Using with non-LI-COR gas analyzer

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

The Smart Chamber logs timestamp, ancillary soil temperature and moisture, location, and other data alongside the analyzer or syringe samples. The data from the other instruments or methods can be merged with Smart Chamber data in SoilFluxPro™ Software to calculate fluxes.

Connecting to the gas analyzer

Configuring the Smart Chamber with a non-LI-COR gas analyzer requires three things.

  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 non-LI-COR gas analyzer. It is strongly recommended that you use these cables with the Smart Chamber, and not cables from a different manufacturer.

Timestamp synchronization

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 non-LI-COR gas analyzer data files in SoilFluxPro software to calculate fluxes, the timestamps for each observation must match. For this, the Smart Chamber contains a network time protocol (NTP) server which can be queried by other devices to sync the device's clock to the Smart Chamber's 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.
  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 sync 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 from an external, non-LI-COR analyzer must not exceed 5 slpm. For the best results however, exhaust not in excess of 2 slpm is recommended so that the exhaust will not have too much effect on the pressure gradients within the chamber.

Determining effective volume

When using non-LI-COR gas analyzers, you must calculate system volume based on the volume of the analyzer used and the length of your tubing.

First, you will need to calculate the effective volume that the non-LI-COR 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 trace gas entering the system from the soil surface and reduces the measured trace gas 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 (mole 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 (mole m-2s-1), where ρ is air density (mole 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 non-LI-COR 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 (moles s-1) delivered to the analyzer, ρ is air density (mole 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 an LI-78xx Trace Gas Analyzer or LI-870 CO2/H2O analyzer along with a non-LI-COR gas analyzer. LI-COR technical support is happy 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, open your Smart Chamber data file, and click the Import tool bar button to launch the Import Data Columns dialog. Click Add Files... to launch a file explorer to add the source file(s) to the source list.

After selecting a source file, the label line and first observation line from the first file in the source list will be visible (A). The expected format for the type of file chosen in the File Format drop-down will be displayed (B). OK means that the data file being imported matches the expected file. Error means the expected type wasn't found. In this case, instead select General Purpose and manually select the format of the data file. Lastly, the list of available data column found in the source file, when parsed according to the expected formats, are visible (C).

Check the desired column labels to import. Note that column(s) used for time and date are shown, but are not checkable. Click OK. Once the columns are imported, you can view them in the Summary View. Observations that contain imported columns are denoted with an asterisk ( * ).

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

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

Note: For calculating fluxes with imported data, it is recommended that you import dry mole fraction/dry mixing ratios. This demonstration was performed using LI-8100A data, which contain water vapor data from the LI-8100A analyzer. Because the Smart Chamber data files do not contain water vapor data by default, you must have this data for your samples, whether they are measured by your non-LI-COR analyzer and imported using the Column Import Routine, or are already included in the Smart Chamber .json file from using a LI-COR gas analyzer that measures water vapor.