smartflux instruction manual - li-cor biosciences

SystemInstruction Manual

The SMARTFlux SystemInstruction Manual

LI-COR BiosciencesGlobalHeadquarters4647 Superior StreetLincoln, Nebraska 68504Phone: +1-402-467-3576 • Toll free: 800-447-3576 • Fax: [email protected] • [email protected] • www.licor.com/env

Regional OfficesLI-COR GmbH, GermanyServing Andorra, Albania, Cyprus, Estonia, Germany, Iceland, Latvia, Lithuania,Liechtenstein, Malta, Moldova, Monaco, San Marino, Ukraine, and Vatican City.LI-COR Biosciences GmbHSiemensstraße 25A • 61352 Bad HomburgGermanyPhone: +49 (0) 6172 17 17 771 • Fax: +49 (0) 6172 17 17 [email protected] • [email protected]

LI-COR Ltd., United KingdomServing Denmark, Finland, Ireland, Norway, Sweden, and UK.LI-COR Biosciences UK Ltd.St. John’s Innovation CentreCowley Road • Cambridge • CB4 0WSUnited KingdomPhone: +44 (0) 1223 422102 • Fax: +44 (0) 1223 [email protected] • [email protected]

LI-COR Distributor Network:www.licor.com/env/distributors

NOTICE

The information contained in this document is subject to change without notice.

LI-COR® MAKES NO WARRANTY OF ANY KIND WITH REGARD TO THE THIS MATERIAL, INCLUDING,BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR APARTICULAR PURPOSE. LI-COR® shall not be liable for errors contained herein or for incidental or con-sequential damages in connection with the furnishing, performance, or use of this material.

This document contains proprietary information which is protected by copyright. All rights are reserved. No part ofthis document may be may be reproduced or translated into another language with prior written consent ofLI-COR®, Inc.

The SMARTFlux System and "SMARTFlux® powered by EddyPro®" are a trademarks of LI-COR®, Inc. EddyPro®Software is a registered trademark of LI-COR®, Inc. All other trademarks and registered trademarks are property oftheir respective owners.

Patents Pending

Printing History

Publication Number: 984-13838

© Copyright 2015, LI-COR®, Inc.

New editions of this manual will include all updates. An update addendum may be used between editions to provideup-to-date information. Revisions are indicated by the revision number. Minor updates, which do not alter the mean-ing of the content, will be incorporated without affecting the revision number.

Version Num-ber

PublicationDate

Changes

1 November 2013 First edition

2 November 2014 Minor Changes

Build Date: Monday, January 04, 2016

ii

iii

CE Marking:This product is a CE-marked product. For conformity information, contact LI-COR Support at [email protected]. Outside of the U.S., contact your local sales office or distributor.

Lead (Pb) Mercury (Hg) Cadmium (Cd)

Chromium VI

Compounds

(Cr6+)

Polybrominated

Biphenyls (PBB)

Polybrominated

Diphenyl Ethers

(PBDE)

Flux Module Assembly X O O O O O

(Pb) 汞 (Hg) (Cd) 六价 (Cr6+) 多溴苯 (PBB)多溴二苯

(PBDE)

通量摸件 X O O O O O

X:表示有毒有害物至少在部件的某一均材料中的含量超出 SJ/T 11363-2006 准定的限量要求o (企可在此 ,根据情况上表中打"X"的技原因行一步的明o )

部件名称有毒有害物或元素

7550-200

O:表示有毒有害物在部件所有均材料中的含量均在 SJ/T 11363-2006 准定的限量要求以下o

Hazardous Substances or Elements

Component Name

7550-200

O: this component does not contain this hazardous substance above the maximum concentration values in homogeneous materials specified in

the SJ/T 11363-2006 Industry Standard.

X: this component does contain this hazardous substance above the maximum concentration values in homogeneous materials specified in the

SJ/T 11363-2006 Industry Standard (Company can explain the technical reasons for the "X")

This device complies with part 15 of the FCC Rules. Operation is subject to the following two conditions: (1) Thisdevice may not cause harmful interference, and (2) this device must accept any interference received, including inter-ference that may cause undesired operation.

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Contents

Section 1. SmartFlux® Overview

What's What 1-1Components 1-2Tools Required 1-3Installation in the LI-7550 1-4Initial Configuration 1-7Configuring Systems with Additional Networked Sensors 1-9

Section 2. Configuring the EC System

Eddy Covariance Checklist 2-1Configuring Eddy CovarianceMeasurements 2-4

System Clock 2-5Configuring the USB Log File 2-6Entering the Site Description 2-7Entering Anemometer Information 2-9Entering CO2/H2O Analyzer Information 2-16Entering LI-7700 Information 2-19Entering Biomet System Information 2-22Connecting with the SmartFlux System 2-24

Begin Logging Data 2-25Verify Flux Computations 2-25Voltage Input 2-27Transferring Logged Data 2-28

Section 3. Running SmartFlux

Express Processing 3-1Automatic Variable Selection 3-1

SmartFlux System Configuration Steps 3-2Automatic Variable Selection 3-4Overview of Advanced Processing 3-5

Advanced Processing Options 3-6Creating a SmartFlux System Advanced Configuration File 3-9Creating an Advanced SmartFlux Configuration File without .ghg Files 3-9Creating an Advanced SmartFlux Configuration File with .ghg Files 3-10Using Planar Fit, In-situ Spectral Corrections and Timelag Optimization in SmartFlux 3-10

Loading a SmartFlux Configuration File 3-13SmartFlux Results Files 3-14

Flux Results 3-14Daily Summaries 3-14Data Backup 3-14

Section 4. Updating Software

Software Updates 4-1Embedded Instrument Software 4-1PC Software Update 4-2

SmartFlux Software Update 4-3Check the Software Version 4-3Update the Software 4-4

EddyPro Software Update 4-4

Section 5. Troubleshooting

Appendix A. Specifications

Appendix B. Warranty

Index

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Section 1. SMARTFlux® OverviewThe SMARTFlux System is an add-on component for LI-COR eddy covariance sys-tems that are based upon the LI-7500RS and LI-7200RS gas analyzers. TheSMARTFlux System includes an all-weather microcomputer processor and GPSantenna. It installs in the LI-7550 Analyzer Interface Unit.

The SMARTFlux System uses EddyPro® Software to process LI-COR® .ghg files. Itprovides:

l Fully corrected eddy covariance results processed by EddyPro in Express orAdvanced mode in real-time with a 30-minute averaging interval.

l GPS location and time keeping for populating metadata location informationand synchronizing system clocks with GPS satellite clocks.

l Input voltage readout for system diagnostics.

For a detailed description of the EddyPro processing algorithms and options, referto the EddyPro Software documentation.

What's WhatIf you just received your SMARTFlux System check the packaging list to verify thatyou received everything that was ordered. The SMARTFlux System includes the fol-lowing items:

l SMARTFlux System - All-weather microcomputer enclosed in a protective hous-ing. Includes a programmed MicroSD card, GPS antenna (part number 9972-061), and mounting bracket. Part number 9972-059.

l Mounting Screws - To secure the SMARTFlux System in the LI-7550. Part number122-10769.

l Power Wiring Harness - To split the LI-7550 power supply. Part number 9972-062.

1-1The SMARTFlux® System


l Ethernet Cable - 30 cm (12 in.) Ethernet cable with a 90° RJ45 plug on one endand straight RJ45 plug on the other. Part number 616-13754.

Description Qty. LI-COR Part No.

SMARTFlux System 1 9972-059GPS Antenna 1 9972-061Mounting Bracket 1 9872-05612" (30 cm) Ethernet Cable 1 616-13754PowerWiring Harness 1 9972-062Mounting Screws (#4) 4 122-107698 GB ProgrammedMicroSD Card1 1 616-1384816 GB ProgrammedMicroSD Card optional 616-14240

ComponentsThe SMARTFlux System components are labeled below:

The power wiring harness included with the SMARTFlux System splits the LI-7550power supply to power both the gas analyzer and the SMARTFlux System. It requiresa 10 to 30 VDC power supply capable of providing 175mA (@12VDC) in additionto the start-up power required for the gas analyzer.

1The MicroSD card runs custom software and should not be removed or replaced. Contact LI-COR if youwant to replace it or upgrade to a large size ([email protected]).

1-2 The SMARTFlux® System

Tools Requiredl Small Phillips screwdriver, (PH1)l 8-pin Turck to 8-pin Turck Ethernet cable (392-10108); Included with

LI-7500RS/LI-7200RS spares kitl 8-pin Turck to RJ45 Ethernet dongle (392-10107); Included with LI-7500RS/

LI-7200RS spares kitl A Windows® PC with to configure the LI-7500RS/ LI-7200RS; see Updating Soft-

ware on page 4-1

Installing the SMARTFlux System will take an experienced technician 15 to 30minutes. Configuring EddyPro® Software Express settings will take about 10minutes. Allow more time if you need to update the instrument software and createan EddyPro Advanced configuration file for the SMARTFlux System.


1-3Tools Required


Installation in the LI-7550The procedure described here is for the retrofit installation. Prior to the installation,update the LI-7500RS or LI-7200RS embedded and PC software. See Software Updateson page 4-1 for details.

