Using analyzers from other manufacturers

Although the Smart Chamber is optimized for use with LI-COR gas analyzers, it can be used with a variety of gas analyzers not manufactured by LI-COR. It may also be used for syringe sampling and other methods of gas analysis such as chromatography, mass spectrometry, or other methods.

The Smart Chamber logs the timestamp, soil temperature, soil moisture, location, and other data. Gas measurements and accurate time stamps will be logged elsewhere - typically by the gas analyzer. Data from the gas analyzer will be merged with Smart Chamber data in SoilFluxPro Software, where you will calculate the flux results.

Connecting to the gas analyzer

Three conditions must be satisfied to use a gas analyzer from another manufacturer with the Smart Chamber:

  1. The analyzer must be able to query the Smart Chamber network time protocol (NTP) server for timestamp synchronization.
  2. Exhaust flow from the analyzer must not exceed 5 slpm to be compatible with the Smart Chamber pneumatics. ≤ 2 slpm is strongly recommended.
  3. The timestamp and file structure from the gas analyzer must be supported by SoilFluxPro Software (supported file types include .csv, .txt, .json, and .81x).

Currently, these features are supported by several models from Picarro, LGR (ABB - Los Gatos Research), Gasmet, and Aerodyne.

Optional sealed and strain-relieved USB-B-to-USB-A cables are available in 1.2- and 2-meter lengths (part numbers 392-17655 and 392-17794, respectively) from LI-COR if you intend to use the Smart Chamber with a gas analyzer. We recommend that you use these cables, not cables from a different manufacturer.

Synchronizing the time stamps

The Smart Chamber contains a GPS receiver for high-precision GPS time data, which is automatically included in Smart Chamber data files. For Smart Chamber data files to be merged with gas analyzer data files in SoilFluxPro Software, the timestamps for each observation must match. The Smart Chamber contains a Network Time Protocol (NTP) server that can be queried by other devices to synchronize the clock to the Smart Chamber GPS time so that the same time stamps are being logged by both devices.

Generally, this synchronization is completed using the following steps.

  1. Connect the Smart Chamber and gas analyzer using a USB or network cable.
  2. For NTP time syncing, the preferred communications protocol is Ethernet. If you use USB (e.g., for Picarro analyzers), you may need to install a device driver on your PC to support "Ethernet-over-USB" communications.
  3. Identify the Smart Chamber NTP server location through the analyzer interface.
  4. Different analyzers have different ways of identifying the location of the Smart Chamber NTP server. Picarro analyzers, for example, have a Windows operating system embedded in the analyzer as a graphical user interface. In the file directory for the analyzer software, a "remote access" .ini configuration file allows users to identify NTP servers for time syncing. In this file, the Smart Chamber server is identified by the Smart Chamber serial number, and a similarly-named "remote access" executable (.exe) file performs the synchronization with the server locations indicated in the .ini configuration file.
  5. Manually query the NTP server to synchronize the devices, or set a task or scheduled job to automatically query the NTP server.
  6. Querying the Smart Chamber NTP server depends on how you interface with your analyzer and locate the Smart Chamber NTP server. Because the Picarro file structure provides an executable file to perform the query, users can manually run the .exe file through the Windows interface command prompt. Alternatively, CRON jobs, shell scripts, or scheduled tasks can also be configured to run the executable at desired intervals, always at instrument startup, etc.

Plumbing considerations

The exhaust flow rate from the gas analyzer must not exceed 5 slpm. For the best results however, exhaust not in excess of 2 slpm is recommended to minimize the effect on the pressure gradients within the chamber.

Determining effective volume

When using gas analyzers, you must calculate system volume based on the volume of the analyzer and the length of the tubing.

First, calculate the effective volume that the gas analyzer adds to your system. The volume of the analyzer will have at least two kinetic effects: 1) it brings additional air to the system, which dilutes gases entering the system from the soil surface and reduces the measured mole fraction rate of change (dC/dt); and 2) it creates a time delay in the onset of a monotonic concentration increase or decrease. Accurate fluxes can still be measured if the added volume is sufficiently small.

The quantitative impact of the added volume on dC/dt can be evaluated by considering the equation used to calculate flux F (mol m-2 s-1). This equation is derived based on the assumption of a single fixed volume V (m3) with homogeneous air density ρ. For simplicity, in this discussion the effects of water corrections are neglected. This, however, does not change the conclusions. Thus,

B‑1

where F is the flux of trace gas (mol m-2 s-1), ρ is air density (mol m-3), dC/dt is the time rate of change in mole fraction of the gas being measured (s-1), and S (m2) is the soil surface area over which the flux occurs. For a flux F, the trace gas mole fraction rate of change dC/dt is proportional to the total number of molecules in the system ρV.

