supporting information an automated flux chamber for
TRANSCRIPT
Supporting Information
An automated flux chamber for investigating gas flux at water – air interfaces.
Nguyen Thanh Duc *1, Samuel Silverstein2, Lars Lundmark3, Henrik Reyier4, Patrick Crill1, David Bastviken4
1 Department of Geological Sciences, Stockholm University, 106 91 Stockholm, Sweden. Email: [email protected]
Phone: +46 8 674 7597 2 Department of Physics, Stockholm University, 106 91 Stockholm, Sweden.
3 Department of Chemistry, Umeå University, 901 87 Umeå, Sweden.
4 Department of Water and Environmental Studies, Linköping University, 58183 Linköping, Sweden.
* Corresponding author
This supporting information contains twenty seven pages, two tables, and seventeen figures.
Overview of AFC The automated flux chamber contains two fundamental connected units: a flux chamber for trapping emission gas and a control box for holding a battery, a power control board, a PIC datalogger board, electrical valves, a pump and sample vials. Figure S1 - S16 illustrate various parts of the AFC system.
Figure S1: General AFC configuration consists of (A) flux chamber and control box including (B1) sampler, (B2) power supply, (B3) power control board, (B4) PIC datalogger. Note: peripheral devices of sampler are connected to male headers on power supply board in order from Pin 1 to Pin 22 which are appropriately controlled via switch name (S1 to S22) in C code.
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(A) Flux chamber
Figure S2: Flux chamber construction. All dimensions are in mm scale.
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Figure S3: Picture of a flux chamber. (a): top view, (b) bottom view, (c) front view, (d) side view
(a) (b)
(c) (d)
(B) Control box
Figure S4: Top view of (left) control box (500×390×180 mm); (right) solar panel (13.5V/5W) mounted on the lid. This control box weight is about 6kg. For safety charge battery, either a commercial charger regulator or a LM317 voltage regulator adjusted to 14.2 V output can be used.
Main switch
Setting button
S6
(B1) Sampler The sampler consists of a sample distribution manifold (Figure S5) and a sample holder (Figure S6 – S9). A completed sampler is illustrated in Figure S10.
Figure S5: Sample distribution manifold including pump, ten 2-way valves which are mounted on a 10 station manifold connect to sample holder by 100 ± 5 mm long polyurethane tubes 3.175 mm i.d. with plastic fitting male luer to barb elbow (e.g. part number LE7230-1 from www.valueplastics.com) and one 3-way valve connected to a balloon made from an inner tube.
Pump
chamber
S7
The sample holder is designed for 118 mL (52 mm outer diameter (o.d.)) and 22 mL (23 mm o.d.) vials. It consists of a sample array and three vial holders. A sample array is an aluminum frame which is bended from an aluminum plate with holes for connectors and needles (Figure S6 and S7). The bottle holder is a plastic block (186 * 57 *40 mm) which is drilled with 21, 23 and 52 mm diameter holes (Figure S8 and S9) for 23 and 52 mm o.d. vials.
Figure S6: Aluminum plate for sample array. Dashed line is cutting line to fold sample array as shown in Figure S7. Drilled holes are in pair as one for sample input to vial and one for brine output from vial. All dimensions are in mm unit.
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Figure S7: Sample array. (a): top view, (b) bottom view, (c) front view, (d) back view
(a) (b)
(c) (d)
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Figure S8: Drawing of vial holder with top view and front view. All dimensions are in mm unit.
S10
Figure S9: Vial holder. (a): top view, (b) bottom view, (c) front view, (d) back view
(a) (b)
(c) (d)
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Figure S10: Pictures of different mounting stages. (a) Bottom view of sample supply manifold mounted to sample holder. (b) Bottom view of sampler after mounting output for brine from vial. (c) Top view of a complete sampler. Brine was collected in a plastic box that can be manually emptied by a syringe to avoid release to the studied system. (d) Back view of a sampler with different needles. For using short needles (25-30 mm), a check valve (e.g. part number SCV12052 from www.valueplastics.com) is used at each sample input. This prevents brine flow backward into sample distribution manifold. Plastic fittings (male luer to female luer: e.g. part number LC78-1 from www.valueplastics.com) are used as brine output from vials. For using long needles (40 mm), no adapter is required.
(a) (b)
(c) (d)
Check valve
Output adapter
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(B3) Power control board The electronic circuit board is designed by the EAGLE software which can be downloaded at
(http://www.cadsoftusa.com/downloads/?language=en)
After installing EAGLE (e.g. freeware version), the powercontrol.brd or powercontrol.sch files (freely download “Power control board design.zip” at ftp://ftp.geo.su.se/ducnguyen/outgoing) can be opened to view design detail (e.g. Figure S11, S12 and S13). The Eagle board files can be sent directly to circuit board manufactures (e.g. Olimex) for production.
Figure S11: Picture of the power control board including top and bottom layers (opened from file powercontrol.brd).
Figure S12: Schema of the power control board (opened from file powercontrol.sch)
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Figure S13: (Left) top view, (right) bottom view of the power control board.
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3-terminal connector for e.g. temperature, methane sensors
12Vdc input
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(B4) PIC datalogger The PIC datalogger design is illustrated in Figure S14 - S16. The dl1.brd or dl1.sch files (available free in “PIC datalogger design.zip” at ftp://ftp.geo.su.se/ducnguyen/outgoing) can be opened by EAGLE to view design detail. Note: for further technical questions about the PIC datalogger, please contact Samuel Silverstein via email: [email protected]. Phone: +46 8 5537 8693
Figure S14: Picture of the PIC datalogger including top and bottom layers (opened from file dl1.brd).
