format Std OutputÓ The optional floating point coprocessor part number 6400 12 is a big help here as well The number of observations B that will be buffered during logging period T s is 9 1 where f is...

Page 270: ...h and without a coprocessor3 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 coprocessor W B f 1 D W T º f f o Ð f 1 Tmax 500 f f 0 Ð 3 These rates depend considerably on what user computations are being done The Table 9 5 data was collected using default c...

Page 271: ...ghtCurve will prompt for the following 1 Desired lamp settings µmol m2 s Enter the PAR values you wish to achieve Type the values separated by spaces such as 1500 1000 800 600 400 200 50 2 Minimum wait time secs The time between a change in the lampÕs target and when the program will begin to check stability to see if an observation can be logged No logging will occur during this period 3 Maximum ...

Page 272: ...which typically takes about 30 seconds there will be a short delay 10 seconds then the maximum wait time and stability checking is entered Thus automatic match ing tends to increase the total time between logging events by about 40 sec onds While LightCurve is running the ÒProgramÓ field will show time in two styles as described in Two Styles for ÒProgramÓ on page 9 22 ÒPrecision AutoLogÓ A new Au...

Page 273: ...gers an interrupt in which the message in the queue is compiled executed and disposed 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 wo...

Page 274: ... the logging frequency for each lamp level You may for example want to record data less frequently during the initial stability period and very frequently when the light changes TimedLamp prompts 1 Get Data from Keyboard or File Press K to enter the programÕs set points from the keyboard if you do this go to Step 3 Or press F to use a previously entered set of points if you do this go to Step 2 2 ...

Page 275: ...ow you are presented with some options Edit these parameters Sunfleck 4 Y N Time s Lamp µmol LogInt s Enter values press esc TimedLamp 60 300 5 30 1800 2 60 300 2 DelLn ClrEnd DelChar CapLock AnyChar 60 seconds at 300 µmol m 2 s 1 logging every 5 seconds 30 seconds at 1800 µmol m 2 s 1 logging every 2 seconds Figure 9 18 The first prompt for TimedLamp Each line you enter corresponds to a program s...

Page 276: ...possible use the next time TimedLamp runs Figure 9 20 escape aborts TimedLamp and E goes back to the edit window DIR User Configs AutoProgs TimedLamp Default Store TimedLamp parameters Data File ÒDfltsÓ ÒJoeÕs testÓ ÒSunfleck 4Ó ÒSunfleck 2Ó Dir CANCEL SELECT Figure 9 20 TimedLampÕs set points can be stored for use next time ...

Page 277: ...should be that is used to prompt the user to enter this time and c what the default value of the wait time will be Thus building an AutoProgram with the AutoProgram Builder consists of picking events in order and answering the questions if any associated with each event When you are done the AutoProgram builder will create the file and store it for you To run the new AutoProgram select it just as ...

Page 278: ... Select the entry entitled ÒBuild a New AutoProgramÓ in the Utility Menu It takes about 10 seconds to load and run Press enter when finally prompted with ÒPress enter to startÓ 2 Select ÒBegin LoopÓ from the menu Highlight ÒB Begin LoopÓ and press enter or else simply press B 3 Make it a Control Loop Press 1 to select a control loop C Wait D Match E Log F Set a control G Prompt for user constants ...

Page 279: ...alue that is never prompted for 6 Edit the default values for the flow control loop YouÕll be given the chance to set the default values for the flow rates Adjust them as you wish and press enter when done 7 Specify the first action within the flow control loop Waiting The first action is the wait so highlight ÒC Wait Fixed TimeÓ and press enter or press C Loop Over what C Flow RH_S_ D FLOW VPD E ...

Page 280: ...es or seconds Press enter YouÕll be asked to specify the default wait time value Press enter when done 8 Specify the second action in the flow control loop Logging The second action is logging so highlight ÒF LogÓ and press enter or simply press F Pick Wait Option C Wait with Logging at intervals B Wait Min Max Stability A Wait Fixed Time Enter time in Minutes or Seconds M S Wait time minutes Ente...

Page 281: ...he program never prompt you but always use the values youÕve specified as the defaults This is nice for rapidly starting an AutoProgram 1 You can have it prompt you always using the de fault values 2 You can be prompted each time with the values entered the last time used as the default Press 0 1 or 2 Main Event 1 B Begin Loop D Match E Log C Wait F Set a control A End Loop Loop Flow Flow Event 3 ...

Page 282: ...you wish to view or edit the AutoProgram that you have created you can do so by accessing the Filer selecting the file and pressing E If you press N to not store the file you will be given a chance to edit the Au toProgram you have created When you exit the editor Standard Editor you can save the file Example 2 A Ci Curves at Various Light Levels This example builds an AutoProgram that does a fami...

Page 283: ...R_µmlÓ as the type Set the prompt string and default values as you wish 5 Select a stability based wait CBA Press C to select ÒC Wait Ó followed by B for ÒB Wait Min Max Sta bilityÓ then A for ÒA SUM ÆCO2 ÆH2O Flow CVsÓ Use Minutes for times and modify the prompts and initial values for the min max and stabil ity values as you wish 6 Match if the DÕs are small DD For the second event in the CO2 lo...

Page 284: ...d Program or End Loop B Begin Loop C Wait D Match E Log F Set a control G Prompt for user constants H Add a remarks record A Flow Flow B Flow H2OS_mml C Flow RH_S_ D Flow VPD E CO2 CO2R_µml F CO2 CO2S_µml G CO2 Control Voltage H Temp Tblock I Temp Tleaf J Light Quantum Flux K Light Control Voltage L Fan Speed A SUM ÆCO2 ÆH2O Flow Cvs B SUM ÆCO2 ÆH2O CVs C ÆCO2 CV only D ÆH2O CV only Action List Co...

Page 285: ...me B Wait Min Max Stability C Wait with Logging at intervals During these waits the instrument will appear to be in New Measurements mode allowing you to monitor channels view real time graphics etc 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 Main Event 3 A End Loop B Control Loop LOOP Flow Fl...

Page 286: ...cified in seconds Prompts and default values for both are established The C option represents a short cut to doing a Type 2 Loop that contains a fixed time wait and a log If you wish to do other events such as matching before each log then you should specify a Type 2 Loop rather than using this wait option D MatchÉ There are some options for matching A Match always B Match if ÆCO2 x C Match if ÆH2...

Page 287: ...ol LoopÓ option for setting the light values G Prompt for user constants This will do the same thing as pressing F5 level 3 User Consts in New Mea surements mode any user constants that have been defined will be prompted for Note This suspends operation until the user responds H Add a remarks record This option does the same thing as pressing F4 level 1 Log Remark in New Measurements mode it adds ...

Page 288: ...Data Logging Making Your Own AutoPrograms 9 44 Using the LI 6400 9 ...

Page 289: ...Part III Working With Files ...

Page 290: ......

Page 291: ...ng 10 10 FILERÕS FILE OPERATIONS 10 11 Viewing File Header Information 10 11 Viewing a Subset of Files 10 12 Viewing and Editing a FileÕs Contents 10 13 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 FILERÕS DISK OPERATIONS 10 18 Space Available 10 18...

Page 292: ...g 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 Physically the files reside on the memory board Figure 10 1 Figure 10 1 The memory board is located on the digital board in the LI 6400 which is the upper full sized board in the console D...

Page 293: ... not matter for letters so the following are equiv alent names MyData mydata MYDATA Dots carry no significance in the LI 6400Õs file system so names like WheatData plot2 aci joe are acceptable What Are Directories Directories provide a mechanism for grouping files logically and can contain the header information name date etc for any number of files or other di rectories Directories have the same ...

Page 294: ...ys Open Open The Root Directory It is helpful to think of the entire file system as a tree of directories branching from a single root The directories that branch immediately from the root are the disks and subsequent directories Figure 10 2 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 fi...

Page 295: ...til all of it is erased Deleting files simply marked those files as unused but the directory information was updated and rewrit ing the directory used up some new disk space Eventually of course the disk will be come full and something needs to be done The normal remedy for a full disk is to defragment it During this pro cess which is not automatic you must initiate it the contents of the disk are...

Page 296: ...or your own use As long as all disks are on line however none of them can be de fragmented The Filer The FILER is a general purpose tool for managing files directories and disks on the LI 6400 file system Some of the functions that you can perform with the FILER include copying deleting renaming and viewing files as well as disk operations such as formatting and defragmenting disks Accessing the F...

Page 297: ...ata Jason MixerTestResults Dir Filter Sort Tag purGe A Ci bad Use the cursor control keys to move the highlight bar Press or to view file time stamp and size Current Directory The file list Which files to display Ò Ó or ÒÓ for all Press labels for more keys or use the short cut keys Table 10 1 The FilerÕs main function key labels and short cuts Label Short Cut Description Dir D Select a directory ...

Page 298: ...ist of files disK K Access the disk keys See Table 10 3 eXecute X Run the highlighted file if itÕs an LPL program Table 10 2 Sort key labels Label Short Cut Description by Name N Sorts files by the file name by Date D Sorts files by the date and time by Size S Sorts files by the file size by Tag T Sorts files by the file tag status selected unse lected or old selected Quit Q escape Return to the m...

Page 299: ...sk Quit Q escape Return to the main level of keys Table 10 1 a The key label that appears here depends on whether there is a disk off line or not Table 10 3 Disk key labels Label Short Cut Description Table 10 4 The Directory function key labels Label Short Cut Description Add A Add a new directory User User 6400 Data User Configs User Configs AutoProgs User Configs AutoProgs Defaults Select new p...

Page 300: ...ied and asked if you really want to purge it Rename R Rename the highlighted directory CANCEL escape Exit the directory selection screen and donÕt change directories SELECT enter Change to the highlighted directory and exit the change screen Print Print the directory list to the Comm Port Find Enter a target and search for the next occurrence ReFind Search for the next occurrence of the current ta...

Page 301: ...2 Tagged 0 Bytes 0 A Ci Iris leaf A Ci Test 4 Data Data Jason MixerTestResults Dir Filter Sort Tag purGe A Ci bad 3146 3256 892 5877 3980 210 User Filter Total 34 Bytes 71962 Tagged 0 Bytes 0 A Ci Iris leaf A Ci Test 4 Data Data Jason MixerTestResults Dir Filter Sort Tag purGe A Ci bad 11 Aug 97 10 Aug 97 07 Nov 97 31 Jul 97 31 Jul 97 11 Aug 97 User Filter Total 34 Bytes 71962 Tagged 0 Bytes 0 A C...

Page 302: ...ed to enter the new Filter string Examples are given in Table 10 5 Table 10 5 Examples of Filters and the files they would include and exclude Filter Includes Files Excludes Files all none 123 123 dat Data123 123 12 3 Data data 1 data x data data 123 junk dat this is long 123 junk 12 junk 1234 User Filter data Total 3 Bytes 962 Tagged 0 Bytes 0 More Data this data is ok Dir Filter Sort Tag purGe D...

Page 303: ...ever is smaller Tagging One File Many of the FILER commands require that files or directories be selected ÒtaggedÓ before the command can be executed These operations include purging copying and printing files Press the Space or Enter keys to tag the highlighted file or press Tag fol lowed by tag One A tag symbol appears next to the file name Figure 5 3 and the highlight moves to the next file Whe...

Page 304: ... size in bytes Table 10 6 Tag function keys Label Short Cut Description Tag all T Tag all files in the current directory list Clr all C Remove all tags from files in the current directory list Retag R After you have performed certain functions e g copying files the tag marker will change to a hy phen to indicate that the command was executed on the tagged files Press Retag to tag these files again...

Page 305: ... 1 Tag the file s to be copied Tag by pressing enter or space or by the Tag function keys 2 Press M for Move or C for Copy Or use the function keys 3 Select the destination A menu of destinations is presented Highlight the desired destination direc tory and press enter Or press escape if youÕve changed your mind 4 Select the overwrite option Your choices are shown in Figure 10 10 Press Y Yes to ov...

Page 306: ... One method of downloading them is to tag them in the Filer and press P or Print The print program that then runs will prompt you for the following information 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 User Filter Total 34 Bytes 71962 Tagged 0 Bytes 0 A Ci bad A Ci Iris leaf A Ci Test 4 Data D...

Page 307: ...un from the FILER by highlighting the file containing the program and selecting eXecute or X After the program is executed you will return to the FILER As an example you can set the communications pa rameters from the FILER by executing the Sys Utility Setcomm program file Utility programs in the directory Sys Utilities are described in Sys Utility Programs on page 21 10 Print headers Y N N Append...

Page 308: ... Press any key to return to the FILER Defragmenting Disks It is periodically necessary to defragment the disks to reclaim space occupied by inactive files During defragmentation all active files are copied onto the Hidden disk see Using the Hidden Disk on page 10 19 The original disk is then reformatted and all inactive files are purged The active files are then copied back to the original disk Th...

Page 309: ...iles that affect the operation of the LI 6400 These files can be reloaded from the system floppy disk To format a disk 1 Access the disk keys In the FILER press the Disk function key or K 2 Select a disk Highlight the disk to be formatted and press enter 3 Read the warning If itÕs ok to proceed and loose everything on the disk press Proceed Other wise press Cancel Using the Hidden Disk The hidden ...

Page 310: ...ng the hidden disk you must create a hidden disk again before defragmenting Make sure that you copy all of the files that you want to save from the disk that is to be hidden see Copying Files in this section All files on the specified disk will be erased when it is hidden To hide the temporary disk 1 Access the disk keys In the FILER press the Disk function key or K 2 Press the HideDisk function k...

Page 311: ... clear the message Defrag menting will ultimately fix the problem Out of Disk Space on _Temp_ _Temp_ or on _Swap_ _Swap When this message occurs it means the hidden disk is out of space This can happen when a full disk is defragmented and the defragment doesnÕt recover any space The remedy to this situation is a two step process 1 Bring the hidden disk on line This is described in Using the Hidden...

Page 312: ...The LPL File System Troubleshooting 10 22 Using the LI 6400 10 ...

Page 313: ... Program Comments 11 10 USING FX ON MACINTOSH 11 10 Installation 11 10 Example 11 11 Program Comments 11 12 USING EW 11 12 Installation 11 12 Examples 11 13 EWÕs Switches 11 17 ODDS AND ENDS 11 21 Text vs Binary Files 11 21 File Name Considerations 11 21 Non standard Serial Port Configuration DOS only 11 23 USING A DATA CAPTURE PROGRAM 11 23 Setting the Communication Parameters 11 23 1000 90 COMM ...

Page 314: ...0 use the Filer to tag and send via print all files you want downloaded LI COR has data capture programs for DOS part number 1000 90 and Macintosh 1000 91 Options 1 and 2 are the best File names and structures are preserved data is error checked and both are quite painless to use Also you neednÕt worry about configuring the LI 6400Õs comm port when using FX or EW itÕs au tomatic Option 3 works but...

Page 315: ... of this Since the LI 6400 is a 9 pin AT device youÕll need a null modem cable to communicate with your computer Many computers and most laptops use a 9 pin AT connector for the RS 232C port in which case an adapter cable such as the 1800 04 from LI COR or a 25 pin to 9 pin adapter is required The LI 6400 is configured with a male 9 pin AT connector on the console Plug the 9 pin end of the 1000 09...

Page 316: ...ause there is only a few second window in which the program tries to establish communications if it canÕt it stops trying Using WinFX WinFX introduced in May 1999 is the Windows version of FX Installation An installer program is located on the ÒUsing the LI 6400Ó CD Edition 2 It can also be downloaded from CORE support in www licor com The installation program will create a directory named WinFX i...

Page 317: ...e Exchange mode Option 3 under File Exchange Mode on page 11 4 then power the LI 6400 on as you click Select in Figure 11 2 4 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 Figure 11 2 Selecting the comm port in WinFX Figure 11 3 WinFXÕs tre...

Page 318: ... it and select the files Click on a file name to select it For multiple files hold ctrl down when you click In Figure 11 5 we are set up to send three files Figure 11 4 Click the destination directory to open it Its name will appear in the active directory window The active directories are shown here Figure 11 5 Select the file s you wish to copy and send them by pressing the appropriate arrow but...

Page 319: ...ns cable falls off battery goes dead file exchange mode is terminated etc the only indication will be the ÒNot ConnectedÓ in the status bar In that case you can click the Connect button to re establish communications Drag and Drop Single files or directories can be copied in either direction this way but not multiple files marked with a check Deleting Files Select the file or files to be deleted t...

Page 320: ...pped legal DOS names to any LI 6400 files with illegal names that were sent to the PC File Name Considerations on page 11 21 In May 1999 version 4 0 was released FX 4 0 is 32 bit friendly and can han dle long file names With the advent of WinFX there is perhaps no need for this program but it remains available Installation All that is needed is the file FX EXE It is available on the 6400 CD and fr...

Page 321: ... Step 3 Enter File Exchange Mode Use one of the three methods described on page 11 4 The when this happens the display on the PC should change to something like in Figure 11 8 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 Figure 11 7 The message displayed while FX waits for an LI 6400 to be connect...

Page 322: ... Files on page 11 21 for a discussion YouÕll also be given the option of overwriting existing files with the same name yes no or only if it is older Each file is copied and will have the same name on the destination as it had on the source However since LPL supports long file names and DOS doesnÕt FX prior to version 4 0 uses a map file to ÒpreserveÓ LPL names on the PC See File Name Consideration...

Page 323: ...em port on your Macintosh 2 Launch FX Double click the FX application icon 3 Establish communications Put the LI 6400 into File Exchange Mode page 11 4 and click on the Con nect button You should be able to navigate through the Macintosh file sys tem and the LI 6400 file system Figure 11 9 Figure 11 9 FX Macintosh shows files and directories on both the LI 6400 and the Macintosh Di rection of file...

Page 324: ... with gibberish binary direc tory information 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 FX1 It is useful for making batch files for routine tasks such as backups Version 2 0 released in May 1999 is 32 bit and supports long file names The data transfer is ...

Page 325: ...LI6400 Examples The EW program is run by typing ew dos lpl switches at a 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 but any subdirectories in either directory will be created if neces sary Note that if the LPL directory cont...

Page 326: ...n do this by adding a baud rate switch to each ew command For example to operate at 115200 baud add b115200 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 above example we have EW EXE in c LI6400 and all data files in subdirectory User of...

Page 327: ...r every data taking session youÕll always have an updated copy of the user disk on your PC 1 Make a subdirectory on the PC YouÕll want a destination directory If we follow our first example weÕll have one named data EW 1 3 Copyright c LI_COR inc 1995 1996 Receive mode No subdirs Establishing contact with the LI 6400 LI 6400 must be in file exchange mode Go aci auto light man light C LI6400 _ File ...

Page 328: ... that are missing ew data user u Archive the user disk This method of backup has the advantage of being potentially quicker than the file by file method just described The disadvantage is that the disk will exist as one binary file on your computer so itÕs not accessible as individual files unless you put it back into the instrument 1 Defragment the user disk This will make the resulting binary fi...

Page 329: ...4 default 1 i irq The interrupt vector for the comm port only needed for non standard comm ports r Send files from the LI 6400 to the computer default files go to the LI 6400 u Skip files that haven t changed Default do all files n Send only this directory Default does all subdirectories as well y Send files in binary form default is text form f name Send this LPL program and execute it before cop...

Page 330: ...oming file The de fault is to overwrite all files regardless of date ew c mydata user joe b115200 r u n Do only the files in the specified directory if there are any subdirectories found in that directory ignore them The default is to include all subdirecto ries ew c li6400 special user configs r n y Do no end of line conversions but rather send the files byte for byte See Text vs Binary Files on ...

Page 331: ...ex ists for the INSTALL program2 and is unlikely to be useful to anyone else m mask To send a particular file or a set of files specify the name or mask with the m switch and are wild card characters means any character or charac ters including nothing while means any character in that location For ex ample ew data user n m grass would transfer any file in the user directory only with ÒgrassÓ some...

Page 332: ...o put user bin back into the LI 6400 type ew user bin user d b115200 Some things to note when using the d switch Disk names are part of the image Consider the following example 1 You download User and store it in us er bin 2 You rename user to junk 3 You then send user bin to Junk by ew user bin junk d What will the LI 6400Õs diskÕs be named Sys and User just like before If on the other hand you d...

Page 333: ...This is the reason that file size may differ after text files are moved by FX or EW from the LI 6400 to a computer File Name Considerations DOS This section pertains to EW EXE below version 2 0 or FX EXE below ver sion 4 0 The LPL operating system in the LI 6400 supports long file names DOS pre Windows did not When files are sent from the LI 6400 to the computer FX DOS or EW will still maintain lo...

Page 334: ...rd File Dialog will prevent you from entering any of these problem characters If you use one of these characters when naming a file on the Macintosh that is to be transferred to the LI 6400 that character will be changed to an underscore at the time of transfer If an LPL file name is too long for the Macintosh 32 characters or more it will be shortened and if it contains a colon which is the direc...

Page 335: ...complish nothing would look like this com1 addr 3f8 irq 4 com2 addr 2f8 irq 3 com3 addr 3e8 irq 4 com4 addr 2e8 irq 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 mat...

Page 336: ...rom 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 Table 11 3 Communication configuration parameters Parameter Acceptable Values Baud Rate 300 1200 2400 4800 9600 19200 38400 57600 115200 Data Bits 7 or 8 Stop Bits 1 or 2 Parity Odd O Even E or None N Handshaking...

Page 337: ...ou type on the PCÕs keyboard should appear on the LI 6400Õs display Verify this If nothing appears on either display there may be a cable problem or the Comm program is not using the right Comm Port If characters are displayed but are not the ones you typed then itÕs a configuration mismatch Make sure the baud rates data bits etc match Once youÕve verified that communications can happen exit Simpl...

Page 338: ...r Macintosh 2 Run the program Double click the 1000 91 icon 3 Configure the Macintosh For version 1 5 or above select ÔLI 6400 Photosynthesis SystemÕ from the Instrument menu to set the Communications parameters In earlier versions of the 1000 91 program select ÔGeneral Õ from the Instrument menu and set the parameters to 9600 8 1 N 4 Configure the LI 6400 On the LI 6400 select ÔConfigure the COMM...

Page 339: ...nted Tag the file s to be printed For how to do this see page 10 13 7 Open a capture file On the Macintosh open a capture file by selecting ÒCapture DataÓ from the File Menu 8 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 9 Close the capture file Once the data has been sent pres...

Page 340: ...Downloading Files Using a Data Capture Program 11 28 Using the LI 6400 11 ...

Page 341: ...uikPik Config 12 6 Using Edit Config 12 7 Storing Plot Definitions 12 10 SELECTING OBSERVATIONS 12 10 Picking the First and Last Observation 12 10 Using Every nth Observation 12 11 Logic Based Inclusion 12 11 Dealing With Strings 12 13 CURVE FITTING 12 14 Configuring for Curves 12 14 Viewing Curve Fit Results 12 15 VIEWING DATA 12 17 PLOTDEF FILE FORMAT 12 19 STORING AND RETRIEVING GRAPHICS IMAGES...

Page 342: ...Mode GraphIt can be used on the file being logged by pressing ViewFile f2 level 1 while logging to memory or a file From OPENÕs Utility Menu The menu selection ÒGraph Stored DataÓ will run the GraphIt Utility pro gram described in the next paragraph Run the program GraphIt Utility ItÕs stored in the Sys Utility directory The program uses the Standard File Dialog to prompt you to select a file then...

Page 343: ...axis 0 Ci Y axis 0 Photo Target File 9 Obs observations Appears only after data has been read and graphed Change to a previously defined and stored plot definition Draw axes points and curves using current plot definition appears only if there is a plot defined Store the current plot definition for later retrieval with QuickPik Appears only if there is a plot de fined Edit which item X X horizonta...

Page 344: ... lines should be quoted Any line beginning with a quote will be ignored when scanning for data The label line can begin with a quote Figure 12 2 illustrates some acceptable data file formats Header info This is skipped The label line is next Obs Photo PAR Tleaf Tair 1 14 2 1001 23 4 22 3 2 12 2 1 1E3 23 5 22 4 3 13 8 2E3 22 4 22 7 This is a remark 4 18 3 1098 23 7 22 9 5 11 1 1008 22 4 22 6 6 17 7...

Page 345: ...it ÒknowsÓ what the first label should be so you probably will never be asked to locate the label line Finding the Data Lines The data set is assumed to extend from the first data line following the label line to the first blank line or the end of the file If this is not the case you can specifically identify the label first data and last data lines described in Se lecting Observations on page 12 ...

Page 346: ...k Config This is quite simple as the following example illustrates To configure for an A Ci curve using QuikPik Config 1 Press QuikPik Config The directory User Configs PlotDefs is accessed using the Standard File Dialog and you can select from the definitions stored there 2 Select ÒA Ci CurveÓ from the menu Figure 12 4 illustrates the resulting plot definition and plot provided of course that the...

Page 347: ...sed on the data Variable Plot symbol Y Axis min Y Axis max X Axis min X axis max X variable X axis 0 Ci Y axis 0 Photo Plot Definition Edit which item X X horizontal axis Y Y left vertical axis Z Z right vertical axis 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 direc...

Page 348: ...can be drawn on either the Y or Z axes youÕll want all the variables for an axis to be of the same magnitude temperatures for example because they are all plotted with a common scaling X axis 0 Ci V change variable R change range Select option or esc Axis being edited and the current definition Figure 12 6 Editing an axis has two parts that can be done independently selecting the vari able s and s...

Page 349: ... is done via Standard Menu Y and Z axes allow up to five vari ables to be included and provide a short cut for doing curves When youÕve selected all the variables you want press escape The X variable is selected from a menu of all the data columns in the data file The Y or Z variable s are se lected from the same menu A shortcut is provided for drawing curves press a number rather than enter to ma...

Page 350: ... whose first character is not a quote starting with the First Data Line The search continues until a blank line is found or until the Last Data Line has been searched 2 Use Every nth Line Between the First and Last Data Lines every nth line is converted to numbers provided it does not start with a quote The default value of n is 1 but the user can set this This is useful for subsampling large data...

