User manual | Supplement - Biogeosciences

Supplement of Biogeosciences, 12, 3849–3859, 2015
http://www.biogeosciences.net/12/3849/2015/
doi:10.5194/bg-12-3849-2015-supplement
© Author(s) 2015. CC Attribution 3.0 License.
Supplement of
Technical Note: Cost-efficient approaches to measure carbon dioxide (CO2 )
fluxes and concentrations in terrestrial and
aquatic environments using mini loggers
D. Bastviken et al.
Correspondence to: D. Bastviken ([email protected])
The copyright of individual parts of the supplement might differ from the CC-BY 3.0 licence.
Content
Manual for adapting and using the CO2 logger for environmental measurements .................. 2
Logger adaptions .................................................................................................................... 2
Connectors ......................................................................................................................... 2
Extension and power supply cables ................................................................................... 3
Protective coating .............................................................................................................. 3
Data communication cable .................................................................................................... 4
Communication with a sensor................................................................................................ 5
Calibration .............................................................................................................................. 6
Assembling the chamber and the sensor protection box ...................................................... 6
Logger settings ....................................................................................................................... 8
Download data ....................................................................................................................... 9
Status codes and error values ................................................................................................ 9
Recommendations of routine for reliable field measurements .............................................. 10
Tests in addition to those described in the main text ............................................................. 11
Influence of temperature and relative humidity on CO2 measurements ............................ 11
Test of chamber response time effects from the sensor protection box ............................ 12
1
Manual for adapting and using the CO2 logger for environmental
measurements
Logger adaptions
Connectors
The CO2 logger used is the ELG module made by Senseair
(http://www.senseair.se/products/oem-modules/elg/). It is sold as a sensor mounted on an
electrical board which needs the following adaptions for the type of use described in our
study:
First, solder connections for calibration, quick start (see below), communication and battery
as shown in Figure S1. Dimensions and type of connections are shown in Table S1.
Figure S1. Positions where connectors should be soldered onto the logger board. The two
upper panels show positions with labels. The use of the connectors is as follows: shorten A+B
for zero calibration and C+D for quick start (see text below for explanations). E (UART
TxD), F (UART RxD) and G (G0) are used for the communication cable (see below) and H
(G+) and I (G0) for battery connection. The lower panel show the board after making the
adjustments.
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Extension and power supply cables
An extension cable from positions E, F, and G in Figure S1 to a connector is practical for easy
connection to the board in the field. To make such an extension cable, use three differently
coloured wire, each about 25 cm long and solder them to the male pin header as shown in
Figure S2 and secure with crimp cables. The other end is soldered onto the board (Figure S1).
Solder battery connection on to the board as shown in Figures S1 and S3. A practical length
of both the extension cable for communication and the power supply cable is 25 cm for the
applications described in this study.
Figure S2. Wiring of the connector from the extension cable from the logger board. The
position of E, F, and G on the board is indicated in Figure S1.
Protective coating
The sensor should be painted with anti-tracking varnish (Ultimeg 2000/372) to protect it from
condensation and water. Before painting, clean the circuit board (but not the sensor
membrane) with ethanol and dry clean with compressed air. Apply a layer of varnish at least
three times (additional varnish layers is better for improved corrosion protection). Areas
marked in Figure S3 should not be covered with varnish.
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Figure S3. A board after applying protective varnish (in this case the varnish had a grey
colour – other colours or transparent varnish is also available). The temperature, relative
humidity, and CO2 sensors and connector areas (encircled) should be protected from varnish.
Data communication cable
To communicate with the sensor a modified TTL-232R-3V3-cable is needed (TTL-232R3V3; FTDI chip; Glasgow, United Kingdom). One part is composed of three differently
colored wires (the same type as for the extension cable described above). One end of this is
attached to a connector, matching the connector in the extension cable and the other end is
soldered to a straight pin header (1x5) that is then connected with the TTL cable (Figure S4).
For details of pins and housing see Table S1.
Table S1. Connections for the sensor.
Component
Dimensions
Straight pin
Pole no. 1x2, pitch 2.54
header
mm
Pin header
Pole no. 1x4, pitch 2.54
mm
Cable socket
Pole no. 1x4, pitch 2.54
mm?
Battery holder
9V, 100 mm
Jumper
Pitch 2 mm
Function
Calibration (A+B), quick start(C+D) and
modification of TTL-cable
Connection cable from sensor
TTL- cable
Battery connection
Calibration and quick start
4
A
B
C
D
E
Figure S4. Illustrations of the connectors needed on the TTL cable for data communication.