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Figure S15: Schema of the PIC datalogger (opened from file dl1.sch)
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Figure S16: (Left) top view, (right) bottom view of the PIC datalogger
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The AFC software The AFC software can be downloaded to the PIC datalogger using the inexpensive Microchip PICkit2 or PICkit3 USB
programmers.
AFC software is written in C and is compiled using the free MPLAB X IDE development software and MPLAB XC16 compiler (run on a computer of Windows, Mac OS, Linux). At www.microchip.com, MPLAB X IDE and MPLAB XC16 can be freely downloaded in “Development tools” of “Design Support” tab from the main page. A user guide and other useful information are also available. Please note that the AFC software was originally developed in MPLAB IDE v8 and MPLAB C30 (freeware which are still available for loading from microchip.com and run on Windows computer) that have recently been superseded by MPLAB X IDE and MPLAB XC16. The AFC project directories for both MPLAB versions are available free of charge at ftp://ftp.geo.su.se/ducnguyen/outgoing in “AFC_C code.zip”.
For setting date and time on the PIC datalogger or for software debugging, the PIC datalogger can communicate with a computer via 9-pin serial port. For a computer without a build-in serial port, a RS232-USB converter cable can be used (example from Farnell website: http://se.farnell.com/jsp/search/productdetail.jsp?SKU=1615838). A terminal application, which is properly setting for RS232 communication, needs to be run on the computer for this purpose. For example, TERMITE is a free serial terminal application for Windows that can be freely downloaded from website http://www.compuphase.com/software_termite.htm. The TERMITE is set with baud rate: 115200, data bit: 8, Parity: none, Stop bit: 1, Flow control: none.
AFC-C code The structure of C code can be read in the following files:
AFC_sensor_lib_DN1.c is function library where all functions of the AFC such as set time, read time, prompt time, set AFC etc. were written.
AFC(designed date)_sensor_main program_v01.c is the main code which users can modify to control the AFC.
Programming idea: There are two versions of AFCs including one with sensors (e.g. pressure, temperature, CH4 and CO2 sensors), and one without sensor. Therefore, the sampling state can be initiated either by the CH4 sensor signal or by time. In the sensor mode, the CH4 sensor keeps monitoring CH4 concentration in the headspace of the chamber. When the CH4 concentration is higher than 646 ppm (equivalent to 3.3V output signal from the CH4 sensor), the sampling state will be initiated after waiting 2 minutes to allow mixing of chamber headspace. This mode is designed for the AFC with CH4 sensor (note that we tested a CH4 sensor as described in
the manuscript file but that we question the long-term stability of this sensor and that there is, to our knowledge, yet no CH4 sensor being suitable in terms of size, power consumption, detection limit, prize and stability). In the timer mode, the accumulation time is set in the SD card and the sampling state is initiated at the end of the accumulation period. This mode can be applied for both of the AFC with/without CH4 sensor. These two modes can be either automatically recognized by the programmable automatic sampler via CH4 sensor signal or set by time as chosen by the user.
Main program design As soon as PIC datalogger is powered up, the program executes as following:
1. Initialize all the peripheral devices (real time clock, RS232 port, SD card, pump and valves) 2. Wait until the main switch is on.
2.1. Refresh the sampler if refresh mode is activated by pressing and holding setting button for 3 seconds while main switch is off. 3. When main switch is on 3.1. Check if user wants to set the real time. 3.2. Open log.txt and sens.txt files on SD card. “log.txt” file records all the status and events of the AFC during deployment with the
real time. “sens.txt” file will save sensor signal with the real time. In case, files cannot open on SD card, the LED will blink. 3.3. Read all set AFC working parameters from SD card and log them back to the “log.txt”. All the working parameters include:
- Accumulation time (for accumulation state) - Number of sample vials, pre-flushing time, gas sampling time, purging time, deflating time (for sampling state) - Frequency to record sensor signals per minute (data to “sens.txt”) - Sampling mode (for sampling state):
“0”: let the AFC automatically chose sampling mode via CH4 sensor signal or set time. “1”: the sensor mode is initiated. “2”: the timer mode is initiated.
3.4 Go to a working loop: - Monitoring the battery level, terminate the working loop when battery goes low. - Recording all sensors signal with the set frequency. - Check which sampling mode is chosen.
o If “0” mode: • Read CH4 sensor signal,
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• if it >=0.100V, initiate sensor mode; • else initiate timer mode
o If “1” mode: initiate sensor mode • Keep read and record CH4 sensor signal • If CH4 sensor signal >= 3.3V and there are still enough sample bottles, start sampling state. • If ((Me_sensor signal >= 1.0) and (Me_sensor signal<= 2.0)) and ((sample bottle = 1) or (sample bottle = 5)), start
sampling state for calibration. • If CH4 sensor signal >= 3.3V and there is no sample bottle left, start ventilation process. • CH4 sensor signal monitors until the main switch is off.
o If “2” mode: initiate timer mode • Keep track of deployment time. • If deployment time = desired accumulation time and there are still enough sample bottles, start sampling state. • If all the sample bottles are used, terminate working loop and blink LED to warn the user until main switch is
off. - Working loop is terminated by turning off the main switch or low battery. All the log.txt and sens.txt files are simultaneously
closed as the working loop is terminated.