Page 351: ...only You could do this with GraphItÕs logic option by specifying only observations with PAR greater than some threshold value such as 1000 µmol m 2 s 1 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 Figure...

Page 352: ...h a vari able column label in the data set Table 1 lists some useful symbols for use in logic statements For this logical expression spaces donÕt matter so for example Table 9 1 LPL keywords for logical expressions LPL Action Add subtract multiply divide Less than greater than Less than or equal greater than or equal Not equal is equal AND OR Logical and logical or Logic for selecting observations...

Page 353: ...uld ac complish the same thing would be simply 1 while one that would exclude all observations of no use at all would be 0 Dealing With Strings Prior to OPEN 3 2 GraphIt would always consider any line that began with a double quote as a remark and would skip over that line Consequently you could not have any quoted field be the first data column or you would never have any observations OPEN 3 2 al...

Page 354: ...Setup Short Cut on page 12 8 For an existing configuration From GraphItÕs main screen press Edit Config then C short cut just press C If only 1 Y or Z variable is defined the curve is simply selected from a menu Figure 12 11 If multiple Y and or Z variables are defined then it is a two part process Figure 12 12 Figure 12 11 Selecting a curve option when only 1 Y or Z variable 0 Dot to Dot 1 Staigh...

Page 355: ...ect a straight line curve Press Edit Config then C and select a straight line as the curve type 3 Ignore the higher Ci values While in the config editor press L to select observation logic Use an expres sion like Z1 Tair none Z2 Tleaf none Y1 Photo none Curve Status Print Find ReFind Cancel Select _ Y1 Photo none Z1 Tair none Z2 Tleaf none Curve Status 0 Dot to Dot 1 StaightLine 2 2ndOrderPoly 3 3...

Page 356: ...ot and curve fit Press REPLOT GRAPH Press escape after viewing the plot 5 View the slope Press View Data then C The display will look similar to Figure 12 13 Photo vs Ci coeffs 5 22275 0 0939082 RMS 0 7112 CurveFit Information Slope Offset Figure 12 13 Polynomial coefficients are presented in ascending order of power ...

Page 357: ...shows the data plotted in the last plot You can also see this after viewing a plot by pressing V instead of escape View Options F File as stored D Data set all vars and obs G Graphed vars obs only C curvefit Coefficients E curvefit Errors Figure 12 14 The screen displayed after pressing View Data Figure 12 15 Viewing with the D option all variables and observations of the data set Use shift and sh...

Page 358: ... Store curve fit info to disk Y N E Curvefit Errors This option shows the coefficients RMS values and the data points and er rors for each defined curve As with the C option you are given the option of storing the information to disk when you exit from viewing it Photo vs Ci coeffs 5 22275 0 0939082 Ci Photo y f x 180 11 3 0 3807 127 7 2 0 4964 76 8 2 16 0 1706 51 4 0 39 0 005872 27 1 2 97 0 2922 ...

Page 359: ...files are binary and are not legible as text If you transfer them to a computer using an FX or EW Chapter 11 be sure to treat them as binary files 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 PLOTDEF X axis ...

Page 360: ... LI 6400 12 Byte 1 Byte 2 Byte 3 Byte 4 Byte 6 Byte 5 etc Image 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 ...

Page 361: ...NS TO RECOMPUTE 13 2 A STEP BY STEP EXAMPLE 13 2 THE DETAILS 13 7 RecomputeÕs Main Screen 13 7 Source File Considerations 13 8 Destination File Considerations 13 11 Customizing the Recompute 13 12 HINTS 13 14 Suppressing a VariableÕs Recomputation 13 14 Multiple Appended Files 13 14 ...

Page 362: ...layer conductance etc can be modified To Change WhatÕs Stored You can select a subset of a data file such as only three variables to be out put To Change WhatÕs Computed You can add quantities to be computed by changing the Compute List file Obviously the computed quantities should depend only on things that are available in the original file A Step By Step Example Suppose you have a file named Ò ...

Page 363: ...ity is found in its Utility Menu Access the FILER Build a New AutoProgram Configure the COMM port File Exchange Mode Graph stored data New File Editor Recompute stored data Set the Time and Date Edit Custom quit Destination Write to buffer LeafArea StomRat BLCond ComputeList User Configs Comps Defau SourceFile undefined Recompute OPEN files Figure 13 2 The recompute programÕs main screen Use and t...

Page 364: ... is between a file and a buffer memory File is generally the better choice unless the source file is quite small and if you arenÕt sure you really want to store the result When you have destination set to a file you are prompted for that file name when you actually start the recompute which weÕll do in a few more steps 5 Specify a change in leaf area Highlight the LeafArea line and press edit Figu...

Page 365: ...fArea entry from No Changeto one of the other choices LeafArea No Change Area No Change Prompt for new values One global value Will ask for the new leaf area for the whole file right now During the recompute ask for a new leaf area as each obser vation is recomputed AREA_cm2 _ Edit ViewSrc quit RECOMP SourceFile MyData Destination Write to file LeafArea One global value 4 4 StomRat One global valu...

Page 366: ...ed Recomputing 8 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 DIR User Write to what file MyData RCMP File AbeÕs data Junk Data MyData ZekeÕs Data Dir CANCEL SELECT Add RDMP to the file name or other wise modify the name to make a new file Figure 13 6 You are prompted for the destination file when you st...

Page 367: ...nt stomatal ratio BLCond Has five possible settings If you are changing leaf area or sto matal ratio then set this to Comput ed The global value and prompted values should be a 1 sided value which is subsequently adjusted for stomatal ratio ComputeList Specify the name of the compute list file to use LogFormat Specify the name of the log format file to use PromptList Specify the name of the prompt...

Page 368: ...ed for the file and the one currently in ef fect you are prompted to select which to use Figure 13 8 If the one used cannot be found you are alerted to this Figure 13 9 and the current one is used Either way you can always set the compute list before recomputing by OPEN 3 2 Thr May 14 1998 14 35 08 ComputeList User Configs Comps Default BLCTable Sys Lib StdBLCTable LightSource Sun Sky 1 0 19 LogFo...

Page 369: ...to be written to the file when recomputing The program uses two pieces of information to build this list 1 The original log format file This is the list of ID values in order that were stored Different Compute List 1 current User Configs Comps Default 2 was User Configs Comps Default MyStuff Use which Compute List 1 2 Recompute OPEN files Or ÒLogÓ or ÒPromptÓ Specified by the file Currently in eff...

Page 370: ...e out from the label which of the presently defined variables if any each data column corresponds to If the program fails to match the label with any known variable you are alerted to the problem 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 CanÕt locate the data label li...

Page 371: ...ile if you choose Destination File Header The recompute program puts itÕs own header information at the start of the recomputed data file as well as a copy of the original header Figure 13 12 If you recompute multiple times youÕll get multiple headers Note Prior to OPEN version 3 2 the recompute program would use the recomputed time stamp rather than the original time stamp as the ÒbaseÓ time for ...

Page 372: ...u choose OpenRecomp 3 2 User MyData OPEN 3 2 Mon Dec 22 1997 12 56 32 ComputeList User Configs Comps Default BLCTable Sys Lib StdBLCTable LightSource Sun Sky 1 0 19 LogFormat User Configs LogFormats Std Output PromptList User Configs Prompts Default none OPEN 2 5 4 Thr Aug 29 1996 11 35 08 ComputeList User Configs Comps Default BLCTable Sys Lib StdBLCTable LightSource Sun Sky 1 0 19 LogFormat User...

Page 373: ..._R Always Recomputed 15 RH_S ALways Recomputed 7 Flow No Change 12 PARi No Change 13 PARo No Change 11 Press No Change 65 CsMch No Change 66 HsMch No Change 23 Status No Change Obs number and time are fixed You canÕt change them User defined variables are usually ÕAlways Re computeÕ but there is a method to skip a vari ableÕs recomputation System variables such as Tair can also be set to ÕOne glob...

Page 374: ...should be aware of 1 The program will recompute until the end of file is reached Blank lines remarks etc will not stop it 2 Only the first data header is considered If you changed log formats or compute lists etc they will not be taken into consideration If this is the case you should split up the source file into mul tiple files before recomputing 3 Non data lines OPEN 3 01 and below All lines th...

Page 375: ...Part IV Configuration Issues ...

Page 376: ......

Page 377: ...rature 14 4 IRGA Temperature 14 5 Water Concentrations 14 5 Carbon Dioxide Concentrations 14 6 Leaf Temperature 14 7 Flow Meter 14 7 In Chamber PAR 14 8 External PAR 14 8 COMPUTED VARIABLES 14 9 Humidity Variables 14 9 Stability Variables 14 10 TIME AND LOGGING VARIABLES 14 11 STATUS VARIABLES 14 12 BOUNDARY LAYER VARIABLES 14 17 LIST OF SYSTEM VARIABLES 14 19 BAND BROADENING CORRECTION FOR WA TER...

Page 378: ...every user variable as well has the following properties 1 A unique ID number This is used as a reference in format files display log and strip chart for ex ample System variables have negative ID values user defined variables have positive ID values 2 Labels for Display and for Logging Display labels are what you see in New Measurements mode Log labels are how the variable is labelled in your out...

Page 379: ...the raw signals from each sensor including for example the battery V the temperature sensors mV the CO2 reference IRGA mV etc Each time these new A D readings are available OPEN computes the sensorÕs readings in meaningful units and some ancillary val ues such as relative humidity which are based on multiple sensors Thus system variables that are associated directly or indirectly with sensors are ...

Page 380: ... calibration coefficients respectively specified by the configuration command2 CalPress ap0 ap1 Air Temperature The air temperature within the IRGA sample cell Ta C is computed from the signal Va mV of a linearized thermistor located just beneath the circulation fan in the sample IRGA shown in Figure 19 26 on page 19 31 The equation is ID 9 14 2 Block Temperature The temperature Tb C of the metal ...

Page 381: ...ncentrations Wr and Ws mmol mol 1 are ID 4 14 5 ID 5 14 6 where the function f x is a 3rd order polynomial whose three coefficients aw1 aw3 the offset term aw0 is always 0 are specified by the configuration command CalH2O aw1 aw2 aw3 Gwr and Gws are gain factors set in the ÒIRGA SpanÓ routine of the Calib Menu of OPEN Setting the H2O Span on page 18 13 The zero drift correction term zw is based on...

Page 382: ...sed for the match correction that is determined every time the IRGAs are matched in New MeasurementÕs Match Mode Carbon Dioxide Concentrations The equations relating reference and sample IRGA signals Vcr and Vcs mV to reference and sample CO2 concentrations Cr and Cs µmol mol 1 are ID 1 14 8 ID 2 14 9 where the function g x is a 5th order polynomial whose five coefficients ac1 ac5 the offset term ...

Page 383: ...bed above for water and Cms and Cmr are the CO2 versions of Wms and Wmr also described above Leaf Temperature The leaf temperature Tl is measured with a chromel constantan thermocouple junction The reference junction is the IRGA block whose temperature Tb is known The thermocoupleÕs signal is amplified to become Vl mV and is related to leaf temperature Tl C by ID 10 14 12 Flow Meter The flow meter...

Page 384: ...Source name fa B CalParGaAs ag CalParLED ae Specifically 14 15 The actinity correction factor fa for the GaAsP sensor allows the ÒsameÓ cal ibration factor ag to be used for various light sources 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 Vqx rela...

Page 385: ... mol 1 and multiply by the total pressure P kPa Thus given a reference measurement of water Wr the reference va por pressure er kPa is ID 53 14 17 while in the sample cell the vapor pressure es kPa is ID 54 14 18 Relative Humidity Relative humidity is the ratio of vapor pressure to saturation vapor pressure The reference and sample relative humidity hr and hs in percent are given by ID 14 14 19 ID...

Page 386: ... or equal to 0 14 24 where the argument e is vapor pressure in kPa and The LPL implementation of function d is named DewPoint Table 15 3 on page 15 15 Stability Variables In New Measurements mode four quantities are displayed that indicate the stability of the ongoing measurements They are found on level e of the stan dard display map and are coefficients of variation for CO2 differential Ccv labe...

Page 387: ...u wish Since new data is measured every 0 75 seconds and n 30 the time period for which any given stability is valid for is 22 5 seconds Time and Logging Variables ID 35 ÒObsStordÓ The number of observations that have been stored since the log file was last opened Note that this will not be the number of observations actually stored in the file if an existing file is opened for appending ID 36 ÒOb...

Page 388: ...e available as system variables ID 31 ÒCO2 H2O Pump Flow Mixr FanÓ This is a string designed to show the status of six hardware components and is available on level J of the standard display map It is simply a composite of the status variables described below ID 25 26 ÒCO2Ó and ÒH2OÓ There are 4 possible values of these string variables The error condition is triggered by too much light blockage i...

Page 389: ... when lowering the concentration or when asking for too low a value see the related troubleshooting discussion starting on page 20 26 Table 14 2 Pump Status states Value Meaning What is Sensed Without Mixer With Mixer 0x0300a 0x0300 0x0100b Off Pump switched off 0 1 ignored OK Pump OK 1 1 1 errc Pump drawing too much current not applicable 1 0 a Pump control output b Digital input port 1 pin 0 c P...

Page 390: ...400 01 CO2 Mixer which means the flow control is done with a diverter valve ID 30 ÒFANÓ The sample and leaf chamber cell mixing fan can have three values 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 Table 14 4 Flow status Value Meaning What is Sensed 0x0300a 0x0103b 0x01...

Page 391: ... Item CO2 IRGAs H2O IRGAs Pump Flow Con trol CO2 Mixer Chamber Fana Possible Values 1 OK 1 OK 0 Off 0 Off 0 Off 0 Off 2 errR 2 errR 1 OK 1 OK 1 OK 4 Slow 3 errS 3 errS 2 err 2 Low 2 Low 5 Fast 4 err 4 err 3 High 3 High LPL Function StatusCO2 StatusH2O StatusPumpb IsPumpOn StatusFlow StatusInj chFanStatec a The value for F is the number of volts that the fan control DAC is set to By default 5 is fa...

Page 392: ...am Commands on page 25 12 ID 57 ÒFwMxCrLpÓ This four digit itÕs actually an 8 character string value provides a control manager status indicator Figure 14 2 A control is marked with a 1 if it is on target and stable or turned off The control manager is discussed in Chapter 7 Table 14 7 Uses of the Program variable When Program Meaning In LPMeasure HH MM SS Time to next step In LPMeasureTilStable H...

Page 393: ...yer conductance to water gbw which is a system variable ID 55 The effective boundary layer conductance which takes into account the ratio K ID 34 of sto mata on one side of the leaf to the other is ID 32 14 31 K is determined by the StomRat configuration command Since boundary layer conductance is also a function of wind speed and leaf area this fixed value option is generally used when not measur...

Page 394: ...1 17 94 EB analysis 1 18 94 The first value is blc at low area 2nd is blc at high area BLCTABLE 1 4 6 leaf area 1 leaf area 2 0 1 0 1 fan 0 1 05 0 646 fan 1 1 50 0 8 2 01 1 12 fan 3 2 2 1 25 2 43 1 42 fan 5 Figure 14 3 Listing of the boundary layer lookup table Ò Sys Lib StdBLCTable The data follows the BLCTABLE string and two values are expected in that line the minimum leaf area and the maximum ...

Page 395: ...l 1 co2_diff_um DC Cs Cr 4 H2OR_mml H2OR Reference H2O mmol mol 1 h2o_1_mm Wr Eqn 14 5 pg 14 5 5 H2OS_mml H2OS Sample H2O mmol mol 1 h2o_2_mm Ws Eqn 14 6 pg 14 5 6 DH2O_mml DH2O DH2O mmol mol 1 h2o_diff_mm DW Ws Wr 7 Flow_µml Flow Flow Rate µmol s 1 flow_um F Eqn 14 13 pg 14 7 8 Tblock C Tblk IRGA Block Temp C tblk_c Tb Eqn 14 3 pg 14 4 9 Tair C Tair Chamber Air Temp C tcham_c Ta Eqn 14 2 pg 14 4 ...

Page 396: ...Numerical status code statusWord page 14 15 24 Battery Battery voltage battery_v Reported in Volts 25 CO2 CO2 IRGA status stat_co2 page 14 12 26 H2O H2O IRGA status stat_h2o page 14 12 27 PUMP Pump status stat_pump page 14 13 28 FLOW Flow Control status stat_flow page 14 14 29 MIXR CO2 Mixer status stat_inj page 14 13 30 FAN Chamber fan status stat_fan page 14 14 31 CO2 FAN The status line statLin...

Page 397: ...p Eqn 14 1 pg 14 4 46 parIn_mv In chamber PAR mV parIn_mv Vqc Eqn 14 14 pg 14 8 47 parOutmV External PAR mV parOut_mv Vqx Eqn 14 16 pg 14 8 48 CRagc_mv Ref CO2 IRGA AGC mV agc_c1_mv AGC voltages on page 20 43 49 CSagc_mv Chamber CO2 IRGA AGC mV agc_c2_mv 50 HRagc_mv Ref H2O IRGA AGC mV agc_h1_mv 51 HSagc_mv Chamber H2O IRGA AGC mV agc_h2_mv 52 totalCV Total stability allRms Tcv Eqn 14 28 pg 14 11 ...

Page 398: ... mol 1 co2_1_offset Cmr Eqn 14 8 pg 14 6 68 HrMch Ref H2O offset mmol mol 1 h2o_1_offset Wmr Eqn 14 5 pg 14 5 69 DOY Day of the year 0É366 clockDOY page 14 12 70 YYYYMMDD Date code integer clockDate page 14 12 101 AuxF1b User defined float auxF1 System Variables for Prompts on page 9 15 102 AuxF2 User defined float auxF2 103 AuxF3 User defined float auxF3 104 AuxN1 User defined integer auxN1 105 A...

Page 399: ...sed over limited ranges of absorber mole fraction pressure and pathlength It can be shown that the Ònon overlapping line approximationÓ applies at ambient pressure and CO2 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 Ja...

Page 400: ...pressure scales the raw voltage much like a gain adjustment All gases are not equally effective in causing pressure broadening of absorp tion lines The equivalent pressure Pe is defined as 14 40 where is the partial pressure of nitrogen and Pi gives the partial pres sures of other diluent non absorbing gases The partial pressure of each non absorbing gas is multiplied by a weighting factor called ...

Page 401: ... instead of nitrogen then 14 41 becomes 14 42 where The foreign gas broadening coefficient for water vapor is denoted in 14 42 to indicate that it uses dry air as refer ence instead of nitrogen A calibration equation similar to 14 38 that includes the pressure broaden ing effects of variable water vapor can be obtained by substituting Pe for P in 14 33 and 14 34 and carrying through the subsequent...

Page 402: ... 14 44 where W has units of mmol mol 1 and w mol mol 1 Literature Cited Burch D E E B Singleton and D Williams 1962 Absorption line broad ening in the infrared Applied Optics 1 359 363 Jamieson J A R H McFee G N Plass R H Grube and R G Richards 1963 Infrared Physics and Engineering McGraw Hill New York 673 pp Wolfe W L and G J Zissis 1978 The Infrared Handbook The Infrared In formation and Analysi...

Page 403: ...ode 15 4 The Label String 15 5 The Description String 15 6 The Equation 15 6 WRITING AND MODIFYING COMPUTELIST FILES 15 7 Some Important Rules 15 7 Compilation Errors 15 10 USER DEFINED CONSTANTS AND REMARKS 15 12 User Constants 15 12 User Remarks 15 12 Using Constants and Remarks 15 12 EXAMPLES 15 13 Water Use Efficiency 15 13 USEFUL VARIABLES AND FUNCTIONS 15 15 THE DEFAULT COMPUTELIST 15 16 OLD...

Page 404: ...e other ComputeList files to appear besides the default one Creating a configuration from the Installation Menu Some items have special ComputeLists associated with them such as the 6400 09 Soil Flux Chamber and the 6400 05 Conifer Chamber so installing those items will cause a new file to appear in the User Configs Comps directory Also just building a configuration for a more conventional chamber...

Page 405: ...t Menu on page 5 15 and press S to store it as a new file or U to store it with out changing the name 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 Choose a ComputeList Edit Current C...

Page 406: ... There are no consequences of duplicating a user variable number other than confusion because only the first occurrence of a particular variable ID will actually be used the duplicate s will be computed but inaccessible Format Code Immediately following the ID number is the optional format code The de fault format for displaying and logging user computations is to use 3 signifi cant digits resulti...

Page 407: ...bel which must be 8 characters or less The variableÕs label is used to iden tify the variable in text graphics and file output Table 15 1 p 1000p and p 1000 expressed using the various format codes Code p 1000p p 1000 Code p 1000p p 1000 F0 3 3141 0 G1 3 3E3 3E 3 F1 3 1 3141 6 0 0 G2 3 1 3 1E3 3 1E 3 F2 3 14 3141 59 0 00 G3a 3 14 3 14E3 3 14E 3 F3 3 141 3141 592 0 003 G4 3 141 3 141E3 3 141E 3 F4 ...

Page 408: ...t in post fix notation The signals the change and there must be spaces between each item 21 Trmmol transpiration mmol m2 s 20 1E3 Multiples an earlier user variable 20 by 1000 101 Plot xxx UCON 0 Defines a floating point user constant Nothing is computed here but this value can be used in other definitions by referencing it as 101 The default val ue of the constant is 0 the argument of UCON 9872 C...

Page 409: ...e new ComputeList is read and implemented and your con figuration will have changed Use the system editor Use the Filer or example to edit a ComputeList file and store it under a new name To actually use the new file you either Choose a ComputeList in the _ComputeList Menu to pick it or use the Config Editor add a ÒCom puteList Ó line and edit it Write one on your own computer Save it as a text fi...

Page 410: ...variable Thus u20 is the variable name of 20 The code that is generated will have a line for each variable assigned to its equation string Thus if the equation string for 20 was 10 15 the line for u20 would appear as in Figure 15 4 Note that Ò 15Ó becomes Òu15Ó You can write it either way If you donÕt want this automatic assignment taking place it can be suppressed with the word NOASSIGN Suppose f...

Page 411: ...by an ÒokÓ or an error If you make a syntax error in an equation string with a NOASSIGN you wonÕt know it until the LPL module that is being generated fails to link and your entire ComputeList is not accepted The ASSIGN function The Assign function allows user variables to be computed during New Mea surements mode but allows them to be skipped during recomputations For example suppose we are measu...

Page 412: ...compiled each vari ableÕs label is printed to the display followed by an ÒokÓ if it compiles correctly1 If there is a problem however you will get a message describing the problem That variable will then not be available for subsequent opera tions EXAMPLE If the definition for Trmmol 20 is changed to 21 Trmmol Transpiration mmol m2 s 20 xyz The symbol xyz will not be found so when Trmmol is compil...

Page 413: ... ComputeList to fail The message will look like Figure 15 7 No user defined quantities will be available Either edit the ComputeList and fix the problem or select another ComputeList Trans ok Trmmol ERROR Unidentified ÕxyzÕ Object FCT recompile Module sys open clfconvert Press Any Key Figure 15 6 Example error message when the unknown variable xyz is put into the defining equation for Trmmol ERROR...

Page 414: ...lot Ó and ÒRateÓ The argument of the UCON function is the initial value of the user constant User Remarks If you wish a constant to contain letters and punctuation in addition to num bers then youÕll need a string remark User remarks are defined just like user constants except instead of UCON use UREM n where n is the desired maximum string length of the remark Using Constants and Remarks To inclu...

Page 415: ...icien cy W will be 15 1 To add water use efficiency to the current ComputeList 1 Access Edit the Current ComputeList Starting from OPENÕs main screen press Config Menu F2 then select _ComputeList Menu 2 Decide where to insert the new variable Since weÕll need both photosynthetic rate and transpiration for this equation scroll down below where they are defined see Figure 15 10 W A 10 6 Ð E 100 StdC...

Page 416: ...Logging Control on page 9 7 You may wish to save the modi fied Log List under a new name 7 Add to Display List If you wish to see the value of the new variable in New Measurements mode add it to the display by using the Display Editor f4 level 6 You may wish to save the modified Display List under a new name 8 Update or Make a New Config File Go to Config Status in the Config Menu and Update or sa...

Page 417: ...anges sign of x ABS x absolute value of x SQRT x square root of x EXP x exponential SatVap T Returns saturation vapor pressure kPa T temp C StdCond E Tf Blc P W Returns stomatal conductance mol m 2 s 1 E transpiration mol m 2 s 1 Tf leaf temp C Blc boundary layer cond mol m 2 s 1 P atmos pressure kPa W ambient water vapor mmol mol 1 DewPoint e Returns the dewpoint temperature C e vapor pressure kP...

Page 418: ...atal cond mol m2 s StdCond 20 Tleaf_c condBL_mol press_kPa h2o_2_mm 30 Photo Photosynthesis umol m2 s 10 co2_diff_um co2_2_um 20 35 CndCO2 Total Conductance to CO2 1 0 1 6 23 1 37 condBL_mol 36 Ci Intercellular CO2 umol mol 35 20 2 co2_2_um 30 35 20 2 38 Ci_Pa Intercellular CO2 Pa 36 press_kPa 1E 3 39 Ci Ca Intercellular CO2 Ambient CO2 36 co2_2_um 25 VpdL Leaf VPD es Tleaf eair SatVap Tleaf_c eAi...

Page 419: ...lexibility to support devices such as the Soil Flux chamber gave rise to an alternative format Com puteList which is termed the 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 ...

Page 420: ...Defining User Variables Old Style vs New Style 15 18 Using the LI 6400 15 ...

Page 421: ...FILES 16 4 The Installation Menu 16 4 Two Examples 16 5 INSTALLATION MENU BEHIND THE SCENES 16 10 Installing a Sensor 16 10 Using Energy Balance 16 11 Boundary Layer Conductance 16 12 MODIFYING CONFIG FILES 16 12 Config Status 16 14 Config Editor 16 15 THE RESET MENU 16 16 ÒConfig File Re InstallÓ 16 16 ÒReset to Factory DefaultsÓ 16 18 ÒReset to User Configuration 16 18 CONFIGURATION COMMAND SUMM...