Panel A and B shows the three coloured wires attached to a connector on one end and to a
straight pin header (1x5) on the other end. Panel C and D shows the connection of this straight
pin header to the TTL cable. Panel E shows the finished data communication cable.
Communication with a sensor
The software UIP5 for communicating with the sensors can be downloaded for free at
http://www.senseair.se/products/software/uip-5/. After installing the software, open the
program and go to the Help menu and check for updates.
Connect and install the cable on the computer and open UIP5. Choose the menu Meter/
Connection configuration. Choose the right COM port and make sure the box ModBus is
checked and save the settings.
Connect a sensor (with the battery connected) and click on connection status in the bottom
right corner of the screen (or Ctrl+d) to connect/disconnect a sensor.
In the control window (the lower right part of the screen) the “Logger” tab is used for starting
and stopping measurements, setting log period, synchronizing logger time with computer time
(RTC), read data to the computer (delivered as text files), and managing the logger memory.
The tab “CO2” can be used for quick calibration as described below.
Note that the logger should always be battery powered when connected to the computer.
Without battery power, connection to the computer will fail. With a bad battery (insufficient
power) the sensor may return unrealistic ppm values while connected. If there are connection
problems, the first step of problem solving should be to change to a new battery.
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Calibration
The recommended calibration is a “zero calibration” i.e. repeated calibration cycles in CO2
free gas (we used N2). To do this, connect the sensor to UIP5 set the log period to 300 s and
set RTC. Disconnect without starting. Connect a jumper to the quick start pins and make note
of the time. After the light stops flashing, connect another jumper to the zero calibration pins.
It is desirable to calibrate many sensors batch-wise. Place the sensors in a gas tight box, glove
box, glove bag or similar and purge with a low but steady flow of nitrogen. If the flow is too
high the CO2 concentration will decrease too fast during each calibration cycle which will
return an error message and automatically stop the calibration. When the sensors have been
calibrating for a minimum of three hours in a zero CO2 atmosphere, remove the jumper from
the zero calibration pins before next measurement cycle starts. Remove the quick start jumper
and connect to UIP5 to confirm the sensor is calibrated.
An alternative, simplified calibration may be used if conditions do not allow a zero
calibration. Via the CO2 window in the UIP5 it is possible to type in the CO2 concentration
around the sensors if known, and press “calibrate” while having the logger turned on at, for
example, 60 s measurement interval. The sensor will then perform a calibration relative to the
typed in value. This option should only be used when the air around the sensor has a stable
CO2 concentration. The calibration cycle should be repeated several times for best results.
After calibration, the sensors should be compared with a reference instrument (e.g. a GC).
This could be done by starting the sensor and placing it in a closed environment with
possibilities to take manual samples. Such a measurement validation procedure should be
executed after each calibration, occasionally during and after use whenever possible, and after
storage, to check when a new calibration is needed.
Assembling the chamber and the sensor protection box
The chambers used in this study were produced from polypropylene plastic buckets covered
with aluminium tape to minimize light induced heating of the chamber headspace (note that
the loggers can be used in any type of flux chamber). Two pieces of Styrofoam were attached
around the rim to keep it floating in the water (Figure S5).
Two plastic boxes were placed inside the chamber. The bigger box (Lock&Lock, 350 ml,
HPL806) contained the CO2 sensor (sensor box) and the smaller one (Lock&Lock, 180 ml,
HPL805) was to protect the battery and the data communication connector from water
(battery box).
The sensor box has a slanting plastic sheet, used as a condensation trap to reduce the
condensation on the sensor in a passive way not consuming power (other ways to reduce
condensation by e.g. pumping air through a desiccant or heating the sensor would consume
significant amounts of power). Ventilation holes were made on one short side (7 mm
diameter, Figure S6). The gap between the plastic sheet and the bottom of the box should be
minimum 1 cm to not restrict air flow too much (Figure S6). Attach the sensor box to the lid
so the sensor is placed on the same side as the ventilation holes. Some of the condensation
will stick on the sheet (instead of the sensor) and drain before reaching the sensor. When
closing the boxes, make sure the cables are in a corner of the lid and not directly by a clasp.
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Figure S5. Inside (left) and outside (right) of the chamber type used. The tube with the 3-way
syringe valve to the right is for manual sampling at the end of selected deployments to check
sensor performance.
Figure S6. Three pictures of the sensor box
with ventilation holes and condensation
protection sheet.