1 Install the SmartFlux ModuleStop datalogging and power off the analyzer. Inside the LI-7550, unplug the Eth-ernet cables from the Ethernet ports, and remove the left two screws that secure thefaceplate. Install the SMARTFlux System as shown in Figure 1-1 below (C).

Note: On early units the faceplate is secured with hex thumb screws. The lefttwo thumb screws should be removed and replaced with screws included withSMARTFlux System. Completely loosen the left two thumb screws and press hardagainst the side of the screw, as shown below (A), and the screw will pop off.

Figure 1-1. In early units (A), loosen the left thumb screws, press firmly to pop them off,and dispose of them. In later units (B), remove the screws and keep them for re-assembly.Install the SMARTFlux System module in the LI-7550 as shown (C).


2 Install the Power Wiring HarnessFirst, remove the power terminal from the circuit board at the bottom of theLI-7550 (A in Figure 1-2 below). It has four leads - brown, white, blue, and black.Install the power wiring harness (B, C) and attach the terminal to the SMARTFluxSystem as shown (D).

Figure 1-2. Install the power wiring harness as shown.


1-5Installation in the LI-7550


3 Install the Data CablesInstall the straight RJ45 terminal of the 30 cm (12 in.) Ethernet cable into the dataterminal at the bottom of the SMARTFlux unit. Install the 90° RJ45 connector intoany one of the LI-7550 Ethernet ports.

Reinstall the other Ethernet cables that were removed during the installation, asshown in Figure 1-3 below.

Figure 1-3. Install the short Ethernet cable (left) in the SMARTFlux System and LI-7550.Any of the three Ethernet ports are suitable for any of the Ethernet cables.

4 Power On the SystemThe hardware installation is now complete. You can connect the power cable topower up the system.


Initial ConfigurationFollow these steps for LI-7550s with the SMARTFlux System pre-installed and for ret-rofit units. To process fluxes with EddyPro Advanced settings, create a configurationfile in EddyPro (see Overview of Advanced Processing on page 3-5).

Windows XP users: Enable IPv6 on your computer before attempting the con-nection. Click Start > All Programs > Accessories > Command Prompt. In thecommand prompt, type "netsh int ipv6 install" and press Enter.

1 Connect a Computer to the Eddy Covariance SystemPower up the gas analyzer and connect the Ethernet cables to your computer. SeeConfiguring Systems with Additional Networked Sensors on page 1-9 if you have anLI-7700, a Biomet system, or a wireless communication system at your site.

2 Connect with the SmartFlux SystemLaunch the gas analyzer PC software and connect to the analyzer. Click theSMARTFlux button. Select the SMARTFlux module and click Connect.


1-7Initial Configuration


3 Configure the Eddy Covariance SystemBe sure that the eddy covariance system is configured properly by entering therequired information in the LI-7500RS or LI-7200RS PC software. See Configuringthe EC System on page 2-1 and the subsequent sections for more information.

IMPORTANT: Some entries in the gas analyzer software are required for theSMARTFlux System or EddyPro software to proceed with calculations. If you donot enter this information or enter it incorrectly, the SMARTFlux System will notcalculate fluxes or will compute incorrect results. Be sure to complete the fieldsmarked below as mandatory and review the Eddy Covariance Checklist on page2-1.

4 Select the Processing ModeSMARTFlux System uses EddyPro Express settings by default. Under the ProcessingOptions tab, click either Use Express Mode or Upload Advanced File and then selectthe file created by EddyPro version 5 or newer. See Loading a SmartFlux Con-figuration File on page 3-13.


Configuring Systems with Additional NetworkedSensors

If your eddy covariance system has additional networked devices, such as anLI-7700 Open Path CH4 Analyzer, Biomet System, and/or a cellular communicationsystem, it is likely that all the Ethernet ports will be occupied by the additional com-ponents. How do you connect over Ethernet when all the Ethernet ports are taken?Keep reading to find out.

This simplest solution is to connect to the LI-7550 with the RS-232 cable and con-figure the networked connections. Another solution is to acquire a 5-port Ethernetswitch (LI-COR part # 616-12721) and install it in the 7900 Biomet enclosure or asmall weather-proof enclosure.

If you cannot connect with RS-232 and you do not have an Ethernet switch, youcan still connect two networked devices and the SMARTFlux System. Here is how:

1. Unplug the Ethernet cable for one of your devices (e.g., the Biomet system) and install an Ethernetcable between your computer and the vacated Ethernet port.

2. In the gas analyzer PC software, Connectwith the device that is still attached to the other Eth-ernet port (e.g., the LI-7700).

3. Then, you can unplug the Ethernet cable for that device (e.g., the LI-7700) and install the Ethernetcable between your computer to the newly-vacated port.

4. Reconnect the Ethernet cable for the device that was disconnected in step 1. Now, Connectwiththat device (e.g., the Biomet system) in the gas analyzer PC software.

5. Unplug the computer's Ethernet cable from the LI-7550 and reinstall the Ethernet cables for thenetworked sensors.

When you've configured the connection for a device in the software, you canunplug and plug in the Ethernet cable without risk. The devices will automaticallyresume communication shortly after the cable is reinstalled.


1-9Configuring Systems with Additional Networked Sensors

Section 2. Configuring the ECSystem

The SMARTFlux System configuration consists of two components: Entering Siteinformation, which is the metadata describing your site and instrument setup (seeConfiguring Eddy Covariance Measurements on page 2-4), and entering Processinginformation, which tells the SMARTFlux System how to process the data (see RunningSmartFlux on page 3-1). Site information is essential for logging complete eddy cov-ariance data sets. Processing information is loaded automatically for express set-tings, but can be customized if you need to use advanced settings.

Eddy Covariance ChecklistTable 2-1 below is a checklist of settings that either must be set or that we recom-mend setting before recording datasets that can be processed by the SMARTFlux Sys-tem or EddyPro® Software. Review this checklist to be sure that everything is setproperly.

Software Field Recommended Setting See Section

Settings > Time

Clock Sync (PTP): Automatic SystemClock on page 2-5

Time Zone: Your time zone

Site Setup > USB Log File

Update Rate (Hz): 10 Hz (recommended; 5 Hz min) Configuring the USB LogFile on page 2-6

File Duration: 30 Minutes

Compress files (.ghg) ✓ (check this box)

When out of space: As desired

Table 2-1. Checklist of mandatory and recommended EC system settings. Note:Some of the settings below are required in order to log valid EC datasets.




Site Setup > Site Descrip-tion

Station name: Name of the station Entering the Site Descrip-tion on page 2-7Canopy height (m): Measured at site

Use SMARTFlux Coordinates ✓ (check this box)

Site Setup > Anemometer

Manufacturer: Make of anemometer

Model: Model of anemometer Entering AnemometerInformation on page 2-9

Head correction appliedinternally:

For the CSAT3, ✓ if true

North alignment: For Gill models, select the anemometersetting

Wind data format: Select the setting set in the anem-ometer

North Offset (°): Measured at site

Height (m): Measured at site

Anemometer > Input Set-tings

Aux1 Type: U; Units: m/s Configuring the Anem-ometer Inputs on page2-12

Aux2 Type: V; Units: m/s

Aux3 Type: W; Units: m/s

Aux4 Type: Ts; Units: °C

Site Setup > CO2/H2O Ana-lyzer

Northward separation (cm): Measured at site Entering CO2/H2OAna-lyzer Information on page2-16

Eastward separation (cm): Measured at site

Vertical separation (cm): Measured at site

CO2/H2O Log Values Select All or Default

Site Setup > CH4 Analyzer (if using an LI-7700)

Table 2-1. Checklist of mandatory and recommended EC system settings. Note:Some of the settings below are required in order to log valid EC datasets.(...continued)



Connect to LI-7700 Select if using LI-7700 Entering LI-7700 Inform-ation on page 2-19Northward separation (cm): Measured at site

Eastward separation (cm): Measured at site

Vertical separation (cm): Measured at site

CH4 Log Values Select All or Default

Site Setup > Biomet (if using a Biomet system)

Connect to Biomet Select if using Biomet system Entering Biomet SystemInformation on page 2-22Sync clock to 7550 ✓ (check this box)

SMARTFlux

Connect to SMARTFlux Sys-tem

Click the SMARTFlux button and selectthe unit

Connectingwith theSmartFlux System on page2-24

Table 2-1. Checklist of mandatory and recommended EC system settings. Note:Some of the settings below are required in order to log valid EC datasets.(...continued)


2-3Eddy Covariance Checklist


Configuring Eddy Covariance MeasurementsThe Site Setup window is where you configure most of the eddy covariance systemsettings. The information entered here will comprise the metadata file, whichdescribes the system setup. The addition of the metadata file inside the .ghg file,while adding a negligible amount of bytes (it contributes about 0.1% to the filesize), allows you to:

l Avoid duplicate retrieving and re-typing of information needed for processingthe file from any external data source;

l Easily store raw data for future reprocessing;l Account for dynamic site parameters that change over the course of the data col-

lection period (e.g., the canopy height of a crop);l To a large extent, simultaneously process files acquired with different set-ups.

IMPORTANT: The SMARTFlux System will not compute flux results if metadataare not entered properly.

Ideally, you are not required to consider the metadata file explicitly, as it is createdand modified by the gas analyzer data logging software and used unobtrusively byEddyPro®. Nevertheless, all information is stored as plain text and can be retrievedand edited at any time.


