PP Systems EGM-5 Operation Manuals

EGM-5

Portable CO2 Gas Analyzer

Operation Manual

Version 1.04

2018 PP Systems. All Rights Reserved

1 March 2018

PP Systems - 110 Haverhill Road, Suite 301 -Amesbury, MA 01913 U.S.A.

Tel: [phone] Fax: [phone]

Email: [e-mail] URL: www.ppsystems.com

Contents

Welcome ....................................................................................................................................................... 7

User Registration .......................................................................................................................................... 7

Service & Warranty ....................................................................................................................................... 8

Contact Information ....................................................................................................................................... 8

Unpacking and Storage of Your Equipment .................................................................................................. 8

Unpacking .................................................................................................................................................. 8

Powering up the EGM-5 for the First Time ................................................................................................... 9

Data Storage ................................................................................................................................................. 9

Technical Specification ............................................................................................................................... 10

Summary of System Design ........................................................................................................................ 11

Overview and Theory .............................................................................................................................. 11

Optional Sensors for use with EGM-5 ......................................................................................................... 13

Internal Sensors and WiFi ....................................................................................................................... 13

O2 Sensor ......................................................................................................................................... 13

H2O Sensor ....................................................................................................................................... 13

WiFi ................................................................................................................................................... 13

External Sensors/Chambers ................................................................................................................... 14

Quantum Sensor ............................................................................................................................... 14

TRP-3 Temperature/PAR Probe ....................................................................................................... 14

SRC-2 Soil Respiration Chamber ..................................................................................................... 15

CPY-5 Canopy Assimilation Chamber .............................................................................................. 15

STP-2 Soil Temperature Probe ........................................................................................................ 16

Soil Moisture and Soil Temperature Sensor ..................................................................................... 16

System Power ............................................................................................................................................. 17

Battery Specification ................................................................................................................................ 17

Power Supply/AC Adapter Rating: .......................................................................................................... 17

Getting Familiar with the EGM-5 ................................................................................................................. 18

Touch Display .......................................................................................................................................... 18

Navigation using the Touch Display ................................................................................................. 19

Power Switch ........................................................................................................................................... 19

Ext Power Jack ........................................................................................................................................ 20

Ext Power LED ........................................................................................................................................ 20

Gas Ports ................................................................................................................................................. 20

Flow Rate ................................................................................................................................................ 20

EGM-5 Operation Manual V. 1.04 2 [e-mail]

USB Flash Drive Port .............................................................................................................................. 21

USB PC Port ............................................................................................................................................ 21

Probe Ports .............................................................................................................................................. 21

Terminal Block ......................................................................................................................................... 22

Analog Voltage Output ...................................................................................................................... 22

Analog Voltage Input ........................................................................................................................ 22

Alarm Relay Outputs ......................................................................................................................... 22

Recommended Cable Interface ........................................................................................................ 23

Absorber Column and CO2 Scrubber ...................................................................................................... 24

Soda Lime (CO2 Scrubber) ............................................................................................................... 24

Routine System Checks Before Starting ..................................................................................................... 25

Touch Display Overview ............................................................................................................................. 26

Heartbeat and Display Update Rate: ....................................................................................................... 26

Splash Screen ............................................................................................................................................. 28

Measurement Mode .................................................................................................................................... 28

Measure Screen ...................................................................................................................................... 28

Readings Screen ..................................................................................................................................... 30

Probe Screen ........................................................................................................................................... 31

Graphic Display Screen ........................................................................................................................... 31

Main Menu................................................................................................................................................... 33

Settings .................................................................................................................................................... 33

Settings 1 Menu ....................................................................................................................................... 34

Zero Settings .................................................................................................................................... 34

Zero Type ......................................................................................................................................... 35

Zero Time ......................................................................................................................................... 36

Alarms Settings ................................................................................................................................. 37

Low CO2 Alarm Setting ..................................................................................................................... 38

High CO2 Alarm Setting .................................................................................................................... 38

Reset Abs Settings ........................................................................................................................... 38

Flow Settings .................................................................................................................................... 39

Pump Power ..................................................................................................................................... 39

Alarm Sound ..................................................................................................................................... 39

Probe Port Settings ................................................................................................................................. 40

Probe Port 1 Settings ........................................................................................................................ 41

Probe Port 2 Settings ........................................................................................................................ 41

EGM-5 Operation Manual V. 1.04 3 [e-mail]

Settings 2 Menu ....................................................................................................................................... 42

Analog Output Settings ..................................................................................................................... 42

Averaging Settings ............................................................................................................................ 43

EGM ID ............................................................................................................................................. 44

Graph Settings .................................................................................................................................. 45

Settings 3 Menu ....................................................................................................................................... 46

Host Measure Settings ..................................................................................................................... 46

WiFi Measure Settings ...................................................................................................................... 48

Memory Measure Settings ................................................................................................................ 48

Host Port ........................................................................................................................................... 49

Reset WiFi ........................................................................................................................................ 50

WiFi Power ....................................................................................................................................... 51

Settings 4 Menu ....................................................................................................................................... 52

Set Clock .......................................................................................................................................... 52

Defaults ............................................................................................................................................. 53

Ship Mode ......................................................................................................................................... 53

Processes ................................................................................................................................................ 54

SRC (Soil Respiration Chamber) Process ........................................................................................ 54

CPY (Canopy Assimilation Chamber) Process ................................................................................ 59

Custom Process ............................................................................................................................... 64

Injection Process .............................................................................................................................. 70

Static Process ................................................................................................................................... 75

Calibration ............................................................................................................................................... 77

CO2 ................................................................................................................................................... 78

O2 Calibration .................................................................................................................................... 80

Touch Calibration .................................................................................................................................... 83

Diagnostics .............................................................................................................................................. 83

ADC (Analog Digital Converter) Diagnostics .................................................................................... 84

Zeros Diagnostics ............................................................................................................................. 85

Hours Diagnostics ............................................................................................................................. 86

Battery Diagnostics ........................................................................................................................... 86

Voltage Diagnostics .......................................................................................................................... 87

Advanced Diagnostics ...................................................................................................................... 87

Information Menu ........................................................................................................................................ 88

About ....................................................................................................................................................... 88

EGM-5 Operation Manual V. 1.04 4 [e-mail]

Contact .................................................................................................................................................... 89

Data Storage ............................................................................................................................................... 89

USB Flash Drive (Memory Stick) ............................................................................................................. 89

Data Storage/Measure Format Settings Table ........................................................................................... 91

Process Data Fields ................................................................................................................................ 91

Measure Format Settings Table .............................................................................................................. 93

Digital Connection Methods ........................................................................................................................ 96

USB ......................................................................................................................................................... 96

Wireless ................................................................................................................................................... 96

Digital Communication Protocols and Software ...................................................................................... 96

EGM-5 Command Set ................................................................................................................................. 96

EGM-5 Auto Strings ................................................................................................................................. 98

“*” String (Power Reset) ....................................................................................................................... 98

“E” String (Error Status) ........................................................................................................................ 98

“M” String (Measurements) .................................................................................................................. 98

“V” String (Versions) ............................................................................................................................. 98

“W” String (Warm up) ........................................................................................................................... 99

“Z” String (Zeroing) ............................................................................................................................... 99

EGM-5 Command Set Table ................................................................................................................. 100

Get/Set Parameter Values Table .......................................................................................................... 106

GAS (Gas Analysis Software) ............................................................................................................... 108

Web Pages ............................................................................................................................................ 110

Communication Summary ..................................................................................................................... 112

Wireless Network Settings..................................................................................................................... 113

Connecting To EGM-5 via Direct Wireless Connection .................................................................. 113

Connecting to EGM-5 via a Local Area Network ............................................................................ 114

Error Messages ......................................................................................................................................... 117

Maintenance .............................................................................................................................................. 119

External Air Filter ................................................................................................................................... 119

Absorber Column and CO2 Scrubber .................................................................................................... 120

Gray Foam Filters ........................................................................................................................... 120

Absorber Filters .............................................................................................................................. 120

End Cap “O” Rings ......................................................................................................................... 120

Soda Lime (CO2 Scrubber) ............................................................................................................. 120

Access to Internal Components ............................................................................................................ 121

EGM-5 Operation Manual V. 1.04 5 [e-mail]

Sampling Pump ..................................................................................................................................... 123

Infrared Source ...................................................................................................................................... 123

Hydrophobic Filter ................................................................................................................................. 123

Battery ................................................................................................................................................... 123

Appendix 1. Soil CO2 Efflux and Net Canopy CO2 Flux ........................................................................... 124

Theory.................................................................................................................................................... 124

Correction for water vapor increase on CO2 efflux ......................................................................... 125

FCO2 Units for measurement of Soil CO2 Efflux ............................................................................ 126

References ..................................................................................................................................... 126

Appendix 2. WiFi Compliance .................................................................................................................. 127

Table C-1 Country Certifications .................................................................................................... 127

Table C-2 Country Transmitter Ids ................................................................................................. 128

Table C-3 Safety ............................................................................................................................. 128

Federal Communication Commission Interference Statement ....................................................... 128

Radiation Exposure Statement ....................................................................................................... 129

EGM-5 Operation Manual V. 1.04 6 [e-mail]

Welcome

Thank you very much for purchasing our EGM-5 CO2 Gas Analyzer. We greatly appreciate your
business and we look forward to working with you and your team for many years to come.

This manual and the information contained within are copyrighted to PP Systems. No part of the
manual may be copied, stored, transmitted or reproduced in any way or by any means including,
but not limited to, photocopying, photography, magnetic or other mechanical or electronic means,
without the prior written consent of PP Systems, Inc.

For applications where failure of this equipment to f unct ion correctly would lead to consequential damage,
the equipment must be checked for correct operat i on and calibration at intervals appropriate t o the
circumstances. The PP Systems' equipment warranty is limited to replacement of defective components,
and does not cover injury to persons or property or other consequential damage.

This manual is provided to help you install and operate the equipment. Every effort has been made to
ensure that the information it contains is accurat e and complete. PP Systems does not accept any liabil ity
for losses or damages resulting from the use of thi s information.

It is the operator’s responsibility to review this information prior to installation and operation of the
equipment. Otherwise, damage may be caused whic h i s not cov ered under our normal warranty policy.

PP Systems is a registered trademark of PP Sy st em s, Inc. All brand names are trademarks or registered
trademarks of their respective owners.

User Registration

It is very important that ALL new customers register themselves with us to ensure that our user’s list is
kept up-to-date. If you are a PP Systems’ user, please go to www.ppsystems.com
Registration in the upper left hand corner.

Only REGISTERED users will be allowed access to the protected “Users” section of our web site. This
section will contain important product inform ation including hardware/software update s, application notes,
newsletters, etc.

Thank you in advance for your cooperation.

and click on Customer

EGM-5 Operation Manual V. 1.04 7 [e-mail]

Service & Warranty

PP Systems' equipment warranty is limited to replacement of defective components, and does not cover
injury to persons or property or other consequential damage.

The equipment is covered under warranty for one complete year, parts and labor included. This, of
course, is provided that the equipment is properly i nstalled, operated and maintained in accordance with
written instructions (i.e. Operator's Guide).

The warranty excludes all defects in equipment caused by incorrect installation, operation or
maintenance, misuse, alteration, and/or accident.

If for some reason, a fault is covered under warranty , it is the responsibility of the customer to return the
goods to PP Systems or an authorized agent for repair or replacement of the defective part(s).

Prior to returning equipment to PP Systems for service, you must first get in contact with our Service
Manager ([e-mail]

) to request a case number for reference and tracking purposes.

Contact Information

PP Systems, Inc.
110 Haverhill Rd, Suite 301
Amesbury, MA 01913 USA
Tel: [phone] Fax: [phone]
Sales: [e-mail]
Support: [e-mail]
Service: [e-mail]
URL: www.ppsystems.com

Unpacking and Storage of Your Equi pment

Unpacking

It is extremely important that you check the contents of your equipment immediately upon receipt to
ensure that your order is complete and that it has arrived safely. Please refer to the packing list to show
all items that are included with your order. DO NO T DISCARD ANY OF THE PACKAGING MATERIAL

UNTIL ALL OF THE ITEMS LIS T ED ARE ACCOUNTED FOR. WE RECOMMEND THAT YOU RETAIN
THE ORIGINAL PACKING FOR FUTURE USE. If you suspect that any of the items listed on the packing

list are not included or damaged, you must conta ct PP Systems or your authorized distributor
immediately.

EGM-5 Operation Manual V. 1.04 8 [e-mail]

Powering up the EGM-5 for the First Ti me

When you receive your new EGM-5 from PP Systems you will need to first connect it up to the external
power supply/charger prior to powering up the instrument. To avoid accidental power up during shipment
we put the instrument into “Ship Mode” (see Ship Mod e on page 53). Therefore, when you are ready to
begin:

1. Locate the power supply/charger and power cord inside the packing box.

2. Connect the AC power cord to the mains and the barrel conne ct or into the EXT Power socket on
the back of the EGM-5.

3. Press the ON/OFF switch to power up the instru m ent. The power switch should now have an
illuminating blue ring indicating power is on.

4. Allow 10-15 minutes to achieve warm-up.

You are ready to go!

Data Storage

For convenience and ease it is very important to not e that all EGM-5 system data is recorded and saved
directly to a USB flash drive (i.e. memory stick or thu m b drive). A USB flash drive is included in the spares
kit (Part No. 43034-1) with every new system.

THEREFORE IT IS IMPERATIVE THAT YOU HAVE A USB FLASH DRIVE WITH YOU AT ALL TIMES
IF YOU WANT TO RECORD DATA WITH YOUR EGM-5. OTHERWISE D ATA WILL HAVE TO BE
RECORDED MANUALLY.

EGM-5 Operation Manual V. 1.04 9 [e-mail]

Technical Specification

Analysis Method

Non-dispersive infrared, configured as an absolute absorptiometer with
microprocessor control of linearization

CO2 Measurement

0-1000 ppm (µmol mol-1)

Readings are automatically corrected for tem perat ure and pressure.

Accuracy

< 1% of span concentration over the calibrated range but limited by the
accuracy of the calibration mixture.

Linearity

< 1% throughout the range

Stability

Auto-zero at regular intervals corrects for sample cell contam ination,
source and detector ageing and changes in electronics.

Warm-up Time

Approximately 15 minutes

Sampling Rate

10 Hz. Sample data is averaged and output every 1.0 seconds.

Sampling Pump

Integral, 5V rotary vane air sampling pump

Gas Flow Rate

100-500 cc/min (280-340 cc/min is optimal). An internal, electronic flow
sensor monitors flow rate.

Terminal Block

External 10 pin terminal connector for; +5V, Groun d, Analog input, Analog
output, and alarm relays.

Analog Input

0-1.0V

Analog Output

0-2.5V (CO2 range selectable)

Alarm

2 relay contacts (Alarm1 and Alarm2), Visual and Audible alarm/warnings.

Communications

USB(USB Mini-B) and Optional Wi-Fi

Air Filter

Internal hydrophobic filter is used to protect analy zer from water.

CO2 Control

High and low user set points

Data Storage (USB)

USB Flash Drive for data storage

Display

2.7” electronic paper touch display with 264 x 176 pixel resolution

Power Switch

Illuminated On/Off power switch

Internal Battery

7.2 Volt - 8.7Ah (63Whr) Li-Ion battery providing up to 16 hours continuous
reduce the operation time.

Power Requirements

12 VDC, 3.0A or AC Adapter (included) 100-240 VAC, 50-60 Hz, 1.0A

Power Consumption

Charging Battery: 30W (12V @ 2.5A)
Normal operation: 6W (12V @ 0.5A)

Gas Connections

2 Quick disconnect style fittings (inlet and exhaust) for use with 1/8” (.125”)
ID tubing

Operating Temperature

0-50 oC, non-condensing. External filtration may be required in dirty
environments.

Enclosure

Durable Cast-Urethane and aluminum, IP43 enclosur e

Dimensions

215 cm W x 200 cm H 120 cm W (Enclosure only)

Weight

1.6 kg

• PP Systems is a registered trademark of PP Systems, Inc.

• All brand names are trademarks or registered trade m arks of their respective owners.

Ranges

0-2000 ppm (µmol mol-1)
0-5000 ppm (µmol mol

-1

0-10000 ppm (µmol mol
0-20000 ppm (µmol mol
0-30000 ppm (µmol mol
0-50000 ppm (µmol mol
0-100000 ppm (µmol mol

)

-1

)

-1

)

-1

)

-1

)

-1

)

operation. If external sensors/accessorie s are used with the EGM-5 it will

Warm up: 12W (12V @ 1.0A)

• PP Systems is continuously updating its products and reserves the right to amend product
specifications without notice.

EGM-5 Operation Manual V. 1.04 10 [e-mail]

Summary of System Design

Overview and Theory

The EGM-5 is designed to function as a self-containe d i nst rument for continuous measurement of CO2 in
air. Its open-path design allows for continuous, unattended air sampling, as the pump introduces fresh
sample gas to the essential component, the IRGA (infrared gas analyzer).

The IRGA forms the core of gas analysis systems that m easure CO
refers to the transmission of a broad-band infra-red wavelength from the IRGA source lamps. A single
IRGA consists of four basic components:

. Non-dispersive infra-red (NDIR)

2

• Infra-red source

• Sample cell of known path length and volume

• Optical interference filter

• Infra-red detector

The theory itself is quite simple – light from mid-infra-red wavelengths is produced by the source and
pulsed through a gold plated cell. The interferen ce f i l t er narrows the bandwidth of the IR source received
by the detector to the signature wavelength absorbed by the target gas molecule, e.g. CO
employs a unique optical filter. As the sample gas fi l l s t he cell, the target gas molecule absorbs IR energy
at the particular wavelength, and the reduction in IR energy reaching the detector is measured. The
higher the target gas concentration, the lower the infra-red signal received at the detector, as defined by
the Lambert-Beer Law of Attenuation.

