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LI-COR 6400-09 Instruction Manual

Soil co2 flux chamber
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6400-09
Soil CO
Flux Chamber
2
Instruction Manual
Publication No. 9710-119
October, 1997
LI-COR, inc.
Environmental Division
4421 Superior Street
P.O. Box 4425
Lincoln, NE 68504 USA
Telephone: 402-467-3576
FAX: 402-467-2819
Toll-free 1-800-447-3576 (U.S. & Canada)
e-mail: envsales@env.licor.com
URL: http://www.licor.com
© Copyright 1997, LI-COR, Lincoln, Nebraska USA

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  • Page 1 Instruction Manual Publication No. 9710-119 October, 1997 LI-COR, inc. Environmental Division 4421 Superior Street P.O. Box 4425 Lincoln, NE 68504 USA Telephone: 402-467-3576 FAX: 402-467-2819 Toll-free 1-800-447-3576 (U.S. & Canada) e-mail: envsales@env.licor.com URL: http://www.licor.com © Copyright 1997, LI-COR, Lincoln, Nebraska USA...
  • Page 2 NOTICE The information contained in this document is subject to change without notice. LI-COR MAKES NO WARRANTY OF ANY KIND WITH REGARD TO THIS MATERIAL, INCLUDING, BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. LI-COR shall not be liable for errors contained herein or for incidental or consequential damages in connection with the furnishing, performance, or use of this material.

  • Page 3: Table Of Contents

    Precautions ..................1-5 Reference ................... 1-5 Section 2. Attaching the Soil Chamber General Description .................. 2-1 Attaching the Sensor Head to the 6400-09 ..........2-3 Section 3. Software Configuring OPEN for Soil Measurements ..........3-1 Creating a Soil Chamber Configuration ..........3-1 Implementing the Soil Chamber Configuration ........
  • Page 4 Section 5. Maintenance Spare Parts Kit ..................5-1 Soil Temperature Probe ................5-1 Making Soil Collars .................. 5-2 Zeroing the IRGAs..................5-3 Zeroing the IRGA While Attached to the Soil CO Flux Chamber .. 5-3 Setting the IRGA Span ..............5-4 Section 6.

  • Page 5: Section 1. General Information

    Soil water evaporation and heating of the air in the chamber head space also induces pressure increases in an unvented chamber. The 6400-09 Soil CO Flux Chamber is vented so that pressures inside and outside the chamber are in a dynamic equilibrium.
  • Page 6 Section 1 the closed system down below the ambient concentration. The scrubber is turned off, and soil CO flux causes the CO concentration in the chamber headspace to rise (Figure 1-2). Data are logged while the CO concentration rises through the ambient level. The software then computes the flux appropriate for the ambient concentration.
  • Page 7 Section 1 General Information...
  • Page 8 Section 1 Pump on ambient Pump off Time Fluxes computed dring the measurement phase of each cycle. Final answer Chamber CO Figure 1-3. (A). Time series of a measurement cycle. Pumping reduced CO air into the chamber brings the CO below ambient.

  • Page 9: Precautions

    If measurements are made on bare soil with no canopy, variation in the measured flux can occur due to dynamic pressure fluctuations at the pressure vent outlet caused by wind effects. The vent on the 6400-09 is shielded to minimize direct wind effects, but you may wish to shield the entire chamber from the wind.

  • Page 11: Section 2. Attaching The Soil Chamber

    Attaching the Soil Chamber General Description Figure 2-1 shows an assembled 6400-09, and Figure 2-2 is an exploded diagram showing the parts of the 6400-09 CO Flux Chamber. Some of the individual parts are described in more detail in Section 5. Figure 2-2 also contains a detailed parts list should you need to order individual parts.
  • Page 12 Section 2 Parts List Description Part # Fan Inlet Duct Hose Barbs 300-02547 Soil Chamber Adapter Manifold O-rings Small 192-02597 (2) Larger 192-00225 (2) Largest 192-02889 (1) Radiation Shield 6564-171 Pressure Relief Fitting 300-02561 Mounting Plate Hose Barb (to Air Supply Manifold #15) 300-02547 Hose Barb (open) 300-00567...