System Clock

IMPORTANT: In order to synchronize instrument clocks with GPS satellitesthrough the SMARTFlux System, PTP time keeping must be enabled.

Click Settings, under the Time tab, set Clock sync (PTP) to Automatic and the time/-location will be updated when the data is received from satellites. When using PTPtime keeping, the other fields (Date, Time, and Time Zone) are populated auto-matically. PTP will override any settings you enter.

If you do not want to use GPS time, simply unplug the GPS antenna cable fromthe SMARTFlux System. This will also disable the GPS location, however.


2-5System Clock


Configuring the USB Log FileData will be logged to a USB flash drive inside the LI-7550 Analyzer Interface Unit.The USB Log File tab is where you configure the Update Rate, File Duration, andthe action to take should the USB flash drive run out of space. The values to belogged to the USB flash drive from the LI-7200RS, LI-7500RS, LI-7700, and BiometSystem datalogger are chosen under the CO2 Analyzer, CH4 Analyzer, and Biomettabs, respectively.

Set the Update Rate (≥10Hz recommended).

Check "Compress files(.ghg)" so data can be pro-cessed by EddyPro orSMARTFlux System.

Select your preference formanaging data when theUSB drive becomes full.

Data can be logged at up to 20 Hz. These files can be split into smaller files at 30minute, 1 hour, 2 hour, or 4 hour intervals. For eddy covariance, select 30 minutes.

Note: Files are split based on the instrument clock. If you choose to split the filesat 15 minute intervals, and start logging at 10:22, the file will be split at 10:30,10:45, 11:00, etc.

All files are assigned a timestamp with the format YYYY-MM-DDTHHMMSS_Instru-mentName.ext, where date and time are year, month, day, and HHMMSS is 24-hour time (e.g. hour 15 = 3:00 p.m.). The file extension appended is either .data,.metadata, or .status.


Entering the Site DescriptionThe Site Description tab is used to enter information about the site. This inform-ation configures the metadata file that is used for flux processing.

IMPORTANT: Some entries in the gas analyzer software are required for theSMARTFlux System or EddyPro software to proceed with calculations. If you donot enter this information or enter it incorrectly, the SMARTFlux System will notcalculate fluxes or will compute incorrect results. Be sure to complete the fieldsmarked below as mandatory and review the Eddy Covariance Checklist on page2-1.

Site name: Name of the research site (e.g., Marsh).

Station name: Name of the flux stations within the site.

Canopy height (mandatory): Site canopy height; meters.

Displacement height: Also referred to as zero plane displacement height, the dis-placement height of a vegetated surface (usually designated d) is the height atwhich the wind speed would go to zero if the logarithmic wind profile was main-tained from the outer flow all the way down to the surface (that is, in the absenceof vegetation). In other words, it is the distance over the ground at which a non-vegetated surface should be placed to provide a logarithmic wind field equal to theobserved one. For forest canopies, the displacement height is estimated to vary


2-7Entering the Site Description


between 0.6 and 0.8 times the height of the canopy. If not entered explicitly,EddyPro computes displacement height as:

2-1d = 0.67 x canopy height

Roughness length: In the logarithmic wind profile, the roughness length is theheight at which wind speed is zero (indicated by z0). It provides an estimate of theaverage roughness elements of the surface. With vegetated surfaces, because thevegetation itself provides a certain roughness, the logarithmic wind profile goes tozero at a height equal to the displacement height plus the roughness length. If notentered explicitly, EddyPro computes roughness length as:

2-2z0 = 0.15 x canopy height

Use SMARTFlux GPS Coordinates (mandatory): Uses GPS location from SmartFluxSystem for the station location.

Note: If you are testing the SmartFlux System in a building, the GPS signals maybe too weak for the system to find the location, and the software will not show alocation. The system will get this information whenever it gets adequate GPS sig-nals.

GPS format (WGS84): Latitude and longitude coordinates are automatically detec-ted by the SmartFlux System or they can be entered manually.

Format Description ExampleDDDMM SS.SSS Degrees, minutes and seconds with North,

South, East, orWest suffix12°20’44” N,98°45’55”W

DDDMM.MMM Degrees and decimal minutes with North,South, East, orWest suffix

12°20.736’ N,98°45.924’ W

Decimal Degrees Decimal degrees with negative numbers forSouth andWest

12. 3456, -98.7654

Latitude (mandatory if "Use GPS Coordinates" is not selected): Site latitude.

Longitude (mandatory if "Use GPS Coordinates" is not selected): Site longitude.

Altitude (mandatory if "Use GPS Coordinates" is not selected): Altitude (in meters)of the research site.


Entering Anemometer InformationThe Anemometer tab allows you to enter information about the sonic anemometer,including the manufacturer and model, data output format, offset from true north,and height. Some of the available options (e.g., North Alignment) will change,depending on the chosen model.

Choose the sonic anemometer manufacturer and model in the menus. LI-COR sup-ports the following sonic anemometer models:

Manufacturer Model(s)CampbellScientific®

CSAT3

Gill Instruments HS-50™ HS-100™ R2 R3-50™

R3-100™ WindMaster™ WindMaster™ Pro

Metek uSonic-3 Class A (or USA-1 Stand-ard)

uSonic-3 Scientific (orUSA-1 Fast)

R.M. Young 81000

Wind data format (mandatory): From the three axis velocities, the wind speed is cal-culated, and output as either signed U, V, and W, as Polar and W, or as raw velocityvalues. The units of output are set during the anemometer configuration.

Choose the wind data format from the menu:


2-9Entering Anemometer Information


l U, V, W (some Gill anemometers): U is defined as toward the direction in linewith the north spar, as shown in the diagram below. V is defined as toward thedirection of 90° counter-clockwise from the N/Reference spar. W is defined asvertically up the mounting shaft.

l Polar, W - The wind speed in the UV plane, with direction in degrees from 0 to359°, with respect to the Reference spar (normally aligned to North).

l Axis velocities - Raw velocity values for U, V, W.

North offset (°): Offset, in degrees (0-359°) from which the Reference spar/axis ororientation of the anemometer varies from geographic/magnetic north.

Important note on North Offset:

EddyPro requires the offset with respect to geographic north as two pieces ofinformation: The offset with respect to geographic north and the magnetic declin-ation. Currently the software does not provide an entry for magnetic declination.For the best results, enter the North Offset to magnetic North. This will createsmall differences in the wind direction between EddyPro and the SMARTFlux res-ults (a constant offset equal to the magnetic declination), but the flux results willbe the same, if all other settings are the same.

Height (m) (mandatory): Sonic anemometer height above the ground, in meters,measured to center of the anemometer sample volume.

Input Settings (mandatory): The button opens the AuxiliaryInputs window, where you configure the measurement type, units, label, and scal-ing coefficients. See Configuring the Anemometer Inputs on page 2-12.

About Sonic Anemometer InputsLI-COR offers a variety of sonic anemometers manufactured by Gill InstrumentsLtd. (Hampshire, England). You can use an anemometer from another man-ufacturer as well, provided it has a linear voltage output and a maximum voltageoutput of ±5V.

When purchased from LI-COR, the Gill Instruments sonic anemometers are con-figured for eddy covariance measurements, however, you will be well served toreview and change the anemometer settings for your site and setup.


For the purposes of the following discussion, we present some settings that are suit-able for a wide range of scenarios:

Field Option

Message Output Format Mode 1 ASCII UVW continuousBaud Rate 19200

Output Rate >20 Hz recommendedMessage Terminator <cr><lf>

Measurement Units m/sAlignment North to SparAveraging (0=off) 0Resolution Normal resolutionMinimumDirection Resolution 50SOS/Sonic Temp Display SOS & Sonic TempDisplay Analogue Inputs Off

Analog Output Mode ±5V recommendedPRT setting OffUnit Identifier QPower onMessage Display Power onMessageRetries Enabled OnInstantaneous Sampling OffCalibration Enabled OnASCII Format Fixed Format

DAC Channel 1 (field) U outputDAC Channel 1 (range) -30 to +30 m/sDAC Channel 2 (field) V outputDAC Channel 2 (range) -30 to +30 m/sDAC Channel 3 (field) W outputDAC Channel 3 (range) -5 to +5 m/sDAC Channel 4 (field) Sonic TempDAC Channel 4 (range) -40 to 70 °CRolling Average for Velocity Fields OffRolling Average Depth 1

Table 2-2. Gill WindMaster settings that are suitable for many EC setups.




Configuring the Anemometer InputsThe Inputs dialog must be configured in order to scale data from the anemometerproperly.

IMPORTANT: It is mandatory to specify the scaling of the wind speed meas-urements to allow EddyPro Software and the SMARTFlux System to read these val-ues and calculate fluxes.

...or...

l The four Auxiliary Inputs (Aux1...Aux4)correspond with U, V, W, and Ts (orSOS) output from the anemometer.

l Type specifies the variable.l Units are the units that will be logged

with the variable.l Label is logged in the data and metadata.

It identifies the variable.l Slope and offset values relate the meas-

ured variable with the voltage.