Note: All the setting parameters (freely download “AFC setting files on SD card.zip” at ftp://ftp.geo.su.se/ducnguyen/outgoing) and data from AFC are saved on the SD card.
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AFC user manual
To compile and install the AFC software on the PIC datalogger with MPLAB IDE v8 and MPLAB C30 - Connect the PICkit to the PIC datalogger. Note: if PICkit2 is used, the programmer will provide power. For PICkit 3, external
3.3V power needs to be provided. - Open MPLAB IDE v8. - Go to “Project” tab and Open the “AFC_sensorsDN1.mcp” file in the “AFC_C code” folder. Note: Please note that the Library
file of libpPIC24Fxxx-coff.a might have to be relocated to “lib/PIC24F” folder where MPLAB C30 was installed on your computer.
- Press “Ctrl+F10” or the “Build All” icon to compile C code. Wait until “Output” window pop up “BUILD SUCCEEDED” - Go to “Programmer” tab and choose PICkit2 (or PICkit3) in “select Programmer” - Click on “Program” in “Programmer” tab to program PIC datalogger. Wait for “Output” window to pop up the following
message: “Programming Target (with date and time) PIC24FJ128GA010 found (Rev 0x3007) Erasing Target Programming Program Memory (0x0 - 0x76FF) (Using Programming Executive) Verifying Program Memory (0x0 - 0x76FF) (Using Programming Executive) Programming Configuration Memory Verifying Configuration Memory PICkit 2 Ready”
- After programming is finished, disconnect the PICkit programmer from the PIC datalogger.
To compile and install the AFC software on the PIC datalogger with MPLAB X IDE and MPLAB XC16 - Connect the PICkit programmer to the PIC datalogger. Note: if PICkit2 is used, the programmer will provide power. For
PICkit 3, external 3.3V power needs to be provided. - Open MPLAB X IDE.
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- In MPLAB X, go to “File” tab on menu bar, "Open Project..." and select the “AFC_sensors.X” file in the “AFC_C code” folder. Note: 1) Check in “Libraries” of “AFC_sensors” in “Projects” window, the library file of libpPIC24Fxxx-coff.a might have to be relocated to “xc16/v1.10/lib/PIC24F” folder where MPLAB XC16 was installed on your computer. 2) Check in “AFC_sensors – Dashboard”, open “Compiler Toolchain”, and double-click on XC16, “Project properties – AFC_sensors” windows will be opened. Check in “Hardware tools” if your programmer e.g. PICkit2 is selected and in “Compiler Toolchain” if XC16 is selected.
- Go to “Run” tab on menu bar and click on "Run Project" or Press “F6” to compile C code and program the PIC datalogger. Wait until “Output” window pop up “Programming completed, Running target..”
- After programming is finished, disconnect the PICkit programmer from the PIC datalogger.
Set real date and time for AFC - Connect the PIC datalogger to a computer via a 9 pin serial null modem cable with a RS232-USB converter cable. - Open TERMITE window. Note: For more information, see section”The AFC Program” below. - Power up AFC system with 12V. - Turn on main switch and then, within 2 seconds, press and hold “Setting” button for 1 second. (Figure S4 “Setting button” - On TERMITE windows will appear "Do you want to change the external date and time? (1 (Yes) or any keys) >" - Press “1” if you want to set date and time. - Real date and time will be retrieved from the computer and saved to the board with a backup battery. - Remove cable and power off AFC when date and time has been set.
Start AFC in field - Power up AFC with a 12V battery. - Press and hold “Setting button” for 3 seconds (with the main switch in the Off position) to activate rinsing function. Note:
The tube and sample deliver system will be flushed by air. - Insert SD card with pre-set files including sampling mode, accumulation time, sample numbers, sampling times, ventilation
times, rinsing time, balloon deflate time, etc (example setting available in folder “AFC setting files on SD card”) - Snap sample vials into the sample holder. Make sure to use needles adapted to the septa/stopper chosen – a mismatch can
cause leakage through septa after sampling. Also try to make the needles go straight through the septum/stopper. - Deploy flux chamber on water surface to initiate the deployment period..
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- Turn on the main switch. Note: Pay attention to the LED indicator - if it blinks, there is a problem. If so, see the trouble shooting part below.
- Close the lid of the control box.
Finish a deployment period - Open the lid of the control box. Note: If the LED indicator blink (on in 1 second, off in 1 second) all sample vials were used. - Turn off main switch. - Remove sample vials.
Continue sampling - Lift flux chamber out of water surface. - Press and hold “Setting” button for 3 seconds (main switch in Off position) to activate rinsing function. - Wait about 45 seconds for finishing rinsing procedure. - Snap in new sample vials. - Deploy flux chamber on water surface. - Turn on main switch. - Close lid of control box.
Stop sampling
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Troubleshooting When turning on the main switch,
- LED indicator blinks fast (on/off in 1/10 second) if there is a problem related to the SD card. Check if: o All files with settings are available. o Or SD cannot be opened. Try to solve by formatting SD card to FAT32 by SD formatter which was freely download
from https://www.sdcard.org/downloads/formatter_3/
Note: AFC may need to be powered off for PIC datalogger restart.
- The LED indicator blinks slow (on in 1/10 second, off in 1 second) if there is a problem caused by low battery. o Solved by either change or recharge of the battery.