The sensor is attached to the lid with M3 polyamide (non-corroding) bolts and nuts (Figure
S7). The boxes are attached to the chamber with M6 polyamide bolts and nuts. All holes are
sealed with rubber sealing. The battery box was made to be as water tight as possible. The
parts for the protective boxes are listed in Table S2.
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Table S2. Chamber parts.
Part
Sensor box
Battery box
Styrofoam collar
Chamber
Bolts and nuts for sensor
Bolts and nuts for sensor box
Dimensions
350 ml, 8 cm x 11.3 cm
180 ml, 6.8 cm x 8.7 cm
2 x 45 cm
8 L, inner radius 12.5 cm, height 12 cm
M3
M6
Figure S7. Sensor placed in lid.
Logger settings
Connect to a sensor and choose the Logger tab (Figure S8). There the Logger Settings, Logger
Status and Logger Data are shown. Table S3 describe the sub categories in Logger Settings
and Logger Status. In the Logger Data window, data saved in the log can be read.
Figure S8. Screenshot of the logger menu in UIP5.
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Table S3. Explanation of Logger Settings in “Logger” tab in the UIP5 software for logger
control.
Setting
Explanation
Allowed frequencies
”Start Sleep” Specifies the delay before start.
0-255
”Log Period” Specifies the time interval between 1-224
measurements
(1 second to ~6 months)
”RTC”
Set Real Time Clock (adjust sensor time to computer time).
”Set”
Activates new settings
”Revert”
Undo the last change in settings.
Log Period specifies the time between measurements in seconds. For example if measuring
pCO2, the Log Period could be set to 3600 s (1 hour) and for flux measurements, 300 s (five
minutes).
Note: All data in the log will be erased each time Log Period is changed.
A measurement is started by clicking Start and stopped by clicking Stop. (Start Sleep
specifies the delay from Start and before the first measurement starts.)
Note: Always set RTC (i.e. the computer clock time) before starting a measurement. In
Logger Settings choose set RTC. If RTC is not set, the time stamps in the log file will be
incorrect.
Download data
Connect a sensor and choose Logger. Stop ongoing measurement, choose Read and then
choose Export (if Export is not activated, try to disconnect and connect the sensor again). To
control what data is exported, choose “save selected part” and “save only data records” in
the export log window appearing. The log file is saved in the desired directory on the
computer as a text file that is easily opened in e.g. Excel for further analysis.
Status codes and error values
Figure S9 shows a short log file. The different status codes are explained in Table S4. More
than one status code can be shown at the same time. The codes 0x70 means that 0x10, 0x20
and 0x40 are active. The value 32767 is used as an ErrorValue for CO2, Temp and RH. If a
measurement for any of the parameters fails the value 32767 will be written in the log. In
most cases errors indicated by status codes or the error value can be resolved by replacing the
battery.
Figure S93. Example of a short log file.
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Table S4. Sensor status codes
Status Meaning
code
0x00
No warning
0x10
Low battery warning
0x20
Low battery alarm
0x40
Error Status
Plausible explanation
Indicating battery voltage < 5.25V. Change battery.
Indicating battery voltage < 4.75V. Change battery.
Indicating failed measurement or internal errors. Can
relate to error measuring CO2, temperature, RH or other
internal errors. Read log file for details.
Recommendations of routine for reliable field measurements
As a routine for measurements the following steps are recommended:
1. Check, and if necessary make a sensor calibration before use. Test the calibration by
comparison with reference gas analyzer (e.g. GC). This can be done with batches of loggers
for increased efficiency.
3. Start the logger and set suitable measurement interval. For flux measurements a shorter
interval is needed (e.g. 1-10 min depending on the system). For pCO2aq measurements the
response time of the system, decided by the headspace equilibration time (in turn regulated by
k and volume to area ratio of the chamber), makes longer measurement intervals (15-60 min)
more adequate to save power and memory space.
4. If using small 9 V batteries – ensure that battery voltage is kept above 7.5 V throughout the
whole measurement period to prevent repeated shutdowns that can result in data loss. This can
be done by adapting the measurement frequency or the interval between battery replacements.
5. Withdraw occasional manual samples from the chambers by syringe to validate logger
measurements by comparison with a reference gas analyzer and for drift correction. In cases
of long term deployments it is highly recommended to collect parallel manual samples
whenever visiting the chamber (at least when starting and ending the deployment).
6. After use for as long as 1- 2 weeks in the field – bring the chambers indoor for proper
drying to minimize moisture accumulation in the measurement cell leading to frequent
condensation events. It is recommended to let the loggers dry after all field use and to store
them under dry conditions to avoid corrosion.