1. Choose the Type of Input.

The Type field allows you to choose from:l U – Horizontal wind speed (m/s) as measured toward the direction in line with

the north spar (see diagram below)l V – Horizontal wind speed (m/s) as measured toward the direction of 90° coun-

terclockwise from the north sparl W – Vertical wind speed (m/s) as measured up the mounting shaftl Ts – Sonic temperature (°C)l SOS – Speed of sound (m/s)

2. Choose the appropriate Units.

The units available are typical wind speed units. The software provides some con-trols over the units that are available with each variable:

Type UnitsOther Other, m/s, cm/s, volts, K, and C

U m/s, cm/s, volts

V m/s, cm/s, volts

W m/s, cm/s, volts

Ts K, C, volts

SOS m/s, cm/s, volts

3. Enter the Label.

The Label will appear in the file header in both the data and/or metadata files. Thelabel cannot be changed for any of U, V, W, Ts, or SOS. The label can be enteredonly when ‘Other’ is selected.




Slope Offset ExamplesThe units selected for each auxiliary input determine the units label recorded in thedata file header, as well as the file header in the metadata file used with EddyPro®Software. As such, it is important convert the anemometer output from voltage todata using the multiplier and offset.

For example, if you have configured your sonic anemometer to output U, V, and Wvalues in volts, but want the data file and metadata file to record these values inm/s, you will need to set the multiplier and offset values to rescale the data.

The following table gives the appropriate values for m (multiplier) and b (offset) tobe used when converting raw voltages into units of m/s, using the default sonicanemometer output ranges of -30 to +30 m/s for U and V, -5 to +5 m/s for W, and -40 °C to 70 °C (and speed of sound 300 to 370 m/s).

U, V-30 to +30m/s

W-5 to +5m/s

Ts-40 to 70°C

SOS300 to 370m/s

Sonic output (V) m b m b m b m b

0-5V 12 -30 2 -5 22 -40 14 300

±5V 6 0 1 0 11 15 7 335

±2.5V 12 0 2 0 22 15 14 335

Example 1: You have configured the Gill WindMaster to output raw voltages forauxiliary input U over the range of 0 to 5 V, and over a full scale wind speed of -30to +30 m/s. You want to convert the raw voltages to wind speed and output the val-ues in units of m/s. What is the wind speed when the sonic anemometer outputs araw voltage value of 0.5 V?

1. Set the Type field to U. Set the Units field to m/s. The Label is set automatically.

2. Enter 12 for the Multiplier (m) and -30 for the Offset (b).

Using the slope intercept equation:

2-3y = m*x + b

the wind speed is calculated as

2-4y = 12(0.5) + (-30) = -24 m/s


Example 2: You have configured the Gill WindMaster to output raw voltages forauxiliary input U over the range of ±5V, and over a full scale wind speed of -30 to+30 m/s. You want to convert the raw voltages to wind speed and output the valuesin units of m/s. What is the wind speed when the sonic anemometer outputs a rawvoltage value of 1.5V?

1. Set the Type field to U. Set the Units field to m/s. The Label is set automatically.

2. Enter 6 for the Multiplier (m) and 0 for the Offset (b).

Using equation 2-3 on the previous page, the wind speed is calculated as

2-5y = 6(1.5) + 0 = 9 m/s




Entering CO2/H2O Analyzer InformationThe CO2/H2O Analyzer tabshows the type of CO2/H2Oanalyzer used (LI-7500RSor LI-7200RS), the values tolog to the USB drive, andthe gas analyzer position rel-ative to the sonic anem-ometer.

The distance between thegas analyzer and sonicanemometer is used toestimate the high-frequencyflux losses. Distances areprovided in a Cartesiancoordinate system, whichallows EddyPro® to determine the distance from a gas analyzer and the anem-ometer.

Important: At least one separation must be different from 0. Values are relativeto the sonic anemometer and measured at the site. Entering wrong values willresult in incorrect flux calculations.

l Measurements must be provided in the indicated units.l The anemometer is the center (0, 0) of the coordinate system.l For all gas analyzers, the distances from the reference anemometer are

provided along the north-south east-west axes.


Figure 2-1. Eastward and northward separation of the gas analyzer relative to the sonicanemometer.

Figure 2-2. Vertical separation of thegas analyzer sample path or inlet rel-ative to the sonic anemometer.

Northward Separation (cm) (mandatory):North or south distance between theLI-7500RS sample path or LI-7200RS inletand the anemometer. Positive values if northand negative values if south of the anem-ometer.

Eastward Separation (cm) (mandatory): Eastor west distance between the LI-7500RSsample path or LI-7200RS inlet and the ref-erence anemometer. Positive values if east andnegative values if west of the anemometer.

Vertical Separation (cm) (mandatory): Verticaldistance between the sample path or inlet andthe reference anemometer. This value is neg-ative if the center of the analyzer intake tubeinlet is below the center of the referenceanemometer sample volume and positive if the inlet is above.


2-17Entering CO2/H2O Analyzer Information


CO2/H2O Log Values (mandatory): Click Default to select data records recommendedfor use with SMARTFlux System and EddyPro Software.


Entering LI-7700 InformationThe LI-7550 Analyzer Interface Unit can be connected to any LI-7700 Open PathCH4 Analyzer that is on the network or connected directly to the LI-7550. Thisenables you to log LI-7700 data in the same dataset collected by the LI-7500RS orLI-7200RS.

Connect with an LI-7700

Click on the button in the Site Setup > LI-7700 dialog box or the LI-7700 but-ton in the dashboard to connect to an LI-7700 CH4 analyzer.

The LI-7700 tab displays a list of LI-7700 instruments available on the network(same subnet as computer). Select an LI-7700 from the list or enter an IP address inthe ‘LI-7700 Hostname’ field (networked device on different subnet mask as com-puter) and click Connect. Click Apply or OK. When you start logging data with theLI-7550 via USB, the chosen data values for the LI-7700 will be logged, as well.

Important: To synchronize the clocks of the LI-7500RS or LI-7200RS and theLI-7700, be sure to configure the PTP time setting in the LI-7700 to Slave orAutomatic.


2-19Entering LI-7700 Information


Enter Analyzer InformationHere you specify the separation between the sonic anemometer and the LI-7700sample volume.

Important: At least one separation must be different from 0. Values are relativeto the sonic anemometer and measured at the site. Entering wrong values willresult in incorrect flux calculations.

Northward Separation (cm) (mandatory): North/south distance between the LI-7700Analyzer and the reference anemometer. Positive values if north and negative val-ues if south of the anemometer (see Figure 2-1 on page 2-17).

Eastward Separation (cm) (mandatory): East/west distance between the LI-7700 Ana-lyzer and the reference anemometer. Positive values if east and negative values ifwest of the anemometer (see Figure 2-1 on page 2-17).

Vertical Separation (cm) (mandatory): Vertical distance between the LI-7700 Ana-lyzer and the reference anemometer. This value is negative if the center of theLI-7700 sample volume is below the center of the reference anemometer samplevolume and positive if the gas sample is above (see Figure 2-2 on page 2-17).


Select Variables

In the Site Setup dialog, click to select the recommended variables for pro-cessing in EddyPro and the SMARTFlux System or click Select All to log all vari-ables.

The LI-7700 data values to be logged to the USB drive are chosen under CH4 LogValues. In addition, you can enable the ‘Log LI-7700 status records (.status)’ checkbox to collect LI-7700 STATUS records. The log values available for the LI-7700Open Path CH4 Analyzer include:

Variable Description

CH4 (µmol/mol) Methane mole fraction1

CH4 (mmol/m3) Methane number densityTemperature (°C) Temperature measured by LI-7700 thermocouplePressure (kPa) Pressure measured by LI-77007700 Auxiliary Input 1 Auxiliary input 17700 Auxiliary Input 2 Auxiliary input 27700 Auxiliary Input 3 Auxiliary input 37700 Auxiliary Input 4 Auxiliary input 4Thermocouple Input 1 Auxiliary thermocouple input 1 (°C)Thermocouple Input 2 Auxiliary thermocouple input 2 (°C)Thermocouple Input 3 Auxiliary thermocouple input 3 (°C)

Signal Strength (RSSI)Signal strength (Residual Signal Strength Indicator (0-100%)

Drop Rate (%) Percentage of 1000 Hz scans dropped (0-100%)Diagnostic Value Diagnostic value, an integer

Table 2-3. LI-7700 variables available for logging in compressed .ghg files.

1For calibrations and mean values; should not be used for eddy covariance calculations.


2-21Entering LI-7700 Information


Entering Biomet System InformationThe LI-7550 Analyzer Interface Unit can be connected to any properly-configuredLI-COR Biomet system on the network to integrate biomet data into the dataset col-lected by the LI-7500RS or LI-7200RS. These data are summarized in EddyPro soft-ware or the SMARTFlux System and can be used in the flux calculations.

Connecting to a Biomet System

Click on the button next to Sutron 9210B or click the Biomet button from thedashboard to open the Settings window, where you can connect to a Sutron data-logger.

The Biomet window displays a list of Sutron 9210B Dataloggers available on thenetwork (same subnet mask as computer). Select a Sutron 9210B from the list, orenter an IP address in the ‘9210 Hostname’ field (networked device on different sub-net mask as computer) and click Connect. Click Apply or OK. When you start log-ging data with the LI-7550, the chosen data values for the 9210B will be logged andsummarized in the SMARTFlux System output.