Figure S17: Variation of CH4 concentration in the FC over 13 day deployment. An example of two weeks deployment with preset of set time mode, 36 hours accumulation, 15 minutes ventilation, 5 minutes deflation and CH4 sensor signal sampling frequency of 1 signal per minute. Ebullitive events were marked as “Eb”.
Eb 1
Eb 2
Eb 3
Eb 4
Eb 5
Eb 6
Eb 7
Eb 8
Eb 9
Eb10
Eb11
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Table S1: Part list of control power board with product number examples from www.farnell.com. Note:*: Rectifier diode can be removed in case peripheral device has built in diode.
Part Device Farnell PN Package Value Qty CS1 CAPACITOR 1236676 E2-5 0.47UF, 63V 1
CS2 CAPACITOR 9451161 E2-5 22UF, 25V 1 C1 - C22 CAPACITOR 9451226 E5-10,5 1000UF, 25V 22
C23, C27 CAPACITOR 9452729 E1,8-4 0.1UF, 63V 2 C25 CAPACITOR 9691944 E3,5-8 470UF, 10V 1
C26 CAPACITOR 9451820 E2-5 47UF, 25V 1 C28 CAPACITOR 9452192 E1,8-4 10UF, 16V 1 D1 RECTIFIER DIODE 5382300 C4111-15 1N5820 1
D2 – D23 DIODE, POWER RECTIFIER 1651094 DO41-10 1N4001-E3/1 22* IC1 V REG LDO +10V, 2940 9493522 TO220V LM2940T-10.0 1
IC2 OP-AMP JFET LOW NOISE 1094351 DIL08 TL071CN IC3 SWITCHING REG 1A ADJ, SMD, 2575 9489878 TO263-5 LM2575S-ADJ 1 IC4 V REG, LINEAR, 3.3V 1469066 TO263-3 LM2937ES-3.3/NOPB 1
IC5 AD620ANZ 1079404 DIL8 AD620ANZ IC6 LMC6484IN/NOPB - Operational Amplifier 1179682 DIL14 LMC6484 1
R1 - R22 RESISTOR, 0.25W 1% 13R 9341307 0207/10 13ohm 21 R23 Thin Film Chip Resistor 9372830 R0805 5.49k 1
R24 – R26, R29 – R47 RESISTOR 1469857 M0805 10k 22 R27 RESISTOR 9341110 0207/12 10k 1 R28 RESISTOR 9341480 0207/12 2k 1
RF1 – RF4 RESISTOR 1469871 M0805 14k 4 RI1 – RI4 RESISTOR 1469884 M0805 2k 4
RS1 RESISTOR 9341102 0207/12 1k 1 RS2 RESISTOR 1879249 0207/12 2.1k 1 T1 - T22 BD677. TRANSISTOR 4399572 TO126V BD677 22
L1 INDUCTOR, PE53118NL 1209559 SFT1030 470UH 1 S1 2 WAY PIN CONNECTOR TO PUMP AND VALVE
SV2 MOLEX - 22-23-2021 - HEADER, PIN, 2WAY 1462926 1 LM35* MOLEX - 22-23-2031 - HEADER, PIN, 3WAY 1462950 4
SV4 MOLEX - 22-23-2041 - HEADER, PIN, 4WAY 1462920 JP1, JP2 LINE SELECTION BY JUMPER 2
Table S2: Part list of PIC datalogger with product number examples from www.farnell.com
Part Device Farnell PN Package Value Qty C1 CAPACITOR 1463377 C0805K 10 UF, 6.3V 1
C2,3,6 - 24 CAPACITOR 1362552 C0805K 0.1UF, 50V 21 C4,5 CAPACITOR 1759195RL C0805 22 pF, 50V 2
IC1 MICROCHIP - PIC24FJ128GA010-I/PF - 16BIT MCU 128K FLASH 8K RAM, SMD 1146522 TQFP100_14x14 PIC24FJ128GA010 1 IC2 EXAR - SP3223EEY-L - TRANSCEIVER RS-232 +3.0V TO +5.5V 9386831 TSSOP20 MAX3223EUP 1
LED2 LED, 3MM, 70°, RED 1581214 LED3MM 1 Q1,2 CRYSTAL, WATCH, 32.768KHZ, CYL, 6PF 1457085 HC49/S 32.768KHZ 2 R1,2,5 RESISTOR 1469884 R0805 2K 3
R9 RESISTOR 9234160 R0805 18K 1 R10 – 15 RESISTOR 1469857 R0805 10K 6
R16,17 RESISTOR 9234098 R0805 4K7 2 SV4 HEADER, STRAIGHT, 40WAY 636393 MA20-2 1 U$2 HEADER, 1 ROW, R/ANGLE, 6WAY 1593430 6-PIN-HDR 1
U$3 ISL1219IUZ - RTC/CALENDAR, BATT BACKUP SRAM, I2C 1360970 MSOP-10 1
U$4 SDCMF-10915W0T1 - CARD, SD, METAL COVER + STANDOFF 9186166 SDCMF-
10915W010 1
U$5 HOLDER, BATTERY, 1 CELL, 20MM
676469 CR2032 1 X1 PLUG, D, PCB, R/A, 9WAY 1099289 M09HP 1
Overview of AFC
(A) Flux chamber
(B) Control box
Main program design
AFC user manual
To compile and install the AFC software on the PIC datalogger with MPLAB IDE v8 and MPLAB C30
To compile and install the AFC software on the PIC datalogger with MPLAB X IDE and MPLAB XC16
Set real date and time for AFC
Start AFC in field
Finish a deployment period
An automated flux chamber for investigating gas flux at water – air interfaces.