For a well-mixed system, when an additional volume Vadded that contains a gas of density ρadded, is inserted into the system, equation B‑1 becomes

B‑2

But ρsystem = Psystem / RTsystem, where R is the universal gas constant, and similarly for the added volume. Substituting these expressions and factoring gives

B‑3

For data processing using SoilFluxPro, an effective volume Veffective for the addition can be defined for the added analyzer and entered into the software.

B‑4

Thus, the total volume used in equation B‑1 becomes simply Vsystem + Veffective and the density is ρsystem. There are inherently small variations in Veffective due to changes in Tsystem and Psystem, but these are generally small and subsequently neglected. In many cases, the impact of an added volume on flux calculations will be modest, as Veffective for many modern trace gas analyzers is small.

In cases where the volume of the addition operates at a non-uniform temperature or pressure, or is not well known, Veffective can be estimated experimentally by plumbing the gas analyzers in a closed loop and injecting a known volume Vinjection (m3) of pure CO2 into the loop. The gas concentrations in the loop pre-injection C1 (mol mol-1) and post-injection C2 (mol mol-1) are defined as:

B‑5

B‑6

where NCO2 is the number of moles of CO2 in the additional volume pre-injection, Nadded is the total number of moles in the additional volume pre-injection, and Ninjection is the number of moles of CO2 injected into the loop. Substituting equation B‑5 into B‑6 and rearranging to solve for Nadded yields:

B‑7

where

B‑8

and

B‑9

Tinjection (K) and Pinjection (Pa) are the temperature and pressure, respectively, of the gas injected into the closed loop. Substituting these into equation B‑7 and following from equation B‑4 yields:

B‑10

In practice it is difficult to know Tinjection and Pinjection with great certainty. Making the assumption that Pinjection = Psystem and Tinjection = Tsystem introduces some error in determining Veffective experimentally, but it allows equation B‑10 to be simplified, eliminating the need to know temperature or pressure:

B‑11

In many cases, the impact of added volume on flux calculations will be modest, as Veffective for many modern trace gas analyzers is small.

Another consideration is time constants. By trapping air making its way around the measurement circuit, the volume of a third-party gas analyzer may also introduce an additional time delay and have other effects that can compromise the flux measurement. The magnitudes of these effects are related to the analyzer’s volume Vadded (m3), its operating pressure and temperature, and the flow rate through it. We can qualitatively assess the kinetic consequences of adding the volume by defining a time constant for the effective volume of the added analyzer. We define a time constant tadded (s):

B‑12

where Uadded is the molar flow rate (mol s-1) delivered to the analyzer, ρ is air density (mol m-3) in the analyzer evaluated at the analyzer’s internal temperature and pressure, and Vadded (m3) is its actual volume.

You will need to follow this protocol to calculate the effective volume and time constant accordingly if you are using a LI-COR Trace Gas Analyzer or LI-870 CO2/H2O analyzer along with a gas analyzer. LI-COR technical support is available to assist you with this configuration.

Merging files in SoilFluxPro

File merging in SoilFluxPro software is currently supported for Picarro, LGR, Gasmet, and Aerodyne analyzers, using the Column Import Routine. The example below uses data from an LGR gas analyzer, though the procedure is identical for Picarro, Aerodyne, and Gasmet datasets.

To perform the Column Import Routine in SoilFluxPro,

  1. Open a Smart Chamber data file.
  2. Click the Import tool bar button to launch the Import Data Columns dialog.
  3. Click Add Files... to launch a file explorer to add the source file(s) to the source list.

  4. Select the file format (LGR in this case).

    After selecting a source file, it will be parsed and the headers, units and flux check box are displayed.

  5. Select an H2O source.

    This is only required if you are calculating a gas flux that needs a water vapor dilution correction.

  6. Enter the Device Name.

    This can be anything you want, but it cannot be blank.

  7. Enter the Tube Length and the Analyzer Volume.

    If a General Purpose file format is selected, adjust the Date & Time settings and the Delimiter setting.

  8. If there is a known time offset between the Smart Chamber and the imported data, enter that into Adjust time of imported data.

  9. Select the variables to import, the units, and whether you want to compute a flux from the data.
  10. If you have selected an H2O source, the parameter is selected automatically.

  11. Click Import.

    Now, when you update the displayed variables, the imported columns will be available under the Meas tab.

  12. When you launch the Recompute dialog, you can now add flux computations based on the imported columns.

For calculating fluxes with imported data, it is best to import dry mole fraction/dry mixing ratios. This demonstration used LI-8100A data, which has water vapor data from the LI-8100A analyzer. Because Smart Chamber data files do not have water vapor data by default, you must provide this data. The data can be measured by a gas analyzer and imported or it may already be included in the LI-8250 or Smart Chamber data file if from a LI-COR gas analyzer that measures water vapor.