View SensorsAfter connection, the software will display a list of biomet sensors configured foruse with the selected Sutron datalogger (under Sensors). Click on any sensor inthe list to display the Sensor Properties (Type, Units, and Value) for the selectedsensor. Note that the Sensors and Sensor Properties are configured through the9210B; this list is for reference only.

NOTE: Enable the ‘Sync clock to 7550’ to synchronize the Sutron 9210B andLI-7550 clocks.

Refer to the Biomet Station Instruction Manual for more information.


2-23Entering Biomet System Information


Connecting with the SMARTFlux SystemThe SMARTFlux System window displays a list of all SMARTFlux Systems that areconnected to your network of sensors. In this window, you select a SMARTFlux Sys-tem and connect to it by clicking the Connect button.

Processing OptionsTwo processing settings are available in the Processing Options tab: Express Modeand AdvancedMode.

l Express settings are used by default. To use Express mode, simply connect withthe SMARTFlux System or click Use Express Mode to activate the setting. SeeExpress Processing on page 3-1.

l To process data with EddyPro Advanced settings, click the Upload Advanced Filebutton and select the .smartflux file created in EddyPro. The file will load andEddyPro. will compute flux results based upon the settings defined within. Referto the EddyPro documentation for more information. See Overview of AdvancedProcessing on page 3-5.


Begin Logging DataUnder the Site Setup menu, each tab has Start, Stop, and Eject buttons.

You can open the logging controls by clicking the log button.

Click Start to begin logging data. Press Stop to quit logging, and Eject to unmountthe USB drive. Always eject the USB drive properly before removing it. After press-ing the Eject button, the LED inside the LI-7550 will turn off when it is safe toremove the drive.

Important: When you stop datalogging, the time-series file that is being col-lected will be saved to USB drive in component form (including the high-speeddata, site metadata, and other files, if applicable), however, it will not be com-pressed into a .ghg file, and subsequently, it will not be processed by theSmartFlux System.

However, you can change the metadata settings or toggle Advanced and Expressprocessing while data is being logged—without stopping datalogging. Theupdated metadata will be recorded in the next .ghg file that the system creates.Under this scenario, all files will still be compressed and processed by theSmartFlux System. To log an uninterrupted series of .ghg files, do not stop log-ging data when you change the metadata or other settings.

Verify Flux ComputationsThe best way to verify that fluxes are calculated is to review the data after 30minutes of collection. To allow time for computation, let the system run for about


2-25Begin Logging Data


35 minutes and then select the Results tab of the LI-7200RS or LI-7500RS software.Computed flux results will be visible.


Voltage InputVoltage input is displayed under the Diagnostics window, General tab:

The voltage is measured by the SMARTFlux System and is displayed for diagnosticpurposes.


2-27Voltage Input


Transferring Logged DataIf the LI-7550 is connectedto a network via Ethernet ora cellular modem, you cantransfer files and managedata on the USB drive froma networked computer.

The file transfer program isinstalled automatically withthe gas analyzer software.Launch it by clicking theDownload button.

To connect to an instru-ment, click Browse to viewa list of instruments on thenetwork. Select the instru-ment, click OK, enter the password (licor) and click Verify Connection. If yourinstrument is not listed, type the IP address in to the IP Address field.

Check the Save login information box if you want the file transfer program toremember this IP address and password the next time you start the program.

USB Drive Information displays the size of the USB drive, available memory, num-ber of .ghg files, number of flux results files, number of daily summary files, thenumber of files in the archive. When new files are transferred, they are then movedto the archive or deleted, depending on the Transfer Options selected.

Transfer Options are used to configure settings and other features:

l Desination: This is where the transferred files will be placed. Ideally, this will bea directory on your computer or a server. Or you can choose a cloud-based ser-vice such as a Dropbox directory on you computer.

l When to transfer: You can Transfer files daily at a scheduled time or Transferfiles now (click the start button).


Note: You can close the application to your system tray (close it, but choose No)so it continues running in the background. Also be sure your computer does notgo to sleep before the scheduled transfer.

l Files to transfer: Select Raw data files (.ghg, .data., metadata) to transfer all rawdata files. Select Flux Results to transfer SMARTFlux System results. Select DailySummaries to download a small summary of the flux results. Select Archivedfiles to copy the archives.Note: When you check a box a corresponding tab will be added to the box. Hereyou can choose which files you want to download.

l After transfer: You can choose Move files to the archive. This is useful if youwant to keep a copy of the files on the USB drive but you want them compressedto save space. You can Delete files from the instrument will remove them fromthe USB drive. Use this option if you want to clear space from the flash drive andyou have backed up the data elsewhere. You can also choose to Do nothing afterthe transfer.

After configuring the transfer and selecting files, click Start.

Tips for Automatic Data Transfer:

l Set the download to begin at 00:15 (1:15 am) if you are using SMARTFlux.That way all the logged files will be processed before the download begins.

l Close the application to your system tray to keep it running in the back-ground.

l Be sure the computer that runs the application is on and not in power savermode.

l Download files daily, if possible, to avoid long wait times for data transfer.

You can also use third-party applications to transfer data, such as WinSCP. In thiscase, use:

l Port: 22l Username: licorl Passord: licor


2-29Transferring Logged Data

Section 3. Running SMARTFluxWhen using SMARTFlux System with express settings, there really is nothing addi-tional for you to do beyond entering site information and configuring your sensors.But, when your site conditions or objectives require advanced settings, you will useEddyPro to create the SMARTFlux advanced configuration file. This section providesa detailed summary of the steps involved with configuring the SMARTFlux withAdvanced settings.

Express ProcessingEddyPro Express mode is the default configuration for the flux computation in theSMARTFlux System. Express settings are loaded automatically unless you specify anEddyPro Advanced configuration file. In most cases, EddyPro Express provides final,fully corrected and valid fluxes that can be directly used for further analysis. In afew special cases, however, Express fluxes may not be fully accurate and only serve adiagnostic purpose.

Automatic Variable SelectionIn standard EddyPro, even when running in Express mode, you still can select thevariables to be used in flux computation, in the Basic Settings > Select Items forflux computation section. More precisely, EddyPro provides default choices based onthe variables described in the metadata file (either embedded in .ghg files, or cre-ated in Project Creation > Metadata file editor), and you can keep these choices orpick other variables. For example, CO2 fluxes from the LI-7200RS can be calculatedfrom CO2 measurements available as either mixing ratio, mole fraction or numberdensity. If all of these measurements are available in the metadata file, thenEddyPro defaults to the mixing ratio, and you are allowed to either keep this choiceor pick one of the other two.

EddyPro defaults, and the order in which other viable variables are listed in thedrop-down menus, reflect best practices suggested by LI-COR and depend on the



deployed instrument(s). The exact same logic is used in SMARTFlux to select thevariables to be used when multiple choices are available. In particular:

l CO2/H2Omeasured by an LI-7200RS: The order of preference is (1) mixing ratio,(2) mole fraction and (3) number density

l CO2/H2Omeasured by an LI-7500RS: Only number density can be used for fluxcomputation

l CH4measured by an LI-7700: Only number density can be used for flux com-putation

l Air temperature and pressure: Precedence is given to measurements from anLI-7700 if available.

l Diagnostics flags: If available for the deployed instruments, diagnostic flags areused to filter out individual raw data based on diagnostic information.

SMARTFlux System Configuration StepsSMARTFlux Configuration mode is used to create an advanced configuration file forthe SMARTFlux System.


To use this mode, check the box, and proceed through EddyPro as you normallywould. The steps are summarized below:

1. Click the SMARTFlux Configuration box.

2. Select New Project or Open Project.

If you are creating a New Project and you do not intend to use planar-fit, automatictime-lag optimizations, or in situ spectral corrections:l Set the Raw Data Directory to a .ghg file with metadata that applies to your site

(see Creating an Advanced SmartFlux Configuration File with .ghg Files on page3-10).

l Select variables and set flags as desired.l Configure Advanced Settings (see Overview of Advanced Processing on page 3-5).If you are creating the SMARTFlux configuration file from an existing project:l Click Open Project and select the project.l Alter any settings that need to be changed.l Configure Advanced Settings (see Overview of Advanced Processing on page 3-5).If you are using planar-fit, automatic time-lag optimization, or in situ spectral cor-rections (see Using Planar Fit, In-situ Spectral Corrections and Timelag Optimization inSmartFlux on page 3-10 for details):l Select a planar-fit file that was generated by EddyPro using data from your site.l Select the automatic time-lag optimization file that was generated by EddyPro

using data from your site.l Select the in-situ spectral corretions file that was generated by EddyPro using

data from your site.3. Click Create Package in the upper right of EddyPro.


3-3SmartFlux System Configuration Steps


4. When prompted, name the package, select a directory and click Create.

The configuration file has a .smartflux extension.5. Upload the SMARTFlux configuration file to the SMARTFlux System.

See Loading a SmartFlux Configuration File on page 3-13.

Automatic Variable SelectionIn standard EddyPro, even when running in Express mode, you still can select thevariables to be used in flux computation, in the Basic Settings > Select Items forflux computation section. More precisely, EddyPro provides default choices based onthe variables described in the metadata file (either embedded in .ghg files, or cre-ated in Project Creation > Metadata file editor), and you can keep these choices orpick other variables. For example, CO2 fluxes from the LI-7200RS can be calculatedfrom CO2 measurements available as either mixing ratio, mole fraction or numberdensity. If all of these measurements are available in the metadata file, thenEddyPro defaults to the mixing ratio, and you are allowed to either keep this choiceor pick one of the other two.