. The CO2 cell

2

CO

molecules have a discrete absorption band at 4. 26 µ m that has very little overlap with any other

2

molecule’s absorption band, so that wavelength prov ides good sensitivity and selectivity. The EGM-5
electronics could be considered another major component, which processes raw analog-to-digital (A/D)
information from the IRGA detector, accurately translating this information into gas concentrations.

EGM-5 Operation Manual V. 1.04 11 [e-mail]

The EGM-5 detector is optimized

for this CO2 waveband (4.26 µm)

The gas sample is of course a mixture of gas molecules, and this can present problems in terms of
accurate detection of concentrations of a specific gas, such carbon dioxide. This effect, foreign gas
broadening (FGB), must be corrected to ensure a cc urate measurement of gas concentrations. With FGB,
the CO
This effect is about 0.1 µmol mol
infra-red absorption, which is detected as an apparent increas e i n [CO

gas in the IRGA cell is somewhat diluted by the increased air volume induced by water vapor.

2

-1

CO2 mb-1 H2O. The presence of water vapor also causes an i ncr ease in

]. This is of a similar magnitude,

2

but opposite to the dilution effect, and the EGM-5 a ut om atically corrects these FGB effects.
The EGM-5 IRGAs are quite stable owing to their con st ruction, calibration and thermal environment, but

various circumstan ces can cause apparent changes over time. Some changes may require recalibration,
although one of the strengths of the EGM-5 is that r ecalibration is not a routine (annual) maintenance t ask
as a result of our innovative “Auto-Zero” function. Our Auto-Zero function corrects for nearly all chan ges
that result in calibration drifts. It minimizes effects on span (gas sensitivity), of sample cell contamination,
lamp aging, changes in detector sensitivity, am pl i f i er gains and reference voltages. Measurements are
ratios based on the Zero reading before IR abso rbance is determined. From the relationship bet ween
absorbance and concentration determined in the factory for each instrument, and the current calibrat i on
factor, the sample concentration is determined.

EGM-5 Operation Manual V. 1.04 12 [e-mail]

Optional Sensors for use with EGM-5

Internal Sensors and WiFi

The O2 and H2O sensors are built into the EGM-5 enclosure.

O2 Sensor

An optional electrochemical O2 sensor can be used with the EGM-5 for measurem ent of oxygen in
addition to CO

• Range: 0-100%

• Response Time: ≤ 15 seconds at 23 ± 2

• Linearity: ± 1.0% of full scale

.

2

o

C

The O
incoming gas stream. Recalibration should not be necessary and based on our experience with this
sensor it should have a working life of approximatel y 4-5 years.

sensor is mounted into a manifold located inside the enclosure and is fitted in-line to sample the

2

H2O Sensor

An optional solid state H2O sensor can be used with the EGM-5 for measurement of H2O in addition to
CO

.

2

• Range: 0-Dewpoint (mb)

• Accuracy: < 2% RH

The humidity sensor is mounted into a manifold located inside the enclosure and is fitted in-line to sample
the incoming gas stream. Readings are displayed and recorded in absolute vapor pressure (mb).
Recalibration of this sensor is not necessary.

WiFi

Optional WiFi is available for use with the EGM-5. Refer to Wireless on page 96 for more information.

EGM-5 Operation Manual V. 1.04 13 [e-mail]

External Sensors/Chambers

The following sensors/chambers are external to the EGM-5 and electrical connection is made to t he
Probe Ports (Probe 1 and Probe 2) located on the ba ck of the EGM-5. See Probe Port Settings on page
40 for more information for proper connection. Ga s c onnections (if applicable) are made to the “Gas I n”
and “Gas Out” ports on the back of the EGM-5.

Quantum Sensor

An optional quantum sensor (Apogee Instruments) is available for use with the EGM-5 for accurate
measurement of PAR (Photosynthetically Active Radiation) and it is specifically calibrated for use in
sunlight conditions. The sensor housing features a fully potted, dome-shaped head, making the sen sor
fully weatherproof for self-cleaning. Never use an abrasive material or cleaner on the diffuser .

• Range: 0-3000 µmol m

-2

s-1

• Calibration Uncertainty: ± 5%

• Measurement Repeatability < 1%

• Long Term Drift: < 2% per year

• Cable Length: 5 meters

An optional leveling unit (ACS039) is also availabl e for use with the quantum sensor. We highly
recommend that you mount the sensor on a horizontal surface and that it is level for best results. To
minimize azimuth error, the sensor should be mou nted with the cable pointing toward true north in the
northern hemisphere or true south in the southern he m i sphere. Azimuth error is typically less than 1%,
but is easy to minimize by proper cable orientatio n.

We recommend recalibration of the quantum senso r every 2 years.

TRP-3 Temperature/PAR Probe

An optional probe can be used with the EGM-5 for meas urement of temperature and PAR. It consists of a
rugged, aluminum housing with black foam cover. It al so includes a standard tripod thread mount for use
with commercially available tripods. The single gas connection for this probe is made to the “Gas In” port
on the EGM-5.

Temperature Sensor (Precision Thermistor)

• Range: 0-50

• Accuracy: ± 0.3

o

C

o

C at 25 oC

PAR Sensor

• Fully cosine corrected

• Range: 0-3000 µmol m

• Accuracy: ± 10 µmol m

-2

-2

s-1

s-1
Cable Length: 1.5 meters
We recommend recalibration of the PAR sensor every 2 years.

EGM-5 Operation Manual V. 1.04 14 [e-mail]

SRC-2 Soil Respiration Chamb er

Our SRC-2 Soil Respiration Chamber is available f or use with the EGM-5
for measurement of closed system, soil CO
connections required, one to the GAS IN port, and the other to the GAS
OUT port on the EGM-5. It is constructed out of rugged PVC with a
convenient handle for placement on the soil surface. An aluminum ring
provides a good seal on the soil surface or on collars.

• Dimensions: 150 mm (Height) x 100 mm (Diameter)

• Volume: 1171 ml

• Area: 78 cm

2

• Cable Length: 1.5 meters

It includes a temperature sensor for measurement of air temperature near
the soil surface.

Temperature Sensor (Precision Thermistor)

efflux. There are two gas

2

• Range: 0-50

• Accuracy: ± 0.3

o

C

o

C at 25 oC

CPY-5 Canopy Assimilation Chamber

Our CPY-5 Canopy Assimilation Chamber is available for use with the EGM-5 for measurement of closed
system, net canopy CO
aluminum ring, which provides a good seal on the soil surface or on collars. It also includes sensor s f or
measurement of air temperature and PAR within the chamber. There are two gas connections required,
one to the GAS IN port and the other to the GAS OUT port on the EGM-5.

• Dimensions: 145 mm (Height) x 146 mm (Diameter)

• Area: 167 cm

• Cable Length: 1.5 meters

Temperature Sensor (Precision Thermistor)

• Range: 0-50

• Accuracy: ± 0.3

PAR Sensor

• Fully cosine corrected

• Range: 0-3000 µmol m

• Accuracy: ± 10 µmol m

flux. It is transparent and constructed out of rugged polycarbonate with an

2

2

o

C

o

C at 25 oC

-2

s-1

-2

s-1
We recommend recalibration of the PAR sensor every 2 years.

EGM-5 Operation Manual V. 1.04 15 [e-mail]

STP-2 Soil Temperature Probe

An optional soil temperature sensor can be used with t he EGM-5 for measurement of soil temperature. It
is commonly used with the SRC-2 Soil Respiration Chamber and CPY-5 Canopy Assimilation Chamber.

It is a rugged sensor with electronics housed in an anodized aluminum
enclosure with stainless steel tip.

• Dimensions: Handle: 200 mm (Length) x 18.7 mm (Diameter)
Tip: 125mm Length

• Cable Length: 1.5 meters

Temperature Sensor (Precision Thermistor)

• Range: 0-50

• Accuracy: ± 0.3

o

C

o

C at 25 oC

Soil Moisture and Soil Temperature Sensor

An optional soil moisture and soil temperature sensor (HydraProbe II - Stevens Water Monitoring
Systems) is available for use with the EGM-5. It is an all-in-one, in-situ sensor t hat can measure both soil
moisture and soil temperature.

Soil Moisture Sensor

• Range: 0-100% ((dry to fully saturated)

Soil Temperature Sensor

• Range: -10

• Accuracy: ± 0.3

Cable Length: 5 meters

o

C-55 oC

o

C at 25 oC

For best results the 3 prongs should be pushed all the way into the ground until the white body of the
sensor is flush with the soil surface.

Recalibration of this sensor is not necessary.

EGM-5 Operation Manual V. 1.04 16 [e-mail]

System Power

Re-Order Information

Part Number

Description

STD561

Mains Charger/Power Supply

The EGM-5 has an internal, rechargeable lithium ion battery pack capable of providing continuous power
to the instrument for up to 16 hours. The EGM-5 is supplied with an external AC power adapter to charge
and/or power the EGM-5.

Battery Specification

• Type: Rechargeable Smart Lithium Ion Battery Pack

• Power: 7.2V, 8.7Ahr, 63Whr

Note, if the EGM-5 is used with external sensors/chambers it will reduce the battery life depending on the
probe connected.

A dead battery (0% capacity) can be fully recharged in approximately 4-5 hours using the power
supply/charger supplied by PP Systems.

To check the battery status, simply power up the instrument and observe the battery capacity nex t to the
flashing heartbeat in the upper left hand corner of the display (see below).

Power Supply/AC Adapter Rating:

• Input: 100-240 VAC, 50-60 Hz, 1.0A

• Output: 12 VDC, 3.3A

EGM-5 Operation Manual V. 1.04 17 [e-mail]

Getting Familiar with the EGM-5

CO2 scrubber

Adjustable Carry

Handle

Flashing Heart
(Power Status)
and battery
capacity

status and
manual Zero
button

Touch display

Polyurethane
shock-absorbing
base and battery
compartment

Touch Display

The EGM-5 features a 2.7” a-Si, active matrix TFT , Electronic Paper Display (EPD) touch panel. T he
panel has such high resolution (117 dpi) that it is abl e t o easily display fine patterns with excellent
readability under sunlight conditions. Due t o i t s bi -stable nature, the EPD panel requires very little power
to update and needs no power to maintain an image.

Features

• a-Si TFT active matrix Electronic Paper Display (EPD)

• Resolution: 264 x 176 pixel

• Ultra-low power consumption

• Super Wide Viewing Angle - near 180°

• Slim & lightweight enclosure

• SPI interface

• RoHS compliant

EGM-5 Operation Manual V. 1.04 18 [e-mail]

Navigation using the Touch Displ ay

Power Switch

USB Flash Drive USB Mini-B

10 Pin Terminal Block

Navigating through the system is simple and easy by pressing black buttons where applicable. Whenever
you see white text inside a black box we refer to this as a butt on (i. e. Main). Pressing on these buttons
will allow you to set up, navigate and operate the EGM-5. Whenever a numeric value is required, a
keypad will appear allowing you to enter the desired values.

Back of EGM-5

External
Power/Charger
socket

External Power
LED Indicator

Probe 1 Input
Probe 2 Input

Gas Out
Gas In

Absorber column
and CO

scrubber

2

Power Switch

The power switch is located in the upper left hand corner of t he back panel. To power up the EGM-5
simply push in the switch. When power is on the illumination ring around the switch will turn blue. To turn
off, simply press the switch again bringing it back to t he flush position. When powered off, the Splash
Screen will be displayed as follows:

EGM-5 Operation Manual V. 1.04 19 [e-mail]

When the EGM-5 is turned off you must wait at least 5 seconds before powering up the instrument. If you
do not wait long enough the system will not power up prop erly.

Please note that the EGM-5 will turn off when the batt ery capacity reaches 0%. If this happens we
recommend connecting up to the charger to recharge the internal battery.

If the EGM-5 was put into ship mode, it will not power on until external power i s appli ed. To bring the
EGM-5 out of ship mode, first connect external power to the instrument, and then turn it on by pressing
the “ON/OFF” button. See Ship Mode on page 53 for more information.

Ext Power Jack

When external power is present, the system will charge the internal battery. A power supply/charger is
supplied with the EGM-5 as standard. When the power supply/charger is connected to t he EGM-5 it will
both operate the instrument continuously and re charge the internal battery when the EGM-5 is powered
on. If connected to the EGM-5 with power off it will recharge t he i nternal battery faster.

Ext Power LED

The amber LED is illuminated whenever the power su pply/charger is connected to the EXT POWER jack
on the back panel.

Gas Ports

There are two gas ports on the EGM-5. Each port is designe d for use with 1/8” (.125”) ID tubing or a
mating quick disconnect. When using the EGM-5 as a stand-alone CO2 analyzer, the sampling line
should be fitted to the GAS IN port and the GAS OUT port should be left open to atmosphere to allow the
sample air to exhaust without restriction. Thi s does not apply when using some optional accessories (e.g.,
the SRC-2 Soil Respiration Chamber or the CPY-5 Canopy Assimilation Chamber).

Flow Rate

The EGM-5 features an internal electronic flow sensor for controlling flow rate between 100-500 cc/mi n.
The flow rate is adjustable by changing the Pump Po wer percentage in Flow Setting. To set/change t he
flow rate from the Main menu, touch Main, Settings and Flow.

Flow Setting
Flow (cc/min): 323
Pump Power (%): 40

EGM-5 Operation Manual V. 1.04 20 [e-mail]

To change Pump Power, press on % value (with black background) and enter your required % from 0-

100. We strongly recommend a flow rate of approximat el y 280-350 cc/min for optimal performance.
Important Note. If the flow rate drops below 50 cc/min, a “low f low" error message will be displayed in

the status box. Typically this is the result of flow restriction caused by either the external air filter or a
blocked internal hydrophobic filter located inside t he EGM-5 enclosure. First, replace the external air f i l ter
connected to the GAS IN port to see if this corrects the problem. I f it doesn’t then the likely problem is a
blocked internal hydrophobic filter See
this filter.

Hydrophobic Filter on page 123 for information related to changing

USB Flash Drive Port

A USB Flash Drive Port is available on the back pane l t o all ow users to save data directly to a USB flash
drive (also commonly referred to as a “thumb drive” or “memory stick”). When a USB flash drive is
inserted into the USB port, the LED indicator will f irst turn red in recognition of the USB flash drive and
then it will flash green indicating that data is being saved to it automatically. If the indicating LED is a
steady green then data is not being saved because the “Interval (sec)” is likely set to 0 under Memory
Measure Settings. See Memory Measure Set t i ngs on page 48 for more information on this.

USB PC Port

The USB PC Port (USB Mini-B) can be used to connect the EGM-5 to a PC. Measured data is
continuously sent through this port. The PP Systems’ GAS software or a terminal emulation program (i.e.
HyperTerminal) can then monitor the measured data. GAS software is supplied on the USB flash drive
supplied with the EGM-5 and it is also available for free download from our website. When using a
terminal emulator, the COM port settings to communicate with the EGM-5 are: 19200 baud, 8 bit, 1 st op,
no parity, no flow control.

Probe Ports

There are 2 digital PROBE PORTS availabl e for use with external sensors/accessories. The current list of
supported probes/sensors include:

• Quantum Sensor (Apogee Instruments)

• TRP-3 Temperature & PAR Probe

• STP-2 Soil Temperature Probe

• SRC-2 Soil Respiration Chamber

• CPY-5 Canopy Assimilation Chamber

• Soil Moisture & Temperature Sensor (Stevens Water Monitoring Systems)

Up to two different probes can be used at the same ti m e, for example, the SRC-2 Soil Respiration
Chamber and the STP-2 Soil Temperature Probe. Note that some combinations of the above probes will
not be possible, for example, the TRP-3 and SRC-2 Soil Respiration Chamber.

EGM-5 Operation Manual V. 1.04 21 [e-mail]

Terminal Block

CO2 Analog Output

GND

Ground connection for CO2 analog output

CO2

Analog output for CO2 (0-2.5V). 0 corresponds to 0 CO2 and 2.5V
corresponds to full scale (defined by user).

Analog Input

GND

Ground connection for analog input

ANALOG IN

Analog input for external sensor (0-1V). The input voltage is displayed and
voltage signal into the appropriate value depending o n the sensor used.

+5V OUT

Additional 5V power supply for external sensors if re quired. It is
recommended that no more than 400mA of current be used.

Alarms

ALARM 2A

Associated with Low Alarm. The relays are rated for 3 0 VDC 1A or 125 VAC

0.3 A.

ALARM 2B

Associated with Low Alarm. The relays are rated for 3 0 VDC 1A or 125 VAC

0.3 A.

ALARM 1A

Associated with High Alarm. The relays are rated for 30 VDC 1A or 125 VAC

0.3 A.

ALARM 1B

Associated with High Alarm. The relays are rated for 3 0 V DC 1A or 125 VAC

0.3 A.

An external 10 pin terminal block is available for CO2 analog output, analog input (for additional sen sor),
+5V OUT and alarms.

saved in the data output as a voltage signal. The user can then convert the

Analog Voltage Output

One analog voltage output is available for the curr ent CO2 reading. The full scale output is 2.5V. The CO2
concentration corresponding to full scale can be set by the user in the Main > Settings 2 > Analog Output
screen. 0 Volts always corresponds to 0 ppm CO
block at the pins labeled CO2 (positive) and GND (negative).

. The analog voltage output is located on the terminal

2

Analog Voltage Input

One analog voltage input is available for general p urpose use. The maximum input voltage is 1.0V. The
input voltage is displayed and saved in the data measurements.

