RRIV Methane Beta Setup

Overview

Beta version RRIV loggers with methane (CH₄) and carbon dioxide (CO₂). Methane sensors use a Figaro NGM2611-E13 metal oxide sensor and CO₂ sensors use a Atlas Scientific infrared carbon dioxide sensor. Sensors were encased in segments of 1-1/4" PVC pipe with one end covered by a 0.005" thick PTFE diaphragm to permit gas exchange with the water.

Tools

2 adjustable wrench 3/8” to 1 ¼”
Pliers 3/8” to 1 ¼”
Mini USB to USB cable
Programming header (Figure 1)
ABS Rubber Cement
Molykote Grease 111

Figure 1: ST Nucleo programming header

Included components

RRIV Data Logger (V0.21)
Enclosed CH₄ sensor
Enclosed CO₂ sensor
ABS sonde housing

Off the shelf components to purchase

Item

Number Needed per Device

Source & Part Number

EPDM O-Ring (Size: Dash Number 341)

McMaster-Carr 9557K316

18-8 stainless steel threaded rod 3/8” – 16 [2']

McMaster-Carr 98804A031

18-8 stainless steel hex nuts 3/8” -16

McMaster-Carr 91845A031

18-8 stainless steel washers 3/8”

McMaster-Carr 92141A031

Tenergy rechargeable NiMH D cell batteries

Tenergy D Cell Batteries

Tenergy NiMH D cell battery charger

Tenergy Battery Charger

Dupont jumper cables F-F

Digikey 1528-1961-ND

Dupont jumper cables M-M

Digikey 1568-1512-ND

Copper Mesh Roll

Home Depot

Initial sensor setup and configuration

Install Microsoft VS Code and then from within VS Code install the PlatformIO extension.
Go to https://github.com/kenchong48/rriv/tree/continuousPower and clone the repository there with github or download manually to a folder on your computer.
- If you clone the repository, you may have to navigate to the continuousPower branch, check with git branch, switch branches with git checkout continuousPouwer
Use dupont jumper cables to connect the programming board to the RRIV logger for communication following Figures 2 and 3- programming header CN4 pins 2, 3, 4, TX, RX to the three RRIV pins 4, 3, 2 on the bottom of the board, then RX and TX on the Nucleo CN10 pins 35 and 37.
Connect the methane sensor plugs to the board as pictured in Figure 4 - red+white into ADC4, purple+green into ADC2, black+blue+orange into ADC1. Plug the remaining 4-pin plug of the CO2 sensor into one of the ports on the back of the board.
Plug the usb cable into the programming board and the computer you are using.
Open VS Code and select the PlatformIO icon on the left side of the VS Code window. On the platformio home screen select open project and navigate to folder containing the RRIV repository you downloaded and select open folder.
Now use the keys CTRL+SHIFT+P (macos: CMD+SHIFT+P) and type serial monitor.
- This will present you with an option for PlatformIO: Serial Monitor.
- While your computer is connected via USB to the RRIV logger is connected to a power source, select the PlatformIO: Serial Monitor. This will open a serial connection that will allow you to give commands to the RRIV logger.
To learn more about the command line interface (CLI) and the commands available check RRIV documentation here or type help into the RRIV CLI command prompt and hit enter.
To configure the sensor paste the following commands in the CLI one at a time (press enter after each command): Command for setting up sampling interval: set-config {"loggerName":"writeOnBoard", "siteName":"7char", "deploymentIdentifier":"15char", "wakeInterval":60, "startUpDelay":0, "burstNumber":60, "interBurstDelay":1} Command that configures the humidity sensor integrated with the methane sensor: set-slot-config {"slot":1, "type":"adafruit_dht22", "tag":"dht", "burst_size":10, "sensor_pin":5} Command that configures the CO₂ sensor: set-slot-config {"slot":2, "type":"atlas_co2", "tag":"atlas", "burst_size":10} Command that configures the CH₄ sensor: set-slot-config {"slot":3, "type":"generic_analog", "tag":"ch4", "burst_size":10, "adc_select":"external", "sensor_port":2}
To test the sensors type the command start-logging while the sensors are connected to the RRIV logger and press enter. This command will continuously report sensor values until you type stop-logging. Note: while the system is logging, values will continuously update sensor performance using the command start-logging. This means that when you are typing stop-logging the letters you type in will be broken up by new lines of data. The device will still read your typing as a single command so keep typing and press enter and the logger will stop.
To beginning using the logger type deploy-now and press enter. Any time the logger is powered up after this it will immediately enter deployment mode after 5 seconds and begin collecting data following the configurations set above. Thus, you can keep the device powered down and add the batteries in the field immediately before deployment.