EddyPro default settings, and the order in which other viable variables are listed inthe drop-down menus, reflect best practices suggested by LI-COR and depend onthe deployed instrument(s). The exact same logic is used in SMARTFlux to select thevariables to be used when multiple choices are available. In particular:

l CO2/H2Omeasured by an LI-7200RS: The order of preference is (1) mixing ratio,(2) mole fraction and (3) number density.

l CO2/H2Omeasured by an LI-7500RS: Only number density can be used for fluxcomputation.


l CH4measured by an LI-7700: Only number density can be used for flux com-putation.

l Air temperature and pressure: Precedence is given to measurements from anLI-7700 if available.

l Diagnostics flags: If available for the deployed instruments, diagnostic flags areused to filter out individual raw data based on diagnostic information.

Overview of Advanced ProcessingAdvanced Mode provides you with the high-level capabilities of the EddyProAdvanced, computing fully corrected flux results in real-time with the processingoptions of your choice.

The SMARTFlux configuration file, needed to run EddyPro in Advanced mode insidethe SMARTFlux System, is created in EddyPro 5 or higher. This, and subsequent ver-sions of EddyPro provide the capability to export a SMARTFlux configuration file,that can then be uploaded via the gas analyzer PC software. Complete doc-umentation is provided in the EddyPro help.

There are additional considerations if you use EddyPro Advanced in SMARTFlux.For many scenarios, you will simply need to configure the advanced settings as yousee best, and load the SMARTFlux configuration file into SMARTFlux following theinstruction provided hereafter.

However, if you wish to use a Planar-fit method for Axis Rotation, the AutomaticTime Lag Optimization option, or one of the in-situ spectral correction methods(Horst, 1997; Ibrom et al., 2007), you will need to process an existing data set from thesite in order to configure the parameters for these settings, as explained in Using Planar Fit,In-situ Spectral Corrections and Timelag Optimization in SmartFlux on page 3-10.


3-5Overview of Advanced Processing


Important: In order for the parameters to be valid, the site must not have under-gone any significant changes between the time when the existing data set wascollected and when the SMARTFlux System is deployed. The instrument con-figuration should remain unchanged during the sampling period if the settingsare to apply to the SMARTFlux System configuration file as well. For closed-pathsystems, the dataset used to optimize time lags and for the spectral assessmentmust refer to a period in which the sampling line did not undergo major modi-fications, such as replacement of tube or filters, change of the flow rate, etc.

When you create the configuration file, only the controls that can be configured forthe SMARTFlux System are enabled, and the other controls are disabled. Similarly toEddyPro Advanced and Express, some controls must be configured, while others areoptional.

Advanced Processing OptionsSimilarly to EddyPro Advanced and Express, some controls must be configured,while others are optional. When you create the SMARTFlux System configurationfile, only the controls that can be configured for SMARTFlux are enabled, and theother controls are disabled. In particular, you will find that:

1. The Project Creation page is not available.

This is because inside SMARTFlux, EddyPro does not need any of the informationthat is entered in the Project Creation page. The file type (LI-COR .ghg), the use ofmetadata (“embedded”) and the use of biomet data (“embedded”) are all predefinedsettings in SMARTFlux.

2. In Basic Settings:

A. The selection of Dataset dates is deactivated because SMARTFlux processes .ghgfiles one by one, as they are created by the gas analyzer software.

B. The Previous results directory is deactivated because this option is not applic-able to SMARTFlux.

C. The Flux averaging interval is deactivated because SMARTFlux operates on a pre-defined interval of 30 minutes. In SMARTFlux there is no option to calculatefluxes on any other time interval.

D. The Master Anemometer is deactivated because LI-COR eddy covariance sys-tems are designed around one only anemometer, which is detected auto-matically in SMARTFlux as the “master”.


3. In Advanced Settings > Processing Options, all processing options are active, and you canselect them as you would do in EddyPro.

4. In Advanced Settings > Processing Options, all processing options are active, and you canselect them as you would do in EddyPro.

The only exception are:A. The Planar Fit Settings... dialogue, which activates when the Planar fit or the

Planar fit with no velocity bias option is chosen as the Axis rotation for tilt cor-rection method, presents only the Planar fit file available option. If you want touse the planar fit method in SMARTFlux, you will have to load a previously cre-ated planar fit file at this time. Refer to Using Planar Fit, In-situ Spectral Cor-rections and Timelag Optimization in SmartFlux on page 3-10 for instruction howto create the planar fit file and more details on how to use it in SMARTFlux.

B. The Time lag Optimization Settings..., which activates when the Automatic timelag optimization option is chosen as a Time lag compensation method, onlygives the Time lag file available option. If you want to use the automatictimelag optimization option in SMARTFlux, you will have to load a previouslycreated timelag optimization file at this time. Refer to Using Planar Fit, In-situSpectral Corrections and Timelag Optimization in SmartFlux on page 3-10 forinstructions how to create the timelag optimization file and more details on


3-7Advanced Processing Options


how to use it in SMARTFlux.

5. In Advanced Settings > Spectral Corrections both low frequency and high frequency cor-rections are available.

However:A. In the Correction for low-pass filtering effects, the method by Fratini et al.

(2012) is deactivated, because this method requires an auxiliary file that is cur-rently not available in SMARTFlux.

B. If an in-situ method is selected (Horst 1997 or Ibrom et al., 2007), only theoption Spectral assessment file available is active, similar to the planar fit andtimelag optimization options discussed above. If you want to use one of thesein-situ methods in SMARTFlux, you will have to load a previously created spec-tral assessment file at this time. Refer to Using Planar Fit, In-situ Spectral Cor-rections and Timelag Optimization in SmartFlux on page 3-10 for instruction howto create the spectral assessment file and more details on how to use it inSMARTFlux.

6. In Advanced Settings > Statistical Analysis, all processing options are active, and you canselect them as you would do in EddyPro with no exceptions.

7. In Advanced Settings > Output Files, most options are active, with the following exceptions:

A. The SetMinimal, Set Typical and Set Thorough pre-selection buttons are deac-tivated, because those pre-selections do not apply completely to SMARTFlux.

B. The Full output file and related settings are deactivated because this file willalways be created by SMARTFlux in a predefined format.


C. The Ensemble averaged cospectra andmodels is unchecked and deactivated,because this output cannot be created in SMARTFlux, were .ghg files are pro-cessed one at a time. To create those outputs, use standard EddyPro instead.

D. All full length (co)spectra outputs are deactivated. These files occupy largeamounts of disk space and are thus not allowed in SMARTFlux. To obtain fulllength (co)spectra files, use standard EddyPro instead.

E. Processed raw data outputs are deactivated. These files occupy large amounts ofdisk space and are thus not allowed in SMARTFlux. To obtain those outputs, usestandard EddyPro instead.

Creating a SMARTFlux System Advanced ConfigurationFileYou need one 30-minute .ghg file from your system in order to create theSMARTFlux configuration file. You can create this file simply by configuring yourEC system and logging data until the system creates a .ghg file. This is required soyou can select the variables to use for flux calculations.

You can also customize the Advanced processing options and select the variablesyou prefer for computing fluxes. In this case, in Basic Settings simply select theRaw data directory where your raw data are stored, and EddyPro will automaticallypopulate the section Select Items for flux computation, as it usually does when usedin the standard mode.

At this point, select the variables, configure the flags, and set the processing optionsof your preference and simply click the Create File button visible on the right sideof the blue SMARTFlux ribbon. This will create a bundle with extension .smartflux

and save it in the selected output directory.

Creating an Advanced SMARTFlux Configuration Filewithout .ghg FilesIf you don’t have any .ghg files from the EC system for which you are going to usethe SMARTFlux System, you can customize the Advanced processing options, butyou will have to rely on EddyPro’s selection of variables to be used for flux com-putation, because at this stage you will have no means to indicate which variablesyou are going to collect and which ones you want to use for fluxes. See AutomaticVariable Selection on page 3-1 for more details on EddyPro default selections.


3-9Creating a SmartFlux System Advanced Configuration File


Once you have chosen the processing options of your preference, simply click onthe Create File button on the right side of the blue SMARTFlux ribbon. This will cre-ate a bundle with extension .smartflux and save it in the selected output directory.

Creating an Advanced SMARTFlux Configuration Filewith .ghg FilesIf you have at least one .ghg file from the EC system for which you are going touse SMARTFlux, you can customize the Advanced processing options, and select thevariables you prefer for computing fluxes on-the-fly. In this case, in Basic Settings

simply select the Raw data directory where your raw data are stored, and EddyProwill automatically populate the section Select Items for flux computation, as it usu-ally does when used in the standard mode.

At this point, select the variables, configure the flags, and set the processing optionsof your preference and simply click the Create File button visible on the right sideof the blue SMARTFlux ribbon. This will create a bundle with extension .smartflux

and save it in the selected output directory.