Nguyen Thanh Duc *1, Samuel Silverstein2, Lars Lundmark3, Henrik Reyier4, Patrick Crill1, David Bastviken4
1 Department of Geological Sciences, Stockholm University, 106 91 Stockholm, Sweden. Email: [email protected]
Phone: +46 8 674 7597 2 Department of Physics, Stockholm University, 106 91 Stockholm, Sweden.
3 Department of Chemistry, Umeå University, 901 87 Umeå, Sweden.
4 Department of Water and Environmental Studies, Linköping University, 58183 Linköping, Sweden.
* Corresponding author
This supporting information contains twenty seven pages, two tables, and seventeen figures.
Overview of AFC The automated flux chamber contains two fundamental connected units: a flux chamber for trapping emission gas and a control box for holding a battery, a power control board, a PIC datalogger board, electrical valves, a pump and sample vials. Figure S1 - S16 illustrate various parts of the AFC system.
Figure S1: General AFC configuration consists of (A) flux chamber and control box including (B1) sampler, (B2) power supply, (B3) power control board, (B4) PIC datalogger. Note: peripheral devices of sampler are connected to male headers on power supply board in order from Pin 1 to Pin 22 which are appropriately controlled via switch name (S1 to S22) in C code.
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(A) Flux chamber
Figure S2: Flux chamber construction. All dimensions are in mm scale.
S4
Figure S3: Picture of a flux chamber. (a): top view, (b) bottom view, (c) front view, (d) side view
(a) (b)
(c) (d)
(B) Control box
Figure S4: Top view of (left) control box (500×390×180 mm); (right) solar panel (13.5V/5W) mounted on the lid. This control box weight is about 6kg. For safety charge battery, either a commercial charger regulator or a LM317 voltage regulator adjusted to 14.2 V output can be used.
Main switch
Setting button
S6
(B1) Sampler The sampler consists of a sample distribution manifold (Figure S5) and a sample holder (Figure S6 – S9). A completed sampler is illustrated in Figure S10.
Figure S5: Sample distribution manifold including pump, ten 2-way valves which are mounted on a 10 station manifold connect to sample holder by 100 ± 5 mm long polyurethane tubes 3.175 mm i.d. with plastic fitting male luer to barb elbow (e.g. part number LE7230-1 from www.valueplastics.com) and one 3-way valve connected to a balloon made from an inner tube.
Pump
chamber
S7
The sample holder is designed for 118 mL (52 mm outer diameter (o.d.)) and 22 mL (23 mm o.d.) vials. It consists of a sample array and three vial holders. A sample array is an aluminum frame which is bended from an aluminum plate with holes for connectors and needles (Figure S6 and S7). The bottle holder is a plastic block (186 * 57 *40 mm) which is drilled with 21, 23 and 52 mm diameter holes (Figure S8 and S9) for 23 and 52 mm o.d. vials.
Figure S6: Aluminum plate for sample array. Dashed line is cutting line to fold sample array as shown in Figure S7. Drilled holes are in pair as one for sample input to vial and one for brine output from vial. All dimensions are in mm unit.
S8
Figure S7: Sample array. (a): top view, (b) bottom view, (c) front view, (d) back view
(a) (b)
(c) (d)
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Figure S8: Drawing of vial holder with top view and front view. All dimensions are in mm unit.
S10
Figure S9: Vial holder. (a): top view, (b) bottom view, (c) front view, (d) back view
(a) (b)
(c) (d)
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Figure S10: Pictures of different mounting stages. (a) Bottom view of sample supply manifold mounted to sample holder. (b) Bottom view of sampler after mounting output for brine from vial. (c) Top view of a complete sampler. Brine was collected in a plastic box that can be manually emptied by a syringe to avoid release to the studied system. (d) Back view of a sampler with different needles. For using short needles (25-30 mm), a check valve (e.g. part number SCV12052 from www.valueplastics.com) is used at each sample input. This prevents brine flow backward into sample distribution manifold. Plastic fittings (male luer to female luer: e.g. part number LC78-1 from www.valueplastics.com) are used as brine output from vials. For using long needles (40 mm), no adapter is required.
(a) (b)
(c) (d)
Check valve
Output adapter
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(B3) Power control board The electronic circuit board is designed by the EAGLE software which can be downloaded at
(http://www.cadsoftusa.com/downloads/?language=en)
After installing EAGLE (e.g. freeware version), the powercontrol.brd or powercontrol.sch files (freely download “Power control board design.zip” at ftp://ftp.geo.su.se/ducnguyen/outgoing) can be opened to view design detail (e.g. Figure S11, S12 and S13). The Eagle board files can be sent directly to circuit board manufactures (e.g. Olimex) for production.
Figure S11: Picture of the power control board including top and bottom layers (opened from file powercontrol.brd).
Figure S12: Schema of the power control board (opened from file powercontrol.sch)
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Figure S13: (Left) top view, (right) bottom view of the power control board.
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3-terminal connector for e.g. temperature, methane sensors
12Vdc input
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(B4) PIC datalogger The PIC datalogger design is illustrated in Figure S14 - S16. The dl1.brd or dl1.sch files (available free in “PIC datalogger design.zip” at ftp://ftp.geo.su.se/ducnguyen/outgoing) can be opened by EAGLE to view design detail. Note: for further technical questions about the PIC datalogger, please contact Samuel Silverstein via email: [email protected]. Phone: +46 8 5537 8693
Figure S14: Picture of the PIC datalogger including top and bottom layers (opened from file dl1.brd).