Alarm Relay Outputs

There are two normally open relay contacts that are activated (closed) when the Low CO2 Alarm (Alarm

1) or High CO
The relays are rated for 30 VDC at 1A or 125 VAC at 0.3 A. The 5V output could be connected to one
side of these relays to create a digital output signal. Relays can also be used to trigger an external device
such as a computer or warning light.

Alarm (Alarm 2) condition occurs. The Alarm limit s are s et in Main > Settings 1 > Alarms.

2

EGM-5 Operation Manual V. 1.04 22 [e-mail]

Recommended Cable Interface

EGM-5 Terminal Block

GND P1

CO2 P2

Shielded cable to external relays or P rogrammable Logic Controller
Typical cable Belden 9609 4C 24 Shield ed. Length 10 Ft M

Shielded cable to Data Logger or Pr ogr ammable Logic Controller
Typical cable Belden 8413 2C 24 Shield ed. Length 10 Ft Maximum.

GND P5

Alarm 2A P7

Alarm 2B P8

Alarm 1A P9

Alarm 1B P10

GND P3

Analog In P4

+5v P6

Shielded cable to Sensor or External Zer o Switch
Typical cable Belden 8413 2C 24 Shield ed. Length 5 Ft Maximum.

When connecting up to external devices via the EGM-5 terminal block we recommend the following cable
type and lengths.

aximum.

EGM-5 Operation Manual V. 1.04 23 [e-mail]

Absorber Column and CO2 Scrubber

The absorber column contains a CO2 scrubbing desiccant commonly referre d to as “soda lime”. When air
passes through this column, it removes all of t he CO
into the EGM-5 periodically switches the flow of gas f rom the analyzer through this column to check the
analyzer zero. This routine ensures long term stability and accuracy of the CO
corrects for such things as sample cell contamination, source aging, detector sensitivity and change s in
electronics. The default Auto-Zero interval i s 20 mi nutes, but this can be changed if required. See Zero
Settings on page 34.

Important Note

It is critical that the soda lime is fresh to ensure that the EGM-5 receives a good zero for long term
calibration and stability of the CO

signal. At present, both self-indicating and non-indicating soda lime

2

can be used with the EGM-5. If using a self-indic at i ng desiccant you can visually determine when the
desiccant is exhausted by change in color. When the desiccant is more than 2/3 exhausted you should
replace it. In addition, the EGM-5 monitors the CO
the display based on use (see below). This is extremely helpful when using a non-indicating CO
scrubber. We recommend changing out the desiccant daily or at minimum when this value gets to 20%.

from the air stream. The “Auto-Zero” function built

2

analyzer. It automatically

2

scrubber condition in the upper right hand corner of

2

2

See Reset Abs Settings on page 38 for information on resetting the CO

scrubber after refreshing the

2

desiccant.

Soda Lime (CO2 Scrubber)

The EGM-5 is virtually maintenance free. However, the condition of the soda lime should be carefully
inspected before each use to ensure stability and accuracy of CO

measurements. Generally speaking,

2

the soda lime should last for several weeks during regular use. However, given the importance of stabi l ity
and accuracy of the CO

signal you should consider changing out this de siccant more frequently as

2

described above (daily).

! CAUTION !

WASH YOUR HANDS AFTER HANDLING SODA LIME

EGM-5 Operation Manual V. 1.04 24 [e-mail]

Routine System Checks Befor e St ar t i ng

The EGM-5 is designed to operate with minimal main tenance. The basic routine system checks are as
follows:

• Make sure the external air filter (Part No. STD558) is fitted to the GAS IN port. This will ensure

that the sample air is filtered before entering the sy st em.

• Check the absorber column on the back and make sure that it is properly seated in its manifold.

You should periodically lubricate all O-rings asso ciat ed with the column (black end caps) with
silicone grease to ensure good seal and to avoid problem s associated with cracks and leaks. Also
ensure that the gray foam filters are in good shape and replace when worn.

• Check the condition of the CO

using self-indicating soda lime you can visually make this determination. If you are using non­indicating soda lime then power up the instrument and check the status (see below). If below 20%
you should change it and reset the absorber column life. See Reset Abs Settings on page 38.

scrubber (i.e. soda lime) and make sure it is fresh. If you are

2

• System Power and Heartbeat - Make sure that the heart symbol is flashing in the upper left

hand corner after the instrument is powered on. Also check the battery capacity next to the heart
to ensure that you have plenty of power to get y ou through your measurements.

EGM-5 Operation Manual V. 1.04 25 [e-mail]

• USB Flash Drive – You must make sure that you have a USB flash drive (memory stick) plugged

in for data storage. If you do not have this you will be unable to save data, and it will have to
be recorded manually.

• Status Box – Inspect periodically for error messages/warnings.

Touch Display Overview

The flowchart on the following page describes an overview of the touch display for the EGM-5. When the
instrument is first powered up, there is a brief period where the Splash screen is shown. After this ti me,
the instrument goes into the warm-up period which i s approximately 10-15 minutes and the Measure
screen is displayed. During and after the warm-up p eriod, the user has the ability to navigate through the
menus as shown in the flowchart below. The following se ct i ons describe each screen and its functionality.

Heartbeat and Display Update Rate:

The flashing heartbeat ♥ icon is updated each time the display is updated (w hether the CO2 or other
values change or not). Normally the display is updated every 1 second. However, in extended mode the
display is updated every 5 seconds (even though data is still being output and recorded every 1 second).
The extended mode saves power and prevents display ghosting. Extended mode begins approximatel y
30 seconds after the last keypress is made on a ny measurement screen. Return to normal 1 second
update rate will occur when:

• Any screen button is pressed

• The heartbeat icon is pressed

• Any new CO2 reading is more than 10% changed from the previous CO2 reading.

EGM-5 Operation Manual V. 1.04 26 [e-mail]

Main Menu

Settings 1

Menu

Settings 2

Menu

Settings 3

Menu

Settings 4

Menu

Settings 2

Menu

Zero

Alarms

Reset Abs

Flow

Alarm Sound

Probe Port

Analog

Averaging

EGM ID

Graph

Host

WiFi

Memory

Host Port

Reset WiFi

WiFi Power

Ship Mode

Set Clock

Defaults

Info

Menu

Diagnostics

Menu

Calibration

Menu

ADC

Zeros

Hours

Battery

SRC

CPY

Custom

Injection

Static

Voltages

Advanced

About

Contact

CO2

O2

Touch Cal

Processes

Splash Screen

CO2

Screen

Variables 1

Screen

Variables 2

Screen

Graphic

Display Screen

EGM-5 Operation Manual V. 1.04 27 [e-mail]

Splash Screen

The Splash screen is always shown on the display when t he EGM-5 is off. When the instrument is first
powered up, the Splash screen is displayed momentarily followed by the Measure screen displayi ng CO
in large text.

Measurement Mode

The Measurement Mode is comprised of four scre ens:

1. Measure screen

2. Readings screen

3. Probe screen

4. Graphic display screen

2

Each screen allows the user to view the EGM-5 data in various ways. The screens can be rotated through
by the user using the left (< -) and right (- >) arrow buttons. Generally speaking, the left arrow brings you
back to the previous screen and the right arrow to t he next available screen. The initial screen is the
Measure screen which displays the value of CO
Readings screen and displays the values of six par ameters in real time; CO
Rate, and Pressure. The third screen is the Probe screen which displays the values of six parameters in
real time; CO
fourth screen Graphic Display screen which displays CO

Each screen contains common features. There is a f lashing
(power status). The percentage value in the top left corner is the percentage of battery remaining. The
percentage value in the top right corner is the percentage of absorber column remaining. Also, a manual
zero can be initiated using the “Z” button. A stat us or error message can be displayed in the Stat us Box.
Each Measurement screen is explained in more detail below.

, PAR, Aux, air temperature (Tair), soil temperat ure (Tsoil) and soil moisture (Msoil). The

2

concentration in a large bold font. The next screen is the

2

, H2O, O2, Temperature, Flow

2

, H2O or O2 concentration graphically over time.

2

♥ icon to confirm that the EGM-5 is on

Measure Screen

The Measure screen is displayed after the Splash screen once the EGM-5 is powered up. For the first 10­15 minutes, the EGM-5 goes into a warm-up period unt i l i t achieves its final temperature of 55°C and a
zero check is performed. During this time, messages are displayed in the Status Box that indicate that t he
instrument is in the warm-up stage (see below). Durin g war m-up, the CO

value is displayed as 0 ppm.

2

EGM-5 Operation Manual V. 1.04 28 [e-mail]

Measure Screen

♥ (Heartbeat)

Pulses on and off to indicate that the system is powe red and operating.
Press to return to normal 1 second display updates.

34%

Percentage of battery life remaining.

Record

Saves current data as a marked record in the USB Memory stick and
also sends the record to the host and WiFi ports

98%

Percentage of CO2 scrubber (soda lime) remaining. We recommend
changing out the scrubber when it gets to 20%.

Z Button

Initiates a manual zero.

CO2

Current measurement of CO2 Concentration (ppm)

Main Button

The Main screen is displayed when this button is selected. See Main

Status Box

Any information or error messages are displayed here.

Right Arrow

Starts the rotation through the 4 available Measurement Mode screens.

At the completion of the warm-up period, the proper CO

value is displayed and the Status Box is blank.

2

Menu on page 33 for more details.

The Main and right arrow buttons are operational during and after the warm-up period. The Main button is
the top level Main Menu for settings and user functionali ty of the system. The arrow button will bring you

to the next available screen. The flashing

♥ icon in the top left corner indicates that the system i s powered

on (power status). The percentage value in the top left corner (34%) is the percentage of battery
remaining. The percentage value in the top right corner (98%) is the percentage of absorber column
remaining. The “Z” button in the top right corner performs a zero when pressed. The Status Box informs
the user of any status or error messages.

EGM-5 Operation Manual V. 1.04 29 [e-mail]

Readings Screen

Readings Screen

♥ (Heartbeat)

Pulses on and off to indicate that the system is powered and operating. Press to
return to normal 1 second display updates.

71%

Percentage of battery life remaining.

Record

Saves current data as a marked record in the USB Memory stick and also sends
the record to the host and WiFi ports

90%

Percentage of absorber column remaining.

Z Button

Initiates a zero.

CO2

CO2 concentration reading (ppm).

Pr

Absolute pressure in sample cell (mb).

Fl

Flow rate reading (cc/min).

H2O

H2O reading if optional H2O sensor is installed (mb).

T

Temperature of the sample gas at the optimal H2O sensor if optional H2O sensor
is installed (°C).

O2

O2 reading if optional O2 sensor is installed (%).

Left Arrow

Displays the previous Measurement Mode screen (t he Measure screen).

Status Box

Any information or error messages are displayed here.

Right Arrow

Continues to the next Measurement Mode screen (the Probe screen).

The Readings Screen displays the values of six par ameters in real time; CO2, H2O, O2, Temperature,
Flow Rate, and Pressure. All of these sensors (if included) are located inside the EGM-5 console. Every
EGM-5 will include CO
these readings will also be displayed and recorded. If the H
readings will show 0.

, Pressure and Flow Rate. If the optional H2O and/or O2 sensor is included then

2

O and/or O2 sensor is not included the

2

EGM-5 Operation Manual V. 1.04 30 [e-mail]

Probe Screen

Readings Screen 2

♥ (Heartbeat)

Pulses on and off to indicate that the system is powered and operating. Press
to return to normal 1 second display updates.

71%

Percentage of battery life remaining.

Record

Saves current data as a marked record in the USB Memory stick and also
sends the record to the host and WiFi ports

98%

Percentage of absorber column remaining.

Z Button

Initiates a zero.

CO2

CO2 concentration reading (ppm).

PAR

PAR sensor reading (μmol m-2 s-1).

Aux

Aux input, also referred to as Analog In (V).

Tsoil

Soil temperature reading (°C).

Tair

Air temperature reading (°C).

Msoil

Soil moisture (%)

Left Arrow

Displays the previous Measurement Mode screen (t he Readings screen).

Status Box

Any information or error messages are displayed here.

Right Arrow

Continues to the next Measurement Mode screen (the Graphics Display
screen).

The Probe Screen displays the values of six parameters in real time; CO2, PAR, Aux(ANALOG IN), air
temperature (Tair), soil temperature (Tsoil) and soil moisture (Msoil). All readings, with the exception of
CO

, are based on optional external sensors which may be used with the EGM-5.

2

Graphic Display Screen

The Graphic display screen shows a real-time display of the CO2 concentration data.

EGM-5 Operation Manual V. 1.04 31 [e-mail]

Graphical Display Screen

♥ (Heartbeat)

Pulses on and off to indicate that the system is powered and operating. Press to
return to normal 1 second display updates.

56%

Percentage of battery life remaining.

Record

Saves current data as a marked record in the USB Memory stick and also sends
the record to the host and WiFi ports

98%

Percentage of absorber column remaining.

Z Button

Initiates a zero.

CO2 Button

Current measurement of CO2 concentration in ppm, and when pressed change s
graphed parameter to CO2

H2O Button

Current measurement of H2O partial pressure in mb, and when pressed change s
graphed parameter to H2O (0 - 30 mb)

O2 Button

Current measurement of O2 concentration in %, and when pressed changes
graphed parameter to O2 (0-100%)

0-2000 ppm

Y-axis range and units (CO2 concentration).

3 min

X-axis time; fixed value of 3 minutes.

Left Arrow

Displays the previous Measurement Mode screen (t he probe screen).

Status Box

Any information or error messages are displayed here.

Right Arrow

Completes the rotation of the Measurement Mode screens and returns to the
Measure screen..

The moving horizontal line below the CO
data is being displayed. The y-axis maximum (CO

concentration value indicates where on the tim el ine t he graph

2

concentration) is the number located under the graph

2

on left side (for example, 10000 ppm). The X-axis ma ximum (time) is the number located under the graph
on the right side. The x-axis maximum is a fixed value of about 4 minutes.

The maximum CO

value can be set in the Graph Settings screen. See Graph Settings on page 45 for

2

more details.

EGM-5 Operation Manual V. 1.04 32 [e-mail]

Main Menu

Main Menu

Settings

Controls major settings of the EGM-5. There a re f our sub menus under Settings.
See Settings on page 33.

Diagnostics

Performs system diagnostics for troubleshooting purposes. See Diagnostics on
page 83 for more details.

Processes

Performs the EGM-5 Processes available depending on probe/sensor used with
the EGM-5. See Processes on page 54 for more details.

Calibration

Used to calibrate the CO2 gas analyzer and O2 sensor and the Touch Screen.
See Calibration on page 77.

Info

Contains version information and contact information.

Back

Returns to the Measure screen.

Status Box

Any information or error messages are displayed here.

The Main Menu screen is displayed when the Main button i s selected in the Measure screen. This menu
is the top level menu for all settings and user functionality of the system.

Settings

There are four settings menus; Settings 1-4. General ly, the settings have been grouped related t o their
common functionality. For example, Settings Menu 1 contains the first tier of major settings for the EGM-

5. Settings Menu 2 contains the second tier set of settings for the EGM-5. Settings Menu 3 contains
options for adjusting the Measurement Format and Interval for the Host, WiFi, and Memory data output s.
Settings Menu 3 also contains settings for the Host P ort , resetting WiFi configuration, and turning WiFi
power on or off. Settings 4 handles the less common set tings of the EGM-5.

EGM-5 Operation Manual V. 1.04 33 [e-mail]

Settings 1 Menu

Settings 1 Menu

Zero

Change/view the settings of the zero parameter s (zero type and time interval for
performing zeros).

Alarms

Change/view the high and low alarm settings built into the EGM-5. The alarm

Reset Abs

Indicate that absorber material has been replaced.

Flow

Change/view the pump power and view the flow rate.

Alarm Sound

Change/view the alarm sound. This setting enable s/ disables the alarm sound.

Probe Ports

Change/view the settings of Probe Ports 1 and 2.

Back

Returns to the Main Menu.

Right Arrow

Continues to the Settings 2 Menu screen.

Zero Settings

Zero Type

There are three types of zeros that can be performed; Automatic, Manual and
User Set. See Zero Type below for more details. We recommend Automatic.

Time (min)

Zero time is the interval between zeros in minutes wh en Z ero Type is set to User
Set. See Zero Time on page 36 for more details.

Back

Returns to the Settings 1 Menu.

This menu contains the first tier and most common settings for the EGM-5 including the Zero, Alarms,
Reset Abs (Reset Absorber Column), Flow, Alarm S ound and Probe Ports settings.

parameters are low and high CO2 alarm set points.

Zero Settings

This function allows the user to change/view the set tings of the zero parameters used by the EGM-5.

EGM-5 Operation Manual V. 1.04 34 [e-mail]

Zero Type

To change the Zero Type, select the button to the right of the “Zero Type:” text in the Zero Settings
screen. The Zero Type Settings will display radio buttons with the current selection indicated.

Press the desired setting (in this case, User Set) eit her directly on the radio button or on the text t o the
right of the radio button.

Then select the Back button to return to the Zero Settings screen. The Zero Settings screen wil l ret urn
with the updated Zero Type value in the button box .

Press the “Back” button to return to the Settings 1 Menu.

EGM-5 Operation Manual V. 1.04 35 [e-mail]

Zero Type Settings

Automatic

This is the recommended Zero Type. The EGM-5 performs a zero on start up,

then again after 3 minutes, then again after 6 more minutes, then after 12

minutes. This is the default mode upon initialization.

Manual

A zero can be initiated at any time and regardless of the Zero T ype Setting by

zeros are performed.