  • Page 13: Attaching The Sensor Head To The 6400-09

    Attaching the Sensor Head to the 6400-09 To attach the sensor head, follow these steps: The sensor head handle must be removed to accomodate the 6400-09. Remove the male end of the leaf temperature thermocouple connector by pulling straight out, and pull the air hose from the underside of the leaf chamber.
  • Page 14 Section 2 To remove the bottom cover (if necessary): Turn the sensor head over and remove the 3 Phillips head screws as shown in Figure 2-5. Sample Air Hose Remove these 3 screws Hose Barb Figure 2-5. Remove the 3 Phillips head screws from the bottom of the sensor head.
  • Page 15 Section 2 Free the wires. Re-assemble the sensor head bottom cover. Be very careful not to pinch any wires when replacing the cover. Remove the handle assembly: Unlatch the handle, and unscrew the knurled leaf chamber adjustment nut (turn clockwise) until it is free of the handle (Figure 2-6).
  • Page 16 Section 2 Rear View Handle Quantum sensor holder Remove these 2 (or 3) screws Figure 2-7. Remove the screws on the back side of the handle. Remove the upper half of the leaf chamber. Unhook the connector from the PAR sensor or LED light source, if necessary.
  • Page 17 Section 2 NOTE: When removing the soil chamber and reattaching the handle, the wires to the log switch need not be threaded beneath the sensor head cover. Remove one fan shroud screw and attach the lamp connector (Figure 2-9). Attach lamp connector here Figure 2-9.
  • Page 18 Section 2 Top View Gasket Lower leaf chamber cuvette Hex head screws (8) Figure 2-10. Remove the 8 hex head cap screws. Attach the soil chamber mounting block with the 8 hex head cap screws from the previous step. The proper orientation of the mounting block is shown in Figure 2-11.
  • Page 19 #192-02889 (1) Figure 2-12. Location of O-rings and cap screws. Attach the 6400-09 body to the sensor head/mounting block assembly using the 4 cap screws (use the 5/64" hex key included), located on each corner of the mounting block (Figure 2-13).
  • Page 20 Figure 2-13. Attach the 6400-09 body to the mounting block. Connect the male and female ends of the thermocouple connectors. Join the sample and reference tubes on the sensor head with the "U" shaped piece of tubing, in the 6400-09 replacement parts kit (Figure 2- 14). Sample and reference...
  • Page 21 Section 2 Connect the air supply tubes on the 6400-09 as described in Section 4, "Check Hose Connections". Attach the chamber and IRGA connectors. Connect the soil temperature probe to the LI-6400 console using the 6400-13 thermocouple adapter assembly (in the spares kit). The adapter plugs into the auxiliary port on the LI-6400.

  • Page 23: Section 3. Software

    Creating a Soil Chamber Configuration Access the Config Menu from OPEN's main screen. Select "6400-09 Soil Chamber" on the Installation Menu. When "Press <enter> to continue" is displayed, press Enter You will be shown a configuration file in a window entitled "The Config (press <esc>)".

  • Page 24: The Soil Chamber Configuration

    Section 3 The Soil Chamber Configuration This section describes changes that the soil chamber configuration makes to the LI-6400 software. OPEN's Main Screen "LI-6400 Soil CO2 Efflux System" is displayed instead of "LI-6400 Photosynthesis System". Calib Menu The Calib Menu has only three entries: "IRGA Zero (CO2S, H2OS)"...
  • Page 25 Section 3 The following keys are new, or have different meanings in soil chamber mode: "AUX OP Params" (level 3, f2). This prompts for three auxiliary operating parameters: "Extra Draw Down (ppm)" - Draw down beyond the window minimum. (See #315, page 3-5). "Dead Time (secs)"...

  • Page 26: User Variables

    Section 3 0) Off 1) Intermediate Obs Only 2) Final Results Only 3) Everything During the measurement cycle, the LI-6400 computes an "observation" every 2.5 seconds. This observation includes a CO efflux value based on a rate of change of CO with time over the previous 7.5 seconds (10 measurements).
  • Page 27 Section 3 Vtot Actual system volume (cm ), accounting for insertion depth *305 InsDpth Insertion depth (cm) dc'/dt Rate of change of CO density corrected for evaporation (see Table 6-1, page 6-3) *307 Vbase Total volume (cm ) at 0 insertion depth Mode Operating mode (0, 1, 2, 3, or 4) 0 - off...

  • Page 28: Autoprograms

    Section 3 AutoPrograms The AutoProgram "Soil Efflux vs CO2" is added to the programs stored in /user/configs/AutoProgs" when the soil CO flux configuration is first created. This autoprogram lets you specify a range of target values to be measured automatically. Software...