S16
Figure S15: Schema of the PIC datalogger (opened from file dl1.sch)
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Figure S16: (Left) top view, (right) bottom view of the PIC datalogger
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The AFC software The AFC software can be downloaded to the PIC datalogger using the inexpensive Microchip PICkit2 or PICkit3 USB
programmers.
AFC software is written in C and is compiled using the free MPLAB X IDE development software and MPLAB XC16 compiler (run on a computer of Windows, Mac OS, Linux). At www.microchip.com, MPLAB X IDE and MPLAB XC16 can be freely downloaded in “Development tools” of “Design Support” tab from the main page. A user guide and other useful information are also available. Please note that the AFC software was originally developed in MPLAB IDE v8 and MPLAB C30 (freeware which are still available for loading from microchip.com and run on Windows computer) that have recently been superseded by MPLAB X IDE and MPLAB XC16. The AFC project directories for both MPLAB versions are available free of charge at ftp://ftp.geo.su.se/ducnguyen/outgoing in “AFC_C code.zip”.
For setting date and time on the PIC datalogger or for software debugging, the PIC datalogger can communicate with a computer via 9-pin serial port. For a computer without a build-in serial port, a RS232-USB converter cable can be used (example from Farnell website: http://se.farnell.com/jsp/search/productdetail.jsp?SKU=1615838). A terminal application, which is properly setting for RS232 communication, needs to be run on the computer for this purpose. For example, TERMITE is a free serial terminal application for Windows that can be freely downloaded from website http://www.compuphase.com/software_termite.htm. The TERMITE is set with baud rate: 115200, data bit: 8, Parity: none, Stop bit: 1, Flow control: none.
AFC-C code The structure of C code can be read in the following files:
AFC_sensor_lib_DN1.c is function library where all functions of the AFC such as set time, read time, prompt time, set AFC etc. were written.
AFC(designed date)_sensor_main program_v01.c is the main code which users can modify to control the AFC.
Programming idea: There are two versions of AFCs including one with sensors (e.g. pressure, temperature, CH4 and CO2 sensors), and one without sensor. Therefore, the sampling state can be initiated either by the CH4 sensor signal or by time. In the sensor mode, the CH4 sensor keeps monitoring CH4 concentration in the headspace of the chamber. When the CH4 concentration is higher than 646 ppm (equivalent to 3.3V output signal from the CH4 sensor), the sampling state will be initiated after waiting 2 minutes to allow mixing of chamber headspace. This mode is designed for the AFC with CH4 sensor (note that we tested a CH4 sensor as described in
the manuscript file but that we question the long-term stability of this sensor and that there is, to our knowledge, yet no CH4 sensor being suitable in terms of size, power consumption, detection limit, prize and stability). In the timer mode, the accumulation time is set in the SD card and the sampling state is initiated at the end of the accumulation period. This mode can be applied for both of the AFC with/without CH4 sensor. These two modes can be either automatically recognized by the programmable automatic sampler via CH4 sensor signal or set by time as chosen by the user.
Main program design As soon as PIC datalogger is powered up, the program executes as following:
1. Initialize all the peripheral devices (real time clock, RS232 port, SD card, pump and valves) 2. Wait until the main switch is on.
2.1. Refresh the sampler if refresh mode is activated by pressing and holding setting button for 3 seconds while main switch is off. 3. When main switch is on 3.1. Check if user wants to set the real time. 3.2. Open log.txt and sens.txt files on SD card. “log.txt” file records all the status and events of the AFC during deployment with the
real time. “sens.txt” file will save sensor signal with the real time. In case, files cannot open on SD card, the LED will blink. 3.3. Read all set AFC working parameters from SD card and log them back to the “log.txt”. All the working parameters include:
- Accumulation time (for accumulation state) - Number of sample vials, pre-flushing time, gas sampling time, purging time, deflating time (for sampling state) - Frequency to record sensor signals per minute (data to “sens.txt”) - Sampling mode (for sampling state):
“0”: let the AFC automatically chose sampling mode via CH4 sensor signal or set time. “1”: the sensor mode is initiated. “2”: the timer mode is initiated.
3.4 Go to a working loop: - Monitoring the battery level, terminate the working loop when battery goes low. - Recording all sensors signal with the set frequency. - Check which sampling mode is chosen.
o If “0” mode: • Read CH4 sensor signal,
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• if it >=0.100V, initiate sensor mode; • else initiate timer mode
o If “1” mode: initiate sensor mode • Keep read and record CH4 sensor signal • If CH4 sensor signal >= 3.3V and there are still enough sample bottles, start sampling state. • If ((Me_sensor signal >= 1.0) and (Me_sensor signal<= 2.0)) and ((sample bottle = 1) or (sample bottle = 5)), start
sampling state for calibration. • If CH4 sensor signal >= 3.3V and there is no sample bottle left, start ventilation process. • CH4 sensor signal monitors until the main switch is off.
o If “2” mode: initiate timer mode • Keep track of deployment time. • If deployment time = desired accumulation time and there are still enough sample bottles, start sampling state. • If all the sample bottles are used, terminate working loop and blink LED to warn the user until main switch is
off. - Working loop is terminated by turning off the main switch or low battery. All the log.txt and sens.txt files are simultaneously
closed as the working loop is terminated.