User Set

When selected, the EGM-5 performs a zero on start up, then again after 3

Zero Time on page 36 for more details.

minutes, then every 20 minutes thereafter. The Zero Time interval is fixed at 20

Important Note

An Auto Zero can be performed at any time either automat i cally or using the “Z" button in the Measure,
Graphic Display, Readings or Probe screens. In thi s c ase, the timer resets back to zero and will perform
another zero when the Zero Time interval has elap sed.

pressing the Z button in the upper right hand corner of t he display. It can also be
initiated externally if required.
In this mode, a zero is performed when a high level signal between 0.7 V and

5.0 V is present on the ANALOG IN pin on the on the terminal block for 3
seconds. The ANALOG IN pin is normally 0 V. A contact closure between the
ANALOG IN pin and the +5V Out pin will initiate a zer o. In this mode, no startup

minutes, then again after 6 more minutes, then aft er 12 mi nutes, then finally after
20 minutes. It then performs zeros at the user-specified interval. It can be set
from 1 to 11,000 minutes (~7 days). For a setting great er t han 40 minutes, see

Zero Time

To change the Zero Time, select the button to the right of the “Time (min):” text in the Zero Settings
display (see display above). A numerical keypad wil l appear. This setting is only available when Zero
Type is in User Set mode.

This numerical keypad will be displayed for any parameter requiring numerical input. A description of the
numerical keypad components, using the example of the Zero Time parameter, is shown in the table
below. In this example, if the OK button is selected, the value of 30 will replace 40 in the Zero Time
parameter in the Zero Settings screen. If Can cel i s selected, Zero Time will continue to display 40
minutes.

EGM-5 Operation Manual V. 1.04 36 [e-mail]

Numerical Keypad

Title (Zero Time)

This is the title of the parameter being modified. In this case, Zero Time is the
title of the parameter.

Units (min)

The units of the parameter are displayed in parent heses. In this case, min or
minutes are the units for this parameter

Range ([1-40])

The valid range of parameter values is displayed in brackets. In this case, the
Zero Time parameter have valid values from 1-40.

Value (30)

The updated value of the parameter is displayed aft er the “=” sign. In this case,
the Zero Time parameter is set to 30.

0-9, . , Del Buttons

These buttons are used to input a numerical value.

OK Button

The OK button accepts the entered value and returns to the previous screen.

Cancel Button

The Cancel button returns to the previous screen without saving any changes.

Alarm Settings

Low CO2 (ppm)

Sets the low CO2 alarm setting. The default low alarm setting is 2 50 ppm .

High CO2 (ppm)

Sets the high CO2 alarm setting. The default high alarm setting is 2000 ppm.

Back Button

Returns to the Settings 1 Menu.

Important Note

PP Systems recommends Zero Time to be set to 40 m i nut es or less. Without frequent auto-zeroing, the
EGM-5 could potentially drift and lose calibration accuracy beyond the 1% specification.

For those customers who are in a very stable environment and where the auto-zero sequence
causes experimental problems, higher than 40 minutes can be used, but it should be used with
extreme caution.

Once the desired values are displayed in the Zero Settings screen, the “Back” button is selected to return
to the Settings 1 Menu.

Alarms Settings

This function allows the user to change/view the l ow (ALARM1) and high (ALARM2) alarm functions t hat
are built into the EGM-5. An alarm consists of an audio beep (if enabled in the Alarm Sound Setting
screen), an information message in the Status Box i n the Measurement Mode screens and a relay switch
closure. There is a relay switch for each alarm: low (ALA RM1) and high (ALARM2).

EGM-5 Operation Manual V. 1.04 37 [e-mail]

Low CO2 Alarm Setting

Reset Abs Settings

YES

Resets the absorber column percentage to 100%. T hi s v al ue is displayed in
Measurement Mode screens in the top right corner of the display.

NO

Cancels out and the absorber column percentage v al ue is not reset. Display
returns to Setting 1 Menu.

To change the Low CO2 Setting, select the button to the right of the “Low CO2 (ppm):” text. The numerical
keypad will appear, allowing the user to enter a new val ue.

The EGM-5 is supplied with a factory default low alar m set t i ng of 250 ppm. A low CO
the result of one of the following scenarios:

• Low or no air flow.

• Absorber column exhausted (soda lime).

• Zero valve failure.

The Low CO

Alarm relay (ALARM1) is closed when the CO2 reading is below the Low CO2 set point.

2

value is typically

2

High CO2 Alarm Setting

To change the High CO2 Setting, select the button to the right of the “High CO2 (ppm):” text. The
numerical keypad will appear, the user to enter a new value.

The default EGM-5 high alarm setting is 2000 ppm.
The High CO
Once the desired values are displayed, select t he “B ack” button to return to the Settings 1 Menu.

Alarm relay (ALARM2) is closed when the CO2 reading exceeds the High CO2 set point.

2

Reset Abs Settings

This function allows the user to indicate that the absorber material in the column has been replaced,
updating the percentage remaining to 100%. This value is displayed in the Measurement Mode screens in
the top right corner of the display.

EGM-5 Operation Manual V. 1.04 38 [e-mail]

Flow Settings

Flow

Flow (cc/min)

Displays the real-time value of the Flow rate (cc/mi n).

Pump Power (%)

Sets the % power of the pump. The range is 0-100%.

Back Button

Returns to the Settings 1 Menu.

This function allows the user to change/view the F l ow rate of the EGM-5.

Pump Power

To change the Pump Power value, select the button t o the right of the “Pump Power (%):” text. The
numerical keypad will appear allowing a new number to be ent ered. After entering the desired value,
press the “S1” button to return to the Settings 1 Menu.

Alarm Sound

This function allows the user to change/view t he set t ings associated with the built-in alarm. This
parameter sets the alarm sound (beep) to either be audible (Yes) or mute (No).

EGM-5 Operation Manual V. 1.04 39 [e-mail]

Alarm Sound Settings

Alarm Sound

Sets the Alarm Sound value to either Yes or No. The default Alarm Sound setting
is Yes.

Back Button

Returns to the Settings 1 Menu.

Status Box

Any information or error messages are displayed here.

Probe Port Settings

Probe Port 1

Sets port 1 probe type. Probe options are: Standard, Quantum, Soil Temperature,
and Soil Moisture.

Back Button

Returns to the Settings 1 Menu.

To change the Alarm Sound value, select the butt on to the right of the “Alarm Sound:” text. The Alarm
Sound settings will be displayed, with the current selection indicated.

Press the desired setting and then the Back button. The Alarm Sound Setting screen will return with the
updated Alarm Sound value in the button text.

Press the “Back” button to return to the Settings 1 Menu.

Probe Port Settings

This function allows the user to change/view the probes that are connected to ports 1 and 2.

EGM-5 Operation Manual V. 1.04 40 [e-mail]

Probe Port 1 Settings

Probe Port 1 Settings

Standard

For use with the following probes manufactured by PP Systems:

• TRP-3 Temperature/PAR Probe

Quantum

For use with the Apogee Quantum Sensor

Soil Temperature

For use with the STP-2 Soil Temperature Probe.

Soil Moisture

For use with the Stevens Soil Moisture Sensor.

Back Button

Returns to Probe Port Settings.

To change the Port 1 probe type, select the button to t he right of the “Probe Port 1:” text. The Probe Port
1 settings will be displayed, with the current sele ct i on indicated.

• SRC-2 Soil Respiration Chamber

• CPY-5 Canopy Assimilation Chamber

Press the desired setting and then the Back button. The Probe Port Settings screen will return wit h the
updated Probe Port 1 value displayed.

Probe Port 2 Settings

Probe Port 2 is for use only with the following 'Standar d' probes manufactured by PP Systems:

• SRC-2 Soil Respiration Chamber

• CPY-5 Canopy Assimilation Chamber

• TRP-3 Temperature/PAR Probe

There is no need to change or set the Probe Port type, the EGM-5 will recognize the Probe that is
attached to the Probe Port 2 and make the appropriat e set ting internally.

Important Note

If you are connecting two probes to the EGM-5 simultaneously, any non-PP Systems manufactured
sensors probes must be connected to Probe Port 1. For i nstance, if you are using both the SRC-2 Soil
Respiration Chamber and Quantum sensor manufactured by Apogee Instruments, the Quantum sensor
should be connected to Probe Port 1 and the SRC-2 Soi l Respiration Chamber to Probe Port 2.

EGM-5 Operation Manual V. 1.04 41 [e-mail]

Settings 2 Menu

Settings 2 Menu

Analog

Change/view the analog output. This parameter cont rols the voltage output of
voltage is fixed at 2.5V.

Averaging

Change/view the CO2 averaging method used by the EGM-5. The CO2
30 ppm.

Graph

Change/view the settings of the CO2 concentration maximum value on the
Graphic display screen. The default value is 1000 ppm.

EGM ID

Assigns an ID number to the EGM-5, useful for situations in which more than
one EGM-5 is used simultaneously. The default ID is 1 .

Left Arrow

Returns to the Settings 1 Menu.

Right Arrow

Continues to the Settings 3 Menu screen.

This menu handles the second tier of settings for the E G M -5 including the Analog, Averaging, Graph,
EGM ID, About and Display settings.

the Digital to Analog (D/A) converter in the EGM-5. The maximum output

Averaging Limit parameter can be modified in thi s s cr een. The default value is

Analog Output Setting s

This function allows the user to change/view the analog output. This setting controls the volta ge and
current output from the D/A converter in the EGM-5.

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Analog Output Settings

CO2 Conc (ppm)

Changes the CO2 concentration (ppm) associated with the max i m um Analog
Output voltage (2.5 V).

Back

Returns to the Settings 2 Menu.

To change the CO

concentration represented by to the maximum analog output value, select the button

2

to the right of the “CO2
be entered.

Conc (ppm):” text. The numerical keypad will appear, allowing a new number to

In the example above, an analog output range of 0-2.5 volts corresponds to a CO

measurement range of

2

0-2,000 ppm. Again, the maximum analog output volt age i s 2. 5V.
After entering the desired value, press the “Back” button t o ret urn to the Settings 2 Menu.

Averaging Settings

This function allows the user to change/view the CO2 averaging method used by the EGM-5.

The default EGM-5 averaging window is 1 second long. An optional running average function is avail able
to improve resolution and reduce the effect of transie nt fluctuations.

Running Average: The instrument’s response time to a step change is 2.5 seconds to reach 66% of a
new value, and 10 seconds to reach 99%, due to the time i t takes samples to reach the IRGA. In other
words, if an instrument goes from measuring Sample Gas A to Sample Gas B, it would take 2.5 seconds
for the CO
measured value will be within 1% of the concentration of CO
average algorithm can smooth out small fluctuations while remaining sensitive to larger differe nces. When
the running average is enabled (by setting Avg Limit great er than 0), the response time is 3.5 seconds to
reach 66% of a new value, and 16 seconds to reach 99%. A special feature of this running average
algorithm is that whenever a new reading differs from t he current running average by more than the CO
Avg Limit value, a new running average begins. Thus, when t he CO
averaging is suspended and the instrument can track changes at the basic instrument data rate of 1
second. When the CO
is 30 ppm. The running average is applied to displaye d data, recorded data, and analog output signal s.

reading to change by 66% of the difference betwe en the two samples; after 10 seconds, the

2

in Sample Gas B. An exponential running

2

concentration is changing rapidly,

2

Avg Limit is set to 0, no running average is perfo rmed. The default CO2 Avg Limit

2

2

EGM-5 Operation Manual V. 1.04 43 [e-mail]

Averaging Settings

CO2 Avg Limit

(ppm)

The CO2 Avg Limit is the threshold that new CO2 readings must exceed in order
The default value is 30 ppm.

Back

Returns to the Settings 2 Menu.

EGM ID

EGM-5 ID

Sets an identifier for use when more than one EGM-5 is employed
simultaneously. The default value is 1.

Back Button

Returns to the Settings 2 Menu.

To change the CO
numerical keypad will appear, allowing a new number to be entered.

After entering the desired value, press the “Back” butt on to return to the Settings 2 Menu.

to trigger the start of a new running average. Value s up to 100 ppm are allowed.

Averaging Limit, select the button to the right of the “CO2 Avg Limit (ppm):” text. The

2

EGM ID

This function allows the user to change/view the set tings of the EGM ID parameter used by the EGM -5.
This parameter sets an identifier for each EGM-5 so data can be differentiated between multiple
instruments.

EGM ID

To change the EGM ID, select the button to the right of the “EGM-5 ID:” text. The EGM ID settings will be
displayed, with the current selection indicated.

EGM-5 Operation Manual V. 1.04 44 [e-mail]

Press the desired setting and then the Back button and the EGM ID Settings Menu will return with the

Graph Settings

Max CO2 (ppm)

This setting determines the maximum CO2 value to be displayed on the y-axis of
step of all processes.

Back

Returns to the Settings 2 Menu.

updated EGM ID setting in the button box.
Press the “Back” button to return to the Settings 2 Menu.

Graph Settings

This function allows the user to change/view the G raph Settings in the Graphic Display screen.

the graph in the Graphic Display screen. This value is also displayed in the final

Max CO

2

To change the Max CO2 value, select the button to the right of the “Max CO2 (ppm):” text. The Max CO2
settings will be displayed, with the current sele ct i on i ndicated.

Press the radio button for the desired setting and then the Back button. The Graphic Settings screen will
return with the updated Max CO

value in the button text.

2

Once the Max CO

Setting is as desired, press the “Back” button to ret urn t o t he Settings 2 Menu.

2

EGM-5 Operation Manual V. 1.04 45 [e-mail]

Settings 3 Menu

Settings 3 Menu

Host

Configures the data format and time interval at whic h m easurement data is
PuTTY).

WiFi

Configures the data format and time interval at whic h m easurement data is
transmitted via the wireless connection and to the Internet.

Memory

Configures the data format and time interval at whic h m easurement data is
sent to the USB memory stick.

Host Port

Change/view the settings of the port connection used by the EGM-5. The
options are USB and WiFi.

Reset WiFi

Restore default factory WiFi settings (if WiFi opt ion is installed).

WiFi Power

Turns the WiFi power on or off.

Left

Returns to the Settings 2 screen.

Status Box

Any information or error messages are displayed here.

Right

Continues to the Settings 4 Menu screen.

This menu contains a number of settings for the EGM-5, including the Host, WiFi, Memory, Host Port,
Reset WiFi, and WiFi Power settings.

sent to the Host via a terminal emulation program (e.g., HyperTerminal or

Host Measure Settings

These settings control the format of measurement data, as well as the interval at which it is sent to the
Host (e.g., a PC running HyperTerminal).

EGM-5 Operation Manual V. 1.04 46 [e-mail]

Host Measure Settings

Format

Determines the measurement data format. Al l data formats are available (M1-

M6). The default is M3. See the Measure Format Settings Table on page 93

for more information.

Interval (sec)

Determines the time interval, in seconds, in which data will be transmitted. A

is 3600 seconds (1 hour). Default is 1 second.

Back Button

Returns to the Settings 3 Menu.

value of 0 disables automatic transmission of measurement data, but zero
operations and Process operations will still be reported. The maximum value

Host Measure Format

To change the Host Measure Format, select the butt on t o t he right of the “Format:” text. The Measure
Format Settings screen will be displayed with the current selection indicated.

Measure Format Settings

Six Measure Format Settings are available. See t he M easure Format Settings Table on page 93 for more
information.

Press the desired setting and then the Back button and the Measure Format Settings Menu will return
with the updated format setting in the button box.

Host Measure Interval

To change the Host Measure Interval, select the butt on to the right of the “Interval:” text. The numerical
keypad will appear allowing a new number to be entered. See numerical keypad description under Zero
Time on page 36 for more details.

Press the “Back” button to return to the Settings 3 Menu.

EGM-5 Operation Manual V. 1.04 47 [e-mail]

WiFi Measure Settings

WiFi Measure Settings

Format

The WiFi data is served as formatted web pages.

Interval (sec)

Determines the time interval, in seconds, in which data will be transmitted. A

is 3600 seconds (1 hour). Default is 1 second.

Back Button

Returns to the Settings 3 Menu.

These settings control the interval at which it is transmitted via WiFi. See Wireless Network S etti ngs on
page 113 for more details.

value of 0 disables automatic transmission of measurement data, but zero
operations and Process operations will still be reported. The maximum value

WiFi Measure Interval

To change the WiFi Measure Interval, select the button to the right of the “Interval:” text. The numerical
keypad will appear, allowing a new number to be entered. See numerical keypad description under Zero
Time on page 36 for more details.

Press the “Back” button to return to the Settings 3 Menu.

Memory Measure Settings

These settings control the format of measurement data, as well as the interval at which it is saved to the
flash drive. See USB Flash Drive (Memory Stick) on page 89 for more details.

EGM-5 Operation Manual V. 1.04 48 [e-mail]

Memory Measure Settings

Format

Determines the measure data format. All data f ormats are available (M1-

M6). The default is M3. See the Measure Format Settings Table on page

93 for a detailed description of each format.

Interval

Determines the time interval, in seconds, in which data will be transmitted.

maximum value is 3600 seconds (1 hour). Default is 1 second.

Back

Returns to the Settings 3 Menu.

Port Connection Settings

Port Connection

Sets the Port Connection to USB or WiFi. The default Port Connection setting is
USB.

Back

Returns to the Settings 3 Menu.

A value of 0 disables automatic transmission of measurement data, but
zero operations and Process operations will stil l be reported. The

Memory Measure Format

To change the Memory Measure Format, select the b utton to the right of the “Format:” text. The Measu re
Format Settings screen will be displayed, wit h the current selection indicated. See Measure Format
Settings Table on page 93 for more details.

Memory Measure Interval

To change the Memory Measure Interval, select the b utton to the right of the “Interval:” text. The
numerical keypad will appear allowing a new number to be ent ered. See numerical keypad description
under Zero Time on page 36 for more details.

Press the “Back” button to return to the Settings 3 Menu.