Page 422: ...he measurements that you want covers a va riety of issues including the proper calibration constants for the sensors being used the mix of variables you want stored and the particular equation set that you deem appropriate to name but three All of these are handled by one ve hicle the configuration file Configuration Files When OPEN is first run one of the things that happens is the selection and ...

Page 423: ...mprise the factory default settings1 Whenever OPEN im plements a configuration this master file is first read and implemented 1 In case youÕre interested this master ÒfileÓ is actually two files Ò Sys Open Con fig Items 1 and Ò dev parm0Ó Figure 16 1 Prompting the user for a configuration file This can happen at power up or when Resetting to User Configuration from the Reset Menu found in the Conf...

Page 424: ...n Menu Figure 16 4 Anytime you wish to add the calibration of an accessory such as an external quantum sensor chamber light sensor LED light source etc or generate a configuration file that makes use of a different chamber or other accessory then select the item in question from the Installation Menu and follow the ensuing directions Note In OPEN 3 01 there is a potential problem with using the In...

Page 425: ... We present two examples of using the Installation Menu to build configura tion files Example 6400 02B LED Source Suppose you already have a 6400 02 red LED source but you have acquired a 6400 02B source as well This example will show you how to install it and easily switch configurations from one to the other 6400 02 or 02B LED Source 6400 05 Conifer Chamber 6400 06 PAM Interface 6400 07 or 11 2x...

Page 426: ... the calibration information YouÕll need the calibration sheet Figure 16 6 for the next three questions Installed 6400 02 or 02B LED Sources 0 47 SI 183 10 Oct 1996 Does the serial number of the item to be installed appear above Y N N Do you wish to add it now Y N Y your responses Figure 16 5 The LED source installation program shows the currently installed sources and gives you the chance to add ...

Page 427: ...n asked Build a configuration file Y N 5 Specify the chamber bottom YouÕll be asked to specify which chamber bottom is being used either the standard 2x3 chamber bottom or the clear bottomed 6400 08 2x3 6 Specify the light source YouÕll be asked to select a light source from a menu Figure 16 7 which will contain all installed LED sources in addition to some standard sources 6400 02B or 02B LED Lig...

Page 428: ... flat plant ma terial such as needles The response here determines a number of configura tion commands including ÒComputeList Ó ÒLogFormat Ó and ÒDisplay Ó 8 Leaf Type Needles or Broadleaves N B The response to the question Enter leaf type Needles or Broadleaves N B determines if the boundary layer conductance will be computed from a look up table broadleaves or if a fixed value is used needles Th...

Page 429: ...berÓ From OPENÕs main screen press Config Menu F2 then select the Installa tion menu 2 View the file Press escape when done 3 Store the file Press Y to store the file Modify the default ÒSoil ChamberÓ name if you desire The installation program will then copy some other support files from sys to user and you are done None of the configurations that can be generated by the Installation Menu ac tual...

Page 430: ...s dev parm0 for the following entries commented or not CalParGaAs CalParLED CalParOut and presents the results in a list such as shown by Figure 16 11 Calibration Data G103950109 CO2Mixer YES 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 CalParGaAs 0 70 GB ...

Page 431: ...pter 15 There are three standard energy balance files that might get used Clear Bottom EB Conifer Chamber EB Default using EB 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 0 48 S...

Page 432: ... Config Editor page 16 15 Frequently however it is not necessary to resort to this to accomplish what you want The Logging Control screen page 9 7 Prompt Control screen page 9 12 and LightSource Control screen page 8 4 are examples of ways to affect the user config file without using the Con fig Editor Table 16 1 Methods of modifying config files Action Affected Configura tion Command AREA F1 leve...

Page 433: ...re the changed config uration as a new configuration file then this can be done with the Config Sta tus described on page 16 14 User 66 full Tue Jun 16 1998 12 29 36 12 25V Menu Menu Menu Msmnts Menu Welcome Config Calib New Utility LI 6400 Photosynthesis System OPEN 3 2 CONFIG Figure 16 12 When the configuration is changed and not stored the CONFIG flag will appear in OPENÕs main screen Too see w...

Page 434: ...e Contents Note that ÒFactory DefaultÓ is an empty file Config Status Current Config Is Factory Default Edit Save saveAs Revert Quit If the current configuration file is NOT saved File Contents as stored changes 1 LightSource Ò6400 02B RedBlue SI 55 Unstored Changes Access the Config Editor Update and Save the Config File Access the Config Editor Revert back to the Ôas storedÕ version Update and S...

Page 435: ...ctual ly happens depends on the item being edited Edit might ac cess a menu of possibilities e g LogDelimiter or prompt for a new value e g AREA or access the Standard File Dialog box e g Displays Remove Remove the highlighted entry This is functionally equiva lent to and more efficient than setting it to the factory de fault value Disable Disables a config command without removing it by turning i...

Page 436: ...C will be the same as ex iting via Cancel The Reset Menu ÒConfig File Re InstallÓ This program will set some or all of the default configuration files back to fac tory defaults It can be used to undo changes you might have made to these files or to get the User disk back into a usable form after it has been format ted or install a default configuration onto an arbitrary disk such as the hidden dis...

Page 437: ...tions Y N Do Prompt Lists Y N Do Strip Chart Definitions Y N Do Config Files Y N The files involved are listed in table Table 16 3 Table 16 3 Files installed by Config File Reinstall Category Destination directory Files to be overwritten AutoPrograms Configs AutoProgs AutoLog Averaging AutoLog LightCurve A CiCurve Buffered AutoLog TimedLamp Remote Control User Computations Configs Comps Default De...

Page 438: ...in the Configs UserPrefs directory After implement ing the master list the user is prompted to select a configuration Figure 16 1 on page 16 3 and it is then implemented Configuration Command Summary The following commands can be used in a configuration file For the most up to date list valid for whatever version of OPEN you are running press the Help function key in the Configuration Menu There m...

Page 439: ...priate for broadleaves in the 2x3 chamber and allows the effective boundary layer conductance to be computed automatically as a function of leaf area and fan speed When using a 2x6 chamber 6400 07 or 6400 11 then use BLCond Sys Lib BLCTable_2x6 If you are using conifers then a fixed value is more appropriate BLCond 5 BndBrdCorr Use band broadening corrections page 14 23 for water vapor when comput...

Page 440: ...ny reason for CalParLED to appear in a user configuration file If for some reason a configuration file contains a LightSource command that specifies an LED source with one value of ae and also a CalParLED that specifies another value of ae the one that takes precedent is whichever one is last in the file CalZero The two values which follow specify IRGA zero drift with temperature for CO2 and H2O r...

Page 441: ...0 02 or 02B then a third parameter ae is expected LightSource 6400 02É fa B ae where ae is the light sourceÕs calibration factor Equation 14 15 on page 14 8 This quantity has historically been specified with the CalParLED command but since OPEN version 3 0 and the introduction of the Light Source Control utility it can also be included in the LightSource command LogDelimiter Data field delimiter t...

Page 442: ...mRat Sets the stomatal ratio parameter K Equation 14 31 on page 14 17 Note that this can be set in New Measurements mode as well f2 level 3 UserChan The three values following the command are signal channel 20 through 23 ground channel 3 through 7 and resolution 0 low 1 high See Analog Input Channels on page 26 22 This marks a comment Any line starting with is ignored Note that the En able and Dis...

Page 443: ...g an Energy Balance Computing what you canÕt measure THE THEORY 17 2 USING ENERGY BALANCE IN OPEN 17 6 How To Do It 17 6 The Details 17 6 Recomputation Considerations 17 9 ENERGY BALANCE AND BOUNDARY LAYER 17 9 FURTHER READING 17 11 ...

Page 444: ...flux L W m 2 17 1 We consider two components to net radiation solar and thermal The solar part we will estimate by converting the incoming PAR reading in the chamber RQ µmol m 2 s 1 to total visible and near IR energy using an empirical measurable with a spectroradiometer conversion factor k and using the leaf absorptivity a averaged over the spec trum of the light source 17 2 The net thermal term...

Page 445: ...ow becomes 17 6 If we let and note that for small DT 17 7 then we can solve 17 6 for DT 17 8 where for most leaves W m 2 K 1 and cP 28 J mol 1 K 1 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 L 44100E Q 2cpgb Tl Ta Ð akR Q 2es T w 273 4 2es T l 273 4 Ð 44100E 2c p g b T l T a Ð DT Tl Ta Ð º T l 273 4 T a 273 4 4 ...

Page 446: ...using an 1800 12 In tegrating Sphere Light Source k a Sun Sky 0 39 0 49 0 19 Mercury 0 33 0 60 0 20 Fluorescent 0 23 0 75 0 18 Tungsten 0 75 0 26 0 20 6400 02 LED Red only 0 18 0 84 0 16 6400 02B LED Red Blue 0 19 0 84 0 15 Metal Halide 0 28 0 61 0 17 k a B º Figure 17 1 Leaf absortance spectrum used in the computations of Table 17 1 0 0 1 0 2 0 3 0 4 0 5 0 6 0 7 0 8 0 9 1 300 400 500 600 700 800 ...

Page 447: ... 5 10 15 20 25 300 400 500 600 700 800 900 1000 1100 W m 2 nm 1 Wavelength nm 6400 02B LED Source 0 0 5 1 1 5 2 2 5 3 300 400 500 600 700 800 900 1000 1100 W m 2 nm 1 Wavelength nm Metal Halide 0 0 5 1 1 5 2 300 400 500 600 700 800 900 1000 1100 W m 2 nm 1 Wavelength nm Sun Sky 0 0 05 0 1 0 15 0 2 0 25 0 3 300 400 500 600 700 800 900 1000 1100 W m 2 nm 1 Wavelength nm Tungsten 0 0 2 0 4 0 6 0 8 1 ...

Page 448: ...he reset menu to implement it 5 If there is a leaf temp thermocouple use it for air temp If you are using a chamber that uses a leaf temperature thermocouple pull it down so that it does not contact the leaf but use it for getting air temperature close to the leaf The 6400 05 Conifer Chamber 6400 07 Needle Chamber and 6400 08 Clear Bottomed chamber all have thermocouples expressly for measuring ch...

Page 449: ...eaf C tLeaf_c 100 21 Trmmol Transpiration mmol m2 s 20 1E3 23 Cond Stomatal cond mol m2 s StdCond 20 101 condBL_mol press_kPa h2o_2_mm 30 Photo Photosynthesis umol m2 s 10 co2_diff_um co2_2_um 20 35 CndCO2 Total Conductance to CO2 1 0 1 6 23 1 37 condBL_mol 36 Ci Intercellular CO2 umol mol 35 20 2 co2_2_um 30 35 20 2 38 Ci_Pa Intercellular CO2 Pa 36 press_kPa 1E 3 39 Ci Ca Intercellular CO2 Ambien...

Page 450: ... bit different EB_DeltaT parIn_um alphaK 1 2 tCham_c tLeaf_C condBL_one 20 The parIn_um value is increased 20 to account for the clear bottom The third variation on the theme is provided by ÒConifer Chamber EBÓ which has no in chamber PAR sensor so the external one must be used Accordingly the call to EB_DeltaT looks like this EB_DeltaT parOut_um alphaK tCham_c tLeaf_C condBL_one 20 Wall Temperatu...

Page 451: ...llowing user equations output formats absorbed radia tion coefficients area boundary layer conductance and stomatal ratio Note however that if you use the leaf temperature thermocouple to measure air temperature as we recommend then you canÕt go back and recompute with out using the energy balance because you will not have a measured leaf tem perature Each of OPENÕs log files contains header infor...

Page 452: ... the paper Equation 14 18 on page 14 9 Solving for one sided boundary layer conductance gb 17 10 and substituting that expression along with RQ 0 into 17 6 leaves us with 17 11 Solving 17 10 for E yields 17 12 Everything in Equation 17 12 is known except leaf paper temperature Tl If Tl can be found by iteration then boundary layer conductance can be deter mined from 17 10 An LPL program is provide...

Page 453: ... 1990 Physiochemical and Environmental Plant Physiology Aca demic 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 ...

Page 454: ...Using an Energy Balance Further Reading 17 12 Using the LI 6400 17 ...

Page 455: ...Part V Maintenance Troubleshooting ...

Page 456: ......

Page 457: ... FLOW METER 18 17 Factory Calibration 18 17 Zeroing the Flow meter 18 17 VIEW STORE ZEROS SPANS 18 18 ZEROING THE LEAF TEMPERATURE THERMOCOUPLE 18 19 6400 01 CO2 MIXER 18 20 Calibrating the CO2 Mixer 18 20 6400 02 B LED SOURCE 18 24 Light Source Calibration 18 24 GAASP LIGHT SENSORS 18 28 Factory Calibration 18 28 Generating a Calibration Correction 18 28 CALIBRATION AND CONFIGURATION FILE SUMMARY...

Page 458: ...span monthly CO2R CO2S CO2 IRGA Flow Flow meter Check zero daily PARi LED Si photodiode Generate control voltage vs output response as needed see Light Source Calibration on page 18 24 PARi no LED GaAsP photodiode Measure adjustment factor for light sources not already in the list See Generating a Calibration Correction on page 18 28 PARo Quantum sensor None Press Pressure sensor Tleaf Thermocoupl...

Page 459: ...igure 16 12 on page 16 13 The calibration also provides data on the IRGAsÕ drift with temperature and this information is provided via the CalZero calibration command User Calibration Zero and Span User calibration actions consist of checking and or adjusting the zero and span There are two parts ÒzeroÓ which is checking the reading with dry CO2 free air in the cell and ÒspanÓ which is checking th...

Page 460: ...ery day using chemicals but ignore the condition of those chemicals Spanning If youÕve got a standard you trust then you can adjust the IRGA to match that standard It shouldnÕt need subsequent adjusting for months and months however If you donÕt have a good standard then donÕt bother with the span Just leave it alone Setting the CO2 and H2O Zero The procedure for checking the IRGAsÕ zero is part o...

Page 461: ...gure 18 1 IRGA zero display while the program loads The prompt appears after a couple of seconds Chamber must be closed To zero CO2 only SCRUB CO2 BYPASS desiccant H2O only SCRUB desiccant Mch off ÒCONFIG JoeÓ CO2R_µml CO2S_µml H2OR_mml H2OS_mml 13 1 5 23 2 234 4 387 AutoCO2 AutoH2O AutoAll Plot Quit Match Valve on or off Press M to toggle Zero CO2 IRGAs only Zero H2O IRGAs only Zero both CO2 and ...

Page 462: ...seconds to do itÕs measurements and calculations and establish new zeros When itÕs done both the CO2R_µml and CO2S_µml values should be within 1 µmol mol 1 of 0 5 Soda Lime full scrub Desiccant full scrub 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 C CO2 Ref Smp H H2O Ref Smp R Ref CO2 H2O S S...

Page 463: ...ou can use air from a tank such as compressed CO2 free air or dry nitrogen Be careful with the latter these tanks may have 10 or 20 µmol mol 1 of CO2 in them and would thus require a tube of soda lime in line to remove it If you have doubts use a tube of soda lime to test it The compressed air should be suitably dry however 1 Use a modest flow rate If you have a way to measure flow from your tank ...

Page 464: ... OPEN 3 2 and above only 5 Match ON if necessary If you are using a single line connected to the sample inlet put the match valve in the proper position by pressing M once the IRGA zero program is running Note that now the reference IRGA will be seeing any leaks that oc cur in the sample cell so make sure there are none chamber tightly closed To shorten the dry down time block the upper half of th...

Page 465: ...le It is therefore a good idea to check the values of these two components to make sure they are both reasonable Figure 18 10 on page 18 18 Not Zero Air The most common problem results from zeroing the IRGAs with air thatÕs not really CO2 free or not really dry LI 6400 PSH 0001 PORTABLE PHOTOSYNTHESIS SYSTEM MODEL SR NO Connect here Match Valve ON Please 1 Close the chamber no leaf 2 CO2 scrub ful...

Page 466: ...be a useful tool is in zeroing the water vapor sam ple cell If both cells are connected with a ÒYÓ as in Figure 18 6 B have the match valve off and zero as described above when the reference cells are sta ble Then turn the match valve on and adjust the H2O sample cell to match the H2O reference value CO2S CO2S H2OS H2OS Chamber must be closed To zero CO2 only SCRUB CO2 BYPASS desiccant H2O only SC...

Page 467: ...e de fined in Equations 14 8 and 14 9 on page 14 6 Checking Setting the CO2 Span Look at Figure 18 6 on page 18 12 1 Select IRGA span from the Calib Menu 2 Set the flow from the tank See the comments under step 1 on page 18 7 3 Attach to the IRGA You have a choice here as shown by Figure 18 6 Attach to the sample inlet on the sensor head and have Match ON or Use a Y connector to split the flow and...

Page 468: ...ast and M to toggle the match valve Figure 18 6 Adjusting the reference CO2 span The span factor should always be near 1 0 is used as a mul tiplier of the IRGA voltage Pressing increases or decreases the span factor for the active IRGA by a factor of 0 001 To change the span factor by 0 010 hold shift down while you press or To change the active IRGA press the F1 through F4 or else use or LI 6400 ...

Page 469: ... 610Õs condensor and the IRGA If condensation happens you will have large errors 2 Set the flow rate Use about a 0 5 l min 1 flow from the LI 610 3 Attach to the IRGA You have the same choice as shown in Figure 18 6 on page 18 12 Here however we would recommend option B splitting the flow and connecting both the reference and sample with Match Off The reason for this is that you will be able to dr...

Page 470: ...ill unequilibrated air from the sample cell enters the reference cell When it sta bilizes 30 seconds set the sample IRGA to read that value Do you see the trick here WeÕve just spanned the reference IRGA so itÕs reading correctly The sample IRGA is seeing slightly drier air because water sorption is still going on and weÕre losing water to the walls of the sample cell When we put match mode on the...

Page 471: ...g label on the tank sent to you H2O Is there water in the condensor Are you asking for a target that is at or above the room temperature You wonÕt get that dew point of course but you will get trouble in the form of condensation somewhere in the line Leak in the chamber The chamber has to be well sealed for this to work 5 Starting in version 3 2 you are not allowed to adjust the span outside of th...

Page 472: ... spans Space doesnÕt permit listing all the reasons why that is a bad idea ÒIRGAs Not ReadyÓ If this message is flashing on your display then there are more pressing prob lems to be addressed see ÒIRGAs Not ReadyÓ Message on page 20 14 and you certainly shouldnÕt be setting the span IRGAs not responding See IRGA s Unresponsive on page 20 16 Storing the Zeros and Spans If the zero and or span adjus...

Page 473: ...lly automatic When you select Flow meter zero in the Calib Menu the flow will be shut off and the system will begin a 10 second count down Figure 18 9 After ten seconds the flow meter signal should read within 1 mV of zero Press OK FLOWMETER ZERO 7 secs to Zero Flowmeter Flowmeter signal 0 7 mV NoAuto Cancel FLOWMETER ZERO Done Flowmeter signal 0 7 mV Adjst Adjst OK When entered the zero rou tine ...

Page 474: ...e the adjustment terms Cmr and Cms in Equations 14 8 and 14 9 on page 14 6 and Wmr and Wms in Equations 14 5 and 14 6 on page 14 5 The values should be between 2 and 2 typically These values are the gain factor terms Gcr and Gcs in Equations 14 8 and 14 9 on page 14 6 and Gwr and Gws in Equations 14 5 and 14 6 on page 14 5 They should be between 0 95 and 1 05 typically These values are the setting...

Page 475: ...ector by pulling straight out 2 Monitor TBlock and Tleaf Configure the New Measurements screen so that you can view both the leaf temperature and block temperature variables Tleaf C and Tblock C respec tively In the default display configuration you can view these variables by pressing H 3 Make them read the same There is a small adjustment screw located on the underside of the sensor head near th...

Page 476: ...ion and that is described below Calibrating the CO2 Mixer Before you start make sure the CO2 source 12 gram cartridge or external tank has been connected for a few minutes In the case of the cartridge make sure itÕs reasonably fresh they only last 8 hours once pierced whether used or not 1 Run the CO2 Mixer Calibration program In OPENÕs calibration menu select _CO2 Mixer Calibrate When prompted OK...

Page 477: ...ter desired max CO2 ppm _ The pump speed is adjusted based on the ratio of what the upper limit of CO2 was measured to be and what you want it to be Type in some value such as 2500 and press enter ÒCONFIG JoeÓ CO2R_µml Status Flow_µml Rangeµml 2110 1 OK 560 0 102 3 Time 7 earlyOK abort Waiting for mixer to stabilize Figure 18 12 While the mixer is stabilizing at itÕs highest value the reference CO...

Page 478: ...ol mol 1 and the lower limit of control is typically 40 or 50 µmol mol 1 This range can be adjusted by varying the pump speed When the 6400 01 is installed the pump runs at a constant voltage and flow control is done by a flow controller downstream of the point of CO2 in jection that diverts air away from the sample path the excess flow is rout ed to the reference path Figure 1 2 on page 1 5 Witho...

Page 479: ...is asked Press Y You should see something like Figure 18 15 You can also see this plot at any later time by selecting _CO2 Mixer Plot Curve from the Calib Menu If the user accepts the calibration it is stored in User Configs Mixer along with ÒCONFIG JoeÓ CO2R_µml Status Flow_µml Rangeµml 2330 1 OK 560 1 18 55 1st set pt 5000mV Time 4 abort Please Stand By Setting the mixer at 8 different set point...

Page 480: ...ctory but will drift as the detector ages This calibration is done at the factory and should be checked every two years It ages As the source ages itÕs maximum output drops This affects the user calibra tion but not the factory calibration The factory calibration has to do with the how the detector ages not the LEDs Light Source Calibration Calibration data relating the LED SourceÕs command signal...

Page 481: ...m generates data for the Õfirst guessÕ of the LED Source control algorithm and need only be run if lamp control seems slow OK to Continue Y N LED Source Calibration Figure 18 17 The LED Source CalibrationÕs opening screen pro vides a fail safe in case you blunder into it while doing some other experiment that you donÕt want interrupted SetPt 1000 mV QNTM 501 µmol m2 s Remaining 32 LED Source WarmU...

Page 482: ...ually implement this calibration data you must respond by pressing Y when asked Figure 18 21 SetPt 100 mV QNTM 45 3 µmol m2 s LED Source WarmUp Figure 18 19 The calibration curve is generated automatically SetPt is the command signal and QNTM is the resulting PAR µmol m 2 s 1 Abort SetPt mV Qntm umol m2 s 10 3 391 100 45 64 1000 507 5 3000 1493 5000 2358 Plot this Y N Figure 18 20 The LED source c...

Page 483: ...ed in Figure 18 22 SetPt mV Qntm ppm 10 3 391 100 45 64 1000 507 5 3000 1493 5000 2358 Implement this cal Y N Figure 18 21 To implement the calibration press Y 50 100 1000 3000 5000 20 097 45 639 507 48 1493 4 2358 Set points mV PPFD µmol m 2 s 1 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 ...

Page 484: ...ting a Calibration Correction A calibration correction factor fa in Equation 14 15 on page 14 8 of the GaAsP sensor in the leaf chamber can be performed for light sources not in cluded in the Light Source menu in the Configuration list Be warned how ever that the results are extremely sensitive to view factors and incident radiation geometry For best results do this procedure with incident radiati...

Page 485: ... labels then press Edit StdFile F2 Add your new correction factor to the list as shown in Figure 18 23 YouÕll need a name in double quotes followed by the fa value followed by a guess at the absorbed energy conversion factor use 0 2 unless you know better 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...

Page 486: ...the Installation Menu in the Config Menu It can however be edited directly by using the program ÒVerify CalibrationÓ described on page 21 20 A typi cal Ò dev parm0Ó is shown in Figure 18 24 Ò dev parm1Ó This file contains user and factory zero and span settings as well as some fac tory determined calibration values for the instrumentÕs A D and D A hard ware Zero and span settings are written to th...

Page 487: ...age 18 27 6 The Configs directory can be installed on any disk See ÒConfig File Re In stallÓ on page 16 16 BOOT BLOCK LCD 2363 BPS 9600 POSREF 4 9982 NEGREF 4 9959 POS12BIT 4 9956 NEG12BIT 4 9959 POS8BIT1 4 9895 NEG8BIT1 0 0154 POS8BIT2 4 9564 NEG8BIT2 4 9883 DEBUG 0 BOOT BLOCK END JW GROUP FuseAware 0 FFlowZero 74 4 UFlowZero 191 4 FZero 237 5 1049 4 3 5 269 4 UZero 276 5 854 4 3 5 269 4 FZerTemp...

Page 488: ...nd Configuration File Summary 18 32 Using the LI 6400 18 ÒConfigs mixerÓ This file contains the latest CO2 mixer calibration generated by executing _CO2 Mixer Calibrate in the Calib Menu It is illustrated in Figure 18 16 on page 18 24 ...

Page 489: ...9 12 Insulation 19 12 Replacing Connector Screws 19 12 THE CHAMBER HANDLE 19 14 Handle Maintenance 19 14 Latch Maintenance 19 14 Latch Return Spring 19 16 Handle Removal 19 16 LEAF TEMPERATURE THERMOCOUPLE 19 18 Thermocouple Maintenance 19 18 Thermocouple Replacement 19 18 LEAF CHAMBERS 19 20 Foam Gasket Care 19 20 Foam Gasket Replacement 19 20 Propafilm Replacement 19 20 Fluorescence Chamber Tops...

Page 490: ...gure 19 1 then before you resort to pliers try wiggling the bottom of the tube left and right as you view the figure as you attempt to loosen the screw Figure 19 1 A chemical tube The only difference between the soda lime tube and the desiccant tube is the label Flow Control Knob Attachment Screw Bottom Cap TOP Do Not open this end DESICCANT Open this end BOTTOM Important To open a tube to replace...

Page 491: ...reassemble the tube make sure the threads are clean and dry No grease please Figure 19 2 Air mufflers in soda lime and desiccant tubes Replacing the Air Mufflers There are two air mufflers attached to the air hoses inside the chemi cal tubes Figure 19 2 These mufflers may become clogged re stricting air flow through the tubes and thus reducing the maximum flow rates This is one of several things t...

