WHOI R/V Atlantis CLIVAR A20 2012 Underway pCO2 data Master Readme file
R/V Atlantis Voyage number: 20-01B

The electronic data in comma delimited ASCII form (.CSV) can be 
found at:

            http://www.aoml.noaa.gov/ocd/gcc/

For further information or special requests regarding data format
contact:

	Mr. Bob Castle
	Atlantic Oceanographic and Meteorological Lab
	4301 Rickenbacker Causeway
	Miami, FL 33149
	
	email: robert.castle@noaa.gov
	Phone: 305-361-4418

****************** Use of AOML CO2 Underway Data **************************
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************* Carbon Cycle Greenhouse Gasses (CCGG) web site] *************

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*********************** Reciprocity Agreement *****************************
* [Adapted from NOAA Climate Monitoring and Diagnostics Laboratory (CMDL) *
************* Carbon Cycle Greenhouse Gasses (CCGG) web site] *************

Use of these data implies an agreement to reciprocate.  Laboratories making
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***************************************************************************

Final QC of this data set was completed on Oct. 11, 2012

Ship:			WHOI Research Vessel Atlantis
Cruise Start:		Bridgetown, Barbados, April 19, 2012
Cruise End:		Woods Hole, MA, May 15, 2012
Chief Scientists:	Michael McCartney
System Operator:	Robert Castle

NOTES:

1. From April 30 at 2341 to May 1 at 0127 there was a failure of the water
flow to the equilibrator.  18 equ values were flagged 4 and 13 equ values
were flagged 3.

2. Also on April 30 at 2341 temperature readings from the ship's TSG
jumped up 2 degrees C.  They returned to normal on May 2 at 0210.
During this time SST values were replaced with values derived from 
equilibrator temperature using the equation SST = EqT - 0.137.  The 
number 0.137 is the average difference between SST and EqT for the
periods immediately preceding and following the problem where the
temperature is within 1 degree C of the equilibrator temperature values
(n = 1460).

3. On April 24 from 1835 to 2012 there was no data from the ship's 
instruments.  SST values during this time were interpolated.

4. On May 8 from 1310 to 1526 the ship's engineers were working on
the uncontaminated seawater system adjusting the water flow.  During
this time all equilibrator values have been flagged 4.

5. On May 12 at 1916 the system shut down when it sensed a water leak.
The problem was corrected and the system restarted at 2121 on May 12.

6. On May 13 at 1350 the standard 2 (356.84 ppm) gas ran out.  After this
time, xCO2 is recomputed using 3 standards instead of 4.

7. Ship's data ends on May 14 at 2036 although the system continued to
operate until May 15 at 0616.  During this time the ship was at anchor
outside Woods Hole waiting for the tide to come in.  All underway values
after May 14 at 2036 have been removed.

8. A time offset of 4.22 minutes has been applied to the SST measurements
to correct for the time it takes water to travel from the bow intake to the
instrument in the Hydro Lab.

9. 11925 Equilibrator headspace gas measurements were made with
11858 good, 17 questionable, and 50 bad.

10. 910 air measurements were made with 890 good, 20 questionable,
and 0 bad.

SAMPLING CYCLE:

The system runs on a cycle during which 4 standard gases, 5 air 
samples from the bow tower and 50 surface water samples (from the 
equilibrator head space) are analyzed on the following schedule:

1. Zero and span of Licor
2. Four standard gases
3. Five air samples
4. Fifty equilibrator headspace gas samples
5. Repeat steps 2 - 4 nine more times
6. Restart from step 1

STANDARDS: (All are calibrated using standards obtained from NOAA/ESRL  in
Boulder, CO and are directly traceable to the WMO scale)

Tank ID	Mole Fraction (ppm) balance air
JB03284 	287.45
JA02646 	463.0
JB02140 	356.84
JB03268 	384.14

DATA FIELDS (* = from ship's instruments):

Group_Ship:			AOML_Atlantis
Cruise ID:			Woods Hole R/V Atlantis Voyage number
JD_GMT:			Decimal year day
DATE_UTC__ddmmyyyy:	Date 
TIME_UTC_hh:mm:ss:	GMT time (24 hour clock)
LAT_dec_degree:		Latitude in decimal degrees
LONG_dec_degree:		Longitude in decimal degrees
xCO2_EQU_ppm:		Mole fraction of CO2 in the equilibrator at 
				equilibrator temperature
xCO2_ATM_ppm:		Mole fraction of CO2 in air in parts per 
				million (ppm)
xCO2_ATM_interpolated_ppm:	Bracketing average air values 
				interpolated to time of current Equ
				measurement
PRES_EQU_hPa:		Barometric pressure in the equilibrator in
				hectopascals
*PRES_ATM@SSP_hPa:	Barometric pressure from ship's barometer,
				corrected to sea level in hectopascals
TEMP_EQU_C:		Equilibrator water temperature in degrees 
				centigrade
*SST_C:			Sea surface temperature in degrees 
				centigrade
SAL_permil:			Salinity from Micro TSG in
				the Hydro Lab practical salinity units
fCO2_SW@SST_uatm:	Fugacity of CO2 in sea water in 
				microatmospheres
fCO2_ATM_interpolated_uatm:	Fugacity of CO2 in air in 
				microatmospheres interpolated to 
				time of Equ measurement
dfCO2_uatm:			Fugacity of CO2 in sea water - fugacity of 
				CO2 in air in microatmospheres
WOCE_QC_FLAG:		Quality control flag for Equ fCO2 values
				and Atm xCO2 values (2 = good, 3 = 
				questionable, 4 = bad)
QC_SUBFLAG:		Subflag text string for values flagged as 3