Step 1-2 should be performed immediately before field use. We recommend building a
database for the measurements in which each logger is given a unique permanent name that is
linked to all data from the logger to record the history for each individual unit.
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Tests in addition to those described in the main text
Influence of temperature and relative humidity on CO2 measurements
In an initial test of temperature effects only, data from five replicate loggers were compared
with syringe samples for analyses by gas chromatography at -17, 5, 8, 20, 27, 37, and 46 °C in
well temperature equilibrated environments taking advantage of Swedish winter outdoor
temperatures (-17 °C) and various temperatures available in our laboratory. The difference
between GC and logger data averaged 1 % and never exceeded 5 % for any of the
temperatures, indicating that the logger response was not biased by temperature. However,
after some of the field tests described in the main text, concerns of possible interaction effects
between temperature and humidity on CO2 values were raised. We performed an additional
sensor performance test as follows: Three replicate and recently calibrated sensors were
mounted together with a weather station (WXT520, Vaisala) logging both temperature and
humidity, and our LGR greenhouse gas analyzer for CO2 measurements (DLT-100), in a
climate room where temperature and humidity was varied. The temperatures used were 5, 10,
15, 20, 25, 30, 35, and 40 °C. At each of these temperatures the relative humidity (RH) was
allowed to increase continuously over 30-60 minutes, from 8 – 95 % while all instruments
logged data with a minimum measurement frequency of 1 minute. To compensate for
differences in sensor response times moving 5 minute averages were compared.
The temperature from the sensors showed a linear correspondence with the weather station as
described by
TWXT = 0.988·TELG - 1.03 (n = 297, R2 = 0.999)
Equation S1
where TWXT and TELG denote temperature measurements in °C from the Vaisala weather
station and the Senseair sensor, respectively. Data from all the three Senseair sensors were
included in Equation S1.
For relative humidity there was a significant interaction effect with temperature.
Therefore the best calibration between RH values from the weather station (RHWXT) and the
sensors (RHELG) was obtained with the multiple regression
RHWXT = 0.934135·RHELG + 0.29414·TELG + 0.912959
(n = 297, R2 = 0.990)
Equation S2
The combined effect of temperature and humidity on CO2 measured by the ELG
sensor (CO2ELG) resulted in a systematic bias with lower values relative to the LGR at low
humidity and higher values at high humidity with this effect being modulated by
temperatures. The maximum difference of CO2 measured with the LGR (CO2LGR) and CO2ELG
(CO2LGR - CO2ELG) was between -6.6 and +7.6 % of CO2ELG. To correct for this we made the
following multiple regression
CO2corr = 153.165 + 0.797236 CO2ELG - 0.799018·TELG - 0.45636·RHELG
(n = 297, R2 = 0.87)
Equation S3
where CO2corr denote corrected CO2 values. Please note that Equation S3 is valid under noncondensing conditions and CO2 levels in the range of 400-550 ppm only. The residual
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difference CO2LGR - CO2corr was unbiased relative to humidity and temperature and ranged
from -1.6 to 2.3 % of CO2corr.
Test of chamber response time effects from the sensor protection box
The plastic box with holes, protecting the sensor from condensation and splashing water
(Figure S6) could potentially delay the response time. To test this we took advantage of the
logger capacity to control one peripheral device and used six chambers with loggers, two of
which were equipped with a computer fan. Two others units were connected to a small
membrane pump that pumped air from inside the protective box right near the sensor to a
sintered aquarium bubble stone right under the water surface within the chamber. This pump
setup were believed to both mix the air in the headspace and also speed up the equilibration
between the chamber headspace and the water which would be beneficial when pCO2aq
measurements are in focus (but obviously not suitable when using chambers for flux
measurements). The two remaining chambers represented reference chambers with no device
for mixing the headspace. CO2 concentrations were measured in all chambers every 2nd hour
for 20 hours. The fan or the pump was run for 3 minutes before each measurement.
The comparison between mixed (by fan or pump) and reference chambers without electrical
mixing of the headspace is shown in Figure S10. No significant difference was seen, which
indicates that the time delay due to the protective box was negligible. A longer delay without
mixing cannot be excluded during calmer conditions (see Fig. 4 and 6). For the fastest
response it is recommended to remove the protective cover whenever possible without risking
sensor integrity.
Figure S10. Comparison of different ways to mix the headspace of floating chambers on a
small pond. Reference chambers had no powered mixing in addition to the natural mixing by
chamber and water movements. “Fan” and “Pump” denote chambers equipped with a fan or a
pump, respectively) to mix the chamber headspace. Two unites of each type was used in this
test. See text for details.
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