Page 492: ...tÕs glass con tainer and close the lid Note that the color of the indicating Drierite may become less distinct after successive regenerations If it turns black youÕve over heated it The CO2 Scrub Tube Use Soda Lime Soda lime calcium oxide and sodium hydroxide removes CO2 from the air stream and adds a bit of water Some brands add more water than others When soda lime becomes very dry it loses effi...

Page 493: ...dry Discussed in Cleaning The End Cap Threads on page 19 3 3 Are the end cap O rings slightly compressed Not too tight but no gaps allowed 4 Make sure the air passage tubes have O rings See Figure 19 3 Also make sure that the mounting surface on the console is clean 5 Not too tight The attachment knob should be just slightly snug to squeeze the air passage O rings a bit ThereÕs no need to tighten ...

Page 494: ...ld the flow adjust bolt and loosen the flow adjust knob with channel lock pliers Turn the nut toward SCRUB to loosen Remove the nut and white washer that is beneath it The flow adjust knob has to go back on oriented the same way so you should mark which face is out when itÕs attached Flow adjust knob Figure 19 4 Removing the flow adjust knob Using a 3 32 hex key remove the three screws on each sid...

Page 495: ...the SCRUB and BY PASS stickers up with a knife then the two loose pieces of the assembly can be removed Peel up with a knife Figure 19 6 Removing 2 of the 3 blocks from the flow ad just assembly If the small tubing remains compressed long enough especially in hot weather they can seal closed If that is the case replace them Also check carefully in the hose barbs and air passages in the clear plast...

Page 496: ... 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 Four discharged batteries connected simultaneously would require approximately 10 to 12 hours to recharge Storing the 6400 03 Batteries Store batteries fully charged and in a cool place if possible During long term storage place the batteries on the charger overnig...

Page 497: ...e out of the lower shell 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 Before installing blow through a new filter in the direction of the white flow arrow to remove any fibers or other debris that may be loose inside The...

Page 498: ...ing the Fuses Remove the card cage as described above There are six fuses located on two different circuit boards there are three fuses on both the backplane board and the flow board Figure 19 8 Table 19 1 lists the replacement fuses that should be used Extra fuses can be found in the spare parts kit Table 19 1 Replacement fuse sizes for the flow and backplane boards Flow Board Fuse Size Protects ...

Page 499: ... back plane board fuses protect the analyzer board flow board and digital boards The flow board fuses protect the thermoelectric coolers and fan F1 Circulation fan 3A F2 TEC 5A F3 TEC 5A F1 Analyzer board 3A F2 Flow board 3A F3 Digital board 1A Back plane board Flow board Air Filter Display Connector ...

Page 500: ... about measuring and replacing the battery Cables Insulation We have found that exposure to UV radiation can sometimes cause shrinkage in the cable insulation This manifests itself in a tendency for a cable to de velop coils and or to pull away from the back of the connector If you detect this happening contact LI COR Replacing Connector Screws Three of the connectors in the LI 6400Õs cable assemb...

Page 501: ...Maintenance Service Cables Using the LI 6400 19 13 Figure 19 9 A connector screw can be removed by firmly pulling it straight out It is held in place by friction Part Number 314 04913 ...

Page 502: ...Latch Maintenance The key to the latch mechanism is the chamber catch rod that little wire shown in Figure 19 11 There are a couple of latching problems that this rod can cause 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 Figure 19 10 Keep ...

Page 503: ...ck handle piece to the left looking down on it from the rear as you squeeze the handle Chamber catch rod assembly Front view installed Side view exploded Part Number 6400 903 90 Bend 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 wir...

Page 504: ...ght have to deal with it is if the spring should fall out of place when the handle is disconnected 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 Figure 19 12 The latch return spring is in the rear of the handle To access remove the bolt in the rear that serves as a hinge ...

Page 505: ...the handle as shown in Figure 19 14 Use a 1 Phillips head screwdriver to remove them Note that the middle screw if there is one is shorter than the other two Allow the han dle to rest at the side of the sensor head with the log button attached Figure 19 13 Unscrew leaf chamber adjustment nut Adjustment Nut This assembly is available as part number 6400 908 Figure 19 14 Remove the 3 screws shown Mo...

Page 506: ... below the bottom half of the leaf chamber Figure 19 15 The thermocouple is terminated with a male thermocouple connector This entire assembly is replaced If the thermocouple junction is broken leaf temperature will read the same as block temperature1 To replace the 6400 04 leaf temperature thermocouple 1 Unplug the connector Remove the male thermocouple connector by pulling straight out 1 Provide...

Page 507: ...nsert the plastic thermocouple holder up through the bottom of the leaf chamber Do not to pinch the thermocouple wires when inserting the holder 5 Position the holder Insert the holder until the thermocouple bead extends just above the lower foam gasket when viewed from the side Figure 19 16 This will ensure that the leaf is in contact with the thermocouple when the chamber is closed If you are us...

Page 508: ...after the gas kets are removed This can be cleaned up with acetone or other solvents if it is a painted metal chamber part Never use solvents on the plastic 6400 05 Conifer Chamber Note A product that weÕve recently come across that works very well for cleaning up gasket adhesive is Oil Floª manufactured by Titan Chemical inc 1240 Mountain View Alviso Rd Sunnyvale CA 94089 408 734 2200 This is a w...

Page 509: ...ape as you could damage the surface of the chamber thereby making it difficult to achieve a tight air seal with the new Propafilm 3 Prepare the new tape Cut a strip of the double sided tape that is slightly longer than the leaf cham ber Lay on a flat cutting surface adhesive side up The tape may be curled slightly hold the corners down with cellophane tape if necessary 4 Attach the tape and trim L...

Page 510: ...bers have holders for fluorescence probes built into the chamber tops The top piece is plastic lined on the inside with Teflon If the inner surface is scratched the Teflon can tear leaving a shad ow causing blemish The chamber tops can be removed by removing the screws that hold it in place There is a layer of silicone cement underneath the chamber top but it wonÕt stick to the top because of its ...

Page 511: ...er a period of storage and prevent the valve from moving There are a few courses of action to take should this hap pen to you Exercise In OPENÕs Welcome menu there is an entry entitled ÒTests and DiagnosticsÓ which leads to a menu containing ÒMatch Valve TesterÓ This program al lows you to ÒmanuallyÓ via the function keys control the match valve DonÕt leave the chamber latched closed with the gas ...

Page 512: ...ch valve free Subsequent exercise using the ÒMatch Valve TesterÓ program is recommended Open Heart Surgery If all else fails or if the problem persists then perhaps a cleaning and lubri cation is warranted To do this lay the sensor head on its back so it is level 1 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 pad...

Page 513: ...e pads make contact 4 Reassemble Replace the match valve and the black cover Make sure that the two wires under the black cover are not pinched 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 LI 6400 PSH 0001 PORTABLE PHOTOSYNTHESIS SYSTEM MODEL SR NO 1 2 3 4 Lift this end Figure 19 20 Remove the match valve cover by removing four ...

Page 514: ...nd instability To change the sensor head soda lime desiccant bottles 1 Open the covers The plastic bottles are located in the analyzer housing in the sensor head They are accessed by removing the cover plate on the left side of the analyzer housing Figure 19 21 There are two bottle covers each with an O ring seal beneath the housing cover Figure 19 23 Pull up on the bottle covers to ex pose the bo...

Page 515: ...ge 4 50 3 Insert the new bottles Insert them lid first into the analyzer housing Seat the bottle cover with the attached O ring and secure the housing cover with the two screws 4 Wait before use When the bottles are changed allow one day for the detector to equilibrate again Magnesium perchlorate is the recommended desiccant Do not use any other desiccant Several grades of magnesium perchlorate ar...

Page 516: ...e chamber bottom by disconnecting the thermocouple exhaust tubing and removing the two screws that hold the chamber in place 2 Remove the 6 screws from each gold mirror Use a 5 64 hex key Be careful They are small screws 3 Clean the mirrors Wash with ethanol or water and wipe dry Hint We have found that a mirror that seems clean when you are looking straight at it may have residue that appears whe...

Page 517: ...ing up To disassemble the sensor head and clean the optical path 1 Remove the handle from the sensor head Described in Handle Removal on page 19 16 2 Remove the upper half of the leaf chamber Remove the 2 screws from the hinge on the rear of the upper half of the leaf chamber Figure 19 24 The upper portion of the leaf chamber can now be moved aside unhook the connector from the PAR sensor or LED L...

Page 518: ...ex key in the spares kit The cover with attached lower half of the leaf chamber can now be removed 4 Clean the windows Moisten a cotton swab and swab the two optical windows for the sample cell Figure 19 26 Figure 19 25 Remove the optical bench cover leave the chamber bottom attached by removing the 8 screws in the manifold Gasket Lower leaf chamber cuvette Top View Hex head screws 8 ...

Page 519: ...o air dry before reassembling the sensor head 5 Reassemble the sensor head Note that there is a thin vinyl gasket on the top surface of the optical bench 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 Figure 19 26 Clean the two optical windows O...

Page 520: ...e filter 1 Remove the CO2 cylinder cover 2 Remove the filter cap After depressurizing the CO2 cylinder remove the filter cap to reveal the filter Figure 19 27 3 Remove the old filter Use the filter hook included to remove the old filter being careful not to scratch the O ring seat Hint pointed tweezers work better 4 Prepare the new filter Remove the paper from around the new filter Roll the filter...

Page 521: ...estrictor Becomes Clogged If the oil filters are not replaced on a regular basis oil from the CO2 cartridges can enter the copper supply tube and clog the flow restrictor If you are unable to attain desired CO2 concentrations while operating the CO2 injector and you are using a fresh CO2 cartridge and oil filter you may have a clogged flow restrictor If oil makes it through the flow restrictor and...

Page 522: ...ap works well and rinse thoroughly with clean water Blow out the tube to ensure no droplets are left inside If any droplets get up into the flow restrictor it will become clogged 3 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...

Page 523: ...the console handle is on the fat side of the case This helps in closing the lid and puts the console in the most protected orientation If shipping to LI COR for repair or recalibration Call for an RTN Return Tracking Number Be sure to includeÉ Éthe console with chemical tubes attached the CO2 source assembly for the mixer if you have one the chamber IRGA and the cable assembly Also in clude all it...

Page 524: ... Atlanta GA 30336 9960 071 Air flow muffler 300 03707 Small O ring seals air passage to console 192 02597 Large O ring for end caps 192 04291 Chemical tube assembly entire 9964 021 Threaded tube only 6564 076 Bottom end cap 6564 071 Labels for desiccant and soda lime tubes 250 04296 Tygon tubing material for small bypass tubes 222 04598 Battery Items Part Number 10 Amp fuse 438 03142 Battery 6400 ...

Page 525: ...erature Thermocouple 6400 04 Propafilm 10 wide order by length 250 01885 Double sided tape per foot 212 04341 Gaskets 2x3 chamber and 3 hole 10 sets 6400 30 Gaskets 2x6 chamber and 3 hole 10 sets 6400 32 Gaskets 6400 05 Conifer chamber 5 sets 6400 31 Gaskets LED source Includes 5 black neoprene gaskets for the lower chamber and 5 3 hole gaskets 6400 33 Needle holding gaskets 5 sets 6400 34 Teflon ...

Page 526: ...2 mixer 9964 039 Spare parts for cylinders O rings filter 9964 041 Flow restrictor assembly 9964 042 Items for Sensor Head IRGA Part Number Latch repair kit has 6564 057 installed 6400 903 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 ...

Page 527: ...r Motor 20 19 MATCH VALVE PROBLEMS 20 21 ÒCO2 has ChangedÓ Message 20 21 ÒExcessive DeltasÓ Message 20 21 ÒCO2R DidnÕt ChangeÓ Message 20 22 Match Valve DoesnÕt Move 20 22 6400 01 CO2 MIXER PROBLEMS 20 23 Stays at Zero 20 23 Instability 20 24 Cartridge Only Lasts a Few Hours 20 25 Slow Achieving a New Value 20 25 CanÕt Achieve Low Values 20 26 CanÕt Achieve High Values 20 26 Calibration Program Gi...

Page 528: ... the chamber or IRGA thatÕs pulling the voltage low enough to shut off the console Note that the analyzer board and flow control board are not turned on until you press Y in response to the ÒIs the cham ber IRGA connected Ó prompt Does the display flicker or show any lines momentarily If no It could be a totally dead battery or blown battery fuse Check the dig ital board fuse Figure 19 8 on page 1...

Page 529: ... a blown fuse or no other battery at all just the charger The first time the analyzer board is turned on such as when you answer Y to ÒIs the chamber IRGA connected Ó the instrument shuts down because the charger cannot provide enough power then immediately powers back on be cause the switch is on and the cycle starts anew The remedy is discussed in Replacing the Battery Fuse on page 19 8 OPEN doe...

Page 530: ... to be an unlinked fragment the program concludes that the disk is not formatted and gives you the opportunity to format it im mediately The only way one could intentionally corrupt a disk like this would be to interrupt a disk image transfer this happens when new system software is installed then power off ÒLost data appended to unknownÓ Message An unlinked fragment see above is made into or appe...

Page 531: ...ouÕll need to edit that file and fix the problem You can either use the Config Editor page 16 15 or simply edit the file with Standard Edit from the Filer highlight the file and press E If the offending command is not in your configuration file and it appears to be a calibration related command then use the program ÒVerify CalibrationÓ see page 21 20 to edit the calibration file and fix the proble...

Page 532: ... draining because capacitor C3 is leaky If C3 is leaky enough it can even prevent the clock from running while the instrument is turned on next section ÒClock StoppedÓ Message OpenÕs main screen displays the time and date which should update each sec ond If the real time clock is not running the message ÒClock StoppedÓ is dis played instead If this happens and the SET CLOCK program ÒSETCLOCKÓ on p...

Page 533: ...g serial number 401 and above are equipped with a back plane board that is modified to allow detection of a blown fuse Two fuses can be detected the analyzer board fuse and the flow board fuse It cannot tell which one is blown just that one or both are blown See Replacing the Fuses on page 19 10 ÒIRGAs Not ReadyÓ Refer to the discussion starting on page 20 14 ÒHigh Humidity AlertÓ The lowest value...

Page 534: ...is message will appear The software senses the pumpÕs status by checking the digital output that controls it If the pump is in fact not operating due to other reasons not being plugged in blown fuse etc it will not cause this message to appear ÒFlow is Too LowÓ The minimum recommended flow is 50 µmol s 1 with a 6400 01 Mixer or 100 without In fixed flow mode if the flow drops below this value the ...

Page 535: ...a lower target humidity or larger VPD Increase the leaf area Wait for the humidity to climb ÒNegative PAR LightSource Cal Ó The ParIn_µm reading is less than 10 µmol m 2 s 1 less than 2 in OPEN 3 01 You likely have the wrong light source specified since Red Blue LED sources generate negative signals while the Red only and the standard cham ber top light sensors generate positive signals Unreasonab...

Page 536: ...due to the nor mal noise in the analyzers Remember that at low rates the noise in the CO2 differential typically 0 4 ppm will become more and more significant So is the variation in DCO2 greater than 0 4 ppm 3 Watch those flow rates For purposes of troubleshooting operate in fixed flow mode and set the flow to about 500 µmol s 1 If you are operating in constant VPD mode or constant RH you could be...

Page 537: ...Considerations on page 4 47 Or there may be moving debris in the sample cell If so it will affect both CO2S_µml and H2OS_mml See Un stable CO2 and or H2O on page 20 16 5 Is the sample cell stable If the reference values are stable but the sample values arenÕt try testing for a leak in the chamber See Sensor Head Leaks on page 20 35 Photosynthesis is stable but ÒcanÕt be rightÓ An example of this p...

Page 538: ...af temperature might be the reason Is the sensor broken Is it mak ing good contact with the leaf Is it well zeroed Negative Boundary Layer Conductance Boundary layer conductance is normally computed from a lookup table based on leaf area and fan speed see Boundary Layer Variables on page 14 17 If you change to a chamber that allows large leaf areas but use the standard 2x3 chamber lookup table you...

Page 539: ...ductance will be too low If you are mea suring leaf temperature is the thermocouple working Is there good contact Is it well zeroed page 18 19 If you are computing leaf temperature energy balance do the values seem reasonable Do you have the right light source specified Pump Flow Problems A useful flow diagram for troubleshooting is Figure 20 14 on page 20 44 CanÕt Achieve High Flow Rates Maximum ...

Page 540: ... the desiccant tube see Chemical Tubes on page 19 2 If this doesnÕt fix the problem open the console See Figure 20 10 on page 20 38 There might be some sort of blockage between the air filter which is next after the desiccant tube and the pump Pull the air intake line from the pump and see if that increases the flow rate If it does youÕve brack eted the problem The problem could also be a bad pump...

Page 541: ...ng when the connector is fully seated When making the connection push the connector in until you hear a snap which we trust wasnÕt a weak bone in your wrist giving out 3 Is the chopper motor running Determine if the chopper motor is stalled see Stalled Chopper Motor on page 20 19 If the chopper motor is running continue with Step 4 Other wise we are down to three possibilities 1 a blown analyzer b...

Page 542: ... factory settings to see if that makes a difference Unstable CO2 and or H2O The noise of the LI 6400 analyzers is typically 0 2 µmol mol 1 for CO2 and 0 04 mmol mol 1 for H2O2 Leaks diffusion inadequate chemicals and fluc tuating inputs are some of the things that can increase apparent signal noise Tracking down a noisy signal This discussion assumes CO2 is the noisy quantity but similar logic app...

Page 543: ...es on page 20 43 Observe the CSagc_mv and HSagc_mv signals They should not be varying by more than a mV or so If they are fluctuating more than that and if the ref erence ones CRagc_mv and HRagc_mv are stable that could indicate that there is debris being blown about in the sample cell If the reference values CRagc_mv and HRagc_mv are jumpy it could be electronics or a chopper motor problem Instab...

Page 544: ...stable temperature or pressure sig nals An IRGA hardware problem is suggested so contact LI COR Readings Obviously Wrong If you just donÕt believe the IRGA readings then try these steps 1 Is it responsive Watch reference readings and go from full bypass on both soda lime and des iccant to full scrub If the IRGAs donÕt respond turn to IRGA s Unrespon sive on page 20 16 2 Zero and Span Check the pre...

Page 545: ...f the cable There could be a faulty connection at work Before doing this set up a strip chart to monitor the IRGAs That makes it easier to detect a jump Stalled Chopper Motor The chopper motor is the motor that spins the filter wheel in the IRGA sensor head This motor should begin to run shortly after the IRGAs are powered on If the chopper motor does not run the ÒIRGAs Not ReadyÓ message will be ...

Page 546: ...r Restarting a Stalled Chopper Motor If you didnÕt hear any evidence of a running chopper motor in the above se quence then you can try starting it 1 Make sure the IRGA is powered Being in OPENÕs Main Screen or in New Measurements mode is sufficient for this 2 Have the pump and fans off so you can hear Same as Step 1 under Determining if the Chopper Motor is Running above 3 Move the filter wheel b...

Page 547: ... just changed or you just made an adjustment on a chemical tube flow knob then the change in CO2 is not indicative of a problem with the system just with your timing Wait for CO2S_µml to stabilize then match Chamber leak If CO2S_µml never does stabilize then you very likely have a chamber leak See Sensor Head Leaks on page 20 35 ÒExcessive DeltasÓ Message This message appears when you try to match...

Page 548: ... the expected change the pre match difference between sample and reference CO2 was larger than 10 µmol mol 1 Reasons for this would be a match valve that is sticking or the air flow tube connecting the chamber to the match valve not being in place or some other flow related problem Match Valve DoesnÕt Move Stuck match valves are discussed in Match Valve Maintenance on page 19 23 CO2R didn t change...

Page 549: ...the regulatorÕs O ring Detach the cartridge holder regulator from the console and check to be sure the large O ring that seals the hole connecting the console and the regulator is in place Figure 20 4 If itÕs not there the leak will prevent the mixer from operating correctly 4 Check the regulator for flow With a pressurized cartridge installed there should be a very slight flow com ing from the ho...

Page 550: ... mouthwash should be replaced as well 2 Use C mode Put the mixer into constant control signal mode in New Measurements press 2 then f3 then C then enter 2000 If the reference cell is much more stable in this mode then the problem is due to the mixer hunting for the proper setting for the concentration you asked for If you were using S mode constant sam ple cell concentration the instability could ...

Page 551: ...ehind this hole and if it gets wet it wonÕt work again The most probable source of a leak is one of the two compression fittings on the copper tubing that goes from the regulator body to the mounting block shown in Figure 19 28 on page 19 34 If that is the case tighten the nut on the copper tubing 1 8 turn at a time until the leak stops The leak could also be at the cap on the ÒTÓ fitting which co...

Page 552: ...o the mixer calibration Calibrating the CO2 Mixer on page 18 20 2 Is the soda lime on full scrub and is it good Turn off the mixer and verify that the reference CO2 goes to zero If it doesnÕt there is a problem with the soda lime or else the IRGA needs to be zeroed 3 Bad valve See The Bad Valve Saga on page 20 28 to see if this could be the problem 4 Valve installed OK If the valve discussed in Th...

Page 553: ...ram gives erratic results for example a curve that looks like steps instead of being smooth check for leaks inside the console in the path that goes to the reference IRGA In particular make sure all the quick connectors have their tubing pushed into them as far as they should see Quick Connectors on page 20 37 If there is a leak in the line going to the reference IRGA CO2 will change too slowly af...

Page 554: ...ad been replaced Determining if You Have a Faulty Valve You do not have a faulty valve if at least one of the following statements is true Your instrument does not have the 6400 01 CO2 mixer option Your instrumentÕs serial number is 437 or above A good valve will have already been installed A Ò6400 909 InstalledÓ sticker is on the bottom Normally this little sticker would be on the bottom plate ne...

Page 555: ...sor bracket a bit to see the color of the tape of the lower valve The valve model number sticker is on this back plate The problem valves will have the model num ber 910 000042 043 If the valve came from a 6400 909 repair kit and is therefore good there will be a red dot painted on this end of the brass piece Figure 20 5 A solenoid valve with yellow tape on the winding The original good valves had...

Page 556: ...ey are supposed to check the following 1 Is the lamp fan running If the lamp fan is running but the LEDÕs are not illuminated go to Step 3 If the fan is not running try blowing on it to make it move If that starts it and brings the light on the problem is that the lamp fan motor might have a Òdead spotÓ and the lamp will not illuminate if the fan motor is drawing too much current Or if the fan is ...

Page 557: ... should be voltage in excess of 100 Volts If the voltage is near 0 A cable or connector problem is indicated Continue with Step 4 If the voltage is about 12V The switching power supply itÕs in the console for the lamp has failed 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 4 Check the 26 pin D connector Make...

Page 558: ...the proper LED light source If itÕs not in the list add it via the Installation Menu PAR Sensor reads negative Chances are you are not using a light source but are configured for a red plus blue one This will leave you with a negative calibration constant for the in chamber light sensor Go to the Light Source Control and select the proper light source such as Sun Sky Source IsnÕt Bright Enough The...

Page 559: ...ctor Table 20 1 on page 20 45 on the back of the chamber IRGA Pins 25 and 26 are on the bottom row right hand end 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 Sys Utility directory and run...

Page 560: ...le end and between 10 and 3 2 Check for a pinched wire Check the metal cover with the serial number label on it beneath the IRGA Figure 20 8 and the wires that come out from beneath it Something may be pinched 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 m...

Page 561: ... the reference is stable try a leak test on the tightly closed chamber Exhale on and around the leaf chamber and see if the sample CO2 responds You should not see more than a 1 or 2 ppm rise in CO2 in a properly sealed cham ber There will always be some effect of breathing near the gaskets due to CO2 diffusion through the gasket material but it is delayed and fairly small If you see rises in exces...

Page 562: ...an occur along the length of the chemical tube at the top creating a channel with re duced CO2 removal scrubber desiccant air baffle pump air baffle divider flow maker air inlet 75 25 To Reference To Sample filter scrubber desiccant divider flow meter air inlet 75 25 To Reference To Sample filter Flow Control CO2 Control air baffle pump air baffle Figure 20 9 Flow schematic with and without the 64...

Page 563: ...inch end wrench or in a pinch needle nose pliers They have rubber gaskets so if they physically touch the surface they screw into that might be tight enough Be careful not to overtighten hose barbs can break Note that there are also four hose barbs on the block to which the chemical tubes are attached Quick Connectors Inside the quick connector is a rubber seal similar to an O ring When a hose is ...

Page 564: ... valves each sealed with an O ring The replacement repair kit for the pump is part number 6400 907 If you disas semble the pump scratch a line down one side so that it can be reassembled in the correct orientation Flow Divider Inside the body of the divider Figure 20 11 are four flow restrictors through which all the flow passes in parallel Check the divider assembly screws for tightness Be carefu...

Page 565: ...d for soil flux mea surements that do not have a CO2 mixer installed Either upgrade to OPEN 3 2 or else do the following 1 Press K in OPENÕs main screen 2 At the ok prompt type 4000 nullonflow and press enter 3 Press escape to return to the main screen 2 Check the auxiliary operating parameters There are 4 parameters 3 in OPEN 3 01 accessible in f2 level 3 AUX OP Params that influence the pumpÕs b...

Page 566: ...g draw down If the CO2 cannot be drawn down even with full flow going though the soda lime try capping the end of the chamber with the white plastic cap If CO2 drops when the chamber is capped but not when it is on the soil surface then perhaps you are trying to achieve to low a concentration or have the flow rate too low or are not scrubbing enough If CO2 doesnÕt drop even with the chamber capped...

Page 567: ...Troubleshooting Soil Chamber Problems Using the LI 6400 20 41 1 2 3 4 5 6 7 8 9 10 12 11 13 14 15 Figure 20 12 Exploded view of the 6400 09 Soil Flux Chamber ...