SYSTEM DESCRIPTION:

On March 22-24, 2012, a General Oceanics underway pCO2 system was installed
aboard the Woods Hole vessel Atlantis for the upcoming A22 and A20 cruises.
This system (SN 107) is normally used on the Ronald H. Brown but was taken off
when the ship went into dry dock and used for these 2 cruises.  This system is 
described in Pierrot et al. (2009) and the general principle of instrumental design can 
be found in Wanninkhof and Thoning (1993) , Ho et al. (1995), and Feely et al. (1998).

The concentration of carbon dioxide (CO2) in surface ocean water is determined by
measuring the concentration of CO2 in gas that is in contact with the water.  Surface
water is pumped from an inlet in the ship's bow to the equilibration chamber.  The
equilibration chamber has an enclosed volume of gas, or headspace, and a pool of seawater
that continuously overflows to a drain.  As the water flows through the chamber, the
dissolved gases (like CO2) partition between the water and the headspace.  At equilibrium,
the ratio of CO2 in the water and in the headspace is influenced most by temperature,
and that relationship is known.  By measuring the concentration of CO2 in the headspace
and the temperature in the chamber, the partial pressure (or fugacity) of CO2 in the
surface water can be calculated.

The concentration of CO2 in the headspace gas is measured using the adsorption of 
infrared (IR) radiation, which results from changes in the rotational and vibrational 
energy state of the CO2 molecule.  The Licor detector passes IR radiation through 
two 6" cells.  The reference cell is flushed with a gas with zero CO2 concentration.  
The sample cell is flushed with the headspace gas.  A vacuum-sealed, heated filament 
is the broadband IR source.  The IR radiation alternates between the two cells via a 
chopping shutter disc spinning at 500 Hertz.  An optical filter selects an adsorption band 
specific for CO2 (4.26 micron) to reach the detector.  The solid state (lead selenide) 
detector is kept at -12 degrees C for excellent stability and low signal noise (less than 
0.2 ppm). 

Several steps are taken to reduce interferences and to increase the accuracy of the
measurements.  The IR adsorption band for water vapor is close to the band for CO2.
After the equilibration chamber, the headspace travels through a drying trap to
remove water vapor.  During each analysis, the headspace gas is compared to a reference
gas of 0 CO2 concentration.  To improve the accuracy of the measurements, four
different gaseous standards for CO2 are analyzed every three hours instead of the
headspace gas.

CALCULATIONS:

The mixing ratios of ambient air and equilibrated headspace air are calculated by fitting a 
second-order polynomial through the hourly averaged response of the detector versus mixing 
ratios of the standards.  Mixing ratios of dried equilibrated headspace and air are 
converted to fugacity of CO2 in surface seawater and water saturated air in order to 
determine the fCO2.  For ambient air and equilibrator headspace the fCO2a, or fCO2eq is 
calculated assuming 100% water vapor content:

	fCO2eq = xCO2eq(P-pH2O)exp(B11+2d12)P/RT
			
where fCO2eq is the fugacity in the equilibrator, pH2O is the water vapor pressure 
at the sea surface temperature, P is the atmospheric pressure (in atm), T is the 
SST or equilibrator temperature (in K) and R is the ideal gas constant 
(82.057 cm^3·atm·deg^-1·mol^-1).  The exponential term is the fugacity correction where 
B11 is the second virial coefficient of pure CO2 

   B11 = -1636.75 + 12.0408T - 0.032795T^2 + 3.16528E-5 T^3

and

   d12 = 57.7 - 0.118 T 

is the correction for an air-CO2 mixture in units of cm^3·mol^-1 (Weiss, 1974). 

The calculation for the fugacity at SST involves a temperature correction term for the 
change of fCO2 due to changes in water temperature which when the water passes 
through the pump and through 5 cm ID PVC tubing within the ship.  The water in the 
equilibrator is typically 0.4 °C cooler than sea surface temperature. For all data before 
2006, the empirical temperature correction from equilibrator temperature to SST is 
outlined in Weiss et al. (1982):

	dln(fCO2)=(Teq-SST)(0.0317-2.7851E-4 Teq - 1.839E-3 ln(fCO2eq))

where dln(fCO2) is the difference between the natural logarithm of the fugacity at teq 
and SST, and Teq is the equilibrator temperature in degrees C.  In 2006, the empirical
temperature correction from equilibrator temperature to SST was changed to:

        fCO2(SST) = fCO2(eq) Exp (-0.0423 (Teq-SST))

where dln(fCO2) SST is sea surface temperature and Teq is the equilibrator temperature
in degrees C.

