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LI-COR LI-6800 Manual

Soil co2 flux chamber
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LI-6800
Soil CO 2 Flux
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  • Page 1 Using the LI-6800 Soil CO 2 Flux Chamber...
  • Page 3 Using the LI-6800 Soil CO Flux Chamber LI-COR Biosciences 4647 Superior Street Lincoln, Nebraska 68504 Phone: +1-402-467-3576 Toll free: 800-447-3576 (U.S. and Canada) envsales@licor.com Regional Offices LI-COR Biosciences GmbH Siemensstraße 25A 61352 Bad Homburg Germany Phone: +49 (0) 6172 17 17 771 envsales-gmbh@licor.com...
  • Page 4 LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. LI-COR shall not be held liable for errors contained herein or for incidental or consequential damages in connection with the furnishing, performance, or use of this material.
  • Page 5 Notes on Safety This LI-COR product has been designed to be safe when operated in the manner described in this manual. The safety of this product cannot be assured if the product is used in any other way than is specified in this manual. The product is intended to be used by qualified personnel.

  • Page 7: Table Of Contents

    Contents Section 1. Introduction to the LI-6800 soil chamber What's what Soil CO2 flux chamber Head mounting bracket Stevens HydraProbe Custom chamber adapter block Soil collars Accessories kit Useful software Bluestem™ OS SoilFluxPro™ Software Introduction to soil gas flux measurements...
  • Page 8 Section 4. Soil variables and constants The SoilConst group The SoilConfig group The SoilData group The SoilComp2 group Section 5. Troubleshooting and maintenance Identifying an issue Bellows pump runs intermittently after the chamber opens or closes Chamber will not open or close, or it opens or closes very slowly Noisy data High initial CO2 concentrations Low flow rate...

  • Page 9: Section 1. Introduction To The Li-6800 Soil Chamber

    Section 1. Introduction to the LI-6800 soil chamber The LI-6800 Portable Photosynthesis System can be used to measure CO efflux from soils when outfitted with the soil CO flux chamber. Here we describe the components of the chamber and the theory of the measurements.

  • Page 10: What's What

    6800 head connector labeled LS. There is also a dock where you can place the soil probe when it is not in use. Head mounting bracket The chamber has a removable mounting bracket that is used to attach the LI-6800 Part number: 9968-285 head to the chamber.

  • Page 11: Soil Collars

    6581-044 installed at the measurement site at least 6 hours prior to measurements (24 or more hours is better). Additional collars can be purchased from LI-COR or made in a shop if you have access to suitable materials. Accessories kit...

  • Page 12: Useful Software

    . The following apps are available free of charge for LI-COR customers: Software Bluestem™ OS Bluestem Operating System runs on the LI-6800. Both the LI-6800 console and head need to run software version 1.3 or newer in order to use the soil CO flux chamber.
  • Page 13 Soil collars, which, after installation, ensure consistency between samples. In contrast with the LI-6800 leaf chambers, which are an open gas exchange sys- tem, the soil CO flux chamber is a closed system. Instead of sample and reference gas analyzers, the LI-6800 uses the reference analyzer in this configuration.

  • Page 14: The Measurement Cycle

    Section 1. Introduction to the LI-6800 soil chamber The measurement cycle When the chamber is placed on a soil collar it will remain open until the meas- urement is started. When the measurement is started, the bellows pump closes the chamber.

  • Page 15: Theory And Equation Summary

    Section 1. Introduction to the LI-6800 soil chamber Theory and equation summary Soil CO flux (F) is computed with the following equation: where V is chamber volume (cm ), P is atmospheric pressure (kPa), W is the water mole fraction in the chamber (mmol mol ), R is the gas constant (8.314 J K...
  • Page 16 Section 1. Introduction to the LI-6800 soil chamber , the flux at t = t , is thus: and flux (F ) at any other target concentration (near C' ) can be computed by target solving equation 1-3 for t such that C' = C'...

  • Page 17: Section 2. Using The Chamber

    In this section we describe how to use the LI-6800 Soil CO Flux Chamber. The LI-6800 console must be running Bluestem OS version 1.3 or newer to use the soil chamber. If you don't have the current software, go to www.licor.com/env/support and download the latest software for the instrument.
  • Page 18 Each tube connects to a corresponding connector on the chamber. Attach the chamber cable to the connector on the head. Remove the connector cover to access the connectors. Reinstall the cover after con- necting the cable. Using the LI-6800 Soil CO₂ Flux Chamber...
  • Page 19 Now you are ready to power on the LI-6800 system. Figure 2-1. The assembled chamber will have two tubes from the LI-6800 head. The cable connects to the terminal on the head.