Page 568: ... 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 CO2R_µml CO2S_µml H2OR_mml H2OS_mml CO2R_mv CO2S_mv H2OR_mv H2OS_mv Flow_µml Prss_kPa ParIn_µm ParOutµm flow_mv press_mv ParIn_mv ParOutmv CRagc_mv CSagc_mv HRagc_mv HSagc_mv uc_20_mV uc_21_mv uc_22_mV uc_23_mV Tblock C Tair C ...

Page 569: ...rce and clean optics these values are typically 0 or less As the optics become dirty these values will in crease Eventually near 5000mV the message ÒIRGAs Not ReadyÓ will ap pear and the CO2 and or H2O status indicators level c in the diagnostics display j in the standard display will stop showing OK User Channel Voltages The spare analog input channels are shown in level i These will show 0 mV if...

Page 570: ...N OFF Solenoid Valve ON OFF Pure CO 2 Exhaust 1 psig Shunt Regulator Flow Meter IRGA Sample Cell IRGA Reference Cell CO 2 Scrub Desiccant Filter Flow Restrictor Buffer Volume Pump Buffer Volume Servo Valve Exhaust Measure Match Pump Loop Input Command Voltage Output Slew Rate Command voltage Pure CO 2 Exhaust Console Pure CO 2 Input Port 50 psig Relief Valve Flow 75 of total Flow 25 of total shunt...

Page 571: ...nnector Comments 26 Pin D Chamber 25 Pin D Console BlockTemp1 22 1 BlockTemp2 10 3 AirTemp1 21 14 AirTemp2 11 16 Match 23 2 Match 24 15 Circ fan 26 19 A normal fan motor has an impedance of 63 Ohms Circ fan 25 7 Tleaf 14 4 Log 1 25 10V 7 11 9V 6 24 Signal Gnd 8 12 Power Gnd 9 13 PAROut 18 5 PARIn 15 17 TECa 4 5 10 23 TEC 2 3 9 22 12V 17 8 TEC Fan 13 21 Lamp 19 18 Warning voltages can exceed 100V L...

Page 572: ...Troubleshooting Useful Information 20 46 Using the LI 6400 20 ...

Page 573: ...ch Valve TesterÓ 21 7 ÒPressure SensorÓ 21 7 ÒSys User Variable SnapShotÓ 21 8 SYS UTILITY PROGRAMS 21 10 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 ...

Page 574: ... 01 CO2 Mixer It takes the mixer through a series of test points and records the time it took the mixer to achieve stability at each point The test points can be entered from the keyboard or from a previously de fined file or a standard test can be run The data to be specified are pairs of set points and wait times The set points are between 0 and 5000 mV and the wait times seconds are the maximum...

Page 575: ... entries in a file for use again by selecting the F from File option From File 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 Table 21 1 Standard test sequence for the mixer Set Point mV Wait Time s Set Point mV...

Page 576: ... program When the test is over the results are shown After viewing the results press escape You are given the option of storing the results Please set the scrub tubes SODA LIME FULL SCRUB DESICCANT FULL BYPASS Then press enter Test in progress Leave SODA LIME FULL SCRUB DESICCANT FULL BYPASS CO2R_µml Status Flow_µml Rangeµml Setting 500mV Time 7 78 2 OK 200 1 0 21 earlyOK 0 21 Abort 23 4 SetPt tim...

Page 577: ... 7 4978 Leaf Fan 8 3 4 Cooling Fan 9 3 4 pin 27 10 3 4 pin 9 11 2150 LCD Contrast 12 1093 CO2R_Zero 13 2108 CO2S_Zero 14 1405 H2OR_Zero 15 1834 H2OS_Zero 16 2652 Flow_zero 17 0 9447 pin 29 18 0 9447 pin 11 19 0 9447 pin 18 Figure 21 1 The list produced by the DAC Status program shows each D A channel and itÕs current value The channels described by pin nnare available for user use For range and re...

Page 578: ...IN out 3 1110 3 in OUT 4 00000000 2 OUT Table 21 2 LI 6400 digital port and pin assignments Port Pins Status 0 1 2 3 4 5 6 7 0 Mixer on off RH Control enable Flow range 1 Flow range 2 TEC on off Lamp on off Cham ber fan on off Match valvea Input Output 1 Pump status Mixer Hi Mixer Lo Flow Hi Flow Lo Log Button 37Pin 4 37Pin 22 Input Output 2 H2O Ref H2O Smp CO2 Ref CO2 Smp Input Output 3 Pump IRGA...

Page 579: ... Note that when you leave this program the match valve returns to the state it was in when the program was entered ÒPressure SensorÓ The pressure sensor test program merely runs the program ÒGeopotentialÓ on page 21 16 Log Button is down When in match mode the right end Match Valve Test Program Toggle Quit of the paddle should be down Match mode is OFF Figure 21 2 The Match Valve manual control pr...

Page 580: ... It can be a diagnostic tool Press escape when done viewing the list a complete example is shown in 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 er SnapShot DataÓ ID Label PresentValue 10 U S 0 832 20 Trans 4 06E 05 21 Trmmol 0 0406 23 Cond 0 00168 30 PHOTO 3 21 35 CndCO2 0 00105 ...

Page 581: ...Fast 31 CO2Þ H2OÞPumpÞFlowÞMixrÞ Fan OK OK OK OK off Fast 32 BLC_mol 2 84 33 AREA_cm2 6 34 STMRATIO 1 35 ObsStord 0 36 ObsTime 3592 2 37 CO2R_mv 1332 1 38 CO2S_mv 1340 5 39 H2OR_mv 467 4 40 H2OS_mv 469 9 41 Tblk_mv 2276 4 42 Tair_mv 2281 5 43 Tleaf_mv 36 7 44 flow_mv 1319 6 45 press_mv 2049 6 46 parIn_mv 0 0 47 parOutmV 0 3 48 CRagc_mv 1228 6 49 CSagc_mv 905 7 50 HRagc_mv 1358 9 51 HSagc_mv 642 0 ...

Page 582: ...ess to most of the analog and digital outputs of the LI 6400 Figure 21 4 The complete list is presented in Table 21 3 This program will power OFF the flow board and the IRGA board OK Y N This sprogram will power ON the flow board and the IRGA board OK Y N 1 IRGA board 2 o FLOW board 3 o Coolers 4 temp target at 0mV 5 fan speed target at 0mV 6 o Lamp 7 target at 0mV Change Revert Quit ÒonÓ ÒoffÓ To...

Page 583: ...oid off o and on This is what the mixer on off button in OPEN controls 12 Étarget Mixer target 0 5000 mV 13 Circulation fanÉ Leaf chamber fan off o and on 14 Étarget Leaf fan speed 0 5000 mV Fast is usually 5000 slow is usually 4000 15 Match valve Match valve on o and off Note reverse logic 16 User Digital Pin 23 0x0400 Digital outputs available on the 37 pin console connector LPL address shown in...

Page 584: ... s 1 and computed leaf temperature C For a one sided value divide the displayed boundary layer conductance value by 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 The theoretical basis of this program is described in Energy Balance And Boundar...

Page 585: ...kPa _EBepsilon 0 95 emissivity _EBsigma 5 67E 8 Steffan Boltzman _EBcp 29 3 heap cap air J mol K _EBbbTair 0 black body rad tair FCT EnergyBalanceAnalysis press vap trans tair tleaf blc _EBtair _EBtrans_mol _EBvap_kPa _EBp_kpa 0 FLOAT t2 0 FLOAT lnRatio 0 FLOAT tleaf 0 FLOAT blc_mol _EBbbTair EBBlackBody _EBtair lnRatio LOG _EBvap_kPa 0 61365 tleaf 240 97 lnRatio 17 502 lnRatio 0 5 tleaf EBIterate...

Page 586: ...EnergyBal temp C computed temp FLOAT t RETURN _EBbbTair EBBlackBody t EBQDenom t _EBtrans_mol EBCpStuff t C _EBtair _EBp_kPa 0 93 _EBcp EBBlackBody t C W m2 273 2 4 _EBsigma _EBepsilon 2 0 EBSatVap t C kPa FLOAT t 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 ...

Page 587: ...Diagnostics and Utilities Sys Utility Programs Using the LI 6400 21 15 EBVpd t C guess EBSatVap _EBvap_kPa ...

Page 588: ...change as you do Press escape to terminate the program ÒGraphics CaptureÓ Graphics Capture will save the current state of the graphics display to a file The file is named using the Standard File Dialog page 5 9 Files created in this manner can be re loaded to the graphics display via the program ÒGraphic RestoreÓ described next Graphics image files can also be downloaded to computer although to do...

Page 589: ...e those that were created using ÒGraphics CaptureÓ described above ÒGraphit UtilityÓ 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 images a ci curve 2 a ci curve 1 Read Graphics from a ci curve 3 a ci curve 4 Dir Help CANCEL SELECT DIR User HalÕs experiment ivy data Plot what file light curve light curve ...

Page 590: ...te Select the field to be changed using and and change that fieldÕs value by pressing and Press Set f5 to implement your changes or Cancel f4 to abandon them Nested Directory Copy User Configs User Select Source Directory User Configs AutoProgs User Configs AutoProgs Defaults Print Find ReFind CANCEL SELECT User Configs AutoProgs TimedLamp Defaults Nested Directory Copy User Configs User Select De...

Page 591: ...s all comm port incoming data on the display 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 Baud Data Stop parity 9600 8 1 N DelLn ClrEnd DelChar CapLock AnyChar Config Captr Send Quit View Edit the Comm Port configuration Capture incoming data into a file...

Page 592: ...data by using the Installation Menu but this program serves as a general purpose alternative Changes made to this file do not take affect until you re run OPEN or change configurations the Ò_Reset MenuÓ Config StopSnd Quit Bytes Sent 12388 this is a remark CO2Mixer YES 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 C...

Page 593: ...Part VI Programming ...

Page 594: ......

Page 595: ...2 8 Naming Convention 22 8 Numerical Objects 22 8 Numerical Arrays 22 9 Char Arrays Strings 22 10 The Back Slash 22 11 FUNCTIONS 22 12 The Function ÒMainÓ 22 12 The Stack 22 12 Post fix 22 13 In fix 22 14 Local Objects 22 15 Local Arrays 22 16 POINTERS 22 17 PTR Arrays 22 18 Passing Parameters 22 19 Undeclarable Foreign Objects 22 20 PUBLIC AND STATIC 22 22 Using PUB 22 22 Using STATIC 22 23 COMPI...

Page 596: ...h computer for example actually has all of this hardware of course but the LPL Operating System for each specific platform will provide software simulation of the missing hardware Thus for example it is possible to program and read an A D converter on a Macintosh just as if it were on the LI 6400 the measured values on the Macintosh of course will be entirely mythical1 LPL applications take the fo...

Page 597: ...nter in Listing 22 1 is a FLOAT declara tion FLOAT x 0 y 0 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 Enter 2 values compute their mean FLOAT define two floating point variables and initialize them ...

Page 598: ...DROP The View From the Stack LPL is a post fix language whose operation centers about an abstraction known as a stack The stack is a ÒLast In First OutÓ list of objects The key to understanding an LPL program is to consider each item keyword string number etc in the program and keep track of what it does to the stack WeÕll go through the program in Figure 22 1 again this time with special emphasis...

Page 599: ... of values assigned is pushed onto the stack Now we do some math to find the average value of x and y Suppose the user had entered 14 for x and 33 3 for y Notice how we seem to have an extra 2 being carried along on the stack This is the 2 that the ENTER command left for us and our example program il lustrates slightly sloppy programming we could have checked this value after the ENTER to see if t...

Page 600: ...encountered causing it to pop a floating point value from the stack and print it Similarly the next fcauses the 33 3 to be popped and printed and the final f pops and prints the 23 65 Thus PRINT cleans the stack except for our left over 2 The final thing our program has to do is wait around for the user to press a key to end the program This is easy First we pop up the standard ÒPress Any KeyÓ mes...

Page 601: ...example the following segment of an LPL program LONG secs 0 thisTime 0 Operation The Stack 3 2 1 19 GETKEY 2 27 20 DROP 2 Table 22 1 Declarable Objects Object Description CHAR Characters are integers that can range in value from 128 to 127 or 0 to 256 INT Short integers are two bytes in length and can range between 32768 to 32767 or 0 to 65536 LONG Long integers are four bytes in length and range ...

Page 602: ...T for any keyword or object name Naming Convention The convention used in this manual is to write LPL keywords in bold upper case variable names with the first letter lower case and function names with the first letter upper case Table 22 2 When function names are multiple words the first letter of each is upper case e g ThisFunction Multiple word variables would be similar except the first letter...

Page 603: ...ber of objects that the array is holding Arrays are declared by appending square brackets to the objectÕs name The brackets can be empty or contain the size of the array The initial values of the array are given between braces If the size is not specified in the square brackets as in def above the size comes from the number of items in the initialization string The initializing sequence for arrays...

Page 604: ...haracter is first encountered when the parser is looking for the initializing string is used for the terminating character of that string Examples of initializing CHARs and CHAR arrays are shown in Figure 22 2 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...

Page 605: ...to be converted into a character If you really want a back slash and not an escape sequence then use two back slashes Ex amples are shown in Table 22 6 Following a inside of a string constant LPL expects to find one of the fol lowing up to 3 digits 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 ...

Page 606: ...operating system is concerned Main or whatever the name happens to be will be the ONLY function executed If there are other functions defined in a program they are not executed unless they are called from Main directly or indirectly When Main is finally done the program is done The Stack 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 t...

Page 607: ...k can be set The default size is 10 items Post fix The default syntax within a function is post fix This means that operations are programmed in order of stack operation To add two values together we would write 17 83 2 5 If we want to go further and store the result in a variable named X we would have to put XÕs address on the stack then do a store command In LPL we would write 17 83 2 5 X The op...

Page 608: ...mind Lines are important Use one statement per line or else use a semicolon as a delimiter Thus we could combine the first two statements of Figure 22 3 into PRINT Enter 2 values to average ENTER y x f f Spaces are not needed When using post fix notation each item must be separated by white space spaces tabs or end of line characters With in fix this is not necessary Pa renthesis square brackets a...

Page 609: ...ure 22 4 the expression 0 INT i puts a 0 on the stack creates a temporary INT named i and with a value of 0 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 FCT Main Prints integers from 1 to 10 0 INT i i is local 1...

Page 610: ... the delimiters must be double quotes Unnamed numeric arrays can also be declared as illustrated by INT 1 2 3 4 5 This type of declaration creates an array that is full size ready 5 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 FCT MyTest 0 FLOAT x 10...

Page 611: ...when executed ABCD BCD Pointers Pointers type PTR are a little more complicated that INT or FLOAT ob jects but provide a lot of power and versatility to the LPL language The Òval ueÓ of a pointer is the address and type of the object to which they point Pointers are initialized by reference to another object Pointers can remain un initialized by substituting a 0 for the destination variable name W...

Page 612: ...mple one can create a PTR array by PTR stuff abc MyFct maxLimit nameList moreStuff abc stuff Element of a PTR array can be different types of objects Note that in the above declaration the 2nd element of moreStuff is itself a PTR array Pointer array declarations can also be nested For example PTR theList PTR INT 5 labelOne PTR INT 5 labelTwo The PTR array theList has two elements each one of which...

Page 613: ... a string and the second is a function The Main function makes the second element operate on the first This program will result in This is a test being printed to the display Passing Parameters 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 Go expects to find three items on the stack waiti...

Page 614: ... Undeclarable Foreign Objects 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 FCT Main Add Add Go Sub Subtract Go Mult Multiply Go Div Divide Go GETKEY DROP Go PTR symbol PTR label PTR action 1 23 FLOAT x 5 67 FLOAT y l...

Page 615: ...h element found in xxx Go2 receives 1 parameter which it assumes is a PTR array with 3 elements 1 the label 2 the symbol and 3 the function to exe cute FCT Main w test file OPEN_FILE IF RETURN THEN PTR file This is a new file n s file PRINT The end s file PRINT file CLOSE Figure 22 10 PTRs and files PTR xxx PTR Add FCT PTR Subtract FCT PTR Multiply FCT PTR Divide FCT FCT Main 1 INT i xxx READY NLO...

Page 616: ...onsidered to be a private object because it is only available to the program that defined it If the program spawns another program the new program will not know any thing about objects belonging to the parent program unless those objects had been declared as public 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 ...

Page 617: ...etails and just outline it in terms of a few functions and vari ables The interface to this package is the function GenPlot that expects to find the x and y data arrays on the stack along with the x and y axes labels 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 INT abc 1 def 10 Private variables FLOAT ...

Page 618: ...directive This saves having to include numerous STATIC keywords We could rewrite the library file described above as shown in Figure 22 15 Ploting library FLOAT STATIC xMin 0 STATIC xMax 0 STATIC yMin 0 STATIC yMax 0 FCT static FindRange STATIC DrawAxes STATIC PlotPoints PUB GenPlot PTR xData PTR yData PTR xLabel PTR yLabel Figure 22 14 Example of using static variables in a library file INCLUDE s...

Page 619: ...PUB GenPlot PTR xData PTR yData PTR xLabel PTR yLabel Figure 22 15 The library file of Figure 22 14 rewritten using the STATIC compiler directive Table 22 8 General purpose compiler directives Directive Argument Use PRINT string Prints a string to the display during compile SEARCH string Add a directory to those being searched to satisfy INCLUDE direc tives INCLUDE string Compile an external file ...

Page 620: ...PEN is already running these objects will be loaded and available Otherwise they must be included As an example of using IFDEF consider the utility Ò sys utility boards offÓ Figure 22 17 This very short application turns off the IRGA and flow con trol boards this can be useful sometimes but not while some other applica tion that is using these devices is running To protect against this happening t...

Page 621: ...dOn FCT main CLEAR This program should not be run now Press Any Key PRINT GETKEY DROP ENDIF IFNDEF FlowBdOn FCT main CLEAR This program will power OFF the flow board and the IRGA board OK Y N PRINT GETKEY UPC Y IF 0 0x0301 DIOSET 0 0x0302 DIOSET THEN ENDIF Figure 22 17 BoardsOff listing ...

Page 622: ...Programming with LPL Compiler Directives 22 28 Using the LI 6400 22 ...

Page 623: ...ce power on 23 32 EVENT HANDLING 23 33 THE FUNCTION KEYS 23 37 I O PROGRAMMING 23 39 Paths 23 41 Transferring Data 23 44 I O Errors 23 45 FILE SYSTEM 23 46 Hierarchical Structure 23 47 Working With Files 23 48 The Trash Directory 23 49 The LI 6400 File System 23 49 MENUS AND EDITORS 23 51 Standard Menus and Editors 23 51 Customized Editors and Menus 23 54 GRAPHICS 23 56 Windows and Coordinates 23 ...

Page 624: ...p item on the stack FLUSH Flush the stack MATHERR Enable disable reporting certain math errors ROT Swap the first and third stack items SHOW Show what s on the stack STKCHECK Enable disable certain stack error checking 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...

Page 625: ...e is 10 If a larger stack is needed the stack can be resized by STKRESIZE The current size of the stack is given by STKSIZE When one application launches another the child application can have itÕs own stack or share the parentÕs Stack sharing is a method of passing data be tween and parent and child application STKSHARE is the keyword control ling this There are two types of errors that can occur...

Page 626: ...cture and the LOOPÉENDLOOP structure Either of these structures can be nested up to 20 deep Figure 23 1 Table 23 2 Flow Control Keyword Summary Keyword Description IF Conditional execution Requires THEN ELSE Optional Used between IF and THEN THEN Marks the end of a conditional LOOP Marks start of an infinite loop NLOOP Marks start of a finite loop ENDLOOP Marks the end of a loop structure BREAKIF ...

Page 627: ...t key codes refer to Keyboard Codes on page 23 29 Illustrates IF THEN and LOOP ENDLOOP FCT Main CLEAR Press Some Keys esc to quit PRINT 1 INT counter LOOP GETKEY INT k Quit on escape k 0x1b BREAKIF 1 5 POSXY counter Key d is PRINT k 255 k 0 AND IF This LOOP allows us to use BREAK s rather than a lot of nested IF ELSE THENs 1 NLOOP k r IF return BREAK THEN k n IF ctrl j BREAK THEN k f IF ctrl l BRE...

Page 628: ...MOVE Shift elements within an array APP Append an item to an array COS Compare two arrays for type and content FIND Find an item in an array FREE Free a dynamically allocated array MAKE Dynamically allocate an array MAKE4 Allocate an array for another application PDRF Pointer dereference 1 step version of PVAL PFIND Pointer version of FIND PICK Select an array element PVAL Pointer version of VAL R...

Page 629: ...lows direct user manipulation of the ready val ue If we were to add the line yy 5 SETREADY to the function testin the above example then the value of yy would become Ò userÓ 1st 5 characters Alternatively yy 100 SETREADY would make the array appear full SETREADY nevers alters actual content so ÒartificiallyÓ filling an array will leave you with whatever happened to be in there Figure 23 2 illustra...

Page 630: ... 23 18 these keywords can operate on elements 1ÉReady of arrays Appending APP can be used to append data onto an array Select 1 element PICK is used to select a specific element in an array to get or change its val ue Select a subset SUBSET will make an array out of a selected subset of another Shift elements AMOVE will shift values within an array I O Tools Some I O tools I O Programming on page ...

Page 631: ...nt we would write 50 x 5 PICK VAL The PICK puts the address of an INT the 5th element of x on the stack The 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 PrintArray1 and PrintArray2 are functionally equivalent they both print out the contents of an integer array whose address INT x 10 1 2 3 4 5 6 7 FCT m...

Page 632: ...rays described in Using PTR arrays on page 23 13 FIND and PFIND are illus trated in Figure 23 8 on page 23 15 Dynamic Allocation A declared array hangs around for the life of a function if itÕs a local array or the life of the application Sometimes it is efficient to dynamically allocate an array That is create it when you need it then dispose of it when youÕre done and recover that memory Such ar...

Page 633: ...e address of the new array is pushed onto the stack followed by a 0 If MAKE fails only a 1 is pushed onto the stack When MAKE succeeds it is up to you to keep track of the address for future reference and this is usually done by as signing a PTR to it In Figure 23 5 a local PTR is assigned we can do that because the array is deallocated using FREE before the function is done If we wanted to use th...

Page 634: ...d The Table 23 4 indicates where declared local and dynamically allocated ar rays are stored Table 23 4 Where arrays exist Type of Array Where it lives Declared global e g INT x 5 1 2 3 The applicationÕs data segment Local e g FCT x hello The local stack ItÕs size is set by the LO CAL directive Allocated with MAKE or MAKE4 Free memory PTR temp 0 FCT Main MakeSpace NOT IF UseSpace KillSpace THEN GE...

Page 635: ... pointer arrays The concept of VAL gets ambiguous then for a pointer array Suppose we have the following declarations INT x 50 y 100 PTR z 2 x y Does the sequence Òz 1 PICK VALÓ meanÉ 1 Éthe value of the pointer That is the type and address of x or 2 Éthe value of what is being pointed at In this case 50 It turns out that VAL has the 2nd meaning But how can meaning 1 be achieved namely getting the...

Page 636: ... itself yields the address of the pointer array element z 1 Note that intermediate pointers if any are hidden If we change the declara tions in Figure 23 7 to be INT x 50 y 100 PTR p x Add a pointer x z 2 p y 1st element is p INT x 50 y 100 PTR z 2 x y FCT Main Print value of x pointed at by z 1 z 1 PICK VAL d n PRINT Change value of x to 75 but get address from z 1 75 z 1 PICK PVAL x d n PRINT Ch...

Page 637: ...3 p2 pfind 0 p3 p1 pfind 2 One way to make sense of these results is to consider what the target object Òlooks likeÓ when operated on by FIND and PFIND Explanations of the FIND and PFIND in Figure 23 8 Table 23 5 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 No INT a 4 b 4 c 5 d 10 PTR ...

Page 638: ...racter arrays The sequence x 1 wqr FIND returns the lowest subscript of array x that points to a pointer array whose 1st element contains the string ÒwqrÓ The result is 2 Similarly the statement x 2 2 3 FIND will produce 3 since this string is contained in the second element of an array pointed at by the 3rd element of x If this is not complicated enough further subscripting is supported by FIND a...

Page 639: ...LI 6400 23 17 which searches the 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 pArray Up to 10 no kidding subscripts may thus be specified ...

Page 640: ...Subtraction Multiplication Division less than less than or equals are they equal greater than greater than or equals Raise to a power ABS Absolute value ACOS Arccosine AND are top two items both non zero 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...

Page 641: ...d maximum value MIN Find minimum value MOD Modulus NOT is top item zero OR is one or the other non zero POLY Polynomial RAD Use radians for trig functions RANDOMIZE Randomizes the seed for the random generator REGRESS Compute coefficients for a polynomial RND Random float between 0 and 1 SIN Sine SQRT Square root SUM Sum a vector TAN Tangent UPC Convert to upper case not equal Table 23 6 Continued...

Page 642: ... Transforms e g ABS absolute value Single Object Transforms Single Object Transforms can operate on values addresses of numeric vari ables or arrays so there are a variety of combinations of things that can be on the stack when a Single Object Transform executes We illustrate the pos sible before and after stack status by the following shorthand INT iArray 5 1 2 3 4 5 FLOAT floatVal 1 234 fArray 5...

Page 643: ...have changed however When an Array is the object of the transform each element of the array is transformed If the array is a PTR array its elements can potentially point at non numeric objects such as function addresses or other PTR arrays so what happens then The rule is this all pointer elements are tracked down pointers to pointers to pointers etc and if the final object is numeric it is trans ...

Page 644: ... of the variable or array are subject to change When the top item on the stack is array d but the target is not targetVal or targetNum the transform is done using each element in d with the targetVal or targetNum holding the cumulative result For example you can sum Array d by the expression 0 d Note that the reverse order Òd 0 Ó would simply add 0 to each element of d accomplishing nothing Table ...

Page 645: ...e top of stack value Target address left on stack Transform is performed on and only on corresponding items between the arrays Target address left on the stack Table 23 7 Two Object Transform combinations Target Object Top of Stack Object Num NAddr Array Table 23 8 Keywords for controlling the display Keyword Description BLKATTR Sets attribute in a specified rectangle window coords CLEAR Clears te...