Note: All the setting parameters (freely download “AFC setting files on SD card.zip” at ftp://ftp.geo.su.se/ducnguyen/outgoing) and data from AFC are saved on the SD card.
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AFC user manual
To compile and install the AFC software on the PIC datalogger with MPLAB IDE v8 and MPLAB C30 - Connect the PICkit to the PIC datalogger. Note: if PICkit2 is used, the programmer will provide power. For PICkit 3, external
3.3V power needs to be provided. - Open MPLAB IDE v8. - Go to “Project” tab and Open the “AFC_sensorsDN1.mcp” file in the “AFC_C code” folder. Note: Please note that the Library
file of libpPIC24Fxxx-coff.a might have to be relocated to “lib/PIC24F” folder where MPLAB C30 was installed on your computer.
- Press “Ctrl+F10” or the “Build All” icon to compile C code. Wait until “Output” window pop up “BUILD SUCCEEDED” - Go to “Programmer” tab and choose PICkit2 (or PICkit3) in “select Programmer” - Click on “Program” in “Programmer” tab to program PIC datalogger. Wait for “Output” window to pop up the following
message: “Programming Target (with date and time) PIC24FJ128GA010 found (Rev 0x3007) Erasing Target Programming Program Memory (0x0 - 0x76FF) (Using Programming Executive) Verifying Program Memory (0x0 - 0x76FF) (Using Programming Executive) Programming Configuration Memory Verifying Configuration Memory PICkit 2 Ready”
- After programming is finished, disconnect the PICkit programmer from the PIC datalogger.
To compile and install the AFC software on the PIC datalogger with MPLAB X IDE and MPLAB XC16 - Connect the PICkit programmer to the PIC datalogger. Note: if PICkit2 is used, the programmer will provide power. For
PICkit 3, external 3.3V power needs to be provided. - Open MPLAB X IDE.
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- In MPLAB X, go to “File” tab on menu bar, "Open Project..." and select the “AFC_sensors.X” file in the “AFC_C code” folder. Note: 1) Check in “Libraries” of “AFC_sensors” in “Projects” window, the library file of libpPIC24Fxxx-coff.a might have to be relocated to “xc16/v1.10/lib/PIC24F” folder where MPLAB XC16 was installed on your computer. 2) Check in “AFC_sensors – Dashboard”, open “Compiler Toolchain”, and double-click on XC16, “Project properties – AFC_sensors” windows will be opened. Check in “Hardware tools” if your programmer e.g. PICkit2 is selected and in “Compiler Toolchain” if XC16 is selected.
- Go to “Run” tab on menu bar and click on "Run Project" or Press “F6” to compile C code and program the PIC datalogger. Wait until “Output” window pop up “Programming completed, Running target..”
- After programming is finished, disconnect the PICkit programmer from the PIC datalogger.
Set real date and time for AFC - Connect the PIC datalogger to a computer via a 9 pin serial null modem cable with a RS232-USB converter cable. - Open TERMITE window. Note: For more information, see section”The AFC Program” below. - Power up AFC system with 12V. - Turn on main switch and then, within 2 seconds, press and hold “Setting” button for 1 second. (Figure S4 “Setting button” - On TERMITE windows will appear "Do you want to change the external date and time? (1 (Yes) or any keys) >" - Press “1” if you want to set date and time. - Real date and time will be retrieved from the computer and saved to the board with a backup battery. - Remove cable and power off AFC when date and time has been set.
Start AFC in field - Power up AFC with a 12V battery. - Press and hold “Setting button” for 3 seconds (with the main switch in the Off position) to activate rinsing function. Note:
The tube and sample deliver system will be flushed by air. - Insert SD card with pre-set files including sampling mode, accumulation time, sample numbers, sampling times, ventilation
times, rinsing time, balloon deflate time, etc (example setting available in folder “AFC setting files on SD card”) - Snap sample vials into the sample holder. Make sure to use needles adapted to the septa/stopper chosen – a mismatch can
cause leakage through septa after sampling. Also try to make the needles go straight through the septum/stopper. - Deploy flux chamber on water surface to initiate the deployment period..
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- Turn on the main switch. Note: Pay attention to the LED indicator - if it blinks, there is a problem. If so, see the trouble shooting part below.
- Close the lid of the control box.
Finish a deployment period - Open the lid of the control box. Note: If the LED indicator blink (on in 1 second, off in 1 second) all sample vials were used. - Turn off main switch. - Remove sample vials.
Continue sampling - Lift flux chamber out of water surface. - Press and hold “Setting” button for 3 seconds (main switch in Off position) to activate rinsing function. - Wait about 45 seconds for finishing rinsing procedure. - Snap in new sample vials. - Deploy flux chamber on water surface. - Turn on main switch. - Close lid of control box.
Stop sampling
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Troubleshooting When turning on the main switch,
- LED indicator blinks fast (on/off in 1/10 second) if there is a problem related to the SD card. Check if: o All files with settings are available. o Or SD cannot be opened. Try to solve by formatting SD card to FAT32 by SD formatter which was freely download
from https://www.sdcard.org/downloads/formatter_3/
Note: AFC may need to be powered off for PIC datalogger restart.
- The LED indicator blinks slow (on in 1/10 second, off in 1 second) if there is a problem caused by low battery. o Solved by either change or recharge of the battery.