INSTRUMENTATION:

ANALYZER:  LI-COR 6262 SN1335 (analog output) infrared (IR) analyzer.

METHOD OF ANALYSIS:  Differential analyses relative to a reference gas which is
close to the CO2 concentration of the middle standard.  Measures dried equilibrator
headspace gas.  Gas flow is stopped prior to IR readings.

DRYING METHOD:  The equilibrator headspace sample gas first goes through an air filter
and a thermoelectric refrigerator (~6 C).  The sample and standard gases pass through
a Perma Pure (Nafion) dryer and a short column of magnesium perchlorate before reaching
the analyzer.  The counter flow in the Perma Pure tube is the reference gas.

EQUILIBRATOR (setup, size, flows):  The equilibrator was fabricated using a filter
housing (ColeParmer, U-010509-00) with ~0.5 L water reservoir and ~0.8 L gaseous
headspace.  Water flow rate is ~1.5 L/min.  Headspace recirculation rate is ~80 ml/min.

ADDITIONAL SENSORS:

Seabird SBE-45 TSG (SN 4559728-0329) attached to the underway system provides 
salinity and temperature measurements of the water flowing into the equilibrator.
Only the salinity measurements are used in the final data file.

A Hart Model 1521 temperature probe was used to electronically log the equilibrator
temperature and was mounted through the top of the equilibrator and its tip was submerged 
about 5 cm.  It was calibrated annually against a Hart Scientific 1560 Black Stack module 
with platinum resistance NIST traceable thermistor.  Based on reproducibility of the annual 
calibrations, the temperatures are believed accurate to well within 0.02 °C.

The barometric pressure was measured with the internal pressure sensor of the Licor.
A Setra Model 239 differential pressure transducer is mounted at the inlet of the equilibrator.  
The Setra output was added to the Licor pressure value since the Licor pressure 
measurement is made at ambient pressure by opening the 3-way solenoid to the vent.

LI-COR 6262 pressure transducer specifications: 
Accuracy (with software correction): +/- 0.1% full scale.
Resolution: 0.002 kPa typical ( = 0.02 hPa).
Signal Noise (peak-to-peak): 0.002 kPa typical ( = 0.02 hPa).

Setra Model 239 differential pressure transducer specifications:
Range:  0 - 0.5 psi ( = 0 - 36 hPa)
Accuracy:  0.11% FS ( = 0.04 hPa)

SHIP'S SENSORS:

SST: SBE 45T located in bow thruster room with the intake ~5 m below the
water line.

Barometric pressure: Sensor is mounted on the forward mast 19.5 m above
the water line and data is corrected for sensor altitude.

SBE45T specifications:
Temperature: Initial Accuracy = 0.002 C
Salinity(PSU): Initial Accuracy = 0.005

Unless noted all sensors are calibrated or cross-checked annually and meet or exceed 
requirements to determine the fCO2_SW @ SST to within 2 uatm and xCO2 to within
0.1 ppm as outlined in Pierot et al. 2009.

REFERENCES:

DOE (1994). Handbook of methods for the analysis of the various
	parameters of the carbon dioxide system in sea water; version
	2. DOE.
Feely, R. A., R. Wanninkhof, H. B. Milburn, C. E. Cosca, M. Stapp and
	P. P. Murphy (1998) A new automated underway system for making
	high precision pCO2 measurements onboard research ships.
	Analytica Chim. Acta 377: 185-191.
Ho, D. T., R. Wanninkhof, J. Masters, R. A. Feely and C. E. Cosca
	(1997). Measurement of underway fCO2 in the Eastern
	Equatorial Pacific on NOAA ships BALDRIGE and DISCOVERER,
	NOAA data report ERL AOML-30, 52 pp., NTIS Springfield.
Pierrot, D., C. Neill, K. Sullivan, R. Castle, R. Wanninkhof, H.
	Luger, T. Johannessen, A. Olsen, R. A. Feely, and C. E.
	Cosca (2009), Recommendations for autonomous underway pCO2
	measuring systems and data-reduction routines.  Deep Sea
	Research II, 56: 512-522.
Wanninkhof, R. and K. Thoning (1993) Measurement of fugacity of CO2 in 
	surface water using continuous and discrete sampling methods.
	Mar. Chem. 44(2-4): 189-205.
Weiss, R. F. (1970) The solubility of nitrogen, oxygen and argon in
	water and seawater. Deep-Sea Research 17: 721-735.
Weiss, R. F. (1974) Carbon dioxide in water and seawater: the
	solubility of a non-ideal gas.  Mar. Chem. 2: 203-215.
Weiss, R. F., R. A. Jahnke and C. D. Keeling (1982) Seasonal effects
	of temperature and salinity on the partial pressure of CO2 in
	seawater. Nature 300: 511-513.