Figure 2: RRIV Logger with the pins that are used to connect the programming board indicated by the orange box. TODO: fix annotation, order for pins is opposite, Green-Blue-Purple

Figure 3: a) The programming board connected to a RRIV logger using a set of five dupont jumper cables. b) a close-up of the programming board with the color of the jumper cable to be connected at each pin indicated.

Figure 4: Methane and humidity sensors plugged into the analog to digital converter (ADC) ports.

Commands and notes for rapid configuration of a device

get-config is used to check the configuration of the settings as they are, the first section displayed is the datalogger settings followed by sensor slot settings
- There is one hardcoded setting to take note of which is continuous_power, whether it is true/false is shown when using get-config.
- To switch this setting one must go to the line settings->continuous_power = true; in the datalogger.cpp file and change true to false, then recompile and flash the code.
- The instance where this should be left as true is when calibrating the methane sensors which benefits from taking continuous measurements and suffers from the sensor module cooling down.
set-config
- loggerName is a colloquial name that has been written on the back of the board in sharpie
- siteName is a 7 character string to indicate where the RRIV is being deployed, this will also be used in the folder structure of CSV output, so should be unique
- deploymentIdentifier is a 15 character string to indicate what experiment is being run
- wakeInterval is in minutes and determines when the board wakes up to begin measurement cycles. 60 indicates to wake up every hour, 1 indicates every minute. The next interval is calculated at the end of a measurement cycle
- startUpDelay is a duration in minutes to delay before starting the measurement cycle
- burstNumber indicates how many burst cycles to complete during a measurement cycle
- interBurstDelay now also works as an interval given in minutes for when to begin taking readings. 1 indicates to take readings at every minute
example of set-config that will need to be customized

set-config {"loggerName":"writeOnBoard","siteName":"7char","deploymentIdentifier":"15char","wakeInterval":1,"startUpDelay":0,"burstNumber":60,"interBurstDelay":1}

set-slot-config:
- slot is a digital slot of data set aside in the EEPROM to hold a sensor configuration
- type is what driver type occupies the slot, these can be found by looking in the registry.cpp and following the "_TYPE_STRING" definitions
- tag is a 5 character prefix for column headers, these should be left alone unless there are multiple of the same sensor in a system
- burst_size is the number of reading cycles that should occur per burst
- sensor_pin only for DHT22 currently, indicates which specific GPIO pin is being used for the sensor
- adc_select only for analog sensors, can be either 'internal' or 'external' and indicates whether the analog sensor data is being processed by the ADC in the MCU or the external one
- sensor_port only for analog sensors, indicates which physical port the sensor is occupying
These can and should be used as they are to setup the AHT, CO2, and CH4 sensors, though once configured should be retained:

  set-slot-config {"slot":1,"type":"adafruit_dht22","tag":"dht","burst_size":10,"sensor_pin":5}

  set-slot-config {"slot":2,"type":"atlas_co2","tag":"atlas","burst_size":10}

  set-slot-config {"slot":3,"type":"generic_analog","tag":"ch4","burst_size":10,"adc_select":"external","sensor_port":2}

To check that all sensors are working properly use start-logging and when satisfied stop-logging
If the DHT is showing errors restart the board using restart then try again
If the serial is showing many I2C errors, disconnect the CO2 sensor and restart, if it is no longer showing I2C errors then manually switch the CO2 sensor from UART to I2C mode, if it is still showing I2C errors then unplug power and USB, hold reset button for a few seconds, then try again, or keep hitting the reset button until the errors clear
To put the system in deployment mode use deploy-now, it will then go to sleep until the next wake interval