Figure S17: Variation of CH4 concentration in the FC over 13 day deployment. An example of two weeks deployment with preset of set time mode, 36 hours accumulation, 15 minutes ventilation, 5 minutes deflation and CH4 sensor signal sampling frequency of 1 signal per minute. Ebullitive events were marked as “Eb”.
Eb 1
Eb 2
Eb 3
Eb 4
Eb 5
Eb 6
Eb 7
Eb 8
Eb 9
Eb10
Eb11
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Table S1: Part list of control power board with product number examples from www.farnell.com. Note:*: Rectifier diode can be removed in case peripheral device has built in diode.
Part Device Farnell PN Package Value Qty CS1 CAPACITOR 1236676 E2-5 0.47UF, 63V 1
CS2 CAPACITOR 9451161 E2-5 22UF, 25V 1 C1 - C22 CAPACITOR 9451226 E5-10,5 1000UF, 25V 22
C23, C27 CAPACITOR 9452729 E1,8-4 0.1UF, 63V 2 C25 CAPACITOR 9691944 E3,5-8 470UF, 10V 1
C26 CAPACITOR 9451820 E2-5 47UF, 25V 1 C28 CAPACITOR 9452192 E1,8-4 10UF, 16V 1 D1 RECTIFIER DIODE 5382300 C4111-15 1N5820 1
D2 – D23 DIODE, POWER RECTIFIER 1651094 DO41-10 1N4001-E3/1 22* IC1 V REG LDO +10V, 2940 9493522 TO220V LM2940T-10.0 1
IC2 OP-AMP JFET LOW NOISE 1094351 DIL08 TL071CN IC3 SWITCHING REG 1A ADJ, SMD, 2575 9489878 TO263-5 LM2575S-ADJ 1 IC4 V REG, LINEAR, 3.3V 1469066 TO263-3 LM2937ES-3.3/NOPB 1
IC5 AD620ANZ 1079404 DIL8 AD620ANZ IC6 LMC6484IN/NOPB - Operational Amplifier 1179682 DIL14 LMC6484 1
R1 - R22 RESISTOR, 0.25W 1% 13R 9341307 0207/10 13ohm 21 R23 Thin Film Chip Resistor 9372830 R0805 5.49k 1
R24 – R26, R29 – R47 RESISTOR 1469857 M0805 10k 22 R27 RESISTOR 9341110 0207/12 10k 1 R28 RESISTOR 9341480 0207/12 2k 1
RF1 – RF4 RESISTOR 1469871 M0805 14k 4 RI1 – RI4 RESISTOR 1469884 M0805 2k 4
RS1 RESISTOR 9341102 0207/12 1k 1 RS2 RESISTOR 1879249 0207/12 2.1k 1 T1 - T22 BD677. TRANSISTOR 4399572 TO126V BD677 22
L1 INDUCTOR, PE53118NL 1209559 SFT1030 470UH 1 S1 2 WAY PIN CONNECTOR TO PUMP AND VALVE
SV2 MOLEX - 22-23-2021 - HEADER, PIN, 2WAY 1462926 1 LM35* MOLEX - 22-23-2031 - HEADER, PIN, 3WAY 1462950 4
SV4 MOLEX - 22-23-2041 - HEADER, PIN, 4WAY 1462920 JP1, JP2 LINE SELECTION BY JUMPER 2
Table S2: Part list of PIC datalogger with product number examples from www.farnell.com
Part Device Farnell PN Package Value Qty C1 CAPACITOR 1463377 C0805K 10 UF, 6.3V 1
C2,3,6 - 24 CAPACITOR 1362552 C0805K 0.1UF, 50V 21 C4,5 CAPACITOR 1759195RL C0805 22 pF, 50V 2
IC1 MICROCHIP - PIC24FJ128GA010-I/PF - 16BIT MCU 128K FLASH 8K RAM, SMD 1146522 TQFP100_14x14 PIC24FJ128GA010 1 IC2 EXAR - SP3223EEY-L - TRANSCEIVER RS-232 +3.0V TO +5.5V 9386831 TSSOP20 MAX3223EUP 1
LED2 LED, 3MM, 70°, RED 1581214 LED3MM 1 Q1,2 CRYSTAL, WATCH, 32.768KHZ, CYL, 6PF 1457085 HC49/S 32.768KHZ 2 R1,2,5 RESISTOR 1469884 R0805 2K 3
R9 RESISTOR 9234160 R0805 18K 1 R10 – 15 RESISTOR 1469857 R0805 10K 6
R16,17 RESISTOR 9234098 R0805 4K7 2 SV4 HEADER, STRAIGHT, 40WAY 636393 MA20-2 1 U$2 HEADER, 1 ROW, R/ANGLE, 6WAY 1593430 6-PIN-HDR 1
U$3 ISL1219IUZ - RTC/CALENDAR, BATT BACKUP SRAM, I2C 1360970 MSOP-10 1
U$4 SDCMF-10915W0T1 - CARD, SD, METAL COVER + STANDOFF 9186166 SDCMF-
10915W010 1
U$5 HOLDER, BATTERY, 1 CELL, 20MM
676469 CR2032 1 X1 PLUG, D, PCB, R/A, 9WAY 1099289 M09HP 1
Overview of AFC
(A) Flux chamber
(B) Control box
Main program design
AFC user manual
To compile and install the AFC software on the PIC datalogger with MPLAB IDE v8 and MPLAB C30
To compile and install the AFC software on the PIC datalogger with MPLAB X IDE and MPLAB XC16
Set real date and time for AFC
Start AFC in field
Finish a deployment period