Host Port

This function allows the user to change/view the set tings of the port connection used by the EGM -5. This
parameter sets the port connection to either USB or WiFi. Refer to the Digital Communication Protocols
and Software on page 96 for more information on this topic.

Port Connection

EGM-5 Operation Manual V. 1.04 49 [e-mail]

To change the Port Connection value, select the button to the right of the “Port Connection:” tex t . The

Reset WiFi

Yes

Starts the initialization process to restore WiFi co nfiguration to factory defaults.

No

Returns to Settings 3 Menu without performing initialization.

Port Connection settings will be displayed, with the current selection indicated.

Press the desired setting and then the Back button. The Port Connection Setting screen will ret urn wit h
the updated Port Connection value in the button tex t.

Press the “Back” button to return to the Settings 3 Menu.

Reset WiFi

This function allows the user to initialize the onboard WiFi device to factory default settings, if the WiF i
option is installed.

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WiFi Power

WiFi Power Setting

WiFi Power

Enables (On) or disables (Off) the WiFi device. D efault is Off.

Back

Returns to the Settings 3 Menu.

This function allows the user to turn WiFi powe r on or off.

WiFi Power Setting

To change the WiFi Power value, select the button to the right of the “WiFi Power:” text. The WiFi Power
settings will be display, with the current selection indicated.

Press the desired setting and then the Back button. The WiFi Power screen will return with the updat ed
WiFi Power value in the button text.

Press the “Back” button to return to the Settings 3 Menu.

EGM-5 Operation Manual V. 1.04 51 [e-mail]

Settings 4 Menu

Settings 4 Menu

Set Clock

Set/Check the system clock (date and time).

Defaults

Initializes EGM-5 back to factory default settings.

Ship Mode

Sets the EGM-5 to ship mode.

Main

Returns to the Main Menu.

Status Box

Any information or error messages are displayed here.

Right Arrow

Returns to the Settings 1 Menu.

Clock

Day

Sets the current day of the month (1-31).

Mth

Sets the current month of the year (-12).

Year

Sets the current year (20XX).

Hr

Sets the current hour (0-23) (24 hour format).

Min

Sets the current minute (0-59).

Back

Returns to the Settings 4 Menu.

This menu contains a number of settings for the EGM-5 including the Set Clock, Defaults, and Ship Mode
settings.

Set Clock

This function allows the user to change/view the EGM-5 real time clock.

The date is displayed as day/month/year and the time i s display on a 24-hour format. Selecting one of the
buttons will cause the numerical keypad to appear, w hi ch will allow a new number to be entered.

EGM-5 Operation Manual V. 1.04 52 [e-mail]

Press the “Back” button to return to the Settings 4 Menu.

Defaults

Yes

Resets EGM-5 to original factory settings then returns to Settings 4 Menu.

undesirable configuration changes.

No

Cancels the initialization process and returns to S etting 4 Menu.

Status Box

Any information or error messages are displayed here.

Defaults

This function allows the user to initialize the E GM -5 t o its factory default values. This feature may be
needed to correct an erroneous calibration, or to simply undo undesirable configuration changes.

This function allows the user to initialize the WMA-5 to its factory default values.
This feature may be needed to correct an erroneous calibration, or to simply undo

After initialization is complete, the EGM-5 system settings will be restored to the predefined factory
defaults. Refer to the Get/Set Parameter Values Table on page 106 for more details.

Ship Mode

This function allows the user to put the EGM-5 into ship mode. The EGM-5 will not respond to presses of
the On/Off button. This mode ensures that the unit i s not i nadvertently powered on during shipment. In
order to take it out of ship mode, the EGM-5 needs to be connected to the power supply/charger provided
with the instrument.

EGM-5 Operation Manual V. 1.04 53 [e-mail]

Ship Mode

Yes

Sets the EGM-5 into ship mode. We recommend putting the EGM -5 int o ship
mode when transporting/shipping the instrument t o avoid accidental power up.

No

Cancels out and the EGM-5 does not go into ship mode. Display returns to
Setting 4 Menu.

Processes Menu

SRC

Starts the Soil Respiration Chamber (SRC) process.

CPY

Starts the Canopy Assimilation Chamber (CPY) process.

Custom

Starts the Custom process (for use with custome r’s own chambers).

Injection

Starts the Injection process using the “Sample Injection Kit” from PP Systems.

Static

Starts the Static process.

Main

Returns to the Main Menu.

Status Box

Any information or error messages are displayed here.

Important Note

In order to get the EGM-5 out of “Ship Mode” you must first connect the power supply/charger to the EXT
POWER jack before turning the instrument on. If you do not have the power supply/charger connected
you will not be able to power up the instrument.

Processes

This menu handles the various processes of the E GM-5.

SRC (Soil Respiration Chamber) Process

This process is used in conjunction with our SRC-2 Soil Respiration Chamber for measurement of closed­system soil CO
rate of change (increase) in the chamber CO
both a linear fit and a quadratic fit to the measured data. The data is checked in the quadratic fit to
determine if the data is linear.

While the EGM-5 is in the SRC measuring mode, addi tional data is added to the output data string:
change in CO

EGM-5 Operation Manual V. 1.04 54 [e-mail]

efflux. In the SRC process, the respiration rate (g m-2 hr-1) is calculated by measuring the

2

concentration over a period of time. The EGM-5 calculate s

2

(dC), process time (dT), Linear respiration rate (L), and Quadratic respiration rate (Q).

2

SRC – Start Process (Step 1)

SRC – Start Process Menu

Back

Returns to the Processes Menu.

Status Box

Any information or error messages are displayed here.

Right Arrow

Confirms and starts the SRC process by displaying t he SRC –Volume and
Area Settings screen (Step 2).

Status Box

Back



Would you like to start the SRC

SRC - Start Process

Autozero

SRC - V and A Settings

Volume (ml):

1171

Area (cm2):

78

Volume/Area Ratio:

15

Status Box

Stop



Def

The first screen asks the user to confirm that t hey would like to start the SRC process.

process or go back?

SRC – Volume and Area Settings (Step 2)

The volume and area settings are defined in this screen.

Important Note. The above values are based on the default volume of the SRC-2 Soil Respiration
Chamber only. You must remember to account for any volume changes for proper calculation of rates. If
using collars, please make sure that you adjust t he volume accordingly.

EGM-5 Operation Manual V. 1.04 55 [e-mail]

SRC – Volume and Area Settings Menu

Def

Sets the volume and area values back to the defaults.

Volume (ml)

Sets the volume of the system. Entries between 1,000 and 2,000 ml are
permitted. Default is 1171 ml.

Area (cm2)

Sets the surface area of the chamber. Entries between 50 and 100 cm2 are
permitted. The default value is 78 cm2.

Volume/Area Ratio

This value is automatically updated when there is a change to either the
Volume or Area values.

Stop

Stops the SRC process and returns to the Processes M enu.

Status Box

Any information or error messages are displayed here.

Right Arrow

Continues to SRC – Termination Settings menu (S tep 3).

SRC – Termination Settings Menu

DT (seconds)

Maximum time for which changes in the chamber CO

concentration are

monitored in a given session. Valid entries range between 10 - 300 seconds.

DC (ppm)

Maximum positive change in CO2 concentration (ppm) allowed in a given
are between 1 - 1,000 ppm.

Delay (seconds)

The amount of time the instrument waits at the start of each session before it
starts calculating respiration. Valid entries are between 5 – 150 seconds.

Stop

Stops the SRC process and returns to the Processes M enu.

Status Box

Any information or error messages are displayed here.

Right Arrow

Continues to SRC – Other Settings menu (Step 4).

Autozero

SRC - Termination Settings

DT (seconds):

120

DC (ppm):

50

Status Box

Stop



Delay (seconds):

9

SRC – Termination Settings (Step 3)

The Termination settings (DT, DC) as well as delay are def i ned in this screen. These settings define the
end conditions for the SRC process. Each new measurement session will begin after the specified Delay,
and will terminate when either the elapsed time reaches the DT value, or when the total change in CO
exceeds a specified threshold (DC), whicheve r oc curs first.

2

session. If total change exceeds this value, the se ssion will end. Valid entries

EGM-5 Operation Manual V. 1.04 56 [e-mail]

2

SRC – Other Settings (Step 4)

SRC – Other Settings Menu

Plot Number

Change/View plot number. Range: 1–1000.

Stop

Stops the SRC process and returns to the Processes M enu.

Status Box

Any information or error messages are displayed here.

Right Arrow

Continues to SRC – Prepare Chamber screen (Step 5).

SRC – Prepare Chamber Menu (Step 5)

CO2

Current measurement of CO2 concentration (ppm).

24

Countdown in seconds, from 25 to 0.

Stop

Stops the SRC process and returns to SRC – Other Settings menu (Step 4).

Status Box

Any information or error messages are displayed here.

SRC - Other Settings

Plot Number:

1

Status Box

Stop



Hold chamber in air for flushing.

SRC - Prep Chamber

CO2

1000

Status Box

24

Stop

The plot number is defined in this screen to allow the user to r eference different sampling plots.

SRC Step 5

This screen instructs the user to prepare the chamber.

EGM-5 Operation Manual V. 1.04 57 [e-mail]

At this stage, the SRC chamber should be held in the ai r t o al l ow it to flush out prior to placing it on the

SRC – Start Measuring Menu

CO2

Current measurement of CO2 concentration (ppm).

5

Countdown in seconds, from 10 to 0.

Stop

Stops the SRC process and returns to SRC – Other Settings menu (Step 4).

Status Box

Any information or error messages are displayed here.

Status Box

dC

Q

dT

Abort

New

L

maxDC 50

maxDT 120

75%

C: 603

Plot

1

CAL

26

24

1.91

-0.77

Place chamber on soil.

SRC - Start Measuring

CO2

1000

5

Status Box

Stop

soil. During the flushing the internal fan of the SRC is sped up to help flush. The number at the top right of
the screen (24 in this case) is the countdown. CO
completed, SRC Step 6 will be displayed.

SRC – Start Measuring (Step 6)

This screen informs the user to place the chamber on t he soil to commence measurement.

concentration is displayed during this step. When

2

At this stage, the SRC chamber should be placed on t he soil . The internal fan is set to a low speed to
provide an even concentration of CO
countdown. CO
be displayed.

Data Plot Screen (Step 7)

This screen displays present values and a graphical representation of the data gathered during the
current session.

concentration is displayed during this step. When completed, the Data Plot Screen will

2

. The number at the top right of the screen (5 in this case) is t he

2

EGM-5 Operation Manual V. 1.04 58 [e-mail]

SRC Data Plot Screen

♥ (Heartbeat)

Pulses on and off to indicate that the system is powered on (power
status).

75%

Percentage of battery life remaining (%).

C: 603

Current measurement of CO2 Concentration (ppm).

Delay/CAL/END

Delay is the countdown in seconds from x t o 0, wher e x is the Delay

value specified in SRC – Termination Settings (Step 3). CAL is the active

been terminated.

dC

The difference in CO2 concentration (ppm) from time = 0 second s.

dT

Elapsed time (seconds) for the current session (i.e. , change in time).

L

Linear respiration rate (g m-2 hr-1).

Q

Quadratic respiration rate (g m-2 hr-1).

Plot

Plot number defined by user in SRC – Other Setting s (S tep 4).

X-axis

Time (1 second interval)

Y-axis

dC (change in CO2 concentration)(ppm)

maxDC

Maximum positive change in CO2 concentration (ppm) allowed in a given
session. This value is defined in SRC – Termination Settings (Step 3).

maxDT

Maximum time for which changes in the chamber CO

concentration are

Settings (Step 3).

Abort

Stops the SRC process and returns to SRC – Other Sett i ngs (Step 4).
Process data is discarded.

Status Box

Any information or error messages are displayed here.

New

Stops the SRC process and returns to SRC – Other Settings (Step 4).
Results are saved to the USB flash drive.

concentration calculating phase. END indicates calculations have

CO

2

2

monitored in a given session. This value is define d in S RC – Termination

Only the individual CO2 measurements are saved to the USB flash drive.

The measurement sequence will terminate when t he m axDC or maxDT is reached. If maxDT is reached
first, the message “Time limit” will appear in the stat us box. If maxDC is reached first, the message “CO2
limit” will appear in the status box.

For more information on the theory and calculation of soil respiration/canopy assimilation, please refer to
Appendix 1. Soil CO

Efflux and Net Canopy CO2 Flux on page 124.

2

CPY (Canopy Assimilation Chamber) Process

This process is used in conjunction with our CPY -5 Canopy Assimilation Chamber for measurement of
closed-system net canopy CO
by measuring the rate of change (decrease) in the chamber CO
both a linear fit and a quadratic fit to the measured data. The data is checked in the quadratic fit to
determine if the data is linear.

While the EGM-5 is in the CPY measurement mode, addit ional data is added to the output data string:
change in CO

(dC), process time (dT), Linear respiration rate (L), and Quadratic respiration rate (Q).

2

EGM-5 Operation Manual V. 1.04 59 [e-mail]

flux. In the CPY process, the assimilation rate (μmol m-2 s-1) is calculated

2

concentration. The EGM-5 calculates

2

CPY – Start Process (Step 1)

CPY – Start Process Menu

Back

Returns to the Processes Menu.

Status Box

Any information or error messages are displayed here.

Right Arrow

Confirms and starts the CPY process by displaying the CPY – Volume and
Area Settings menu (Step 2).

Status Box

Back



Would you like to start the CPY

CPY - Start Process

Autozero

CPY - Vol and A Settings

Volume (ml):

2427

Area (cm2):

167

Volume/Area Ratio:

14.5

Status Box

Stop



Def

The first screen asks the user to confirm that t hey would like to start the CPY process.

process or go back?

CPY – Volume and Area Settings (Step 2)

The volume and area settings are defined in this screen.

Important Note. The above values are based on the default volume for the CPY-5 Canopy Assimilation
Chamber only. You must remember to account for any volume changes in order for the instrument to
properly calculate assimilation rates. If using collars, please make sure that you adjust the volume
accordingly.

EGM-5 Operation Manual V. 1.04 60 [e-mail]

CPY – Volume and Area Settings Menu

Def

Sets the volume and area values back to the defaults.

Volume (ml)

Sets the volume of the system. Entries between 1,000 and 5,000 ml are
permitted. Default is 2427 ml.

Area (cm2)

Sets the surface area of the chamber in cm2. Entries between 150 and 200
cm2 are permitted. The default value is 167 cm2.

Volume/Area Ratio

This value is automatically updated when there is a change to either the
Volume or Area values.

Stop

Stops the CPY process and returns to the Processes M enu.

Status Box

Any information or error messages are displayed here.

Right Arrow

Continues to CPY – Termination Settings menu (Step 3).

CPY – Termination Settings Menu

DT (seconds)

Maximum time for which changes in the chamber CO

concentration are

monitored in a given session. Valid entries range between 10 - 300 seconds.

DC (ppm)

Maximum negative change in CO2 concentration (ppm) allowed in a given
are between 1 - 1,000 ppm.

Delay (seconds)

The amount of time the instrument waits at the start of each session before it
starts calculating respiration. Valid entries are between 5 – 150 seconds.

Stop

Stops the CPY process and returns to the Processes M enu.

Status Box

Any information or error messages are displayed here.

Right Arrow

Continues to CPY – Other Settings Menu (Step 4).

Autozero

CPY - Termination Settings

Status Box

Stop



DT (seconds):

120

DC (ppm):

50

Delay (seconds):

9

CPY – Termination Settings (Step 3)

The Termination Settings (DT, DC) as well as Delay are defined in this screen.

2

session. If total change exceeds this value the ses sion will end. Valid entries

EGM-5 Operation Manual V. 1.04 61 [e-mail]

CPY – Other Settings (Step 4)

CPY – Other Settings Menu

Plot Number

Change/View plot number. Range: 1–1000.

Stop

Stops the CPY process and returns to the Processes M enu.

Status Box

Any information or error messages are displayed here.

Right Arrow

Continues to CPY – Prepare Chamber menu (Step 5).

CPY – Prepare Chamber Menu

CO2 (ppm)

Current measurement of CO2 concentration (ppm).

24

Countdown in seconds, from 25 to 0.

Stop

Stops the CPY process and returns to CPY Step 4.

Status Box

Any information or error messages are displayed here.

CPY - Other Settings

Plot Number:

1

Status Box

Stop



Hold chamber in air for flushing.

CPY - Prep Chamber

CO2

1000

24

Status Box

Stop

The plot number is defined in this screen.

CPY – Prepare Chamber (Step 5)

This screen instructs the user to prepare the chamber.

EGM-5 Operation Manual V. 1.04 62 [e-mail]

At this stage, the CPY chamber should be held in the air to allow it to flush out prior to placing it on the

CPY – Start Measuring Menu

CO2 (ppm)

Current measurement of CO2 concentration (ppm).

5

Countdown in seconds, from 10 to 0.

Stop

Stops the CPY process and returns to CPY – Other Settings (Step 4).

Status Box

Any information or error messages are displayed here.

Status Box

Abort

New

maxDC 25

maxDT 30

75%

C: 603

dC

Q

dT

L

Plot

26

24

1.91

-0.77

1

CAL

Place chamber on soil.

CPY - Start Measuring

CO2

1000

Stop

Status Box

5

soil. During this step, the internal fan of the CPY is sped up to help flush the chamber. The number at the
top right of the screen (24 in this case) is the countdown. CO
When completed, the process will proceed t o t he CPY – Start Measuring screen (Step 6).

CPY – Start Measuring (Step 6)

This screen instructs the user to place the chambe r on the soil to commence measuring.

concentration is displayed during this step.

2

At this stage, the CPY chamber should be placed on t he soil. The internal fan is set to a low speed to
provide an even concentration of CO
countdown. CO
displayed.