Using Planar Fit, In-situ Spectral Corrections andTimelag Optimization in SMARTFluxIn order to use planar-fit, in-situ spectral corrections or timelag optimization in theSMARTFlux System, EddyPro needs to access the respective “planar_fit”, “spectral_assessment” and “timelag_optimization” files, referred to as “additional con-figuration files” hereafter. These files contain summaries of calculations performedon relatively large datasets (Table 3-1 on the facing page) and that apply also to datato be collected in the future.

For example, you can use three-months of data to calculate a spectral assessment,and then use this spectral assessment that is summarized in a short text file, to cor-rect fluxes calculated from data collected after those three months, if the system con-figuration didn’t change to such an extent, that the spectral assessment is no longerrepresentative. Similar considerations apply to the planar fit and the timelag optim-ization procedures. Refer to EddyPro documentation for more details on when andhow to use these three advanced procedures.


The additional configuration files are created by EddyPro (3.0 and above), whenused in the standard desktop mode. If you have been running your EC system – forwhich you intend to user SMARTFlux—for some time, you may already have createdone or more of these files, or you may have a .ghg dataset suitable for creatingthem, if the corresponding implementation is deemed necessary to calculate accur-ate fluxes (again, refer to EddyPro documentation to learn more about when it issuggested to use these options). If you do not have previously collected .ghg files,then you will need to run the system for a suitable amount of time (for exampleusing SMARTFlux in Express mode), then use EddyPro in desktop mode to createthe additional configuration files of your interest, and then provide them toSMARTFlux as explained below.

EddyPro Advanced Setting Recommended Data-set

Planar Fit Settings 2 weeks minimum; < 2months

Time Lag Optimization 1 to 2 months or more

Spectral Corrections, Assessment of high frequencyattenuation

1 month or more

Table 3-1. Recommended dataset durations for Advanced settings.

Thus, assuming that you have a sufficiently long .ghg dataset (Table 3-1 above), theprocedure to correctly configure SMARTFlux to use planar-fit, in-situ spectral cor-rections or timelag optimization is illustrated here, using the in-situ spectral cor-rections as an example. Analogous procedures shall be followed for the planar-fit orthe timelag optimization.

1. Open EddyPro (5.0 or above recommended) in normal desktop mode and complete the ProjectCreation and Basic Settings pages as usual (refer to EddyPro documentation if needed).

In the Advanced Settings > Spectral Corrections, configure Corrections for low-pass filtering effects to use one of the in-situ methods, i.e. Horst (1997), Ibrom etal. (2007) or Fratini et al. (2012). In the same page, customize the settings toinstruct EddyPro to use the dataset of your choice and to filter data appropriately, soas to obtain a sound assessment of spectral attenuations. Click Run and when this iscompleted, locate the spectral assessment file (it contains the string “spectral_assess-ment” in the file name) in the subdirectory \spectral_analysis that you will findinside the selected Output folder. This is the file that you will use for SMARTFlux.

2. Open EddyPro (5.0 or above) in SMARTFlux Setup Mode.


3-11Using Planar Fit, In-situ Spectral Corrections and Timelag Optimization in SmartFlux


Configure everything as explained in the previous sections. In the Advanced Set-tings > Spectral Corrections, configure Corrections for low-pass filtering effects touse one of the in-situ methods among Horst (1997) and Ibrom et al. (2007) (themethod of Fratini et al. (2012) is currently not usable in SMARTFlux). In the “Spec-tral assessment file available” entry, select the spectral assessment file createdearlier. Then proceed normally and when done, click on the Create File button tocreate the .smartflux bundle, as explained above.An analogous procedure can be used to create and use the planar fit and thetimelag optimization configuration files.


Loading a SMARTFlux Configuration FileNote: EddyPro Express settings are loaded by default so you only need to load aconfiguration file if you use EddyPro Advanced settings.

To connect with a SMARTFlux System, see Connecting with the SmartFlux System onpage 2-24. To load an EddyPro Advanced configuration file:

1. Create the SMARTFlux configuration file (see Overview of Advanced Processing on page 3-5)

2. Open the SMARTFlux System dialog.

3. Select the Processing Options tab, and click the Upload Advanced File button. Read thewarning dialog.

4. Browse to the file created in EddyPro (extension *.smartflux) and select it.

After loading the file, the SMARTFlux System will compute flux results based uponthe defined Advanced settings. Be sure to turn on datalogging first as described inBegin Logging Data on page 2-25.


3-13Loading a SmartFlux Configuration File


SMARTFlux Results FilesThe SMARTFlux System writes EddyPro results files to the USB flash drive in theLI-7550. In addition to the raw .ghg files (including any .data and .metadata files),you can retrieve flux results files, daily summary files, and archived files.

Flux ResultsThese are the output files from EddyPro. They follow a format typical of EddyProoutputs, as described in detail in the EddyPro help(http://www.licor.com/env/help/eddypro/index.html).

Daily SummariesThese logged data summaries, typically named something like YYYY-MM-DD_AIU-xxxx_Summary, include the high-speed data logged in the LI-7550 analyzer interfaceunit. These are the variables selected in Entering CO2/H2O Analyzer Information onpage 2-16.

The EddyPro summaries, typically named somethings like YYYY-MM-DD_EP-Sum-mary, include the half-hour eddy covariance flux results. This file is created at theend of each day by collecting the results of each 30-minute file and placing them ina row. The variables included in this file are specified in EddyPro automatically ifyou select Basic processing or manually if you select Advanced processing (seeAdvanced Processing Options on page 3-6).

Data BackupAn emergency data backup archive is stored on the MicroSD card, which may beuseful if data are lost for any reason. The backup files are limited to the latest filesrecorded—the oldest files are overwritten when the MicroSD card gets full. Do notdepend upon the MicroSD card as a primary backup for your data, however,because old files are automatically overwritten by new ones.


http://licor.com/env/help/eddypro6/index.htm


Software UpdatesWe recommend running the most current software at all times, including both theembedded instrument software for the LI-7500RS/LI-7200RS and the PC applic-ation. You can acquire the software from the LI-COR® web site: www.licor.-com/env/support

On the support web site, select your instrument, then select "Software." Downloadboth the Instrument (Embedded) Software and the Windows Interface Software.

Embedded Instrument SoftwareTo update the embedded instrument software:

1. Connect your instrument to the gas analyzer using an Ethernet cable, as shown. Power on the gasanalyzer.

Important: There must be a USB drive in the LI-7550 USB port.

The Instrument (Embedded) Software is a zipped file named something similar toLI-7xxx_embedded-7.0. Unzip the files and save them.

2. Double-click the file called update7x00.


http://www.licor.com/env/support

http://www.licor.com/env/support


3. Click Browse... and select the instrument from the list. You may need to allow the application topass through your computer's firewall.

4. Select the gas analyzer from the list and clickUpdate Software.

The update will take about 5 minutes.

Important: Do not close the software, let your PC go to sleep, or power off the instru-ment during the update process. The software will notify you when the update iscomplete. If the update fails for any reason, repeat steps 2 and 3.

If you are updating from embedded version 4.x.x or earlier, you must also run theFPGA update. To check if this update is necessary click the Check FPGA button.Note: Do not check the FPGA version until you update the system software.If the FPGA update is needed the Update FPGA button will become enabled in theapplication. The update takes approximately 8 minutes.

Important: Do not close the software or reset the instrument while the update is takingplace. The software will notify you once the FPGA programming is finished.

5. After updating the software, check all your instrument configuration settings. The instrumentshould retain all settings through a software update, but in unusual circumstances, some settingsmay be lost.

Troubleshooting: Getting an update error? There must be a USB drive installedin the LI-7550 USB port before you can update. Also, if the drive is inserted forthe first time, the instrument will take a few minutes to connect with the drive.

PC Software UpdateTo update the PC Desktop Software:

1. The PC Desktop Software is an executable file named something similar to LI-7xxx_win-7.0.Double click to launch the installer.

2. Follow the Windows Installation wizard to install the application.


SMARTFlux Software UpdatePeriodically LI-COR® will release updated software for SMARTFlux System. Softwareupdates will include bug fixes, new features, or performance improvements. Werecommend that you keep the software on your instruments up-to-date.

Check the Software VersionThe SMARTFlux System software version and IP Address are displayed in the Con-nect window in the gas analyzer software.


4-3SmartFlux Software Update


Update the SoftwareYou will be notified by email if and when we release a critical software update.Download updated software from the technical support website:http://www.licor.com/env/support/

On the support web site, select your instrument, then select "Software," and savethe update package to your computer.

To update the software:

1. Unzip the compressed update package and double click the file called "flux updater.exe".

Each SMARTFlux System that is on your network will be visible in the Flux Updaterwindow.

2. Select the module you want to update and clickUpdate Firmware.

The updater will load the new system files. This process takes about 30 seconds to aminute to complete. Do not power off the device while it is updating.

3. After the update is complete, you can verify the software version in the updater or in the gas ana-lyzer software (see Check the Software Version on the previous page).

EddyPro Software UpdateTypically, EddyPro® Software will notify you automatically if a software update isavailable. You can also check for updates. EddyPro 5 or greater is required to usethe SMARTFlux System.

To update EddyPro:

In EddyPro® Software, click Help > Check for Updates... (or press Ctrl + U).EddyPro will check for updates and ask you to download the update.

Otherwise, you can go tohttp://www.licor.com/env/products/eddy_covariance/software.html and downloadthe newest version.