Page 646: ...ay in which text operations are confined There are two types of units PUTDISP Restores window text and attribute PUTTEXT Puts text into a rectangle display coords PUTWINDOW Set current window info SCRLOCK Locks unlocks vertical scrolling SETATTR Sets attribute for subsequent printing SETCURSOR Sets cursor type WINDOW Establish a window display coords Table 23 8 Continued Keywords for controlling t...

Page 647: ...re 23 12 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 Hello world Hello world Row 1 Col 1 Display units Row 1 Col 1 Window Units Row 4 Col 13 Display Units Figure 23 12 Text windows ...

Page 648: ... cursor type Also the cursor can be moved to any location within the current window by the POSXY keyword The keyword GETWINDOW loads the current window status including at tribute and cursor information into an array 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 betwee...

Page 649: ... 1 1 3 20 7 2 WINDOW Normal 0 SETATTR Full height cursor 2 SETCURSOR Save attributes for window 1 w1 GETWINDOW Set normal attrib for border 0 SETATTR Make window 2 22 3 40 7 2 WINDOW Inverse 1 SETATTR No cursor 0 SETCURSOR Save attributes for window 2 w2 GETWINDOW LOOP GETKEY INT k k 0x1b BREAKIF flop NOT VAL IF w1 activeWIndow ELSE w2 activeWindow THEN activeWindow PUTWINDOW k c PRINT activeWindo...

Page 650: ...copy text between the display ignoring any windows and an LPL CHAR array or PATH At tribute is ignored although PUTTEXT can be made to impose an attribute on the destination rectangle Frequently it is desired to save the contents of the display beneath a window so that when the window is removed the display can be returned to the way it was before GETDISP and PUTDISP accomplish this easily It is i...

Page 651: ...ro then the key is an ascii key and the low byte is the value Thus pressing the key A will generate a key code of 97 hex 61 while shift A generates 65 hex 41 If a non ascii key is pressed such as a cursor control key or a function key then the high byte is non zero and contains the identifier for that key Table 23 11 on page 30 The low byte Table 23 12 on page 23 31 con tains modifier key informat...

Page 652: ...ble 23 11 Non Ascii Key Codes High Byte The Key Variable Namea High Byte The Key Variable Name High Byte labels _Labels 0x12 f1 _F1 0x60 home _Home 0x24 f2 _F2 0x61 end _End 0x23 f3 _F3 0x62 pgup _PgUp 0x21 f4 _F4 0x63 pgdn _PgDn 0x22 f5 _F5 0x64 _UpArrow 0x26 f6 0x65 _DnArrow 0x28 f7 0x66 _LeftArrow 0x25 f8 0x67 _RightArrow 0x27 f9 0x68 _Back 0x08 f10 0x69 escape _Esc 0x1b f11 0x6a enter _Enter 0...

Page 653: ...e Bits 2 thru 7 Bit 1 Bit 0 unused Control Shift Table 23 13 Clock Keyword Summary Keyboard Description CTIME Convert seconds print time and date in formatted string DATE Convert seconds to year month day DAYOFWK Convert seconds to day of week DAYOFYR Convert seconds to Julian day of year GETMS Get ms since power on GETTDS Get current date and time in seconds SECS2TD Convert seconds to time and da...

Page 654: ...ME The current date and time in seconds since the base time is obtained by GETTDS and set by SETTDS LPL provides several tools for doing time conversions DATE converts sec onds since the base time to day month and year while TIME extracts the hours minutes and seconds SECS2TD converts seconds into date and time while TD2SECS goes the other way DAYOFWK and DAYOFYR converts seconds to day of the wee...

Page 655: ...sired event and if it has occurred handle it Table 23 14 Event Handling Keyword Summary Keyword Description HALT Terminates an IDLE IDLE Wait for something to happen OFFA2D Cancel A D converter interrupt OFFCOMM Cancel comm port interrupt OFFCYCLE Cancel regular timer interrupts OFFKBD Cancel keyboard interrupt OFFSOFT Cancel softkey interrupt OFFTIC Cancel 1 second interrupt OFFTIME Cancel real t...

Page 656: ... LPL hides much of this work from the programmer It turns out that to actually implement the outline in Figure 23 15 one only needs to a register the functions to be called and b write those functions Figure 23 16 illustrates how this actually looks in LPL We register the functions to be called using the ON LPL keywords FCT EventLoop LOOP KeysReady IF HandleKeys THEN ClockReady IF HandleClock THEN...

Page 657: ...ds one for which we had registered a function it calls that function for us LPL can handle a number of events Table 23 15 in the manner outlined by the listing in Figure 23 16 To illustrate consider the AutoProgram Remote Control whose listing is shown in Figure 23 17 Table 23 15 Events Supported by LPL Event KeyWord User presses any key on the keyboard ONKBD User presses a function key ONSOFT A c...

Page 658: ...REAKIF ENDLOOP Cleanup LPCleanup buff CLOSE OFFCOMM Gets called on receipt of line feed CHAR line 500 FCT GotIt line 0 SETREADY line c n buff ENTER DROP line COMPILE NOT IF PTR fct fct fct FREE THEN Figure 23 17 Listing of the AutoProgram Remote Control The program sits endlessly in New Measurements mode LPMeasure and incoming data from the comm port is collected in a buffer COMM buff XFER Ev ery ...

Page 659: ...ribed in this section work during IDLE See ÒEvent HandlingÓ on page 33 The strategy is to define how many function keys you want to ÒcreateÓ MAKESOFT then what each keyÕs label and function is ONSOFT During IDLE the user can scroll through the keys if there are too many to show at one time using the labels key and if he presses one the function happens automatically OFFSOFT and FREESOFT dis able a...

Page 660: ...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 FCT Main Illustrate use of function keys CLEAR 0 1 2 0 5 MAKESOFT 0 plain text for label delimiter the delimiter is a space 1 inverse labels 2 labels 2 lines high 0 donÕt save background beneath the labels 5 total of 5 function key...

Page 661: ...ored When GLOBALKEYS is off you cannot change a function key definition label or function without exiting the IDLE I O Programming The ability to move information to and from devices is critical to any com puter and LPL provides an abundance of tools for doing that task Table 23 17 I O Keyword Summary Keyword Description BENTER Binary enter from a path BPRINT Binary print to a path CLOSE Close any...

Page 662: ...en a path to a circular queue PATHSTAT Get path status PRINT Send formatted or unformatted data to a path PUTCH Write a byte to a path RESET Set fill and empty pointers to 0 RESETDFC Reset to platform default default file convert in and out SEARCH Search a path for the occurrence of something SETDFCIN Set default file convertin SETDFCOUT Set default file convertout SETEMPTY Set empty reading point...

Page 663: ...hile the operating system takes care of all the messy details involved with the various devices or memory that are at the oth er end of the Path LPL supports Paths to a variety of devices Table 23 18 When an application is launched four standard paths are provided and are accessible by the keywords LCD COMM ARGS and KBD Alternate paths to these devices or paths to other devices are opened by the v...

Page 664: ...acter from the empty location updating the regis ter Path Filters 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 Table 23 19 PATH Status Registers Name Description TYPE Describes what the path is pointing t...

Page 665: ...ce for any path Table 23 20 Path Filters Code Convert From Convert To e cr lf or cr lf lf E cr lf or cr lf cr lf n cr lf or cr lf cr tn n spaces n 0 16 tab Tn tab n spaces n 0 16 s xdd or ddd ascii character S nonprintable characters xdd k Byte pairs If 1st byte is null it is stripped otherwise k sequence out put K Does reverse of ÒkÓ filter bytes are padded with nulls except for the k se quence B...

Page 666: ...e path to another and depending on what type of paths are involved can do it simultaneously with 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 FCT Main Open a path to the display OPEN_LCD IF RETURN THEN PTR di...

Page 667: ...om input data I O Errors The keyword IOERR returns the error if any that has most recently hap pened for any path Possible errors are given in Table 23 21 The keyword IOCLEAR resets the error number for a path to 0 no error Table 23 21 I O Error codes Error Number Condition 0 No error 1 Attempting to write to a full path 2 Attempting to read from an empty path 3 Attempting to move a pointer outsid...

Page 668: ...KE Make a directory DIRSAVE Make sure file system is up to date DIRSET Set current working directory DSKFORMAT Format a disk DSKISSWAP Is a disk off line and available for swap space DSKOFFLINE Take a disk off line DSKONLINE Take a disk on line DSKPACK Defragment a disk DSKSPACE How much space on a disk FCOPY Copy a file FERASE Erase a file FGETTDS Get file time and date FGETWP Get write protect s...

Page 669: ...g three disks named Dir A Dir B and Dir C is shown in Figure 23 22 FSETTDS Set file time and date FSETWP Write protect a file or directory FSIZE Get file size FTRASH Returns the trash location FTYPE Determine if exists or file or directory FUPDATE Update changed portion of a file FWPICK Pick file from a list of possibilities OPEN_FILE Open a a path to a file OPEN_FILE_ASK Open a path to a file usi...

Page 670: ...N_FILE_ASK When a file is opened a Path is cre ated and all data transfer operations take place through the path 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 The Root Dir A Dir B Dir C Dir A Dir A File 1 File 2 File 3 File 1 File 2 File 1 File 1 File 1 File 2 File 2 D...

Page 671: ...e FERASE keyword does not move the file to the Trash If you wish to use the trash instead of FERASE then use this code sequence fileName 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 c...

Page 672: ... flashdisk3 for example If one opens the ÒfileÓ dev flashdisk3 to read one will be reading the binary image of that disk including directory information file fragments and everything else valid or invalid in sequence 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...

Page 673: ...ghlighted 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 Table 23 23 LPL Menu and Editor Keywords Keyword Description MESSBOX Put up a message in a window STDLINE Single line edit STDEDIT Multiple line edit STDMENU Standard menu function SETTARGET Set editor search target GETTARGET Return current editor...

Page 674: ...we must pass the STDMENU function a Path instead of a simple CHAR array because STDMENU uses the Path status registers to tell us where the cursor was when the user exits 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 CHAR menuItems This is item 1 This is item 2 and item 3 and 4 and 5 an...

Page 675: ...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 CHAR menuItems This is item 1 This is item 2 and item 3 and 4 and 5 and 6 nand 7 nand 8 nand lastly 9 FCT Main 5 1 25 8 2 2 My Menu WINDOW Open a path to the CHAR array menuItem...

Page 676: ... with customized behavior Also SET TARGET GETTARGET allow program control over searching for targets in an editor or menu The Display Editor in OPEN is an example of a custom ized menu 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 Sys Lib CEDefs which contains us...

Page 677: ...oggleMenuBar IDLE ResetWindow edPtr EDCLOSE menu CLOSE Write the initial contents of the menu to the path passed to this function DEBuildMenu PTR menu DEKeys GETKEY INT k k _Esc IF DEQuitTest RETURN THEN k 127 IF is it ascii k LWC DROP If ÕaÕ thru ÕzÕ jump to that format line k a k z AND IF edPtr CEHomeToggle k a 1 workingFmtList READY MIN edPtr CEJumpToLine edPtr CEToggleMenuBar THEN ELSE If itÕs...

Page 678: ...lot a 5x5 image centered at pen location user units GIGET Copies a graphics image to a buffer user units GINIT Initializes Resets graphics GIPUT Puts a graphics image on the display user units GISIZE Gets required size of a graphics image user units GLABEL Label in graphics mode at pen position GLSIZE Determine height and width in pixels of a label GMDGET Gets graphics drawing mode GMODE Sets grap...

Page 679: ... share com mon hardware the ÒinteractionÓ between text and graphics images is set by GTMODE and sensed by GTMDGET and can be any of the following or exclusive or and and Note that on the display of the LI 6400 there is ÒinterferenceÓ between text highlights inverse and blinking and graphics mode text modes will not be shown when graphics mode is also on GRMOVE Graphics pen relative move user units...

Page 680: ...ing window to any range of real numbers that is desired The keywords GHEIGHT and GWIDTH return the height and width of the current graphics window The default graphics window at power on and after the reset function GINIT is full size it fills the physical graphics display The window can be reduced by the keyword GWINDOW which specifies a new graphics window and PWC coordinate system To find the c...

Page 681: ... and FLOAT scale 4 0 1 1 360 1 1 FCT Main Reset the scaling GINIT Turn off text turn on graphics clear the graphics display 1 GRAPH 0 ALPHA GCLEAR Get the dimensions of the graphics display GWIDTH INT pixelsWide GHEIGHT INT pixelsHigh DEG Scale the plotting area scale GSCALE Draw a sine curve DrawACurve New window in the lower left 1 3 of the display 0 pixelsHigh 3 pixelsWide 3 0 GWINDOW Re draw s...

Page 682: ...dinate pair Labels and symbols can be done with GLABEL which draws a string start ing at the pen location and GICON which plots a 5x5 pixel image at the pen location GLORG specifies where the label is to be relative to the current pen location Figure 23 29 Thus if GLORG is 8 the label will appear to the left of the pen location centered vertically GLSIZE returns the height and width of a label in ...

Page 683: ...tes 20 4 GMOVE 0 GLABEL 200 4 GMOVE 720 GLABEL 100 4 GMOVE DEGREES GLABEL 2 7 GMOVE 1 GLABEL 2 60 GMOVE 1 GLABEL Make a box for plotting and change to user coordinates graphBox GWINDOW fromAngle 1 1 toAngle 1 1 GSCALE Draw axes lines 0 1 GMOVE 0 1 GDRAW 0 0 GMOVE 720 0 GDRAW This routine fills ÕangleÕ with angles and ÕcosineÕ is filled with corresponding cosines FillArrays angle SIZE INT n toAngle...

Page 684: ...rwrites old graphics information For example where lines intersect should the pixels be on or off The possibilities are listed in Table 23 25 The effects of the graphics drawing mode is illustrated in Figure 23 32 Table 23 25 Graphics Drawing Modes Mode Name Action 0 default Draw or erase without checking existing graphics state 1 or 2 eor 3 and 4 not Invert then Mode 0 Figure 23 31 Labelled cosin...

Page 685: ...his 1 rect2 GBOX mode2 GMODE Example 1 uses this 1 rect2 GBOX Example 2 uses this 2 rect1 GBOX rect2 1 PICK VAL 30 GMOVE label GLABEL 0 GMODE rect2 1 PICK VAL 4 GMOVE label GLABEL rect1 add DROP rect2 add DROP Example 1 The solid rectangles and the lower labels are drawn first using mode 0 The mode is changed to the indicated values and the open rectangles and upper labels are drawn Example 2 The ...

Page 686: ... Measurements strip chart mode works RS 232 Communications LPL provides several tools for dealing with the Comm Port The utility program Sys Utility SETCOMM described on page 21 19 illus trates the use of COMMSTATUS and COMMCONFIG Its listing is shown in Figure 23 33 Table 23 26 COMM Port Keyword Summary Keyword Description BLKREC Block receive BLKSEND Block send COMMBREAK Set Momentary break cond...

Page 687: ...ect 2 2 38 4 FCT setcomm 0 CHAR cline 40 commRect GETDISP PTR hold commRect 2 1 Baud Data Stop Parity WINDOW cline COMMSTATUS cline STDLINE IF cline COMMCONFIG IF 1 Bad Configuration MESSBOX THEN ELSE 1 Config unchanged MESSBOX THEN hold PUTDISP Figure 23 33 Listing of the program SETCOMM ...

Page 688: ...d Each channel has an address starting with 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 Table 23 27 Analog Measurement Keyword Summary Keyword Description AINUM Returns the number of analog input channels ground chan nels a...

Page 689: ... new reading would be the average over the last 4 seconds for exam ple to help smooth the noise Having defined the groups we then can identify the channels that are to be included in each group Note that in LPLÕs scheme of things the same channel can be included in multiple groups One could for example measure a thermocouple in two dif ferent ways by including it in two different groups One group ...

Page 690: ...r 0 to 5 Must have already been defined via AIGDEF The reference e g ground channel Referred to by number 0É7 The range This is not currently used but still must be present Just say 0 The address of the destination variable This must be a FLOAT or a FLOAT array Thus every channel gets linked to a FLOAT variable that you must maintain Make sure the destination variable will always exist using a loc...

Page 691: ... readings for this group should the operating system buffer for you 0 means no buffering LetÕs focus for the moment on the third parameter the time interval Each group has some time interval at which new readings will be ready However just because readings are available doesnÕt mean that they automatically go anywhere they donÕt They are buffered until you say you want them which is done via AIGET...

Page 692: ... main Define the A D stuff Setup IF RETURN THEN CLEAR IN CMBR_mV OUT_CMBR_mV PRINT 1 8 POSXY Press esc to quit PRINT GetReadings group ONA2D keys ONKBD AISTART IDLE AISTOP a2d AICLOSE AIFREE Setup Open a structure AIOPEN IF AIOPEN Failed PGD 1 RETURN THEN a2d qSize avgCnt count secs group a2d AIGDEF IF AIGDEF Failed PGD 1 RETURN THEN 1 NLOOP dum 0 0 group 0 a2d AICDEF IF BREAK THEN dum 0 0 group 1...

Page 693: ...I 6400 has 24 analog channels Table 23 28 and 8 reference channels Table 23 29 Note that the library file Sys Lib StdAnalogIn provides variable names for these channels which should be used rather than the num bers Table 23 28 LI 6400 Analog Input Channels Channel Channel Descriptions Variable Name 0 Zero reference channel aZeroChan 1 Span reference channel aSpanChan 2 Battery aBattChan 3 CO2 Refe...

Page 694: ...s ÒlostÓ because it was not accessible on the 37 pin connector of the first LI 6400s In LI 6400s having serial numbers 401 and above it is used for blown fuse detection Table 23 29 LI 6400 Reference Channel Descriptions Channel Channel Description Variable Name 0 Reference ground aRefGnd 1 IRGA ground aIrgaGnd 2 Flow board ground aFlowGnd 3 Chamber ground aChamGnd 4 Pressure ground aPressGnd 5 Spa...

Page 695: ...o number 0 to 19 The range of each and itÕs resolution is found using the AOMIN AOMAX and AORES functions Table 23 30 D A Control Keywords Keyword Description AONUM Returns the number of analog output channels AOMIN Returns the minimum allowed value of an analog output channel AOMAX Returns the maximum allowed value of an analog output channel AORES Returns the resolution of an analog output chann...

Page 696: ...log 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 INT lamp 2 d a for lamp delta 200 shift amount uparrow 0x2600 dnarrow 0x2800 escape 0x1b FCT main 1 0x0302 DIOSET flow board on 1 0x0005 DIOSET lamp on Keys ONKBD CLEAR Press up and down arrows n PRINT escape to quit PRINT 0 ChangeLa...

Page 697: ... pin is designated using a 16 bit integer The high byte is the port and the low byte is the pin 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 Table 23 31 Digital I O keywords Keyword Description DIONPORTS Returns the number of DIO ports DIONPINS Returns the number of pins on a partic...

Page 698: ...um useful value is 10 ms setting it to 0 would ef fectively stop all counters High Speed Counter For higher speed pulse counting pin 3 on the 37 pin external connector can be used It is triggered by the falling edge of a pulse The keyword HSCOUNTS returns the number of pulses detected since the last call Table 23 32 LI 6400 digital port and pin assignments Port Pins Status 7 6 5 4 3 2 1 0 0 Match ...

Page 699: ... 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 The number of counts that is the number of times this happened is accessible via the keyword DIOERR which returns the count and resets the counter ...

Page 700: ...line mode LINK Load and compile source code add to an application LPL Return the version number of the operating system MEM Find the amount of memory and largest contiguous piece MEMMAP Outputs the heap map MODSIZE List compiler size directives for one or more modules PTRTOLL Converts an LPL address to address and type RUN Launch a program SETID Change the owner of an allocated item SETMODNUM Set ...

Page 701: ...cation compile a function that will below to any parent or itself Compiling and Linking Structures The LINK keyword compiles and links any LPL structure functions PTR ar rays etc to any existing application Modules Applications contain one or mode modules A module is a source file and an application collects source files together with the compiler directive IN CLUDE As each module is added to the ...

Page 702: ...en runs The active one sys lib stdshell is what runs when you press K in OPENÕs main screen Select sys open start whose listing is shown on Figure 3 55 on page 3 66 A Pick App C Chars D Doubles and floaters F Functions L Longs and ints M Miscellaneous P Pointers U User private symbols Y all public sYmbols Z LPL Keywords sys lib stdshell Figure 23 36 DEBUGÕs main menu Shows a list of all active app...

Page 703: ...gure 23 38 The function list of sys open start Table 23 34 What is displayed in the miscellaneous section of the debugger ITEM Description Compiler Directive Local Stack LOCAL For each module Name The module name Static Symbols The symbol table addresses of the root and each block for this module Typically there are no static symbols because they are stripped after compilation The size and the num...

Page 704: ...ltage drops below 10 5V When the low warning is disabled the instrument will run until the battery voltage reaches about 7V GETBATT returns the battery state 0 1 or 2 for ok low and critical POWEROFF does what youÕd think it does and RE START is the equivalent of power off then back on Table 23 35 LPL keywords involving battery and power Keyword Description LOWWARN Enable Disable low battery warni...

Page 705: ...Reference Keyword Summary SYNTAX SUMMARIES 24 2 LPL Type Declarations 24 2 Compiler Declarations 24 8 DEFINITIONS 24 11 Single Value Transforms 24 13 Two Value Transforms 24 13 Two Value Logical Transforms 24 15 THE REFERENCE 24 16 ...

Page 706: ...s CHAR Character declaration 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 PUB STATIC size name value value name name Value decimal 0x hexidecimal Õ character Õ CHAR value string string ...

Page 707: ...ries Using the LI 6400 24 3 DOUBLE High precision floating point declaration Item Description Range name valid LPL name size integer 1É32767 value integer or floating point PUB STATIC size name value value name name DOUBLE value ...

Page 708: ...lement in the un named array 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 FCT PUB STATIC name LPL Keyword name numeric string name declaration Õ character Õ declaration CHAR INT LONG FLOAT DOUBLE PTR name array initialization name size function definition Note 1 Note 2 ...

Page 709: ... Item Description Range name valid LPL name size integer 1É32767 value integer or floating point FLOAT PUB STATIC size name value value name name value Item Description Range name valid LPL name size integer 1É32767 decimal hexidecimal INT PUB STATIC size name value value name name Value decimal 0x hexidecimal Õ character Õ value ...

Page 710: ...24 LONG Long integer declaration character Item Description Range Item Description Range name valid LPL name size integer 1É32767 decimal hexidecimal character LONG PUB STATIC size name value value name name Value decimal 0x hexidecimal Õ character Õ value ...

Page 711: ...ect name valid LPL name size integer 1É32767 array initialization specify each array element function definition PTR PUB STATIC size name object name name ptr initialization name ptr initialization CHAR INT LONG FLOAT DOUBLE array initialization FCT function definition string object name PTR ptr initialization ...

Page 712: ...ion DATA Declares data space for this application IFDEF IFNDEF Compiler logic Item Description Range Bytes Creates a code segment 1 to 64000 CODE Bytes Item Description Range Bytes Creates a data segment 1 to 64000 DATA Bytes Item Description Range Directive LPL compiler directive or decla ration IFDEF IFNDEF ENDIF Directive ...

Page 713: ... this application If the name contains one or more spaces it should be quoted INCLUDE filename Item Description Range Bytes The number of bytes to use for local objects Default 1000 1 to 64000 LOCAL Bytes Item Description Range Bytes The number of bytes to make a name segment Multiple segments are allowed 1 to 64000 NAMES Bytes Item Description Range String The first non whitespace character follo...

Page 714: ...ts that this module defines 1 to 4096 PRIVCOUNT count Item Description Range count The number of public objects that this module defines 1 to 4096 PUBCOUNT count Item Description Range directory The name of the directory to be add ed to the list of directories to be searched when finding a file to be in cluded If the name contains one or more spaces it should be quoted SEARCH directory Item Descri...

Page 715: ...e Thus using the same vari able names we would write arr first last SUBSET Make the subset PTR tempHdr Make local PTR for the result To do this same function using in fix notation the order of the arguments stays the same 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 Item Description...

Page 716: ...ither an address Addr or else a numeric value Long or Double Rect name NArray windowb or Num left Num top Num right Num bottom Num name A Long or Double numeric value Text name Path or CArray Addr name Address of any LPL object NObj name Long Double or NAddr Logic name Num that is evaluated to be 1 or 0 Fct name Address of an LPL function Path name Address of a path NAddr name Address of numeric o...

Page 717: ... ments are shown in Figure 24 2 Table 24 2 Examples using ABS a single value transform LPL Code Result 12 ABS Puts 12 LONG on the stack 48 4 ABS Puts 48 4 DOUBLE on the stack arr1 ABS Sets every element of arr1 to its absolute value Figure 24 1 Single value transform stack requirements Initial Num a Final Double or Long b or Initial NObj c Final NObj c or Initial Array b Final Array b Figure 24 2 ...

Page 718: ...DOUBLE 100 200 Puts 300 LONG x 1 Adds 1 to the value of x and leaves the address of x on the stack 1 x If x 3 leaves 4 on the stack 0 xArray If xArray 1 2 3 4 leaves sum 10 on the stack xArray yArray Adds corresponding elements to xArray 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 ...

Page 719: ...r1 to 1 arr1 5 5 Sets every element of arr1 to 1 if it was equal to 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 Initial Num targetNum Num b NObj c Array d Final Long result 0 false 1 true or Initial NObj targetVal Num b NObj c Array d Final NObj targetVal object value will be 1 or 0 or ...

Page 720: ... 24 13 The assignment operator Initial Num x NAddr target Final or Initial Addr x Addr target Final The assignment operator is used for numerics strings and pointers Logical compare Initial Final see Two Value Logical Transforms on page 24 15 Do not use this operator to compare arrays use COMPARE for that Logical negative compare Initial Final see Two Value Logical Transforms on page 24 15 Table 2...

