Software

Configuring OPEN for Soil Measurements

To make soil CO2 flux measurements, a configuration file must first be created. After that, anytime you wish to use the soil chamber, select this configuration file from the list of configurations presented at power up, or when you change configurations (Config Menu -> Open...).

Creating a Soil Chamber Configuration

Follow the steps in Figure 28‑18.

Figure 28‑18. Creating a soil chamber configuration.

Selecting An Existing Soil Chamber Configuration

Once a soil chamber configuration has been created, you can select it from the list of configurations that are presented at power up, or when “Open...” is selected from the Config Menu (Figure 28‑19).

Figure 28‑19. Prompting the user for a configuration file.

OPEN’s Main Screen

When configured for soil flux measurements, OPEN’s Main Screen appears as in Figure 28‑20. The only change from normal is the title.

Figure 28‑20. OPEN's main screen.

The Calibration Menu

While configured for soil flux measurements, the flow meter and reference IRGA are not used, so the Calibration Menu is slightly changed (Figure 28‑21).

Figure 28‑21. The soil flux Calibration Menu.

Also, the zeroing and spanning routines are a bit different, and some replumbing is necessary. This is explained later in IRGA Calibration.

New Measurement Mode

New Measurements mode has some new variables and function keys.

Figure 28‑22. New Measurements with the soil flux configuration. Function key level 7 has most of the controls.

The function keys are described below, and the new variables are discussed in Table 28‑2.

Function Keys

Figure 28‑23 shows the function keys in New Measurements while configured for soil CO2 flux. The important group of keys is on level 7.

Figure 28‑23. The soil flux measurements are controlled from level 7.

The following function keys are new - or have different meanings - for the soil configuration:

Target= (f1 level 7,). Sets Target and Delta. The target is the CO2 concentration at which you want the measurement taken, and the delta defines the operating window around that target. For example, if you specify a target of 360 ppm and a delta of 20 ppm, the measurement will occur while the CO2 rises from 340 to 380 ppm. Once above 380 ppm, the pump will pull the CO2 back down to 340 ppm (minus any extra draw down ddMargin) for another cycle).

Cycles= (f2 level 7). Sets NumCycls, the number of repetitions to perform. The key label shows the current repetition number, and the maximum number of repetitions (e.g. 1/3 is the first of three).

START (f3 level 7). Starts/stops the measurement cycle. (While a measurement is in progress, the label will be Stop.) If no log file is open when Start is pressed, you will be prompted for one. If a file is open, you will be prompted “Append to the current log file? (Y/N)”. If you respond N, you are prompted for a new log file name.

It is possible to do a measurement without logging to any file. Simply press escape when asked for the file name, and press N for the subsequent prompt “Log to COMM port? (Y/N)”. (The other way to accomplish this is to turn off logging, as described next.)

Logging… (f4 level 7). Selects what is stored in the log file (if a log file is open) during a measurement. The dialog box is shown in Figure 28‑24.

Figure 28‑24. Logging options (f4 level 7).

During the measurement cycle, the LI-6400 computes an intermediate observation (Mode = 3) every 2 seconds (see #310 in Table 28‑2). This observation includes a CO2 efflux value based on a rate of change of CO2 with time over the previous 10 seconds, which corresponds to 20 samples. (For versions 3.x and 4.x, it is 10 samples over 7.5 seconds.) In addition to the rate of change of CO2, the intermediate observation includes the mean CO2 for that interval. At the end of the cycle, when CO2 has reached the upper limit (Target + Delta), a final result (Mode = 4) record is computed by regressing the rates of change of CO2 (dc’/dt) against the mean CO2 concentration (C2avg), and computing the CO2 efflux rate (EFFLUX) appropriate for the target concentration. Typically, you only need to store the final result record (option 2), but the other options are available.

Edit Params (f5 level 7).This key provides access to all the soil flux parameters, and allows them to be viewed, edited, stored and retrieved (Figure 28‑25).

Figure 28‑25. The Edit Params screen.

The entire list looks like this:

To edit any of the parameters, place the cursor on that line, and press f2 (Edit).

Figure 28‑26. Changing a setting.

If the value of any setting is different from its value as last stored with the configuration file, it appears with an asterisk (Figure 28‑27).

Figure 28‑27. Changed values (un-stored) are indicated by *.

The Undo key (f4) allows any or all un-stored values to be reverted back to their stored condition (Figure 28‑28).

Figure 28‑28. The UNDO key in action.

The Import key (f3) allows soil settings to be imported from any stored configuration file that has them, or from soil config files that may exist from older versions, if you’ve upgraded from OPEN 6.0.x (Figure 28‑29).

Figure 28‑29. Importing a set of soil parameters.

Display Map

The default soil configuration has the display arranged as shown in Table 28‑1.