Section 5. TroubleshootingThe SMARTFlux System relies upon both a properly-functioning sonic anemometerand LI-7500RS or LI-7200RS. If the errors seem related to the performance of thegas analyzer, it may be helpful to ensure that each component of the system is work-ing properly.

SMARTFlux System powers on or off unpredictablyl Check the power supply connections along the system power supply and correct

any faulty connections.l Check the connections on the SMARTFlux System wiring harness and tighten

any loose fittings.

SMARTFlux System not connectedl Check the LED lights on the Ethernet cable connections. If they are flashing,

that indicates that SMARTFlux System is communicating with the LI-7550.l Restart SMARTFlux System by cycling the power (unplug and then plug in the

power cable from the SMARTFlux System unit).

SMARTFlux System results are not identical toEddyPro desktop results

l Configuration settings are not the same. Review the configurations and ensurethat they are identical.

l North Offset/Magnetic declination are set differently. See Important note on NorthOffset: on page 2-10.

l Software versions not identical. Although we attempt to test every possible scen-ario, there are cases that may lead to slight offsets in flux results. We fix bugs asthey are identified. Ensure that you are running the most up-to-date version of


Section 5. Troubleshooting

EddyPro and SMARTFlux System software. Contact LI-COR® technical support([email protected]) if you are unable to resolve the issue.


Appendix A. SpecificationsData Storage: 8 GB or 16 GB removable micro SD card with custom boot loader

(contact LI-COR® for a replacement, not user servicable).1Data Communication: Ethernet, TCP/IPOperating Temperature Range:

SwissBit MicroSD card; 8 GB: -25 to 85 °CDelkin MicroSD card; 8 GB or 16 GB: -40 to 85 °C

Relative Humidity Range:0 to 95% (non-condensing)Input Voltage: 10 to 30VDC, 2.1 WSystem Input Current (total): 150 mA (190 mA max) @ 12VDCDimensions w/ bracket (LxWxH): 8.4 in x 3.75 in x 0.95 in (213.4 mm x 95.25

mm x 24 mm)GPS Antenna Diameter: 2.4 in (61 mm)GPS Accuracy:

GPS Standard Positioning Service: <15m; 95% typicalWAAS: <3 m; 95% typical

Weight: 0.5 lbs. (0.23 kg)

1Specifications subject to change without notice.

A-1The SMARTFlux® System

Appendix A. Specifications

A-2 The SMARTFlux® System

Appendix B. WarrantyEach LI-COR, inc. instrument is warranted by LI-COR, inc. to be free from defectsin material and workmanship; however, LI-COR, inc.'s sole obligation under thiswarranty shall be to repair or replace any part of the instrument which LI-COR,inc.'s examination discloses to have been defective in material or workmanshipwithout charge and only under the following conditions, which are:

1. The defects are called to the attention of LI-COR, inc. in Lincoln, Nebraska, in writing within oneyear after the shipping date of the instrument.

2. The instrument has not been maintained, repaired or altered by anyone who was not approved byLI-COR, inc.

3. The instrument was used in the normal, proper and ordinary manner and has not been abused,altered, misused, neglected, involved in an accident or damaged by act of God or other casualty.

4. The purchaser, whether it is a DISTRIBUTOR or direct customer of LI-COR or a DISTRIBUTOR'S cus-tomer, packs and ships or delivers the instrument to LI-COR, inc. at LI-COR inc.'s factory in Lincoln,Nebraska, U.S.A. within 30 days after LI-COR, inc. has received written notice of the defect.Unless other arrangements have been made in writing, transportation to LI-COR, inc. (by air unlessotherwise authorized by LI-COR, inc.) is at customer expense.

5. No-charge repair parts may be sent at LI-COR, inc.'s sole discretion to the purchaser for install-ation by purchaser.

6. LI-COR, inc.'s liability is limited to repair or replace any part of the instrument without charge ifLI-COR, inc.'s examination disclosed that part to have been defective in material or workmanship.

There are no warranties, express or implied, including but not limited to anyimplied warranty of merchantability of fitness for a particular purpose onunderwater cables or on expendables such as batteries, lamps, thermocouples,and calibrations.

Other than the obligation of LI-COR, inc. expressly set forth herein, LI-COR,inc. disclaims all warranties of merchantability or fitness for a particular pur-pose. The foregoing constitutes LI-COR, inc.'s sole obligation and liability withrespect to damages resulting from the use or performance of the instrument

B-1The SMARTFlux® System

Appendix B. Warranty

and in no event shall LI-COR, inc. or its representatives be liable for damagesbeyond the price paid for the instrument, or for direct, incidental or con-sequential damages.

The laws of some locations may not allow the exclusion or limitation on impliedwarranties or on incidental or consequential damaged, so the limitations hereinmay not apply directly. This warranty gives you specific legal rights, and you mayalready have other rights which vary from state to state. All warranties that apply,whether included by this contract or by law, are limited to the time period of thiswarranty which is a twelve-month period commencing from the date the instru-ment is shipped to a user who is a customer or eighteen months from the date ofshipment to LI-COR, inc.'s authorized distributor, whichever is earlier.

This warranty supersedes all warranties for products purchased prior to June 1,1984, unless this warranty is later superseded. To the extent not superseded by theterms of any extended warranty, the terms and conditions of LI-COR’s Warrantystill apply.

DISTRIBUTOR or the DISTRIBUTOR's customers may ship the instruments dir-ectly to LI-COR if they are unable to repair the instrument themselves even thoughthe DISTRIBUTOR has been approved for making such repairs and has agreed withthe customer to make such repairs as covered by this limited warranty.

Further information concerning this warranty may be obtained by writing or tele-phoning Warranty manager at LI-COR, inc.

B-2 The SMARTFlux® System

Index

AAdvanced Eddy Covariance Flux Pro-

cessing, 3-10Air Pressure, 3-5Anemometer, See Sonic Anemometer

BBackup, 3-14Biomet

about, 2-22connecting, 2-22

CClock

GPS, 2-5Compression, 2-6Connecting

Biomet system, 2-22LI-7700, 2-19SMARTFlux, 1-7

DData

logging, 2-6Data Backup, 3-14Diagnostic Flags, 3-5Diagnostics

voltage in, 2-27

EEastward Separation, 2-17, 2-20Eddy Covariance

CH4 Log Values, 2-21

CO2/H2O Log Values, 2-18gas analyzer information, 2-16instruments, 2-4logging datasets, 2-6Site Setup, 2-4sonic anemometer inputs, 2-10

EddyProadvanced mode, 3-5

Ethernet Cableconnection, 1-2, 1-7, 2-22installing, 1-6part number, 1-2

GGHG Software

update, 4-1GPS

antenna, 1-1, 1-2, 1-2clock, 1-1, 2-5format, 2-8location, 1-1

IIn-situ Spectral Corrections, 3-10Installing SMARTFlux, 1-4IP Address

SMARTFlux, 4-3

LLI-7700

connecting, 2-19Logging Data

important note, 2-25start, 2-25

C-1Index

MMeteorological measurements, 2-22MicroSD Card, 1-1, 1-2Mixing Ratio, 3-4Mole Fraction, 3-4

NNorthward Separation, 2-17, 2-20Number Density, 3-4

PPlanar Fit, 3-10Power

cycling, 5-1Power On, 1-6PowerWiring Harness

connection, 1-2installing, 1-5part number, 1-2

PTP Clock, 2-5

RResults Files, 3-14

SSensor Separation, 2-17, 2-20Site Information

entering, 2-7SMARTFlux

advanved mode, 3-5clock, 2-5configuration file, 3-13connect, 2-24connecting hardware, 1-6connecting software, 1-7IP Address, 4-3

Software UpdateEddyPro, 4-4GHG, 4-1LI-7200RS, 4-1LI-7500RS, 4-1SMARTFlux, 4-3

Sonic Anemometerinputs, 2-12

Sonic Anemometer Information, 2-9Spectral Corrections, 3-10Sutron, 2-22

TTimelag, 3-10

UUSB

terminal, 1-2

VVariables

selection, 3-4Vertical Separation, 2-17, 2-20Voltage

system, 2-27

Index

C-2The SMARTFlux® System

LI-COR Biosciences

Global Headquarters

4647 Superior StreetLincoln, Nebraska 68504Phone: +1-402-467-3576Toll free: 800-447-3576Fax: [email protected] • [email protected] • www.licor.com/env

LI-COR GmbH, GermanyServing Andorra, Albania, Cyprus, Estonia, Germany, Iceland, Latvia, Lithuania, Liechtenstein, Malta, Moldova, Monaco, San Marino, Ukraine, and Vatican City.LI-COR Biosciences GmbHSiemensstraße 25A61352 Bad HomburgGermanyPhone: +49 (0) 6172 17 17 771Fax: +49 (0) 6172 17 17 [email protected] • [email protected]

LI-COR Ltd., United KingdomServing Denmark, Finland, Ireland, Norway, Sweden, and UK.LI-COR Biosciences UK Ltd.St. John’s Innovation CentreCowley RoadCambridgeCB4 0WSUnited KingdomPhone: +44 (0) 1223 422102Fax: +44 (0) 1223 [email protected] • [email protected]

LI-COR Distributor Network: www.licor.com/env/distributors

Regional Offices

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