                                       TO VIEW PROPERLY YOU MAY NEED TO SET YOUR
                                       BROWSER'S CHARACTER ENCODING TO UNICODE 8
                                       OR 16 AND USE YOUR BACK BUTTON TO RE-LOAD 



CRUISE REPORT:  A05
(Updated JUL 2010)




HIGHLIGHTS

                        Cruise Summary Information

          WOCE Section Designation  A05
Expedition designation (ExpoCodes)  74DI20040404
                   Chief Scientist  Stuart Cunningham/SOC-JRD
                             Dates  Apr 4, 2004 - May 10, 2004
                              Ship  RSS Discovery
                     Ports of call  Santa Cruz de Tenerif - Freeport, Grand Bahama

                                              27° 54' N
             Geographic Boundaries  79° 56' W           13° 22' W 
                                              24° 29' N
                          Stations  125
      Floats and drifters deployed  1 Argo float deployed
    Moorings deployed or recovered  0

                        Chief Scientist Contact Info.:
              Stuart Cunningham • National Oceanography Centre
                University of Southampton Waterfront Campus 
                     European Way, Southampton SO14 3ZH
            Phon: +44 (0) 23 8059643 • Email: scu@noc.soton.ac.uk








SOUTHAMPTON OCEANOGRAPHY CENTRE


CRUISE REPORT NO. 54
RRS Discovery Cruise 279
04 APR - 10 MAY 2004

A Transatlantic Hydrographic Section at 24.5°N

Dr. Stuart A. Cunningham


2005


James Rennell Division for Ocean Circulation and Climate
Southampton Oceanography Centre
University of Southampton
Waterfront Campus
European Way
Southampton                                          Tel: +44 (0)23 8059 6436
Hampshire   SO14 3ZH                                  Fax:+44 (0)23 8059 6204
UK                                                 Email: scu@soc.soton.ac.uk



ABSTRACT

The cruise report describes the acquisition and processing of transatlantic 
hydrographic, current, chemistry and other measurements made during three 
cruises in Spring 2004 at a latitude of around 24.5°N from shallow water near 
Africa to shallow water just off Palm Springs beach on the eastern seaboard 
of the USA. During the principal cruise, RRS Discovery Cruise D279 (4th April 
to 10th May 2004), 125 full depth CTD and lowered acoustic Doppler current 
profiler (LADP) stations were completed between the USA and Africa and 
continuous underway observations were made of currents in the upper 1000m 
using a ship mounted 75kHz ADP and of surface salinity and temperature. At 
each station up to 24 water samples were captured for the analysis of oxygen, 
salinity, nitrate, silicate, phosphate, CFC11, 12, 113 and CCl4 (carbon 
tetrachloride), discrete total inorganic carbon (TCO2), discrete total 
alkalinity (TA) and, discrete partial pressure of CO2 (discrete pCO2). Direct, 
near real-time measurements of the air-sea turbulent fluxes of momentum and 
sensible and latent heat in addition to various mean meteorological 
parameters including testing of a new Licor sensor to determine its 
suitability for making direct measurements of the air-sea CO2 flux were also 
made. Atmospheric dust samples were gathered on a daily basis. Two prior 
cruises D277 (26th February to 16th March) and D278 (19th to 30th March) 
completed 33 full depth CTD/LADP stations in the Florida and Deep Western 
Boundary Currents, including continuous underway observations of currents in 
the upper 1000m and of surface salinity and temperature. No LADP or chemistry 
measurements were made during these cruises. The three cruises provide one 
CTD and one CTD/LADP transect of the Florida Current, two Florida Current 
transects at 5knots with the shipboard ADP continuously seeing to the bottom 
for high accuracy well resolved direct velocity measurements, one section of 
16 CTD stations across the Deep Western Boundary Current and a 125 station 
transatlantic section with a full suite of physical and chemical 
measurements. The principal scientific objective is to estimate the 
circulation across 24.5°N, using for the first time, LADP profiles at each 
station as constraints in an inverse study. Using this circulation and the 
transatlantic distribution of temperature and other properties we will 
calculate the Atlantic heat and property fluxes. We will also define the size 
and structure of the Atlantic Meridional Overturning Circulation (MOC) to 
compare to results from a recently deployed transatlantic mooring array 
designed to continuously measure the size and structure of the MOC. The 
24.5°N section has now been occupied five times since 1957 (including the 
2004 section reported here). Therefore, we will analyse temporal trends of 
temperature to see if the widely report warming of the thermocline and 
intermediate waters and cooling of deep water is continuing. Carbon 
measurements were also obtained in 1992 and 1998 so this section provides a 
unique decadal view of anthropogenic carbon fluxes.