  • Page 20: Connecting Soil Sensors

    SDI-12 communication protocol, and no configuration is necessary. Sim- ply connect the cable and power on the LI-6800. The cable connector has a mark- ing that faces up and a key that must be aligned before the connector can be tightened.

  • Page 21: Installing Soil Collars

    Section 2. Using the chamber Check the box called and enter the offset in the Using 9968-162 T/C Adapter(s) appropriate field. If the measured value is below the actual temperature, enter a pos- itive number; if the measured value is above the actual temperature, enter a neg- ative number.

  • Page 22: Insertion Depth

    3 cm, but with greater extension there is increased shading and perturbation of air movement. Over the long term, these perturbations could result in changes of evaporation rate, soil temperature, and soil moisture. Using the LI-6800 Soil CO₂ Flux Chamber...

  • Page 23: Measuring The Chamber Offset

    Section 2. Using the chamber Measuring the chamber offset The chamber offset is used to determine the volume of air inside the soil collar, which is in turn used to calculate the total system volume. The total system volume is an important part of the flux calculation, so it should be determined as accurately as possible.

  • Page 24: Overview Of The Software

    Section 2. Using the chamber Overview of the software When the 6800-19 Custom Chamber block is detected by the LI-6800 head, one of the computational options presented is . Select this option to power on 6800-09 Soil the light source connector in the head, into which the soil chamber should be plugged;...
  • Page 25 Section 2. Using the chamber have check boxes that, if checked, simplify your choices to settings that are appro- priate for the 6800-19 chamber. If unchecked you can alter other settings, if you deem necessary. are computational constants used in the flux calculation. These can Constants be found in the Data Dictionary under the group called SoilConst...
  • Page 26 The purpose of the flux estimates is to help you know if the measurement is suf- ficiently long enough, or perhaps too long. Basically, if the estimates are still chan- ging significantly by the end of the repetition, the repetition duration is not long enough. 2-10 Using the LI-6800 Soil CO₂ Flux Chamber...
  • Page 27 Figure 2-4. Results after 3 out of 4 repetitions are completed. Performing a soil flux measurement does not require a normal LI-6800 log file to be open. If one is open, then at the end of each repetition, a log will happen auto-...
  • Page 28 Section 2. Using the chamber Figure 2-5. In the page, you can examine all of the repetitions together. Results 2-12 Using the LI-6800 Soil CO₂ Flux Chamber...
  • Page 29 Section 2. Using the chamber Soil tab Every soil measurement is stored in a file (whether or not a normal LI-6800 .json data file is open) in , in a folder named for the day on /home/licor/logs/soil/ which the measurement occurred. Each measurement has a unique number that increments each time.
  • Page 30 Section 2. Using the chamber 2-14 Using the LI-6800 Soil CO₂ Flux Chamber...

  • Page 31: Section 3. Measurement Tutorial

    Preparations Prior to conducting your first measurement, consider the following: Install the soil chamber on the LI-6800 head and assemble the system. Install soil collars at least 6 hours prior to the first measurement (24 or more hours is better).
  • Page 32 Whether you are using a Stevens HydraProbe or another soil temperature probe, press it into the soil near the collar. Start the measurement. Under , tap . During a measurement, the LI-6800 displays both Measure Flux Start C' and estimates of F as a function of time. C is plotted every 0.5 seconds and...

  • Page 33: Logging Soil Co2 Flux Data In A Standard File

    Section 3. Measurement tutorial When the measurement is complete a curve is fit and displayed, and the flux estim- ate is given. Logging soil CO flux data in a standard file A soil gas exchange measurement is always captured in a .json file. If you have a normal log file open, a record is logged there after each repetition.

  • Page 34: Enabling Prompt On Log

    Figure 3-1. Part of a normal LI-6800 log file, viewed in a spreadsheet. You can manually log at any time by pressing the log button, and the LI-6800 will log the latest values of the SoilConst, SoilConfig, and SoilComp2 records. Manual logging is independent of the state of a soil measurement.

  • Page 35: Viewing Results

    Section 3. Measurement tutorial Viewing results After you've completed a measurement you can review the results on the LI-6800. Under the tab, , you see a list of all files logged. Select the one Soil Flux Soil Files you want to view and then tap .
  • Page 36 Section 3. Measurement tutorial Using the LI-6800 Soil CO₂ Flux Chamber...