Table 28‑1. The default soil display map for New Measurements mode.
Group Label Description
A CO2S_μml Sample cell CO2 (μmol CO2 mol-1)
H2OS_mml Sample cell H2O (mmol H2O mol-1)
RHcmbr% RH in the soil chamber (#321)
RHirga% RH in the IRGA (#323)
B EFFLUX Soil Efflux (#320)
C2avg Average CO2 (#302)
Wavg Average water concentration (#303)
C Tsoil_C Soil temperature (#322)
Tsch_C Soil chamber temperature (#324)
Program Status State of the measurement (#31)
D Vtot Total volume (computed) (#304)
InsDepth Insertion depth (#305)
Target Target concentration (#313)
Delta CO2 range (#314)
E Press_kPa Atmospheric pressure (kPa).
Flow_μml Flow rate (μmol s-1)
dC/ct Rate of change of CO2 (#300)
dW/dt Rate of change of H2O (#301)
F Tblock°C Block temperature
Tair°C Temperature in the IRGA sample cell
Tsch_C Temperature in the soil chamber (#324)
Tsoil_C Temperature of the soil temperature probe (#322)
G HH:MM:SS Real time clock
Program Shows AutoProgram status
CHPWMF Status word (summary of line J)
Battery Battery voltage
H CO2 Status of CO2 IRGAs
H2O Status of H2O IRGAs
Pump Status of pump
Flow Status of Flow controller
Mixr Status of CO2 mixer
Fan Speed of chamber fan
I CRagc_mv Reference CO2 AGC (automatic gain control) signal, in mV
CRagc_mv Sample CO2 AGC signal
HRagc_mv Reference H2O AGC signal
HSagc_mv Sample H2O AGC signal

User Variables

The soil CO2 flux configuration makes use of a compute list file named “/User/Configs/Comps/Soil Efflux Eqns.LPL”, which defines a number of user variables and constants (Table 28‑2).

Table 28‑2. User defined variables and constants for the Soil Configuration.
ID # Label Description How to Change1 LPL variable name
5.2 and up 5.1 and bleow
300 dC/ct Mode=3: Rate of change of CO2
Mode=4: Meaningless (last Mode=3 value)		     co2Slope
301 dW/dt Mode=3: Rate of change of H2O
Mode=4: Meaningless (last Mode=3 value)		     h2oSlope
302 C2avg Mode=3: Average CO2
Mode=4: The target CO2.		     co2Mean
303 Wavg Mode=3: Average H2O
Mode=4: Meaningless (last Mode=3 value)		     h2oMean
304 Vtot Total Volume (including IRGA), computed by the software:
Vtot = Vbase - Area * InsDepth		     soilChamSysVol
305 InsDepth Insertion depth (cm). Distance from chamber edge to the top of the soil surface. f5 level 7 f5 level 7 soilInsDepth
306 dc’/dt Mode=3: Dilution corrected CO2 density
Mode=4: Dilution corrected density regressed to target concentration.		     dcdt
307 Vbase Volume (cm3) at 0 depth. Includes IRGA. f5 level 7 Note2 soilChamBaseVol
308 Area Soil area (cm2) f1 level 3 f5 level 7   soilArea
310 Mode 0 - Measurement not active
1 - Pump is on, drawing CO2 down
2 - Pump off, waiting to start. (CO2 still too low)
3 - Computing intermediate observations
4 - Final result		     opMode
311 Smpls Mode=3: Number of samples used in the intermediate observation that was logged.
Mode=4: Number of intermediate observations of dc’/dt used for the final regression.		     numSamps
312 Program Status Mode=0: "0:Stopped"
Mode=1: "1. Pumping Down"
Mode=2: "2:Waiting to start"
Mode=3: "3:Measuring"
Mode=4: "4:Compute Final"		     srState
313 Target Target CO2 μmol/mol. Computations and logging are performed while the CO2 is rising from Target - Delta to Target + Delta. f1 level 7 f5 level 7 f1 level 7 targetCO2
314 Delta CO2 Delta μmol/mol. deltaCO2
315 ddMargin Extra Drawdown (ppm). Mode 1 (drawdown) ends when the CO2 concentration drops below Target - Delta - ddMargin. f5 level 7 f2 level 3 ddSafetyMargin
316 DeadTime Dead Time (secs). Minimum time between when the pump turns off, and when measurements begin. postPumpDeadSecs
317 MnMsrTime Min Measure Time (secs). Minimum length of the Mode 3 part of a measurement. minMeasureTime
318 NumCycls Number of cycles to do. 1 cycle is drawdown (Mode=1) through final result (Mode=4). f2 level 7
f5 level 7		 f2 level 7 numCycles
319 ddFlow Flow during draw down (Mode=1). f5 level 7 f2 level 3 ddFlow
320 EFFLUX Mode=3: Flux for intermediate observation
Mode=4: Flux for final result.		     soilEfflux
321 RHcmbr% Relative humidity in the soil chamber     rhsc
322 Tsoil_C Temperature of the external soil probe     tSoil
323 RHirga% Relative humidity in the IRGA     rhOut
324 Tsch_C Air temperature in the soil chamber.     tLeaf_c
330 R(C)m Mode=3: Meaningless
Mode=4: Slope of dc’/dt vs. C2avg		     dcdtSlope
331 R(c)b Mode=3: Meaningless
Mode=4: Intercept of dc’/dt vs. C2avg.		     dcdtOffset