CPY Data Plot Screen (Step 7)

This screen displays present values and a graphi cal representation of the data gathered during the
current session.

concentration is displayed during this step. When completed, CPY Step 7 will be

2

. The number at the top right of the screen (5 in this case) is t he

2

EGM-5 Operation Manual V. 1.04 63 [e-mail]

CPY Data Plot Screen

♥ (Heartbeat)

Pulses on and off to indicate that the system is powered on (power
status).

75%

Percentage of battery life remaining.

C: 603

Current measurement of CO2 Concentration (ppm).

Delay/CAL/END

Delay is the countdown in seconds from x t o 0, wher e x is the Delay

value specified in CPY – Termination Settings (Step 3). CAL is the active

been terminated.

dC

The current difference in CO2 concentration (ppm) from time = 0
for display purposes the negative values are inve rt ed.

dT

Elapsed time (seconds) for the current session (i.e. , change in time).

L

Linear assimilation rate (μmol m

-2 s-1

).

Q

Quadratic assimilation rate (μmol m

-2 s-1

).

Plot

Plot number defined by user in CPY – Other Setti ngs (Step 4).

X-axis

Time (1 second interval)

Y-axis

dC (change in CO2 concentration)(ppm)

maxDC

Maximum negative change in CO2 concentration (ppm) allowed in a

3).

maxDT

Maximum time for which changes in the chamber CO

concentration are

Settings (Step 3).

Abort

Stops the CPY process and returns to CPY – Other Set tings (Step 4).
Process data is discarded.

Status Box

Any information or error messages are displayed here.

New

Stops the CPY process and returns to CPY – Other Set tings (Step 4).

concentration calculating phase. END indi cat es calculations have

CO

2

seconds. Normally in assimilation, CO2 concentration is decreasing, but

given session. This value is defined in CPY – Termination Settings (Step

2

monitored in a given session. This value is define d in CPY – Termination

Only the individual CO2 measurements are saved to the USB flash drive.

Results are saved to the USB flash drive.

The measurement sequence will terminate when t he m axDC or maxDT is reached. If maxDT is reached
first, the message “Time limit” will appear in the status box. If maxDC is reached first, the message “CO 2
limit” will appear in the status box.

For more information on the theory and calculation of soil respiration/canopy assimilation, please refer to
Appendix 1. Soil CO

Efflux and Net Canopy CO2 Flux on page 124.

2

Custom Process

This process is available for users that want to use t heir own custom chambers with the EGM-5. Since it
is assumed that you are using your own chambers there are no “defaults” built into the system. It is y our
responsibility to make sure that you enter the appropriate values where required in order to ensure prope r
calculations.

EGM-5 Operation Manual V. 1.04 64 [e-mail]

Custom – Start Process (Step 1)

Custom – Start Process Menu

Back

Returns to the Processes Menu.

Status Box

Any information or error messages are displayed here.

Right Arrow

Confirms and starts the Custom process by displaying the Custom – Volume
and Area Settings menu (Step 2).

Status Box

Back



Would you like to start the custom

Custom - Start Process

Autozero

Custom - V and A Settings

Volume (ml):

2000

Area (cm2):

100

Volume/Area Ratio:

20

Status Box

Stop



The first screen asks the user to confirm that they would like to start the Custom process.

process or go back?

Custom – Volume and Area Settings (Step 2)

The volume and area settings are defined in this screen.

Important Note. You must remember to account for any vol um e changes in order for the instrument to
properly calculate assimilation rates. If using collars, please make sure that you adjust the volume
accordingly.

EGM-5 Operation Manual V. 1.04 65 [e-mail]

Custom Step 2 Menu

Volume (ml)

Sets the volume of the system. Entries between 10 a nd 100,000 ml are
permitted.

Area (cm2)

Sets the surface area of the chamber in cm2. Entries between 1 and 10,000
cm2 are permitted.

Volume/Area Ratio

This value is automatically updated when there is a change to either the
Volume or Area values.

Stop

Stops the Custom process and returns to the Proces ses Menu.

Status Box

Any information or error messages are displayed here.

Right Arrow

Continues to the Custom – Termination Settings menu (Step 3).

Custom – Termination Settings Menu

DT (seconds)

Maximum time for which changes in the chamber CO

concentration are

monitored in a given session. Valid entries range between 10 - 300 seconds.

DC (ppm)

Maximum change in CO2 concentration (ppm) allowed in a given session. I f
1 - 1,000 ppm.

Delay (seconds)

The amount of time the instrument waits at the start of each session before it
starts calculating respiration. Valid entries are between 5 – 150 seconds.

Stop

Stops the Custom process and returns to the Processes Menu.

Status Box

Any information or error messages are displayed here.

Right Arrow

Continues to the Custom – Other Settings menu (St ep 4).

Autozero

Custom - Termination Settings

Status Box

Stop



DT (seconds):

120

DC (ppm):

50

Delay (seconds):

9

Custom – Termination Settings (Step 3)

The Termination settings (DT, DC) and Delay are defined in this screen.

2

total change exceeds this value the session will end. Valid entries are between

EGM-5 Operation Manual V. 1.04 66 [e-mail]

Custom – Other Settings (Step 4)

Custom – Other Settings Menu

Plot Number

Change/View plot number. Range: 1–1000.

Tair (°C)

Air temperature inside chamber (oC).

Stop

Stops the Custom process and returns to the Processes Menu.

Status Box

Any information or error messages are displayed here.

Right Arrow

Continues to the Custom – Prepare Chamber screen (Step 5).

Custom – Prepare Chamber Menu

CO2 (ppm)

CO2 concentration.

Stop

Stops the Custom process and returns to the Custom – Other Settings menu
(Step 4).

Start

Continues to the Custom – Start Measuring scre en (Step 6). Note: It is up to
the user to determine the amount of time required to fl ush a custom chamber.

Status Box

Any information or error messages are displayed here.

Custom - Other Settings

Plot Number:

1

Status Box

Stop



Tair (°C):

25

Flush chamber.

Custom - Prep Chamber

CO2

1000

Status Box

Stop

Start

The plot number is defined in this screen.

Custom – Prepare Chamber (Step 5)

This screen prompts the user to prepare the chamber.

EGM-5 Operation Manual V. 1.04 67 [e-mail]

At this stage, the Custom probe should be held in the ai r t o al l ow it to flush out prior to placing it on the

Custom – Start Measuring Menu

CO2 (ppm)

CO2 concentration.

5

Countdown in seconds, from 10 to 0.

Stop

Stops the Custom process and returns to Custom Step 4.

Status Box

Any information or error messages are displayed here.

Status Box

Abort

New

maxDC 25

maxDT 30

75%

C: 603

dC

Q

dT

L

Plot

26

1.91

-0.77

1

CAL

24

Place chamber on soil.

Custom - Start Measuring

CO2

1000

5

Stop

Status Box

soil. CO
countdown for flushing the chamber; it is up to the user to determine the amount of time required to flush
a custom chamber. Once the chamber has been ad equately flushed, pressing the Start button will allow
the process to continue to the Custom – Start Measuring screen (Step 6)

Custom – Start Measuring (Step 6)

This screen instructs the user to place the chambe r on the soil to commence measuring.

concentration is displayed during this step. Unlike the SRC and CPY Processes, there is no

2

At this stage, the Custom probe should be placed on the soil. The number at the top right of the screen (5
in this case) is the count down from 10-0 seconds. CO
completed, the Custom Data Plot screen (Step 7) will be di splayed.

Custom Data Plot Screen (Step 7)

This screen displays present values and a graphi cal representation of the data gathered during the
current session.

EGM-5 Operation Manual V. 1.04 68 [e-mail]

concentration is displayed during this step. Whe n

2

Custom Data Plot Menu

♥ (Heartbeat)

Pulses on and off to indicate that the system is powered o n (po wer
status).

75%

Percentage of battery life remaining.

C: 603

Current measurement of CO2 Concentration (ppm).

Delay/CAL/END

Delay is the countdown in seconds from x t o 0, wher e x is the Delay

value specified in Custom – Termination Setti ngs (Step 3). CAL is the

have been terminated.

dC

The current difference in CO2 concentration (ppm) from time = 0
seconds.

dT

Elapsed time (seconds) for the current session (i.e. , change in time).

L

Linear respiration rate (g m-2 hour-1).

Q

Quadratic respiration rate (g m-2 hour-1).

Plot

Plot number defined by user in Custom – Other Sett i ngs (Step 4).

X-axis

Time (1 second interval)

Y-axis

dC (change in CO2 concentration)(ppm)

maxDC

Maximum negative change in CO2 concentration (ppm) allowed in a
(Step 3).

maxDT

Maximum time for which changes in the chamber CO

concentration are

Termination Settings (Step 3).

Abort Button

Stops the Custom process and returns to Custom – Other Settings (Step
drive. Process data is discarded.

Status Box

Any information or error messages are displayed here.

New Button

Stops the Custom process and returns to Custom – Other Settings (Step

4). Results are saved to the USB flash drive.

active CO

2

given session. This value is defined in Custom – Termination Settings

monitored in a given session. This value is defined in Custom –

4). Only the individual CO2 measurements are saved to the USB flash

concentration calculating phase. END i ndicates calculations

2

EGM-5 Operation Manual V. 1.04 69 [e-mail]

Injection Process

The injection process is a technique used to measure the concentrations of small samples of gas, us ual ly
collected in sampling jars and transferred to the EGM-5 with a syringe. The injection process is an
improvement over static sampling and yields more reliable and consistent results.

Measurement Principle

The concentration of CO2 in a gas sample is calculated by injecting the sampl e i nto a fixed flow of gas
with a known CO
until they return to baseline. This is similar to the Puls e T racer Gas Technique used for HVAC duct flow to
infer the unknown flow rate by measuring the concentration of a known mass of tracer gas injected into
the duct over time. In our case, the gas flow rate F is known, the syringe volume V is known, but the
sample (or tracer gas) concentration is unknown.

The concentration in the syringe is calculated as:

concentration (the baseline CO2 level) and integrating the resulting CO2 measurements

2



= () 

 



= 



_



_





60







Where

CO
CO

(ppm) = calculated CO2 concentration inside syringe (“integrated” CO2)

2 INT

(ppm) = baseline CO2 readings before the measurement phase (aver aged over 10

2_ b

readings)
CO

(ppm) = CO2 readings during the measurement phase

2_m

Δt (s) = sample interval, typically 1 second
F (ml min

-1

) = flow rate

V (ml) = syringe volume

The process consists of two phases: Baseline P hase and Measurement Phase. The Baseline Phase
establishes a baseline measurement of CO

concentration by passing CO2-free gas through the EGM-5

2

and calculating the average concentration over 10 measurements at a 1-second interval. Upon
completion of the Baseline Phase, the instrument will enter the Measurement Phase. In this phase the
sample is slowly injected, and the measured CO
Measurement Phase. Any gas with a known, constant CO
a gas with zero CO

concentration can be readily produced with an absorber column filled with soda lime.

2

concentrations are integrated over the duration of the

2

concentration can be used as a baseline, but

2

Sample Injection Kit (Part No. ACS037)

PP Systems offers a Sample Injection Kit (Part No. ACS037),
which includes a fully assembled and leak-tested injection
port with 4 spare septa, as well as an absorber colum n to
establish a zero baseline.

The syringe is user supplied (not included with the kit ) and
the soda lime is not included with this part but it is included
with the EGM-5 as standard.

EGM-5 Operation Manual V. 1.04 70 [e-mail]

The injection port includes a 9mm low-bleed septum that can withstand up to 50 injections (per the

Injection – Start Process Menu

Back Button

Returns to the Processes Menu.

Right Arrow Button

Confirms and starts the Injection process by displaying the Injection – Settings
screen (Step 2).

manufacturer’s specification). For best results, we recommend changing the septum every 25 inject i ons.
The septum has a guide hole and accommodates syri nges up to 22 gauge, but we recommend at least

18 gauge for best results. The syringe is not include d i n the kit and must be provided by the user. The
injection technique is relatively insensitive t o the volume of the syringe, but it should be at least a size
where you could comfortably inject gas for at least 3 seconds continuously. For this reason alone,
syringes with a volume of at least 10 ml (e.g. 10- and 25-ml sy ringes) are recommended. The injection
rate should not exceed 3 ml/s, due to the risk of over-p ressurizing the IRGA and causing damage to the
instrument. We recommend glass syringes if available (e.g. typical GC syringes), but plastic
(polypropylene) syringes will work as well.

The injection process works best for samples with concentrations greater than 100 ppm. The process will
work at lower concentrations, but percent error will be significantly larger.

Injection – Start Process (Step 1)

The first screen asks the user to confirm that t hey would like to start the Injection process.
To begin a sample injection measurement, first fill the absorber column of the Sample Injection Kit wit h

fresh soda lime and ensure it is oriented vertically throughout the process. Connect the open end of the
kit to the GAS IN port on the back of the EGM-5.

EGM-5 Operation Manual V. 1.04 71 [e-mail]

Injection – Settings (Step 2)

Injection – Settings Menu

Syringe Volume(ml)
Button

Volume of injection syringe. Valid entry range is between 1.0 – 1,000.0 ml.

Correction Factor
Button

This user defined factor can be used to scale calculated gas concentrations to
make them match a known reference gas standar d. Range: 0.50 – 2.00.

Stop Button

Stops the Custom process and returns to the Processes Menu.

Right Arrow Button

Continues the Injection process to Injection S t ep 3 sc reen.

Injection – Sample Setting Menu

Sample Number
Button

Sample number of measurement.

Stop Button

Stops the Custom process and returns to the Processes Menu.

Start Button

Starts the Injection Process and displays the Injection Baseline Phase screen
(Step 4).

The syringe volume and correction factor settings are defined in this screen.

Injection – Sample Setting (Step 3)

The sample number is defined in this screen. Once the Start button is pressed, the Injection process will
begin. Before you press Start, take your syringe sa m ple (e.g., from a chamber or airbag) if you have not
done so already. We recommend that you draw more gas from your sample source than required, and
then squeeze out excess. For example, for a 10 ml sample y ou should draw at least 11 ml into your
syringe, and then slowly push the plunger to the 10 ml mar k.

EGM-5 Operation Manual V. 1.04 72 [e-mail]

Injection – Zero (Step 4)

Perform Zero

Yes Button

Does a Zero then proceeds to Measuring screen (Step 5).

No Button

Proceeds to Measuring screen (Step 5).

The next screen prompts the user whether to perform a zero or not. Since an autozero occurring during
an injection measurement would disrupt the process, normal timed zeros are disabled. It is
recommended that a zero be performed at the start of each measurement sequence. But it is not
required to perform one every single measurement.

Injection Step 5 – Baseline Phase

This is the Baseline Phase. For the first 10 seconds, the EGM-5 will record the baseline reading, which is
the CO
Injection Phase begins. We recommend inserting the needle from your syringe into the septum at this
point in time to avoid contamination of the sample about to be injected into the EGM-5.

concentration of the air before the sample is injected (typically 0 ppm). After 10 seconds the

2

EGM-5 Operation Manual V. 1.04 73 [e-mail]

Injection Baseline Phase Menu

♥ (Heartbeat)

Pulses on and off to indicate that the system is powered on (power
status).

100%

Percentage of battery life remaining.

C

Current CO

2

concentration in tubing (ppm).

M

Calculated CO2 concentration inside syringe (ppm).

B

Average baseline of CO

concentration (ppm).

BSLN

Indicates that the process is in the Baseline phase for the first 10
readings.

X-axis

Time (seconds). It is fixed at 180 seconds.

Y-axis

CO

2

concentration in tubing (ppm).

250 ppm

CO2 concentration maximum. This is set to be ¼ of the Max CO2 value

this graph shows 250 ppm.)

Abort Button

Stops the Injection process and returns to Injection – Settings (Step 2).
Process data is not saved to the USB flash drive.

New Button

Stops the Injection process and returns to Injection - Settings (Step 2).
Injection Process results are saved to the USB flash drive.

2

for the Graph setting and can be modified under Main > Sett ings >
Settings 2 > Graph. (For example, when Max CO2 is set to 1000 ppm,

If the baseline (B) does not drop to either 0 or a very small num ber (typically 1-3 ppm), then there is either
a leak in the system, or the system has not adequate l y “zeroed”. Try aborting the process, wait 2-3
minutes, and try again. If the problem persists, check the Injection setup for leaks and ensure that t he
absorber column is properly seated and contains fre sh soda lime.

Injection Step 6 – Injection Phase

During the Injection Phase, the syringe should be slowly and steadily injected into the airstream t hrough
the septum. The injection rate should not exceed 3 ml/second to avoid over-pressurization of the syst em
(in other words, it should take the user at least 3 seconds t o i nject a 10 ml syringe).

EGM-5 Operation Manual V. 1.04 74 [e-mail]

Injection Step 6 Menu

♥ (Heartbeat)

Pulses on and off to indicate that the system is powered on (power
status).

100%

Percentage of battery life remaining.

C

Current CO

concentration in tubing (ppm).

M

Calculated CO

concentration inside syringe (ppm).

B

Average baseline of CO

concentration (ppm).

INJT/END

INJT Indicates that the process is in the injection pha se. END
indicates CO

2

concentration calculations have been terminated.

X-axis

Time (seconds). It is fixed at 180 seconds.

Y-axis

CO

2

concentration in tubing (ppm).

250 ppm

CO2 concentration maximum. This is set to be ¼ of the Max CO2

1000 ppm, this graph shows 250 ppm.)

Abort Button

Stops the Injection process and returns to the Injectio n Baseline menu
(Step 4). Process results are not saved to the USB flash drive.

New Button

Stops the Injection process and returns to Inject i on Baseline menu
(Step 4). Injection Process results are saved to the USB flash drive.