Once the sensor has been deployed

When the system has been recovered, if the system has been fully drained of power then disconnect the power source, if the system is still powered, hit the physical reset button (Black push button) before disconnecting power
At this point you can remove the SD card and copy the data from it, then move folders into the oldData folder(we've been preserving old data on the SD cards for now), the file structure is Data/{siteName}/epochTimestampAtFileCreation.CSV
Take the logger out of the case and connect the programming board to the device as described above (Figure 2)
Open up the serial monitor in VS Code
Power up the device with batteries or a wall outlet
Once the device is fully booted up and you have reached the command prompt, you have 5 seconds to press the letter 'i' and then press enter. This puts the device back into interactive mode for further use

Data

The DHT22 reports temperature in degrees Celsius and relative humidity in percentage
CO2 data is reported in ppm
Methane data is reported as a digital reading, which can be converted to volts by reading*5/4096 or millivolts reading*5000/4096, 5V being the voltage to the ADC and sensor, and 4096 being 2^12, which is the precision of the ADC

Sonde assembly

Figure 5: Assembly of the extended sensor housing Figure 5: Assembly of the extended sensor housing

Part assembly:
- Use the ABS cement to secure the central housing ABS section into both the open sides of the couplers. Follow directions on the ABS cement to do so. Leave to cure in a ventilated space for 2hours
- Apply a coat of Molykote 111 around the large O-rings and add them around the short sections of ABS in the couplers

Case Assembly:

Add 2 nuts onto each of the 6 steel threaded rods, around 1" and 8" from the same end, then add washers to them one from each end of the rod.
Add the 6 rods through an acrylic end plate (does not have the holes for the cable glands / sensors) and affix each rod with another washer and nut.
Apply Molykote to the O-ring of the cable gland and attach with sensors through the sensor plate, hand tighten or use pliers. If the O-ring is displaced the it is too tight.
Rest the sensor plate on the open set of washers and visually level the nuts as best as possible, the goal is to keep the plate flat.
If deploying follow next steps, if doing a submersion test, proceed directly to sealing.

Deploying:

Add RRIV board to battery assembly using Velcro.
Place board + battery assembly into center of rods, taking care to ensure no wires go around the rods. Then orient so that the dowel rod can sit flat on the acrylic plate and connect the sensors.
Set RRIV board to deployment mode by connecting to serial, checking sensors are working using start-logging (stop-logging when done checking), then using the command deploy-now.
Slide housing around the assembly, check for wires trapped underneath, mainly the blue wire of the CO2 sensor, then add dessicant pack in from the top.
Wrap copper mesh around the sensor cage and affix with cable ties.
Proceed to sealing

Sealing:

Add top plate and hand tighten washers and nuts onto each rod.
Make one round of tightening the nuts in pairs across from each other using one or two sets of pliers, making ~180 degree turns and hand tightening the other nuts after each pair.
Hand tighten the nuts on the sensor plate up towards the top plate, then repeat step 4.
Check each top nut by trying to make a 90 degree turn on each, they should all feel similarly tight.
Visually check the seal formed on the O-ring against the acrylic plate, you should not see the O-ring deform or have anything trapped underneath it, restart if you do.

Figure 6: RRIV in extended sensor housing Figure 6: RRIV in extended sensor housing

Submersion tests (conducted without RRIV electronics in case):

30 minutes and 1 hour are good checking points for initial leaks. 24 hours for next day.
In the event of a severe leak during testing, check sensor cases have not also flooded which can happen if the water traverses through the wires/cables of the sensor. If they have flooded, the PTFE should be cut to allow the case to drain, then dried; sensor cases can be remade if the sensors are still functioning. Otherwise, allow sensor cables to dry fully before using them.

Stock tank submersion Submerge horizontally in a stock tank and weigh down the main housing to test the entire case

5gal bucket submersion test Submerge vertically in a 5gallon bucket to test just the sensor plate and cable glands

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Last updated 6 months ago