  • Page 29: Section 4. Making Measurements

    These topics are covered in Sections 2 and 3. There are two different methods of making measurements. The 6400-09 can be inserted directly into the soil for measurements, or it can be used with "soil collars"...

  • Page 30: Measuring With Soil Collars

    Section 4 Measuring With Soil Collars Soil collars should be installed several hours to one day before making a measurement. You can test to see if the flux has stabilized by making a measurement immediately after installing the collar, and then make subsequent measurements over time.

  • Page 31: Check Hose Connections

    IRGA. 2. Check Hose Connections The general plumbing arrangement between the LI-6400 and the 6400-09 is shown in Fig. 4-1. Note that there is a piece of black shrink wrap on one of the hoses leading from the soil chamber; this hose is connected to the hose leading to the sample and reference inlets on the LI-6400 console.

  • Page 32: Measurement Procedure

    To do this, lay the chamber on its side and monitor soil chamber CO concentration (CO2S). Install the 6400-09 at the measurement location. Insert the soil temperature probe to an appropriate depth (typically 5 to 10 cm), near the Soil CO Flux Chamber.
  • Page 33 Section 4 Enter the number of cycles the instrument should perform at any given location (menu level 7, f2). Select whether you want to save final computed values, intermediate instantaneous observations, or both (menu level 7, f4). Press Start (menu level 7, f3). You will be prompted to enter a name for the log file if one is not already open.

  • Page 35: Section 5. Maintenance

    Maintenance Spare Parts Kit This kit contains some common replacement parts for the 6400-09. If you need to re-order any individual parts, please refer to the part numbers shown in Table 5-1 below. More part numbers are shown in Figure 2-2, page 2-2.

  • Page 36: Making Soil Collars

    1.75” (4.4 cm) long or longer, depending on your soil type and experiment, and bevel one edge with a grinding wheel so that it can be pressed into the soil. Soil collars are also available from LI-COR at a nominal cost under part #6560-228 (1 each).

  • Page 37: Zeroing The Irgas

    Section 5 Zeroing the IRGAs In order to zero the sample analyzer, it is necessary to replumb the system. Zeroing the IRGA While Attached to the Soil CO Flux Chamber Plumbing changes for zeroing the IRGA: Disconnect the To-Sample tube (it has black heat shrink) from the jumper shown below (Figure 5-8).

  • Page 38: Setting The Irga Span

    Section 5 Setting the IRGA Span Connect the span gas directly to the sample analyzer inlet. Do not connect to the console. NOTE: If you also want to check the span of the reference analyzer, connect the gas directly to it when you are ready.

  • Page 39: Section 6. Equation Derivation

    Equation Derivation The mass balance of CO for the 6400-09 soil flux chamber (Figure 6-1) is given by In = Storage + CO ∂ ρ ∂ where s is the soil surface area (m ) enclosed by the chamber, v is the...
  • Page 40 Section 6 The mass balance of water vapor is given by Water In = Storage + Water Out ∂ ρ ∂ where f is the flux of H O coming from the soil surface (mol H and w is the water vapor concentration (mol H O mol If we assume that evaporation is the sole cause of the leakage, then u = sf and we can write...
  • Page 41 Section 6   ×   P kPa     ρ     8 314     − ×   V cm      =     ...
  • Page 42 Section 6 Table 6-1. The terms of the LI-6400's soil flux equation (6-10). Symbol Description Units Soil Config LABEL µmol CO Soil flux of CO EFFLUX Atmospheric Press_kPa pressure Total system Vtot volume Enclosed soil area Area °C Air temperature in Tsch_C chamber µmol CO...
  • Page 43 Specifications System Volume (0 insertion depth): 991 cm Soil Area Exposed: 71.6 cm (11.1 in. 80.0 cm (12.4 in. ) with supplied PVC soil collar Diameter: 9.55 cm (3.76 in.) Air Temperature Thermocouple: Range: ± 50 °C of reference junction Type E: Reference Junction: Optical housing block thermistor Accuracy: ±...
  • Page 44 Warranty Each LI-COR, inc. instrument is warranted by LI-COR, inc. to be free from defects in material and workmanship; however, LI-COR, inc.'s sole obligation under this warranty shall be to repair or replace any part of the instrument which LI-COR, inc.'s examination discloses to have been...
  • Page 45 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 consequential damages.

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