2

2

2

value for the Graph setting and can be modified und er Main >
Settings > Settings 2 > Graph. (For example, whe n M ax CO2 is set to

Typically during an injection, the first value will rise quickly and drop back to zero; correspondingly , the
value of M will increase quickly as the value of C peaks and then plateaus at a constant value. Once C
has dropped to 0 ppm (or a very low background value), wait 3-5 seconds to make sure M has stabilized
and take note of the value. This value is also recorded on t he USB memory stick, if a memory stick has
been inserted.

Errors from injection measurements are typi call y larger than flow-through methods (larger error s could
come from both instrumental and handling sour ces), so it is recommended that you measure the same
sample multiple times and calculate an average whenever possible.

Static Process

If static sampling is selected, the user can inject s am ples directly into the sample cell through the port
labelled GAS OUT rather than having the sample pumped through it. This is normally done using a
syringe with 1/8” tubing on the end which can easily fit over the GAS OUT port on the EGM-5. For static
measurements injected directly into the “Gas Out” p ort, we recommend a minimum sample volume of 5
ml.

Note: The system will still perform its regularly sch eduled zeros even if a Static measurement is ongoing.
A warning will be displayed 2 minutes before the zero and again 1 minute prior. The onboard pump will
turn on during the zero. Upon completion of the zero t he pum p wil l again switch off.

The general procedure for taking a Static measurement is as follows:

1. Navigate to Main > Processes > Static.

2. Press the right arrow button to begin the Static Proce ss.

3. A zero is automatically performed.

4. After the zero is completed (the sample pump is now off), the system is ready for a sample

injection.

EGM-5 Operation Manual V. 1.04 75 [e-mail]

5. Inject your sample (minimum of 5 ml) directly into the GAS OUT port. We recommend a slow,

Static – Start Process Menu

Back

Returns to the Processes Menu.

Status Box

Any information or error messages are displayed here.

Right Arrow

Confirms and starts the Static process by displaying t he S tatic Data Plot
screen (Step 2).

Z 24.0

Abort

New

75%

Z

1000 ppm

Status Box

Back



Would you like to start the Static

Static - Start Process

C

Pr

531

1022

180 sec

concentration will be higher

steady injection rate of approximately 6 ml/sec ond. Initially, the CO
(due to pressure) and then will drop to the actual con cent ration and should remain stable. Once
the reading stabilizes, take note of the value. This val ue is also recorded on the USB memory
stick, if a memory stick has been inserted. To start a new measurement, press New. Remove the
syringe from the GAS OUT port to allow the sy st em t o flush properly.

2

Static – Start Process (Step 1)

The first screen asks the user to confirm that t hey would like to start the Static process.

process or go back?

Static Data Plot (Step 2)

Upon entry to this screen, a zero will be performed.

EGM-5 Operation Manual V. 1.04 76 [e-mail]

Static Step 2 Menu

♥ (Heartbeat)

Pulses on and off to indicate that the system is powered on (power
status).

75%

Percentage of battery life remaining.

Z

Initiates a zero.

C

Current CO

concentration in the IRGA (ppm).

Pr

Atmospheric pressure (mb).

X-axis

Time, 1 second interval. It is fixed at 180 seconds.

Y-axis

CO

2

concentration in the IRGA (ppm).

1000 ppm

CO2 concentration maximum. This is the same value as the Max CO2
Settings > Settings 2 > Graph.

Abort

Stops the Injection process and returns to the Processes Menu. Static
Process results are not saved to the USB flash drive.

Status Box

Any information or error messages are displayed here.

New Button

Stops the current Static process and saves results to the USB flash
performed.

Calibration Menu

CO2

Initiates CO2 calibration.

O2

Initiates O2 calibration.

Touch Cal

Calibrates the touch screen display.

Back Button

Returns to the Main Menu.

Status Box

Any information or error messages are displayed here.

2

value for the Graph setting and can be modified und er Main >

drive. Clears graph to begin another Static process. No zero is

Calibration

This menu handles the calibration of CO2 IRGA, the O2 Sensor and the Touch Screen.

EGM-5 Operation Manual V. 1.04 77 [e-mail]

CO2

Calibration

CO2 Conc (ppm)
Button

CO2 concentration (ppm) of the calibration reference gas.
Entering a value will begin the calibration process

Actual CO2

The current CO2 Reading based on the Scale Factor

CO2 Scale Factor

The current Scale Factor being used

Stop Button

Returns to the Calibration Menu.

This menu allows the user to recalibrate the CO2 gas analyzer. Before proceeding with an instrument
recalibration, it is critical that:

• The absorber column is properly seated in its manifold

• The soda lime (CO

scrubber) is fresh.

2

• The EGM-5 has been on for at least 30 minutes.

• The Gas Out port is unobstructed.

Connecting Calibration Gas to the EGM-5

During calibration, the signal from the CO2 detector is referenced against a gas of known CO2
concentration. The EGM-5 calibration procedure uses two reference points:

1. Zero CO

absorber column.

2. Span (reference) gas, a user-provided gas with a known CO

accurate (+/- 1%) certified source.

It is vital that both of these references are accurate. F or greater accuracy, cylinder mixtures should be
traceable to NIST (National Institute of St andards and Technology) standards. The zero gas will onl y be
accurate if the soda lime in the absorber column is fr esh.

Assuming that a calibration gas mixture is used to calibrate the EGM-5, follow these instructions:

1. To avoid excess pressure in the sample cell and possible damage to the analyzer, you must place a
T-fitting between the reference gas source and the GAS IN port on the EGM-5. One end of the T­fitting should be left open in order to relieve exce ss p res sure, as follows:

, generated from air that has been scrubbed of CO2 through the soda lime in the

2

concentration, typically from a very

2

EGM-5 Operation Manual V. 1.04 78 [e-mail]

CO2

Pressure

Shut-off

“T”

Gas In

Regulator

GAS

Cylinder

Valve

To vent

Gas

~ 250ml/min

Port

2. The pressure regulator on the reference source should be set to a very low pressure, such that the
flow rate of excess gas from the open end of the T-fitting should be approximately 250 ml/min.

3. Select the button to the right of the “CO2

Conc (ppm):” text. The numerical keypad will appear

allowing a new number to be entered.

4. Enter the CO2 concentration of the reference gas. This value must match the certified CO2
concentration of the reference source and be greater than or equal to the anticipated measurement
range of the instrument. For example, if the anticipated measurement range of your samples will be 0

- 350 ppm, the instrument should be calibrated using reference gas with a CO2 concentration
between 350 – 400 ppm.

5. The EGM-5 will then perform a zero. At completion of successful zero, a similar message to the
following will be displayed:

6. Note, the displayed value may not be the value you entered in step 3 above. When the Actual
CO2 value has stabilized (i.e., not changing by more than 1 ppm after 30 seconds), press the Right
arrow. To cancel without performing a Calibration, press Stop.

EGM-5 Operation Manual V. 1.04 79 [e-mail]

Calibrate

Set CO2

The CO2 concentration value entered at the beginning of the Calibration Process.

Actual CO2

The current CO2 reading.

Stop Button

Returns to the Calibration Menu with no changes.

OK Button

Calculates new Scale Factor and goes to next screen. Press to continue once the
seconds).

Actual CO2 value is stable (i.e., not changing by mor e t han 1ppm after 30

Note, the Actual value may not be the value you entered in step 4 above. When the Actual CO2
value has stabilized (i.e., not changing by more than 1 ppm after 30 seconds), press the OK button. To
cancel without performing a Calibration, press Stop.

If the process is successful, the screen below will be displayed and the new calibration constant will be
stored in non-volatile memory. If the process i s unsuccessful, the message “Calibration: failed.” will be
displayed and no changes made.

The Back button returns the user back to the Main Menu.

O2 Calibration

This function allows the user to recalibrate t he internal O2 sensor used with the EGM-5. Before
calibrating, confirm that:

• The WMA-5 has been on for at least 30 minutes.

• The Gas Out port is unobstructed.

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Calibration

O2 Conc Button

O2 concentration (%) of the calibration referen ce gas.
Entering a value will begin the Calibration Process

Actual O2

The current O2 reading based on the Scale Factor

O2 Scale Factor

The current Scale Factor being used

Stop Button

Returns to the Calibration Menu.

Air with

Pressure

Shut-off

“T”

Gas In

Connecting Calibration Gas to the EGM-5

During calibration, the signal from the O2 sensor is referenced against a gas of known O2 concentration.
For greater accuracy, reference gas mixtures should be accurate to at least +/- 1% and traceable to NIST

standards.
Follow these instructions to calibrate the EGM-5 O2 sensor:

1. To avoid excess pressure in the sample cell and damage to the analyzer, you must place a T-fitting
between the reference gas source and the GAS IN port on the EGM-5. One end of the T-fitting should
be left open in order to relieve excess pressure, as f oll ows:

Regulator

O2

GAS

Cylinder

EGM-5 Operation Manual V. 1.04 81 [e-mail]

Valve

To vent

Gas

~ 250ml/min

Port

2. The pressure regulator on the reference source should be set to a very low pressure, such that the

Calibrate

Set O2

The O2 concentration Value entered at the beginning of the Calibration Process.

Actual O2

The current O2 Reading

Stop Button

Returns to the Calibration Menu with no changes.

OK Button

Calculates new Scale Factor and goes to next screen. Select this button when the
seconds).

flow rate of excess gas from the open end of the T-fitting should be approximately 250 ml/min.

3. Select the button to the right of the “O2

Conc (ppm):” text. The numerical keypad will appear allowing

a new number to be entered.

4. Enter the O

concentration of the reference gas. This value must match the certified O2 concentration

2

of the reference source and be greater than or equal to the anticipated measurement range of the
instrument.

5. The EGM-5 will then perform a zero. After completion of successful zero, a similar message to the
following will be displayed.

6. Note, the Actual displayed value may not be the value you entered in step 3 above. When the
Actual O

value has stabilized (i.e., not changing by more than 0.1% after seconds), press the OK

2

button. To cancel without performing a Calibration, press Stop.

Actual O2 value is steady (i.e., not changing by more than 0. 1% after 30

If the process is successful, the screen below will be displayed and the new calibration and linearizat i on
constants will be stored in non-volatile memory. If the process is unsuccessful, the message “Calibration:
failed(xx).” will be displayed, where xx is the error code. See EGM-5 Command Set Table on page 96 for
a description of calibration error codes.

EGM-5 Operation Manual V. 1.04 82 [e-mail]

Performing touch

Touch screen to

The Main button returns the user back to the Main M enu.

Touch Calibration

This function allows the user to calibrate the t ouch s creen display. Follow the on-screen prompts t o
complete the process.

screen calibration.

continue.

NOTE: This function can also be initiated by holding a finger on the screen while powering up the EGM-5.
If your touch screen is not reacting to your touch:

1. Turn the instrument off.

2. Place your finger anywhere on the touch display and turn system power on and wait for the next

screen to appear.

3. Proceed as directed with the touch screen calibration.

Diagnostics

This menu monitors and reports key system diagnost ics associated with EGM-5 hardware. It is gen erall y
used for troubleshooting and diagnosing potenti al problems associated with the instrument.

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Diagnostics Menu

ADC (analog digital
converter)

Initiate zeros and view readings from the Analog t o Digital (A/D) Converter,
which are digital representations of CO2 values.

Zeros

Displays the A/D counts for the last 7 zero operations.

Hours

Displays the amount of time (in hours) that the contro l l er and I RGA have
operated over their lifetime.

Battery

Displays the percentage of battery remaining, t he voltage and current of the

battery, and an estimate of time remaining bef ore t he battery is completely

discharged.

Voltages

Displays the external voltage, the flow sensor vol t age, the Aux (Analog Out)
voltage and the O2 sensor voltage.

Advanced

Displays more advanced diagnostics functions. These functions are password
protected, and are for PP Systems use only.

Back

Returns to the Main Menu.

ADC Diagnostics

CR

This is the reading from the 16 bit A/D converter for t he CO2 detector.

Diagnostics
Mode (Measure)

Modify the Diagnostic Modes setting. The options are Measure or Zero. The text
on the button indicates the current mode.

CZ

This is the A/D count reading from the last zero.

Start Zero

Initiates a zero.

Back

Returns to the Diagnostics Menu.

ADC (Analog Digital Converter) Diagnostics

This function allows the user to change/view the Diagnostic Mode, initiate a zero and view A/D count
readings.

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Diagnostic Mode

Diagnostics Mode Setting

Measure

Puts the EGM-5 into “Measure” mode. In Measure mode, the CR value shoul d
read approximately 35000-45000 for CO2 concentrations around 400 ppm.

Zero

Puts the EGM-5 into “Zero” mode. In “Zero” mode, the A/D value for CR should

Back

Returns to the Diagnostics display.

Status Box

Any information or error messages are displayed here.

Zero Diagnostics

1-7

The zero ADC value of the last seven zeros.

Back

Returns to the Diagnostics Menu.

To change the Diagnostic Mode, select the butt on to the right of the CR reading. The Diagnostic Mode
Setting screen will be displayed, with the current selection indicated.

.

Press the desired Diagnostic Mode setting and then t he Back button. The Diagnostics screen will return
with the updated Diagnostics Mode value in the button text. In Zero mode, sample gas is continuously
passed through the absorber column until the user returns to Measure Mode, or until the unit performs an
Auto Zero.

read approximately 40000-50000 if fresh soda lime is present in the absorber
column. The CR value in “Zero” mode should always be gre ater than the CR
value in “Measure” mode.

Zeros Diagnostics

This screen displays the last 7 zero values.

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Hours Diagnostics

Hours Diagnostics

Controller (hr)

Displays the total amount of time (in hours) that the c ontroller has operated.

IRGA (hr)

Displays the total amount of time (in hours) that the I RGA has operated.

Back

Returns to the Diagnostics Menu.

Battery Diagnostics

Charge (%)

Displays the percentage of battery charge remai ni ng.

Voltage (V)

Displays the battery voltage.

Current (A)

Displays the average battery current in Amps over t he past 60 seconds. A
battery is being charged.

Time Left (M)

Displays the estimated remaining run time in minutes assum i ng the average
current does not change. A value of 65535 is displayed during battery charging.

Back

Returns to the Diagnostics Menu.

This screen displays the amount of time (in hours ) t hat the controller and IRGA have operated in the
instrument’s lifetime.

Battery Diagnostics

This screen displays the percentage of battery remaining, the voltage and current of the battery, and the
time remaining before the battery is completely discharged.

negative value indicates discharge current and a positive value indicates the

EGM-5 Operation Manual V. 1.04 86 [e-mail]

Voltage Diagnostics

Battery Diagnostics

External (V)

Displays the applied voltage when power is supplied by the power adapter.

Flow Sen (V)

Displays the flow sensor voltage.

Aux (V)

Displays the Aux (Analog Out) voltage.

O2 Sen (V)

Displays the O2 Sensor voltage.

Back

Returns to the Diagnostics Menu.

Advanced Diagnostics

****

Displays a number entry screen for the operator to enter their PIN.

Back

Returns to the Diagnostics Menu.

This screen displays the external voltage, the flow sensor voltage, the Aux voltage and the O2 sensor
voltage.

Advanced Diagnostics

This screen prompts the user to enter a password in orde r to view advanced diagnostics features. The se
functions are reserved for PP Systems service & trou bleshooting use only.

EGM-5 Operation Manual V. 1.04 87 [e-mail]

Information Menu

Information Menu

About Button

Provides information about serial numbers and the f irmware versions

Contact Button

Information to contact PP Systems

Back Button

Returns to the Main Menu.

About

Controller SN

Displays the Controller serial number. This is the also the instrument serial
number.

Controller VN

Displays the Controller version number.

IRGA SN

Displays the IRGA serial number.

IRGA VN

Displays the IRGA version number.

Display VN

Displays the Display version number.

Back Button

Returns to the Settings 2 Menu.

About

This function allows the user to view hardware and software serial and version numbers.

Press “Back” to return to the Info Menu.

EGM-5 Operation Manual V. 1.04 88 [e-mail]

Contact

Contact

Contact

Contact information for PP Systems.

Back Button

Returns to the Information Menu.

Data Storage

Data is stored directly to a USB Flash Drive for conv enience. Generally speaking the data form at will
default to the proper M type format required for the sp ecific sensor/chamber being used. All data is stored
as a .txt file in standard ASCII format making it very easy to open and view in Excel. See the following
sections for more information on data storage and measurement formats.

USB Flash Drive (Memory Stick)

The USB Type A port on the back panel is designed specif ically for a USB flash drive (commonly referred
to as a memory stick or thumb drive). Most memory stick s can be used and one is provided with the
EGM-5. If you are using your own memory stick, ensure it i s f ormatted as FAT32 with a 512-byte sector
size for best performance.

Data recording begins when a flash drive is inserted into the USB port on the EGM-5 unless the Interv al i s
set to 0 seconds under “Memory Measure Settings”. Dat a recording ends when the flash drive is removed
from the USB port. The data format depends on what has been defined for the Measure Memory Format
in the Memory Measure Settings screen. The record ing i nterval is defined in the Memory Measure
Settings screen, under “Memory Measure Interval”. For more information about data format and recording
interval see Memory Measure Settings on page 48.

When the memory stick is inserted for the first tim e, a directory named “EGM5” is created. A filename is
created within the directory using the following form at:

YYMMDDWI.txt
Where:

• YY is the last 2 digits of the calendar year.

• MM is the 2 digit month.

• DD is the 2 digit day.

• W is the EGM ID (0-9).

• I is the increment of the file if there is more than one file created in a day.

EGM-5 Operation Manual V. 1.04 89 [e-mail]

Each time the memory stick is removed and then reinserted, or when the instrument is power cycled, a
new file is created and the increment ‘I’ is increased. Any files in this directory with extensions other t han
.txt do not contain valid data and may be deleted or ignored.