Page 721: ... the top of the stack an address Initial Obj a Final Obj a LONG returnVal 1 yes 0 no Related Keywords TYPE AICDEF Define an analog input channel Initial FAddr dest Num range Num ground Num group Num chan A2dPtr atd Final Long code 0 ok non zero failed See Analog Measurements on page 23 66 For a discussion of the AI_ keywords see Analog Measurements on page 23 66 Table 24 6 Parameters for AICDEF de...

Page 722: ...ts on page 23 66 Table 24 7 Parameters for AIGDEF qSize The number of final readings that the operating system should buffer This value must be between 1 and N where c 4 14 N 64000 and c is the number of channels in the group avgCnt The number of raw readings that should be averaged to gether for each final reading count The number of raw readings that should be taken during the time interval secs...

Page 723: ...on zero failed AIPREP must occur after groups and channels are defined AIOPEN AIGDEF AICDEF and before the A D is started AISTART AIREADY Group status readings lost readings available Initial Num group Final Long numLost Long numReady When an A D is running this function will return information about readings avail able or lost for a particular group To capture readings use AIGET or AITGET AISTART...

Page 724: ...ero Initial Final see Two Value Logical Transforms on page 24 15 Related Keywords NOT OR AOMAX Returns max signal that can be put on a D A channel Initial Num chanNum 0 AONUM 1 Final Double mV Related Keywords AOSET AORES AOMIN Table 24 9 Parameters for AITGET timeDest The address of the FLOAT variable or array that will contain the time information If readings are greater than 1 then timeDest sho...

Page 725: ...ted Keywords AOVAL AOVAL Returns the current value of a D A channel Initial Num chanNum Final Double mV Related Keywords AOSET APP Append item or array onto an array Initial Array toAdd Array dest or Initial NObj toAdd NArray dest or Initial Addr toAdd PArray dest Final Related Keywords READY GETREADY SIZE Example Figure 23 3 on page 23 9 ARGS Provides a path to arguments if any for that applicati...

Page 726: ... 3 degrees whereas 1 0 1 5 ATAN2 yields 123 7 and 1 0 1 5 ATAN2 yields 56 3 BEEP Turn on beeper for a specified time Initial Num milliSecs Final The beep is a background process It does not halt program execution If KBDCLICK is on pressing a key will terminate the beep BENTER Binary enter Initial Obj dest Path source Final Long byteCount 1 if error No filtering Path Filters on page 23 42 is done o...

Page 727: ...al Final See Two Value Logical Transforms on page 24 15 Computes the exclusive or of two LONGS Related Keywords BINAND BINCMP BINIOR BSHIFT BINIOR Binary inclusive or Computes an inclusive or for two LONGs If a value is not LONG an internal con version is done first Related Keywords BINAND BINCMP BINEOR BSHIFT Table 24 11 BINCMP Effect Before After 0 1 1 0 Table 24 12 BINEOR Truth Table 0 1 0 0 1 ...

Page 728: ...to work BPRINT Binary print Initial Obj source Path dest Final LONG byteCount 1 error If source is a PTR array then multiple objects can be sent No filtering is done on bi nary transfers Related Keywords BENTER PRINT BREAK Exit a LOOPÉENDLOOP Initial Final BREAKIF Conditional exit from a LOOPÉENDLOOP Initial Num a Final BREAKIF is functionally identical to the sequence IF BREAK THEN BSHIFT Binary ...

Page 729: ...or location to the right edge of the text window Initial Final The display attribute for that portion of the line is set to the SETATTR value Related Keywords CLEAR SETATTR WINDOW COMM Provides the standard path to the comm port Initial Final Addr path This path is common to all applications and cannot be closed by any of them Related Keywords LCD ARGS KBD COMMBREAK Set a break condition on the Co...

Page 730: ...guration string Initial Text dest default is LCD Final Related Keywords COMMCONFIG COMMUART Returns the UART status for the Comm port Initial Final Long statusByte bit 0 break received 1 framing error 2 parity error Example 6 means framing error and parity error COMPARE Compare two arrays Initial Array arr1 Array arr2 Final LONG result 1 same 0 different Arrays are the same if 1 they are the same ...

Page 731: ...0 on page 23 43 Related Keywords GETCONVERTIN CONVERTIN SETDFCIN PRINT ENTER PUTCH XFER COS Cosine Initial Final See Single Value Transforms on page 24 13 Units depend on RAD and DEG CTIME Converts seconds since base time to a time and date string 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 TI...

Page 732: ...YOFWK DEBUG Access the debug utility Initial Final DEBUGV Show the error dialog box Initial Path errors Final errors can contain anything but normally it would be the message path used for COM PILE or LINK DEG Enable Òdegrees modeÓ for trig functions Initial Final The scope of DEG is the application The default mode is RAD Related Keywords RAD DEVNAME Returns the device name for a disk Initial Tex...

Page 733: ...irectional ports Determine status and ability with DIOSTATUS DIOERR Number of digital port resets have occurred Initial Final Long count See Digital Errors on page 23 77 DIOGET Returns status of a portPin Initial Num portPin e g 0x0302 Final Long highLow 1 high or 0 low DIOGETPORT Get state of multiple pins in a port Initial Num maskWord Num port Final Long stateWord Set bits in mask determine wha...

Page 734: ...al Text dest Final The default dest is the standard path LCD Related Keywords DIRSET DIRERASE Remove a directory from the file system Initial Text filename Num all non zero remove dir even if not empty Final Long error 0 ok 1 dir not found 2 not empty 1 failed Related Keywords FERASE DIRMAKE Create a new directory Initial Text newName Final Long error 0 ok 1 failed Note that you cannot create a di...

Page 735: ...at completely erase a disk Initial Text fileName Final Long error 0 ok non zero failed The disk stated or implied by fileName is the one formatted DSKISSWAP Is there swap space available Initial Final Long code 0 yes 1 no Related Keywords DSKPACK DSKONLINE DSKOFFLINE DSKOFFLINE Take a disk off line make available for swap space Initial Text filename Final Long error 0 ok 1 failed Note All files an...

Page 736: ...EditInfoPtr edInfo Final Do not do any further processing once edInfo has been disposed Related Keywords EDOPEN EDCTL Perform an editor function or series of functions Initial Num code EditInfoPtr edInfo or Initial Narray codes EditInfoPtr edInfo Final Perform an editor function or series of functions code values are given in Table 24 16 Related Keywords EDOPEN For a discussion of the ED_ keywords...

Page 737: ... 0x30 Move cursor right 0x35 Move to start of previous word 0x31 Move cursor left 0x36 Page left 0x32 Move cursor up 0x37 Page right 0x33 Move cursor down 0x38 Page up 0x34 Move to start of next word 0x39 Page down 0x40 Jump to the beginning 0x43 Jump to end of current line 0x41 Jump to the start of the last line 0x44 Jump to top of window 0x42 Home on current line 0x45 Jump to bottom of window 0x...

Page 738: ...Conditionals and Loops on page 23 4 ENTER Read values of variables from a source Initial 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 Table 24 17 EDSTAT codes and Results Code Result Code Result 0 Error code for previous operat...

Page 739: ...preted A format string can contain multiple format directives which take the form Reps Width Type Table 24 18 Format string scan format directives Always marks the start of a format directive Optional If present no assignments are made there doesnÕt need to be a corresponding address on the stack to accept any values Reps Optional Used when the target address is an array If present it is one of n ...

Page 740: ... read a floating point value assign it to y User Defined Radix If the source contains numeric values that are not decimal they can be read and con verted using the user defined radix type code ÕrÕ The character immediately following the ÕrÕ determines the radix or base to be used This character should be the highest value character in the base binary Õ1Õ decimal Õ9Õ hex ÕfÕ base 36 ÕzÕ etc For exa...

Page 741: ...r 0 ok Related Keywords DIRERASE FGETTDS Return the last modified date for a file or directory Initial Text filename Final Long secsSinceBaseTime To interpret secsSinceBaseTime see Real Time on page 23 32 Related Keywords FSETTDS FTYPE TIME DATE CTIME SECS2TD Table 24 21 Format string examples Format String What is Done f Read a floating point value 5c Read the next 5 characters append to an array...

Page 742: ... Comparing Arrays on page 23 10 FINDADDR Given a variable name return itÕs address Initial Text name Num sysID Final Long 1 not found or Final Addr address Long 0 The default sysID is the current application FINDTOKEN does the opposite FINDTOKEN Returns an objectÕs name given itÕs address Initial Text tokenDest Num 1 Addr obj or Long address Num sysID or Initial Text ownerDest Num 2 Addr obj or Lo...

Page 743: ...ted Keywords FPARSE FMOVE Move a file to another directory Initial Text source Text dest Num overwriteFlag 0 donÕt non zero ok Final Long error 0 ok 1 not found 2 dest illegal or exists 1 failed The source file is removed Related Keywords FCOPY FPARSE Break a file specifier into path and file name Initial Text pathDest Text nameDest Text fullSpecifier Final If fullSpecifier doesnÕt start with a or...

Page 744: ...zero failed To convert secs to real time see Real Time on page 23 32 Related Keywords FGETTDS FSETWP Set the write protect status of a file or directory Initial INT onOff Text specifier Final Long error 0 ok non zero failed Related Keywords FGETWP FSIZE Get the size of a file Initial Text filename Final Long bytes 1 if doesnÕt exist Related Keywords FTYPE FTYPE Returns the type of a file Initial T...

Page 745: ... to all parent and child directories but the files shown in each directory are only those that match the pattern This function is the one that is called when the user enters a wild card character in a filename in the main LPL OS menu such as when prompted for a file to run or edit The use of the Standard File Dialog usually renders this function unnecessary Related Keywords OPEN_FILE_ASK FX Enter ...

Page 746: ...N Get the default convertin filter for files Initial Text dest default LCD Final Related Keywords GETDFCOUT SETDFCOUT SETDFCIN RESETDFC GETDFCOUT Get the default convertout filter for files Initial Text dest Final Related Keywords GETDFCIN SETDFCOUT SETDFCIN RESETDFC GETDISP Store text and attribute information for a rectangle Initial Rect area Final DispInfo dest Related Keywords PUTDISP See Mani...

Page 747: ...lse the value last set by SETMODNUM if no modules have been linked since then If sysID is 0 then the current application is assumed GETTARGET Retrieves present search target for the system editor Initial Text destination default LCD Final Related Keywords SETTARGET GETTDS Get seconds since base time Initial Final LONG tdSecs Related Keywords SECS2TD SETTDS For timing with resolution higher than 1 ...

Page 748: ...ALE GMODE GPLOT GLABEL Table 24 23 GETWINDOW PUTWINDOW Array Information Element Item Element Item 1 Left column 5 Cursor Col 2 Top row 6 Cursor Row 3 Right column 7 Text Attribute 4 Bottom row 8 Cursor Type 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 Byte 1 Bit 7 Byte 1 Bit 6 Byte 1 Bit...

Page 749: ...ack on the display Initial Text source Rect rect user units Final Related Keywords GIGET GISIZE Returns the array size necessary for a graphics image Initial Rect rect user units Final Long bytes Related Keywords GIGET GIPUT GLABEL Print a label on the graphics screen Initial Text message Final Related Keywords GMOVE GLORG GLSIZE GLOBALKEYS Determines behavior on ONKBD and ONSOFT Initial Logic onO...

Page 750: ...des on page 23 62 GPGET Is pixel at this location on or off Initial Point point user units Final Long 1 on or 0 off Related Keywords GSCALE GPPUT GIGET GPLOT Plot characters or draw a line Initial Num code 0 line non zero plot NArray horizUserUnits NArray vertUserUnits Final If code is not zero it is interpreted as the character to be plotted Otherwise a line is drawn connecting the coordinates Re...

Page 751: ...es automatic scrolling in the horizontal and vertical Automatic scroll ing will occur whenever the pen is moved or drawn out of the current graphics win dow If scrolling is enabled the graphics window scaling is automatically adjusted to keep the new pen location visible Note that when scaling is adjusted both max and min values are adjusted by the same amount GSHIFT Shift part of the graphics dis...

Page 752: ...elated Keywords GWINDOW GWINDOW Define a graphics window Initial Rect newWindow Final Units are pixel hardware coordinates User scaling is not affected by this command the user scaling will be in effect in the new window Related Keywords GWIGET HALT Terminate an IDLE or TIDLE Initial Final Related Keywords IDLE TIDLE HASCOPRO Is there a coprocessor installed Initial Final Long Logic 1 yes 0 no HID...

Page 753: ...ed The xArr array must be sorted in ascending or descending order IOCLEAR Clears the error code for a path Initial Addr path Final Related Keywords IOERR IOERR Returns the latest error if any for a path operation Initial Addr path Final LONG errorNumber 0 none 1 read EOF 2 write EOF 3 seek EOF See I O Errors on page 23 45 Related Keywords IOCLEAR ISEMPTY Is a path empty Initial Final LONG logic 1 ...

Page 754: ...esc exits this mode Related Keywords COMPILE KBDREPEAT Set the repeat interval when a key is held down Initial Num milliSecs Final LCD Provides the standard path to the display Initial Final Addr path This path is common to all applications and cannot be closed by any of them Related Keywords COMM ARGS KBD LGT Log base 10 Initial Final See Single Value Transforms on page 24 13 Related Keywords LOG...

Page 755: ...T DOUBLE PTR MAKE MAKE4 LOOP Program looping Initial Final Related Keywords NLOOP ENDLOOP BREAK BREAKIF LOWWARN Enable disable low battery warning Initial Num onOff 0 off 1 on Final Related Keywords GETBATT LPL Return the LPL version number Initial Text dest default LCD Final LWC Lower case Initial Final See Single Value Transforms on page 24 13 Related Keywords UPC Table 20 21 The optional code p...

Page 756: ...n application goes out of scope ends any arrays that have been allocated but not FREEd are disposed of automatically Related Keywords FREE MEM MAKE MAKESOFT Create function key structure Initial Num de Num dc Num le Num nLines Num mode Num nKeys Final See The Function Keys on page 23 37 Related Keywords FREESOFT ONSOFT MATHERR Enable disable math error corrections Initial Num onOff 0 report errors...

Page 757: ...inal LONG keyCode Mode 0 does not pause execution to wait for the user The message goes up and exe cution continues There is no automatic cleanup Mode 1 waits for the user to press any key after the message is displayed When this happens the message and frame go away and the underlying display is restored If no frame labels are defined ÒPress Any KeyÓ will appear on the lower frame Mode 2 also wai...

Page 758: ...DE nn DATA nn NAMES nn PRIVCOUNT nn PUBCOUNT nn STATCOUNT nn MOVETEXT Copy a block of text and attribute within a text window Initial Num toLeft Num toTop Rect area Final toLeft toTop and area are in relative window coordinates NEXTKEY See what is next in the keyboard queue without removing it Initial Num Final NUM result keyCode or 1 if queue is empty To decode keyCode see Keyboard Codes on page ...

Page 759: ...unction Final Execute function every time character is received during the ongoing or subsequent T IDLE An overlapped transfer XFER from the comm port must be ongoing Related Keywords IDLE TIDLE OFFCOMM ONCYCLE Enable interrupt of a timer Initial Num seconds Num timerNum 1 2 or 3 Fct function Final Define a function to be periodically called during the ongoing or subsequent T IDLE This is the same...

Page 760: ...r the function key information ONKBD and ONSOFT interaction If no function keys are defined MAKESOFT not in effect then any function key stroke is passed to the ONKBD function If function keys are de fined MAKESOFT in effect then function key strokes do not pass through to the ONKBD function If function keys are defined but a function key is pressed for which no ON SOFT function was defined then t...

Page 761: ...th keywords PRINT ENTER etc and the normal array keywords APP ENTER etc and also that there is no immediate interaction between the SETREADY keyword and the SETFILL or SETEMPTY key words Related Keywords CLOSE OPEN_COMM Open a path to the Comm port Initial Final Addr path Long 0 or Final Long 1 Every application has available to it the standard path COMM One reason to open an other path to the com...

Page 762: ...D One reason to open another path to the keyboard would be to implement different filtering without changing the standard filters associated with KBD Related Keywords CLOSE Table 24 26 Options for FILE_OPEN opts File exists File doesnÕt exist r ok Error w Opened and truncated File created a Opened for appending File created Table 24 27 OPEN_FILE_ASK parameters code Optional Value doesnÕt matter Th...

Page 763: ...g 1 The actual size of the queue may differ from the requested size Queues are sized 7 15 31 63 127 255 511 1023 2047 4095 8191 16383 or 32767 bytes If a different value is requested the next largest size is used but is never larger than 32767 Related Keywords CLOSE OR Logical OR Initial Final See Two Value Logical Transforms on page 24 15 Related Keywords AND NOT PATHSTAT Get status information f...

Page 764: ...m subscript or Initial Num subscript Array arr Final Addr address If subscript is 0 or greater than the array size an error will result Related Keywords VAL PVAL SIZE See Array Operations on page 23 6 POLY Computes a polynomial Initial Double Array coeffs Num arg Final Double result The power of the polynomial is determined from the number of values in the coeffi cient array coeffs 2 values 1st or...

Page 765: ...ber of elements to output or for all elements The optional delim character is used if specified as the delimiter between ele ments flags Optional The flag characters are and space as indicated by Table 24 31 width Optional If present specifies the minimum num ber of characters to print padding with blanks or zeros precision Optional If present specifies the maximum number of characters to print fo...

Page 766: ...ith E x or X unsigned hex int g floating point in e or f form based on precision ld or li signed long G floating point in E of f form based on precision lo signed octal long c character lx or lX unsigned hex long s string lu unsigned decimal long p pointer address k outputs an unsigned int as kHHLL where HH is the high byte in hex and LL is the low byte in hex Table 24 33 PRINT Format Examples Ite...

Page 767: ...PTRTOLL Converts an LPLÕs address into address and type Initial ADDR Ptr Final Long address LONG type Related Keywords USES PUTCH Add a character to a path Initial Num theChar Addr Path Final LONG result theChar if ok or 1 on error Related Keywords GETCH PUTDISP Redisplay text and attribute information Initial DispInfo old Final This disposes the structure pointed at by old so donÕt use it again R...

Page 768: ...dr p Final PAddr final Related Keywords VAL RAD Enable Òradians modeÓ for trig functions Initial Final Related Keywords DEG and all trig functions RANDOMIZE Randomize the random generator seed Initial Final Related Keywords RND READY Returns the number of elements in the array Initial Array arr Final Long number Related Keywords SETREADY SIZE REGRESS Do a linear regression Initial Num power DArray...

Page 769: ...to pressing shift ctrl escape on the keyboard and should be done after loading a disk image Related Keywords POWEROFF RETURN Exit from a function Initial Final RND Generate and random number between 0 and 1 Initial Final Double value Related Keywords RANDOMIZE ROT Exchange the 1st and 3rd items on the stack Initial Obj a Obj b Obj c Final Obj c Obj b Obj a Related Keywords SWAP DUP DROP RUN Launch...

Page 770: ...lag Final Long return 1 if found 0 if not flag given in Table 24 36 The path pointers are changed only if return is not 0 SECS2TD Convert seconds since base time to time and date Initial Num secsSinceBase Final Num secs Num min Num hour Num day Num month Num year Convert seconds since base time to the time and date numerical Related Keywords TD2SECS TIME DATE CTIME SETATTR Set text attribute for s...

Page 771: ...inal See Path Filters on page 23 42 Related Keywords SETDFCIN GETDFCIN GETDFCOUT RESETDFC SETEMPTY Sets the empty pointer for a path Initial Num offsetBytes Num Ref from 0 start 1 current 2 end Addr Path Final Related Keywords PATHSTAT SETFILL SETFILL Set the fill pointer for a path Initial Num offsetBytes Num Ref from 0 start 1 current 2 end Addr Path Final Related Keywords PATHSTAT SETEMPTY SETI...

Page 772: ...e arrayÕs header Related Keywords READY SIZE SETTARGET Sets the search target for the system editor Initial Text target Final Related Keywords GETTARGET SETTDS Sets the system clock Initial Num secsFromBase Final Related Keywords GETTDS TD2SECS SHOW Show n items on the stack Initial Num numItems Path dest default LCD Final SHOW does not affect the stack unless pushing numItems and dest onto the st...

Page 773: ...ring up the exit menu Related Keywords STDMENU STDLINE EDOPEN STDLINE Edits a line of text Initial Text line Final LONG result 1 enter pressed 0 escape pressed The window is borderless and lies between the current cursor position and the right edge of the active text window If the text object is too large to fit in the window the text scrolls horizontally in the window NOTE The text object changes...

Page 774: ... Initial Num newSize number of items Final This also flushes the stack Related Keywords STKSIZE STKSHARE Enable disable stack sharing Initial Num yesNo 0 no sharing non zero stack sharing Final Stack sharing applies to subsequent child applications launched by the current appli Table 24 38 StdMenu Flag Bit Value Description 0 1 Highlighted menu bar 1 2 Put cursor to start of current line at exit 2...

Page 775: ...g array This is convenient for limiting searches or confining transformations to a region of an array whose lower bound is not 1 When the lower bound is 1 you can accomplish the same thing by setting the ready value SETREADY temporarily IMPORTANT tempHdr is created on the local variable stack so becomes invalid once the current function is exited SUM Returns the sum of numeric objects in an array ...

Page 776: ...pe of the object on the stack Initial Obj a Final Obj a LONG type UNGETCH Put a character back into a path Initial INT charCode Addr path Final LONG result charCode or 1 if path is full Related Keywords GETCH PUTCH UNGETKEY Put a back into the keyboard queue Initial INT keyCode Final LONG result keyCode or 1 if queue is full Related Keywords GETKEY NEXTKEY UNLINK Remove one or more modules from an...

Page 777: ...om LINK using control code 2 or 3 Related Keywords LINK XREF PTRTOLL FINDTOKEN VAL Get the numeric value of an object Initial NAddr a Final LONG or DOUBLE value or Initial PAddr p Final Addr final Related Keywords PVAL WINDOW Open a text window on the display Initial Rect area Num border Num pos Text lab1 Num pos Text lab2 Final border is 0 none 1 single line or 2 double line Label positions are s...

Page 778: ...al XREF Generate a cross reference for an application Initial Text filename Path dest Final Table 24 39 XFER Combinations To Keyboard Display CommPort File Buffer or Queue From Keyboard Error OK Overlapped Overlapped Display Error Error Overlapped Overlapped Comm Port Overlapped Overlapped Error Overlapped File Buffer or Queue OK OK Overlapped OK ...

Page 779: ... 12 LED Source Control 25 15 CO2 Control 25 16 Flow Control 25 17 Temperature Control 25 18 Fan Control 25 18 AUTOPROGRAMS AND THE CONTROL MANAGER 25 19 Interaction with Variable Tracking 25 19 LOW LEVEL CONTROL TOOLS 25 19 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...

Page 780: ... edit an existing program Autoprogram Format AutoPrograms are small LPL application programs designed to run on top1 of OPEN While there is no limit to the scope of what an AutoProgram can be made to do typically these programs log data in some sort of automatic fash ion while perhaps maintaining control over one or more conditions in the leaf chamber LetÕs look at a simple but fully functional LP...

Page 781: ...ies the number of times through the loop Within this structure the 60 second delay is done by 60 LPMeasure LPMeasure creates a New Measurements mode like setting for a fixed amount of time and when it is over the global variable lpAbort tells us if the user wishes to abort the program This happens when the user presses escape during LPMeasure This brings up the AutoProgram exit dialog box Figure 2...

Page 782: ... time defaults CHAR defaultFile ÒAutoLog dfltsÓ progName ÒAUTOLOGÓ INT logInterval 5 quitAfter 5 matchEvery 0 This array holds the list of things to be prompted for with a call to LPPrompts2 below PTR user PTR logInterval Ò nLog every __ secs Ò PTR quitAfter ÒAdd __ observations Ò PTR matchEvery ÒAuto match every __ obs 0 none Ò FCT main progName LPSetName progName Ò f sÓ PRINT defaultFile user LP...

Page 783: ...ht Curve with stability checking 960822 Tech Note 14 modification wait time defaults 970502 remembers last time defaults 980309 delta based matching CHAR defaultFile ÒLightCurve DfltsÓ These default values are used if there is no last time defaults file found FLOAT lampVals 20 2000 1500 1000 500 200 100 50 20 0 stable 1 0 matchIf 20 INT minWaitTime 120 maxWaitTime 200 pmWait 10 PTR user PTR lampVa...

Page 784: ...e maxWaitTime LPMeasureTilStable lpAbort BREAKIF Match fct is below MatchFct Log LPLog log the data i 1 DROP increment ENDLOOP LPDeregLoop LPCleanup must be done MatchFct co2_diff_um ABS matchIf IF LPMatch 10 LPMeasure THEN ÒA CiCurveÓ This program is described on page 9 21 A Ci Curve rev 2 3 16 95 960822 Tech Note 14 modification 970502 remembers last time defaults 980309 delta based matching CHA...

Page 785: ...mixerAvail NOT IF 1 ÒSorry Need a CO2 Mixer for this Ó MESSBOX DROP RETURN THEN IsCO2MixerOn NOT IF 1 ÒTurn on the CO2 Mixer and get it stabilized before running this Ó MESSBOX DROP RETURN THEN ÒA Ci CurveÓ DUP LPSetName Ò f s nÓ PRINT MixerGetTarget SWAP DROP INT theTarget defaultFile user LPPrompts2 IF RETURN THEN 1 INT i LPPrep target LPMixerTarget co2Vals READY LPRegLoop NLOOP LPLoopStat If as...

Page 786: ...undled with OPEN 3 0 980515 Updated for 3 2 INT wndw 4 1 2 39 7 Maximum steps is 60 3 To increase this change the number 60 to something bigger values 60 changed 0 LONG lastTime 0 logMS 0 CHAR defaults 40 ÒDfltsÓ defaultDir 80 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 Pi...

Page 787: ...VAL LPSetLamp values i 2 PICK VAL 1000 50 logMS i 3 DROP n i 3 LPSetProgress time LPMeasure lpAbort BREAKIF ENDLOOP buff CLOSE LPCleanup ResetComp ResetUpdate User types in parameters using Standard Edit FromKeyboard PTR buff 0 INT rtn wndw 1 1 ÒTime s Lamp æmol LogInt s Ó 5 ÒEnter values press esc Ó WINDOW LOOP buff STDEDIT Ò x1bSREÓ 2 2 ÒOptionsÓ 6 ÒPress A KeyÓ Ò esc abort nS store this then ru...