  • Page 37: Section 4. Soil Variables And Constants

    Table 4-2. Soil measurement settings. Meas Description Rep duration Time (s) chamber is closed for each repetition. Dead band Delay (s) after closing to begin computations. # Reps Number of repetitions per measurement. Using the LI-6800 Soil CO₂ Flux Chamber...

  • Page 38: The Soildata Group

    Value comes from Pa in group Meas Computed RH in the soil chamber. dCdry/dt Rate of change of Cdry over previous 2 seconds F-to An estimate of what the final flux will be at time t Using the LI-6800 Soil CO₂ Flux Chamber...

  • Page 39: The Soilcomp2 Group

    Section 4. Soil variables and constants group SoilComp2 When a rep is finished, a record is published. SoilComp2 Table 4-4. SoilComp2 record published at the end of a repetition. Label Description MeasNum Measurement number. RepNum Repetition number. F_target Flux computed Cdry = C_target. F_to Flux computed at Cdry = C_o.
  • Page 40 Section 4. Soil variables and constants Using the LI-6800 Soil CO₂ Flux Chamber...

  • Page 41: Section 5. Troubleshooting And Maintenance

    In this section we describe how to identify problems with the chamber and how to solve them. The troubleshooting in this section is specific to the soil CO flux chamber. You may need to refer to the LI-6800 instruction manual for additional troubleshooting and maintenance procedures. Identifying an issue Here we begin by describing some basic issues related to the operation of the instru- ment and the data that it provides.

  • Page 42: Noisy Data

    Try to get the water out as soon as possible, and consider calling technical support. Bad pump? If you cannot hear the pump run, it may have failed. In this case, con- tact technical support to learn how to replace the pump. Using the LI-6800 Soil CO₂ Flux Chamber...

  • Page 43: Replacing The Bellows Pump Air Filter

    Section 5. Troubleshooting and maintenance Replacing the bellows pump air filter There is one air filter in the pneumatic circuit that drives the bellows. The filter can become clogged, which will affect the performance of the pump. Do not run the pump if you think the filter is clogged.

  • Page 44: Maintaining The Gaskets

    The other two gaskets are on the bot- tom of the chamber, beneath the metal flange that surrounds the soil collar. These two gaskets, especially the white foam gasket, may need to be replaced more reg- ularly. Using the LI-6800 Soil CO₂ Flux Chamber...

  • Page 45: Foam Gasket

    Section 5. Troubleshooting and maintenance Foam gasket The foam gasket is the most easily damaged. Inspect the foam gasket before you start making measurements each day. If the foam is torn or compressed, or if it appears as though the foam will not make a good seal you should replace it. You do not need to remove the gasket plate when replacing the foam gasket.
  • Page 46 Remove the adhesive backing from the new gasket and install the gasket around the bottom of the chamber bowl. Trim the ends of the gasket so both sides are touching, then apply Loctite to glue the ends together. Reassemble the chamber. Using the LI-6800 Soil CO₂ Flux Chamber...

  • Page 47: Appendix A. Specifications

    Operating range: -20 to 45 °C Accuracy: ±0.5 °C over 0 °C to 70 °C Soil Collars Inside diameter: 20.32 cm Outside diameter: 21.34 cm Height: 11.43 cm 21.34 cm (8.4") outside diameter 11.43 cm (4.5") 24° Using the LI-6800 Soil CO₂ Flux Chamber...
  • Page 48 Appendix A. Specifications Using the LI-6800 Soil CO₂ Flux Chamber...

  • Page 49: Appendix B. Warranty

    Inc.'s examination discloses to have been defective in material or workmanship without charge and only under the following conditions, which are: The defects are called to the attention of LI-COR, Inc. in Lincoln, Nebraska, in writing within one year after the shipping date of the instrument.
  • Page 50 The foregoing constitutes LI-COR, Inc.'s sole obligation and liability with respect to damages resulting from the use or performance of the instrument and in no event shall LI-COR, Inc. or its representatives be liable for damages beyond the price paid for the instrument, or for direct, incidental or con- sequential damages.
  • Page 52 Regional Offices LI-COR Biosciences GmbH Siemensstraße 25A 61352 Bad Homburg Germany Phone: +49 (0) 6172 17 17 771 envsales-gmbh@licor.com LI-COR Biosciences UK Ltd. St. John’s Innovation Centre Cowley Road Cambridge CB4 0WS United Kingdom Phone: +44 (0) 1223 422102 envsales-UK@licor.com LI-COR Distributor Network: www.licor.com/env/distributors...

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