Even if the Measure Interval is set to 0, Zero Operations and P rocess data are still sent to the USB, even
though CO

Refer to Error Messages on page 117 for disk erro rs.

measurement data is not.

2

EGM-5 Operation Manual V. 1.04 90 [e-mail]

Data Storage/Measure Form at Settings Table

General M Format

Mtype

1-6

Date

dd/mm/yy

Header

Time

hh:mm:ss (24hr)

Plot No.

0-999

Rec No.

1-9999

CO2 Ref

CO2 reading in parts per million (ppm = µmol mol-1)

Measured Data

AP

Atmospheric pressure in millibars (mb)

Flow

Sample flow (cc/min)

H20 Ref

H2O reading in millibars (mb) (if optional H2O sensor
is installed).

RHT

Temperature of RH sensor (˚C) (if optional H2O sensor
is installed).

O2 Ref

O2 percentage (if optional O2 sensor is installed).

Error Code

Aux (Analog Out)
Voltage

Volts

PAR

PAR: µmol m-2 s

-1

Temperature Soil

˚C

Temperature Air

˚C

RH

Relative Humidity (%)

Parameter 1

Process

Parameter 2

Parameter 3

Parameter 4

Parameter 5

This table describes the different data storage i nformation and measurement formats available in t he
EGM-5.

M

Probe Data

Data

Process Data Fields

The process data fields are based on the measurem ent mode used with the EGM-5. The 5 different
modes available are:

1. Measure mode

2. SRC or Custom mode

3. CPY Mode

4. Injection mode

5. Static mode

EGM-5 Operation Manual V. 1.04 91 [e-mail]

Process Data Format (measure mode)
Parameter 1

Probe Type

0-19

Process

Data

Parameter 2

Battery %

Battery charge (0-100%)

Parameter 3

Zero %

Absorber capacity (0-100%)

Parameter 4

Bat Volts

Battery voltage (volts)

Parameter 5

Bat Time

Battery time remaining (minutes)

Process Data Format (SRC, CUSTOM mode)
Parameter 1

Process

20, 60

Process

Parameter 2

DC

Change in CO2 concentration (ppm)

Parameter 3

DT

Process runtime (seconds)

Parameter 4

SRL Rate

(Assimilation): grams (CO2) m2 Hour-1

Parameter 5

SRQ Rate

(Assimilation): grams (CO2) m2 Hour-1

Process Data Format (CPY mode)
Parameter 1

Process

50

Process

Parameter 2

DC

Change in CO2 concentration (inverted) (ppm)

Parameter 3

DT

Process runtime (seconds)

Parameter 4

SRL Rate

(Respiration): µmol m2 s-1

Parameter 5

SRQ Rate

(Respiration): µmol m2 s-1

Process Data Format (Injection mode)
Parameter 1

Process

30,31

Process

Parameter 2

C_F

Correction Factor (0.5 – 2.0)

Parameter 3

Volume

Syringe sample volume (cc)

Parameter 4

Base

CO2 Baseline (ppm)

Parameter 5

CO2 int

CO2 Integration value (ppm)

Process Data Format (Static mode)
Parameter 1

Process

40

Process

Parameter 2

n/a 0 Parameter 3

DT

Process runtime in seconds

Parameter 4

CO2

CO2 reading (ppm)

Parameter 5

n/a

0

Data

Data

Data

Data

EGM-5 Operation Manual V. 1.04 92 [e-mail]

Measure Format Settings Table

Measure Format Setting

Setting

Description

M1

M1 is Header and Measured data only. The parameters are comma delimited.

• System Error: Displays error code message. (See Error Messages table)

M2

M2 is Measured data only. The parameters are comma deli m i ted. There are 8

• System Error: Displays error code message. (See Error Messages table)

M3

M3 is Header, Measured data, and Probe data only. The parameters are comma

825, 23.4, 25.7, 12<CR>

This table describes the 6 different Measure Formats for data output. Note: A CRC, or Cyclic Redundancy
Check, may be appended to measurement data to ensure its integrity. In the examples below, the CRC
parameter is turned off and there are no CRCs conc atenated to the end of a message. <CR> represents
a carriage return (ASCII 13).

There are 12 fields.
An example is:

M1, 03/06/15, 09:32:15, 1, 0003, 1094, 1004.2, 327, 0.0, 00.0, 20.41, 00<CR>
The format is as follows:

• M1: Specifies the data format.

• Date: dd/mm/yy

• Time: hh:mm:ss

• Plot No: 0-999

• Record No: 1-65535

• CO

• Air Pressure (mb): Atmospheric pressure

• Flow Rate (cc/min): Rate of flow.

• H

• H

• O

(ppm): CO2 reading in parts per million (ppm = µmol mol-1)

2

0 (mb): H2O reading

2

0 Sensor Temperature (°C): Temperature of the ga s sample.

2

(%): O2 reading

2

fields.
An example is:

M2, 1094, 1004.2, 327, 0.0, 00.0, 20.41, 00<CR>
The format is as follows:

• M2: Specifies the data format.

• CO

(ppm): CO2 reading in parts per million (ppm = µmol mol-1)

2

• Air Pressure (mb): Atmospheric pressure

• Flow Rate (cc/min): Rate of flow.

0 (mb): H2O reading

• H

2

0 Sensor Temperature (°C): Temperature of the gas sample.

• H

2

(%): O2 reading

• O

2

delimited. There are 17 fields.
An example is:

M3, 03/06/15, 09:32:15, 1, 0003, 1094, 1004.2, 327, 0.0, 00.0, 20.41, 00, 0.000,

EGM-5 Operation Manual V. 1.04 93 [e-mail]

The format is as follows:

• RH: Percent Humidity

M4

M4 is Measured data and Probe data only. The parameters are comma delimited.

• RH: Percent Humidity

M5

M5 is Header, Measured data, Probe data, and Process data. The parameters are

• Plot No: 0-999

• M3: Specifies the data format.

• Date: dd/mm/yy

• Time: hh:mm:ss

• Plot No: 0-999

• Record No: 1-65535

• CO

(ppm): CO2 reading in parts per million (ppm = µmol mol-1)

2

• Air Pressure (mb): Atmospheric pressure

• Flow Rate (cc/min): Rate of flow.

0 (mb): H2O reading

• H

2

0 Sensor Temperature (°C): Temperature of the gas sample.

• H

2

(%): O2 reading

• O

2

• System Error: Displays error code message. (See Er ror Messages table)

• Aux Voltage (volts): Analog Output Voltage.

2 s-1

• PAR: (ppm = µmol m

)

• Tsoil: Temperature (°C)

• Tair: Temperature (°C)

There are 13 fields.
An example is:

M4, 1094, 1004.2, 327, 0.0, 00.0, 20.41, 00, 0.000, 825, 23.4, 25.7, 12<CR>
The format is as follows:

• M4: Specifies the data format.

• CO

(ppm): CO2 reading in parts per million (ppm = µmol mol-1)

2

• Air Pressure (mb): Atmospheric pressure

• Flow Rate (cc/min): Rate of flow.

0 (mb): H2O reading

• H

2

0 Sensor Temperature (°C): Temperature of the gas sample.

• H

2

(%): O2 reading

• O

2

• System Error: Displays error code message. (See Er ror Messages table)

• Aux Voltage (volts): Analog Output Voltage.

2 s-1

• PAR: (ppm = µmol m

)

• Tsoil: Temperature (°C)

• Tair: Temperature (°C)

comma delimited. There are 22 fields.
An example is:

M5, 03/06/15, 09:32:15, 1, 0003, 1094, 1004.2, 327, 0.0, 00.0, 20.41, 00, 0.000, 0,

23.4, 0, 0, 1 ,76 ,89.56, 7.231, 480<CR>
The format is as follows:

• M5: Specifies the data format.

• Date: dd/mm/yy

• Time: hh:mm:ss

EGM-5 Operation Manual V. 1.04 94 [e-mail]

• Record No: 1-65535

• CO2 (ppm): CO2 reading in parts per million (ppm = µmol mol-1)

M6

M6 is the raw format containing raw data (A/D values) from the IRGA. It is comma

• System Error: Displays error code message. (See Error Messages table)

• Air Pressure (mb): Atmospheric pressure

• Flow Rate (cc/min): Rate of flow.

0 (mb): H2O reading

• H

2

0 Sensor Temperature (°C): Temperature of the gas sample.

• H

2

(%): O2 reading

• O

2

• System Error: Displays error code message. (See Er ror Messages table)

• Aux Voltage (volts): Analog Output Voltage.

2 s-1

• PAR: (ppm = µmol m

)

• Tsoil: Temperature (°C)

• Tair: Temperature (°C)

• RH: Percent Humidity

• Parameter 1 (See Process Data Fields on page 91)

• Parameter 2 (See Process Data Fields on page 91)

• Parameter 3 (See Process Data Fields on page 91)

• Parameter 4 (See Process Data Fields on page 91)

• Parameter 5 (See Process Data Fields on page 91)

delimited.
An example is:

M6, 44572, 50675, 17603, 17600, 37340, 50292,0x0040<CR>
The format is as follows:

• M6: Specifies the data format.

• CO

A/D Counts: Proportional to the CO2 reading.

2

• Air Pressure A/D Counts: Proportional to the atmosp heric pressure
reading.

• Temperature Probe1 A/D Counts: Proportional to the temperature of probe

1.

• Temperature Probe2 A/D Counts: Proportional to the temperature of probe

2.

• Lamp A/D Counts: Proportional to lamp current.

• Last Zero CO

: Reports A/D counts of the last zero value.

2

EGM-5 Operation Manual V. 1.04 95 [e-mail]

Digital Connection Methods

There are two methods of connecting to the EGM-5 to view digital data:

1. PC USB port

2. Wireless (if WiFi Option is installed).

USB

A USB cable (Mini-B to Type A) can be used to connect the EGM-5 to a host device such as a PC, laptop
or tablet. This cable is supplied by PP Systems with every EGM-5. When using a terminal emulator, the
COM port settings to communicate with the EGM-5 are: 19200 baud, 8 bit, 1 stop, no parity, no flow
control.

Wireless

If WiFi option is installed, there are two additional con nect i on methods available: First, a direct wireless
connection (up to 15m) between any wireless device ( e. g., phone, tablet, or laptop) and the EGM-5 can
be made without any additional hardware or routers. Second, the EGM-5 can be connected to the
customer’s wireless router, which makes it acce ssible via the customer’s Local Area Network (LAN). The
customer’s network may also be configured to allow remote connections to the EGM-5 over the Internet if
firewall settings and security protocols are pr operly configured (see your Network Administrator). PP
Systems is not responsible for any security risks associated with modifying network or firewall settings.

Digital Communication Protocols and Software

Once a connection is made to the EGM-5 as described in the previous section, communication software
is needed to read, display, and record data. This section describes three methods for reading EGM-5
data and changing settings: the EGM-5 Command Set, for direct communication using EGM-5 ASCII
character strings; GAS Software, for a Windows based graphical user interface with graphing and
logging; and Web Pages, which are available only wi th the WiFi Option.

EGM-5 Command Set

When a computer is connected to the EGM-5 using a US B cable, a communication protocol and
command set comprised of ASCII characters and strings allows receipt of EGM-5 data and setti ng of
EGM-5 parameters. A terminal emulation program (e.g. , HyperTerminal or PuTTY) is generally used for
this, but other custom software may also be used to observe and interact with the EGM-5 using these
commands.

Measured data is continuously output by the EG M -5. T he time interval can be modified using the Host
Measure Interval setting (default is every 1 seco nd). The data format is dependent on the Host Measure
Format setting. Refer to Host Measure Settings on p age 46 for more information.

Sending a command

To initiate a command, the Host (e.g., a PC running HyperTerminal) sends an ASCII string in comma­delimited format to the EGM-5. The command can be sent wit h or without a CRC-8 (9-bit Cyclic
Redundancy Check). If a CRC-8 is sent, a ‘C’ follows the CRC-8 value.

For example,
Host sends command without CRC-8: S,1,25<CR>
Host sends command with CRC-8: S,1,25,080C <C R>

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The CRC calculation includes everything but the CR C itself and the ‘C’ character. In the example above,
the CRC was calculated from the string “S,1,25,”.

The command is processed by the EGM-5 after the command string terminator <CR> is received.
Only commands that are less than 90 characters in length will be successful. If a CRC-8 is present, the

CRC-8 also needs to be correct in order for the command to be suc cessful.
On successfully receiving the command string, EGM-5 sends an acknowledgement by sendin g to the

Host a ‘+’ followed by a <CR>.
On a failure, a ‘–‘ is sent back to the Host with a <CR>.
A failure can be caused by a string longer than 90 characters or an incorrect CRC.

Receiving a response

Depending on the value of the CRC parameter, a CRC will/ wil l not be appended to the command
received from the EGM-5. If the CRC parameter valu e i s ‘0’ (C RC Off), no CRCs will be appended to any
of the commands received from the EGM-5. If the CRC parameter value i s ‘1’ (CRC On), CRCs will be
appended (including the ‘C’) to all commands received from the EGM-5. See Get/Set Parameter Values
Table on page 106 for more details on turning off /on the CRC.

For example,
With CRC=0 (CRC Off):
Received from EGM-5: G,1,25<CR>

With CRC=1 (CRC On):
Received from EGM-5: G,1,25,043C<CR>

The following table describes the EGM-5 Comm and Set that can be used by the Host to communicate
with the EGM-5. Note, the examples shown below have CRC disabled (CRC=0). There are two ty pes of
commands; Auto and Standard. Auto commands are commands that the EGM-5 will send without bei ng
prompted by the user. For example, the ‘W’ (Warm Up) command is automatically sent by the EGM-5
when it is warming up. Standard commands are commands that are sent by the user. Standard
commands can be only a single character, or a single character followed by one or more parameter s. A l l
commands are terminated with <CR> which represen ts a carriage return (ASCII 13).

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EGM-5 Auto Strings

EGM-5 Auto Command Set

String

Type

Description

*

Auto

E

Auto

In this example, 11 is the code for the Low CO2 Alarm.

M

Auto

Settings Table on page 93 for more details.

V

Auto

01.01 is the IRGA firmware version number

Auto Strings are text strings that are sent by the EGM-5 automatically under certain states and conditions

“*” String (Power Reset)

Sent immediately after the EGM-5 is turned on or reset.
Example:

*<CR>

“E” String (Error Status)

Transmitted whenever an error is detected. The E string contains an Error Code that
indicates the problem. See Error Messages on page 117 for more details.

Example:
E,11<CR>

“M” String (Measurements)

The M string is sent on a fixed interval. The interval a nd the string format may be
modified. When the interval is set to 0 the M string sto ps s ending automatically, but
can be manually polled by sending the “M” command.

Example:
M3, 03/06/15, 09:32:15, 1, 0003, 1094, 1004.2, 327, 0.0, 00.0, 20.41, 00<CR>

In this example, the Measure Format setting had been set to 3. See

Measure Format

“V” String (Versions)

This is sent once right after the EGM-5 is powered on, or if the system is reset. The V
string contains the serial numbers and software versions of the EGM-5 controller, the
IRGA and the Display.

Example:
V,EGM500007,01.02,IRGA00001,01.01<CR>

In this example,

EGM500007 is the EGM-5 serial number

01.02 is the EGM-5 firmware version number
IRGA00001 is the IRGA serial number

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W

Auto

“W” String (Warm up)

59.47 is the Remaining Zero Column Capacity

Z Auto

operation.

The W string is transmitted every second during ini tial warmup, until the operating
temperature is reached. No “M” strings are sent du ring this time. The W string contains
the IRGA temperature, Battery Percent, and the Zero Column Percent.

Example:
W,55.0, 80, 59.47<CR>

In this example,

55.0 is the IRGA temperature (°C).
80 is the Battery % of Charge

“Z” String (Zeroing)

The Z string indicates a zero in progress. During a zero operation, the EGM-5
transmits the Z string every 1 second, until the end of the zero operation. No “M”
strings are sent during this time. This command can b e i ni t i ated by the user or by the
EGM-5 itself.

Example:

Z, 025<CR>
Z, 024<CR>
…

In this example, 025 and 024 represent the number o f seconds remaining in the zero

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EGM-5 Command Set Table

EGM-5 Standard Command Set

Command

Type

Description

‘

Character

“ ’ ” Command (Comment)

+<CR>

A,x,y

Character

“A” Command (Relays on/off)

In this example, ALARM1 relay would be set to on.

B

Character

“B” Command (Status info)

C,d,a,c

Character

Parameters

“C” Command (Calibration)

d = device

This command ignores any characters between the quote and <CR>.
This is useful for documentation; for example, it allows comments in a
configuration file to be ignored when the file is uploaded.

Example:
Sent from Host: ‘ This file sets all the default val ues<CR>

Received from EGM-5:

Parameters

with

This command is the diagnostic toggle for the alarm relay.
x=’1’ for ALARM1 Relay
x=’2’ for ALARM2 Relay

y=’0’ for Relay Off
y=’1’ for Relay On

Example:
Sent from Host: A,1,1<CR>

Received from EGM-5:
+<CR>
A,1,1

This command returns 5 Parameters: Battery Capacity (%), Battery Voltage
(Volts), Battery Current (Amps), Battery t i me remai ning (minutes), and Absorber
remaining (%).

Example:
Sent from Host: B<CR>
Received from EGM-5:
+<CR>
B,100, 7.2, 0.546, 752, 99.1<CR>

In this example,
Battery Capacity (%) = 100%
Battery Voltage (Volts) = 7.2 Volts
Battery Current (Amps) = 0.546 Amps
Battery time remaining = 752 minutes
Absorber remaining (%) = 99.1%

with

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