KEYWORDS

CTD, ADCP, METEROLOGY, NUTRIENTS, CFC, CARBON TETRACHLORIDE, CARBON, 
ATLANTIC, CIRCULATION, MERIDIONAL OVERTURNING CIRCULATION, LOWERED ADCP, 
SHIPBOARD ADCP, OCEAN SURVEYOR, ATMOSPHERIC CHEMISTRY, D278, D278, D279, 
OXYGEN


CONTENTS
Scientific Personnel	
Ship's Personnel	
Acronynms	
Acknowledgements	
1.  Introduction  
2.  Scientific Background  
3.  Objectives  
4.  Basic Observational Strategy  
5.  Itinerary  
6.  Narrative  
7.  D279 Bridge Timetable Of Events  
8.  Ctd Operations - D279  
9.  Ctd Data Processing And Calibration  
10. Sbe35 Deep Ocean Standards Thermometer  
11. Water Sample Salinity Analysis  
12. Winches  
13. Adcp And Battery Pack  
14. Lowered Acoustic Doppler Current Profiler  
15. Lowered Acoustic Doppler Current Profiler Data Processing Software Test 
    Suite  
16. Navigation And Shipboard Acoustic Doppler Current Profiler  
17. Ashtech 3df Gps Attitude Determination  
18. Ocean Surveyor 75khz Shipboard Acoustic Doppler Current Profiler  
19. 150khz Shipboard Acoustic Doppler Current Profiler  
20. Measurement Of Dissolved Oxygen  
21. Measurement Of Nutrients  
22. Autoflux - The Autonomous Air-Sea Interaction System  
23. Surface Met Data  
24. Salinity Calibration Of Underway Data  
25. Bathymetry  
26. Shipboard Instrumentation And Computing  
27. Carbon Parameters (Cbn)  
28. Halocarbons  
29. Atmospheric Sampling  
30. Trial Float Deployment  
31. Dissolved Oxygen Microelectrode Sensor  


SCIENTIFIC PERSONNEL

D277, 26th Feb to 16th March 2004

Principally a moorings deployment cruise {Cunningham, 2005 #1247} but 
including a CTD/LADP and SADP section across the Florida Current at 27°N 
between 79° 12.23'W and 79° 51.89'W and a SADP section across New Providence 
Channel to measure the transport of water flowing west into the Florida 
Current.


Table 1:  D277 scientific and technical personnel.

                     Stuart Cunningham   PS (SOC)
                     Darren Rayner       Scientist (SOC
                     Pedro Vélez Belchi  Scientist (IEO)
                     Stephen Whittle     OED
                     Ian Waddington      OED
                     John Wynar          OED
                     Robert McLachlan    OED
                     Elizabeth Rourke    OED
                     Christian Crow      OED
                     Peter Keen          OED

                           10 persons          


D278, 19th March to 30th March 2004

Principally a moorings deployment cruise {Cunningham, 2005 #1247}) but 
including a CTD/LADP and SADP section along the Abaco Mooring Array at 26.5°N 
between 71° 58.12'W and 76° 53.67'W to measure properties and transport of 
the Deep Western Boundary Current.


Table 2:  D278 scientific and technical personnel.

                     Stuart Cunningham  PS, SOC
                     Darren Rayner      SOC
                     Harry Bryden       SOC 
                     Marc Lucas         SOC
                     Jochem Marotzke    MPI
                     Johanna Baehr      MPI
                     Clotilde Dubois    MPI
                     Fiona McLay        MPI
                     Bill Johns         UoM
                     Lisa Beal          UoM

                     Deb Shoosmith      UoM
                     Mark Graham        UoM
                     Robert Jones       UoM
                     Ian Waddington     OED
                     John Wynar         OED
                     Robert McLachlan   OED
                     Christian Crow     OED
                     Jeffrey Benson     OED
                     Jeffrey Bicknell   OED
                     Chris Hunter       OED

                           20 persons


D279, 4th April to 12th May, 2004

  Transatlantic hydrography.


Table 3:  D279 scientific and technical personnel.