Page 788: ...OX ÔYÕ IF buff FromKeyboard RETURN THEN 0 RETURN Returns 0 for abort 1 for ok User selects how to enter input parameters PickParams PTR buff buff RESET CheckDir ÒKFÓ 2 2 ÒTimed Lamp ProgramÓ Ò nGet data n K from Keyboard n F from FileÓ MESSBOX INT k k 0x1b IF 1 RETURN THEN k ÔKÕ IF buff FromKeyboard RETURN THEN k ÔFÕ IF buff FromFile RETURN THEN Does the default directory exist CheckDir theConfigD...

Page 789: ... fullSpec OPEN_FILE NOT IF PTR file file dest XFER file CLOSE THEN THEN StoreDefaults PTR source 0 0 source SETEMPTY 1 fullSpec ÒStore TimedLamp parametersÓ OPEN_FILE_ASK NOT IF PTR dest source dest XFER dest CLOSE THEN compEvery is described in Table 26 3 on page 26 5 FCT SetComp 0 compEvery ResetComp 2 compEvery hiResUpdateTime is described in Table 26 2 on page 26 4 FCT SetUpdate 1 hiResUpdateT...

Page 790: ...ial Final See LPRegLoop LPLog Logs another observation to the log file Initial Final LPLogComment Logs a string to the log file as a comment Initial Text remark Final This function builds a quoted string made up of the current time HH MM SS fol lowed by remark and outputs it to the log destination LPLoopStat Register a loop Initial Final See LPRegLoop LPMatch Matches the IRGAs Initial Final This f...

Page 791: ... you are shown the AutoProgram exit dialog box Figure 25 2 Pressing A will set the global variable lpAbort to 1 this should be checked in the Au toProgram immediately after calling LPMeasure or LPMeasureTilStable Pressing T will also terminate LPMeasure or LPMeasureTilStable but lpAbort will be set to 0 LPPrep Required Initial Final This is required if LPMeasure or LPMeasureTilStable is going to b...

Page 792: ...the loop Inside the loop call LPLoopStatus to update the counter and the display When the loop is done call LPDeregLoop to deregister the loop These are the tools used by the AutoProgram Builder and were designed to han dle nested loops in a reasonable fashion LPSetName Defines the Autoprogram name Initial Text name Final name will appear in the Autoprogram exit dialog LPSetProgress Sets the AutoP...

Page 793: ...ts of value depend on typeCode Table 25 1 LampGetTarget Gets the current lamp control id and target value Initial Final DOUBLE value LONG typeCode Us this to determine the current control method and target value typeCodes are given in Table 25 1 LampSetTargetVal Sets the current target value without changing control type Initial Num value Final Control type remains the same Only the target changes...

Page 794: ...eCode Table 25 2 MixerGetTarget Get the current target value and control mode Initial Final Double value LONG typeCode Use this function to get the current control type and target value typeCodes are given in Table 25 2 MixerSetTargetVal Sets the target value independent of control mode Initial Num value Final Sets a new target without changing the control type Table 25 2 CO2 mixer control typeCod...

Page 795: ...ypeCode Table 25 3 FlowGetTarget Get the current control mode and target value Initial Final Double value Long typeCode Use this to determine the current set point and control type typeCode values are given in Table 25 3 FlowSetTargetVal Set new target value independent of control mode Initial Num value Final Table 25 3 Flow control typeCodes typeCode Meaning 1 Pump off 2 Constant flow µmol s 1 3 ...

Page 796: ...d control type Table 25 4 CoolSetTargetVal Set the cooling target independent of control mode Initial value Final Fan Control These functions affect the chamber mixing fan LPSetFanSpeedVal Set fan speed volts Initial Num volts 0 off through 5 full speed Final FINAL Intermediate values 4 38 will work here as well LPSetFanOSF Set fan speed Off Slow Fast Initial Num selection 0 1 or 2 for off slow fa...

Page 797: ...d the quantum flux target will indeed be set to that val ue but sometime within the following 30 seconds the control manager will reset the target to the external quantum sensor value Thus the target setting AutoProgram commands listed below will override variable tracking for up to 30 seconds but after that the variable tracking takes over Low Level Control Tools The control manager is defined as...

Page 798: ...l Long logic 1 yes 0 no Returns the state of the digital output dio_pump NullOnFlow Set flow control for constant flow Initial Num setPoint mV Final Sets flow control circuit to null on flow meter signal target value mV given by set Point This command unsets digital output dio_null 0x0001 and sets D A channel da_null_set 0 NullOnRH Set flow control for constant humidity Initial Num setPoint mV Fin...

Page 799: ...ect 0x0000 Co2MixerPowerOff Powers off the CO2 injection circuit Initial Final See comments above Co2MixerOn Sets solenoid to allow CO2 injection Initial Final The flow of pure CO2 is switched into the flow circuit Uses digital output dio_co2 0x0303 Co2MixerOff Sets solenoid to bypass CO2 injection Initial Final The flow of pure CO2 is switched out of the flow circuit so no mixing takes place IsCo...

Page 800: ...ital output dio_cool 0x0004 and D A channel da_cool_fan to 0 V Cooling Are coolers on Initial Final Long Logic 0 off 1 on Returns state of digital output dio_cool Cooling_setpt Sets block cooling set point C Initial Num temp C Final Sets D A channel da_chamber_temp 4 Lamp Control Functions SetLamp_mv Sets the lamp control value 0 5000 mV Initial Num setPoint mV Final If mV is 0 lamp is turned off ...

Page 801: ...ogic 0 off 1 on Returns state of digital output dio_irgabd StatusH2O Returns the status of the water IRGAs Initial Final Long status 1 ok 2 bad ref 3 bad sample or 4 both ref and sample This information comes from 2 digital inputs dio_h2o1 and dio_h2o2 0x0200 and 0x0201 StatusCO2 Returns the status of the CO2 IRGAs Initial Final Long status 1 ok 2 bad ref 3 bad sample or 4 both ref and sample This...

Page 802: ...se digital output dio_fan 0x0006 to be set and D A channel da_chamber_fan 7 to be set to 1000 times the speed Otherwise dio_fan is unset Example Using the Library As an example of how to use the tools in Sys Lib StdControls consider the stand alone program shown in Figure 25 4 This program prompts the user for a command voltage and then sets the lamp accordingly INCLUDE Ò Sys Lib StdControlsÓ FCT ...

Page 803: ...7 Example 1 Using New MeasurementÕs Fct Keys 26 9 Example 2 Periodic Actions 26 11 Example 3 Hooks in AutoPrograms 26 12 NEW STYLE COMPUTELIST FILES 26 16 The userList Pointer Array 26 18 Soil Flux Example 26 20 USING SPARE CHANNELS 26 22 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 ...

Page 804: ...ction New Style Com puteList Files on page 26 16 lists a number of these variables and what they control How to add a Patch command to a configuration file 1 Access the Config Editor In the Config Menu select Config Status then press Edit f1 2 Add a dummy line or select a blank line Put the cursor where you want the new line press Add and select the AREA 6 entry 3 Make the line a comment Highlight...

Page 805: ...figuration file is actually processed The section OpenÕs Hooks on page 26 7 describes more powerful method for modifying OPEN Table 26 1 Samples of Patch commands and what they do Patch Description 3500 3 AOSETa a The entire configuration line would be Patch 3500 3 AOSET Sets analog output 3 pin 12 to 3500 mV 0 logBeepTime Turn off log beeping 200 logBeepTime Make log beeps 0 2 seconds long 1 0x04...

Page 806: ...Õt change it if itÕs shaded Description lowResGroup INT 0 Group number for all non IRGA chan nels hiResGroup INT 1 Group number for all IRGA channels groupQueue INT 1 Buffer size for accumulating readings hiResUpdateTime FLOAT 75 Update time New readings available every __ seconds Low and Hi resolu tion channels both use this period hiResCount INT 16 Number of raw readings per update time lowResCo...

Page 807: ...t if itÕs shaded Description ukey1 ukey2 ukey3 ukey4 ukey5 INT 31É35 Use for defining the five user defined function keys maxKeys INT 35 Determines max of function keys in New Msmnts mode compEvery INT 2 Determines how often user computations are done 0 every time new measure ments are available 1 every other time 2 every 3rd time etc matchStableLimit FLOAT 2 CO2 range limit ppm for de termining Ò...

Page 808: ...d in sys open open log Name Type Valuea a DonÕt change it if itÕs shaded Description logBufferOpen INT 0 or 1 0 logging inactive 1 logging active Do not set this variable logBeepTime INT 200 Duration of beep when log ging in milliseconds obsInPad INT 0 Number of observations logged since destination opened System variable 35 obsOneTime Long 0 Time and date seconds des tination was opened ...

Page 809: ...omputeList The safest way to take advantage of OPENÕs hooks is put one or more include fileName directive s into your ComputeList file that will link module s containing functions to do the activities that you want The names of these functions are very important and Table 26 5 lists the required name along with what the default actions are Before a ComputeList is processed all of these hooks are r...

Page 810: ...c LogFromButton UpdateClock CompStability UserEverySec HookPreComps Called every 2 25 seconds prior to doing the User Computations FCT CompPrep UserPreComps HookPostComps Called every 2 25 seconds just after the User Computations FCT Nothing UserPostComps HookWatchDog Called every 10 seconds in New Mea surements mode to check for problems such as IRGA s Not Ready FCT WatchDog UserWatchDog HookNewM...

Page 811: ...ys is the most impor tant since that is how weÕll get our key defined The other hook UserNM Figure 26 1 The file Ò User Configs Modules LI 610 Fct KeyÓ It uses two hooks by defining the functions DefUserKeys and UserNMStartUp Module to control an LI 610 with fct key 1 level 7 in New Measurements mode internal stuff STATIC 1 FLOAT targetDP 20 0 Uses D A port number 3 That s pins 12 and 13 signal an...

Page 812: ...he our key FCT Def610Key targetDP Target g to_string Change610Target ukey1 ONSOFT The function to_string is a handy tool for building a temporary string and is defined in sys open open utl Since ONSOFT requires a function key number we use ukey1 rather than 31 f1 level 7 is 31 f2 is 33 etc ItÕs safest to use the variables defined in sys open open msr ukey1 ukey2 ukey3 ukey4 and ukey5 when defining...

Page 813: ...gging etc The hook we want is UserNewReadings since that is called each time we have new measured values The only other thing we need is the variable names of the four quantities see Table 14 8 on page 14 19 The module is shown in Figure 26 2 To use this store it in the user configs modules directory and include it in whatever ComputeList you wish A useful addition to this module would be a functi...

Page 814: ...from 0 75 seconds to 1 5 seconds 3 Speed up how often calculations are done Change it from every 2 25 seconds to 1 5 seconds Thus computations are done at the same rate as measurements are being made The listing of ÒAveraging AutoLogÓ follows with some margin notes AutoLog with Averaging for OPEN version 3 To log the number of readings in each average include auxN3 sys value 106 in the log list FL...

Page 815: ...gs New readings less often all comps and screen updates done with each one Change update times hiResUpdateTime FLOAT oldUpdate compEvery INT oldComp readingsEvery hiResUpdateTime 0 compEvery A2dProgram GETMS totalDuration 60000 stopTime matchAfter matchCount 2 LPMeasure LOOP stopTime GETMS 1000 logInterval INT n numLogged DUP n SWAP LPSetProgress logInterval LPMeasure ComputeMeansAndLog lpAbort BR...

Page 816: ...ining functions are involved with the data averaging UpdateTotal update values 1 INT i actionList READY NLOOP totals i PICK actionList i PICK VAL DROP i 1 DROP ENDLOOP numAdded 1 DROP ComputeMeansAndLog numAdded NOT IF RETURN THEN actionList READY INT n totals n SETREADY totals numAdded DROP 1 INT i n NLOOP totals i PICK VAL actionList i PICK i 1 DROP ENDLOOP numAdded auxN3 LPLog 0 auxN3 0 numAdde...

Page 817: ...tivity while this program runs we could add a call to oldFct somewhere in MyAc tivity It is very important to restore HookNewReadings to itÕs original value before the AutoProgram ends If we donÕt HookNewReadings will be pointing at a block of deallocated memory and will likely crash OPEN the next time it gets called Changing Update Times The ÒAveraging AutoLogÓ program also modifies the way the A...

Page 818: ...utility for generating a new style ComputeList from an old style it is found in the ComputeList Menu entry in the Config Menu 10 U S flow area ratio flow_um area_cm2 100 0 20 Trans Transpiration mol m2 s 10 h2o_2_mm h2o_1_mm 1000 0 h2o_2_mm 21 Trmmol Transpiration mmol m2 s 20 1E3 23 Cond Stomatal cond mol m2 s StdCond 20 Tleaf_c condBL_mol press_kPa h2o_2_mm 30 Photo Photosynthesis umol m2 s 10 c...

Page 819: ... PTR 36 Ci s8 u36 g83 Intercellular CO2 umol mol 0 g13 PTR 38 Ci_Pa s8 u38 g83 Intercellular CO2 Pa 0 g13 PTR 39 Ci Ca s8 u39 g83 Intercellular CO2 Ambient CO2 0 g13 PTR 25 VpdL s8 u25 g83 Leaf VPD es Tleaf eair 0 g13 PTR 27 VpdA s8 u27 g83 Air VPD es tair eair 0 g13 FCT ComputeUserValues u10 flow_um area_cm2 100 0 u20 u10 h2o_2_mm h2o_1_mm 1000 0 h2o_2_mm u21 u20 1000 u23 StdCond u20 Tleaf_c cond...

Page 820: ...sts for example Each item in the pointer array is itself a pointer that must contain 8 items Figure 26 5 and optionally a 9th item Table 26 6 Figure 26 5 The elements of each PTR array that make up userList PTR 10 U S s8 u10 g83 flow area ratio 0 g13 ID Display Label Log Label or 0 if same as Display Label Display Label Format String Display Format String The Variable The Description Log Format St...

Page 821: ... ever be included in a Log List If you wish to use the display label for this just enter a numeric value like 0 instead of a string 8 Log Format String The format you wish used for the variable if it is logged Note that while you may display a number with something like Ò 8 1fÓ you may not want to consume 8 spaces all the time when you log so you would use the corresponding Ò 1 1sÓ 9 Optional Can ...

Page 822: ...ÒdcÕ dtÓ s8 dcdt df3g Òrate of change of co2 densityÓ sad lf4g PTR 307 ÒVbaseÓ s8 soilChamBaseVol df4g Òvol cm3 at 0 depthÓ sad lf4g 2 PTR 310 ÒModeÓ s8 opMode df8d Ò0 4Ó sad lf1d PTR 311 ÒSmplsÓ s8 numSamps df8d Ò obs of slopes or efflux ratesÓ sad lf1d PTR 312 ÒProgram StatusÓ Ò 18sÓ srState Ò 18sÓ ÒStatusÓ ÒPgStsÓ Ò 18sÓ PTR 313 ÒTargetÓ s8 targetCO2 df8d ÒTarget CO2 æmol molÓ sad lf1d 2 PTR 31...

Page 823: ...teUserValues 0 FLOAT density 0 FLOAT va rhsc 100 0 eAir_2_kPa SatVap Tleaf_c tSoil chan21_mv 10 0 soilChamSysVol soilChamBaseVol area_cm2 soilInsDepth va soilChamSysVol area_cm2 IF opMode 3 density 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 ...

Page 824: ...nput channels All you have to do is add the UserChan configuration command to the configuration file and edit it so that it reflects the signal and ground channels being used by the sensor Choose the resolution high or low A channel measured with high resolution is sampled at the same rate as the gas analyzers and is subject to the AvgTime configuration command Signals measured with low resolution...

Page 825: ...signal updated Once at the start of OPEN This is probably most easily done by inserting a PATCH command into the configuration file This will execute every time that configuration is imple mented For example suppose you need to provide 4 volts to some device as part of a particular configuration If you are using channel 10 for this you would add PATCH 4000 10 AOSET to your configuration file That ...

Page 826: ...n analog output that is proportional to photosynthetic rate edit the ComputeList definition of photosynthesis to be 30 Photo Photosynthesis umol m2 s 10 co2_diff_um co2_2_um 20 AOSET 30 5000 0 30 0 3 This uses D A channel 3 and scales the signal so that 5V is 30 µmol m 2 s 1 Whenever you feel like it no programming required A simple method of setting a D A channel is to do the AOSET manually from ...

Page 827: ...ommands 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 Table 26 11 Spare digital channels LPL ID Pin 37 Pin Connector LPL ID Pin 37 Pin Connector 0x0400 23 0x0404 25 0x0401 5 0x0405 7 0x0402 24 0x0406 26 0x0403 6 0x0407 8 5 V pin 1 Digital Ground pin 20 Digital Output pin 5 10K Ohm ...

Page 828: ...if the input is low An input channel can be used to count pulses 10 Hz and this is discussed in Digital I O on page 23 75 For higher frequency pulse counting see High Speed Counter on page 23 76 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 ...

Page 829: ...rates a method of connecting a switch Software Use the HSCOUNTS LPL keyword Summary of the ConsoleÕs 37 Pin Connector The LI 6400 consoleÕs 37 pin connector assignments are listed in Table 26 13 The shaded entries pins 10 21 and 28 are outputs that are wired in parallel with some component in the LI 6400 and would not normal ly be controlled by a user application Digital Ground pin 20 Pulse counti...

Page 830: ...or 15 Analog Input Ground 6 Analog Input Channels on page 26 22 16 Sample H2O raw analog output 17 Analog Input Ground 7 Analog Input Channels on page 26 22 18 Analog Input 22 19 Analog Input 21 20 Digital Ground Use with digital I O 21 Digital Output 0x0007 Match mode 22 Digital Input 0x0107 Digital Input on page 26 26 23 Digital Output 0x0400 See Digital Output on page 26 25 25 Digital Output 0x...

Page 831: ...Valve 20 28 9864 111 Quantum Chamber Mount 18 28 A aborting a program 5 16 About this unit menu item 3 8 AC indicator LED 19 8 Access the FILER menu item 10 6 A Ci curve AutoProgram 9 21 discussion 4 30 with light curve 9 38 actinity correction 14 8 Add fct key Config Editor 16 15 Filer 10 9 AddGrp fct key 9 9 Add Remark fct key 9 5 Adjust fct key 18 17 adjusting the latch 4 4 agc signals 20 15 mo...

Page 832: ... 3 19 storing 19 8 Battery label 14 20 baud rate 11 24 setting in boot screen 5 19 setting in OPEN 21 19 BDH soda lime 4 50 beep duration 26 6 in log sequence 9 14 on key press 23 29 when logging 9 7 black body radiation 17 2 BLC_mol label 14 20 BLC1_mol label 14 21 BLCond label 14 20 BlkÉ fct keys 5 14 BlkT fct key 7 16 block temperature control option 7 16 equation 14 4 ref for leaf temp 18 19 v...

Page 833: ...21 CO2 label 14 12 _CO2 Mixer Calibrate menu item 18 20 CO2 Mixer 6400 01 calibrating 18 20 config command 16 20 controlling 7 13 introduction to using 3 33 preparing 2 7 service 19 32 status 14 13 troubleshooting 20 23 with external tanks 2 10 _CO2 Mixer Plot Curve menu item 18 23 CO2 Mixer Test menu item 21 2 CO2 response curve 4 30 CO2R didnÕt change enough 4 37 20 22 CO2R fct key 7 14 CO2 R S ...

Page 834: ...ays Diagnostic 20 42 Configs Modules LI 610 Fct Key 26 9 Configs Prompts 9 17 configuration introductory tour 3 51 reference 16 18 Configuration Examples Menu 3 10 Configure the COMM port menu item 11 23 Conifer Chamber 6400 05 installing 16 5 temp measured in 17 6 conifers 3 51 connecting to computer 11 3 connector chamber pinout 20 45 console 37 pin 26 27 IRGA 20 15 LED source 20 31 screws 19 12...

Page 835: ... 10 2 Digital Status menu item 21 6 dilution correction 1 10 Dir fct key Filer 10 9 Std File 5 11 directories changing Std File 5 11 creating 10 10 definition of 10 3 Filer functions 10 9 removing 10 10 renaming 10 10 root 10 4 Disable fct key 16 15 disK fct key 10 18 disk not formatted 20 4 disks archiving 11 16 binary images 11 20 definition of 10 3 defragmenting 10 18 Filer functions 10 18 form...

Page 836: ... number 20 33 program control 25 18 status 14 14 14 15 troubleshooting 20 33 LED source 20 30 temp control 3 36 FAN label 14 14 FCV label 14 20 file exchange mode 11 4 File Exchange Mode menu item 11 4 file formats boundary layer table 14 17 ComputeList 15 3 Display config 6 7 LED source calibration 18 27 light sources 18 29 LogList config 9 10 mixer calibration 18 24 PlotDefs 12 19 PromptList con...

Page 837: ...ist editor 9 14 CLOSE FILE 9 6 Close Logging 9 7 Clr all Filer 10 14 ClrAll LogList editor 9 9 ClrEnd 5 6 CO2 R S 18 10 CO2R S 18 14 CO2S 7 14 CO2V 7 15 Copy 10 15 Curvs n 6 10 CUSTOM 13 12 Data Set Pick 12 10 Defrag 10 18 DelChar 5 6 DelLn 5 6 Dir Filer 10 9 Std File 5 11 Disable 16 15 disK 10 18 Display Editor 6 4 Display List 6 3 Display QuikPik 6 3 dUplct 10 16 earlyOK LED Calib 18 25 Mixer Ca...

Page 838: ... Show Items 9 7 Space 10 18 Store Config 12 10 Store Image 12 19 Store 18 18 Tag all 10 14 tag One 10 14 Tag 10 14 Toggle 9 9 Track PAROut 7 19 View Data GraphIt 12 17 View File 12 2 VIEW GRAPH 6 9 View 10 13 VPD 7 10 WhatÕs Missing 9 7 WhatÕs What 6 4 XYPlot LOG 6 9 in New Msmnts 6 3 in Standard Edit 5 13 in Standard Line Editor 5 6 in Standard Menu 5 3 in the Filer 10 7 RTG control 6 8 FUSE mess...

Page 839: ...Invert fct key 10 14 IRGA Span menu item 18 12 IRGA Zero menu item 18 5 IRGAs calibration discussion 18 3 checking zero 4 4 chopper motor 20 19 CO2 equation 14 6 connecting and disconnect ing 3 5 H2O equation 14 5 interchanging 2 5 maintenance 19 26 noise 20 16 temperature equation 14 5 troubleshooting 20 14 IRGAs Not Ready 20 7 Is the chamber IRGA connect ed 3 4 J Jamieson J A 14 26 JumpTo fct ke...

Page 840: ...balance 17 2 positioning sensor 19 19 replacing sensor 19 18 sensor equation 14 7 viewing 3 19 zero 18 19 LeafT fct key 7 16 leaks finding 20 35 long discussion 4 42 short discussion 1 3 _LED Source Calibrate menu item 18 24 _LED Source Plot Curve menu item 18 26 LED source 6400 02 02B calibration 18 24 installation example 16 5 installing 2 15 introduction to using 3 39 maintenance 19 22 performa...

Page 841: ...ge enough 4 37 CO2 has changed 20 21 CO2 has changed leak 4 38 CO2R didnÕt change enough 20 22 DidnÕt match Unsta ble CO2S 4 40 DidnÕt match Valve stuck 4 40 Excessive Deltas 20 21 Excessive deltas 4 38 Flow is Low 4 36 New Msmnts BLOWN FUSE 20 7 Chamber Fan is Off 20 8 Flow Too Low 20 8 High Humidity Alert 20 7 IRGAs Not Ready 20 7 NeedÉdrier target 20 9 NeedÉwetter target 20 8 Negative PAR 20 9 ...

Page 842: ...ot fct key 18 6 polyurethane tubing 19 7 powering the LI 6400 2 18 preparation check lists 4 2 Press label 14 19 press_mv label 14 21 pressure and IRGA noise 20 17 checking sensor 4 3 sensor equation 14 4 sensor location 20 38 viewing 3 19 Pressure Sensor menu item 21 7 Print fct key Filer 10 16 Standard Edit 5 14 Standard Menu 5 4 printing files 10 16 ProgPrgs label 14 16 Program label 14 16 Prom...

Page 843: ..._ label 14 19 RH_S fct key 7 10 RH_S label 14 20 RH_S_ label 14 20 Richards R G 14 26 root directory 10 4 RSPNS fct key 7 12 run a program from a program 23 78 from LPL screen 5 21 from Standard Edit 5 16 S saturation vapor pressure equation 14 9 Save fct key Config Status 16 14 SaveAs fct key Config Editor 16 15 Config Status 16 14 Display editor 6 5 LogList editor 9 9 PromptList editor 9 14 RTG ...

Page 844: ...ted Directory Copy 21 18 SETCLOCK 21 18 SETCOMM listing 23 65 SETCOMM 21 19 Simple Terminal 21 19 Verify Calibration 21 20 system software 2 19 system variables list of 14 19 properties of 14 2 T tab in FX DOS 11 10 in Standard Edit 5 15 Tag all fct key 10 14 Tag fct key 10 14 tag One fct key 10 14 tagging files 10 14 Tair label 14 19 Tair_mv label 14 21 tape double sided 19 21 Tblk label 14 19 Tb...

Page 845: ...or pressure deficit controlling 7 10 viewing 3 18 vapR_kPa label 14 21 vapS_kPa label 14 21 variable control targets 7 5 names in OPEN 15 15 Verify Calibration program 21 20 View Data fct key GraphIt 12 17 View fct key 10 13 View File fct key 12 2 VIEW GRAPH fct key 6 9 View Installed Cal Items menu item 16 5 View Store Zeros Spans menu item 18 18 VPD fct key 7 10 VpdA label 3 18 VpdL label 3 18 W...

Page 846: ...Index I 16 Using the LI 6400 ...

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