                 Stuart Cunning  PS                      SOC
                 Louise Duncan   PI LADP                 SOC
                 Steve Alderson  PI SADP, Nav            SOC
                 Hannah Longwor  PI CTD, Salts, Samples  SOC
                 Rachel Hadfiel  PI Underway obs         SOC
                 Amanda Simpson  PI Bathymetry           SOC
                 Margret Yellan  PI Autoflux             SOC
                 Robin Pascal    Autoflux                SOC
                 Richard Sander  PI Nutrients, Oxygen    SOC
                 Abigail Patten  Oxygen                  SOC
                 Angela Landolf  Nutrients, Oxygen       SOC
                 Rhiannon Mathe  Oxygen                  SOC
                 Ute Schuster    PI Carbon               UEA
                 Gareth Lee      Carbon                  UEA
                 Maria Nielsdot  Carbon                  UEA
                 David Cooper    PI CFC                  UoM
                 Charlene Grail  CFC                     UoM
                 David Teare     PI CTD technical        OED
                 Peter Keen      CTD                     OED
                 Martin Bridger  TLO                     OED
                 Richard Phipps  Mechanical              OED



Table 4:  D279 watches.

Physics
0800-1600          1600-2400          0000-0800
Louise Duncan      Robin Pasca        Richard Sanders
Hannah Longworthl  Margret Yelland    Steven Alderson
                   Rachel Hadfield    Amanda Simpson

CTD Technical
1200-1600          1600-0200          0200-1200
Martin Bridger     Peter Keen         David Teare

Oxygens and Nutrients
0800-1600          1600-2400          0000-0800
Angela Landolfi    Abigail Pattenden  Richard Sanders
                                      Rhiannon Mather

Carbon
0800-1600          1600-2400          0000-0800
Maria Nielsdottir  Ute Schuster       Gareth Lee

CFCs
1400-0200          0200-1400
David Cooper       Charlene Grail



SHIP'S PERSONNEL
Table 5:  Ship's personnel for D277, D278 and D279.

Rank                           D277                   D278                      D279
----------------------  ------------------  ------------------------  ------------------------
Master                  Roger Chamberlain   Roger Chamberlain         Roger Chamberlain
Chief Officer           Derek Noden         Richard Warner            Richard Warner
2nd Officer             John Mitchell       Phil Oldfield             Phil Oldfield
3rd Officer             Annalaara K-Willis  Darcy White               Darcy White
Chief Engineer          Sam Moss            Sam Moss                  Bernard McDonald
1st Engineer            Martin Holt         Stephen Bell              Stephen Bell
2nd Engineer            Antony Healy        John Harnett              John Harnett
3rd Engineer            Gary Slater         Chris Uttley              Chris Uttley
ETO                     Dean Hurren         Dennis Jakobaufderstroht  Dennis Jakobaufderstroht
CPO (Deck)              Greg Lewis          Greg Lewis                Iain Thomson
CPO (Scientific)        Stephen Smith       Martin Harrison           Martin Harrison
PO (Deck)               Andy MacLean        Andy MacLean              Andy MacLean
SG1A                    Stephen Day         Mark Moore                Gerry Cooper
SG1A                    Robert Dickinson    Robert Dickinson          Alan McPhail
SG1A                    Robert Spencer      Robert Spencer            Robert Spencer
SG1A                    William McLennan    William McLennan          Ian Cantile
MM1A                    Donald MacDiarmid   Donald MacDiarmid         John Smyth
SCM                     Keith Curtis        Keith Curtis              Edward Staite
Chef                    Paul Lucas          Stephen Nagle             John Haughton
Assistant Chef          Walter Link         John Giddings             John Giddings
Steward                 John Giddings       Alastair Harkness         Alastair Harkness
Deck Technician         Michael Minnock                -                         -
Extra CPO (Scientific)  Michael Trevaskis   Simon Avery
Extra SG1A                                  Gerry Cooper                         -  
Total                   22                  23                        22


ACRONYNMS
Acronyn  Meaning
-------  ---------------------------------------------------
CFC      Chloroflurocarbon
CTD      Conductivity, temperature and depth instrument
EC       Eddy correlation
i/b      In board
ID       Inertial dissipation
IEO      Institutio Espanol de Oceanografia, Tenerife, Spain
JRD      James Rennell Division
LADP     Lowered acoustic Doppler current profiler
MBL      Maximum breaking load
MPI      Max Planck Institute
o/b      Out board
OED      Ocean Engineering Division, SOC
PI       Principal Investigator
PS       Principal Scientist
SADP     Shipboard acoustic Doppler current profiler
SOC      Southampton Oceanography Centre
TLO      Technical Liaison Officer
u/s      unserviceable
UEA      University of East Anglia
UoM      University of Miami
UPS      Uninterruptible power supply


ACKNOWLEDGEMENTS

Particular thanks go to Captain Roger Chamberlain who participated in cruises 
277 to 279. Without the good working relationship we developed through all 
three cruises not nearly so much scientific work would have been completed. 
During the cruise there were ongoing worries about the new winch system. Some 
teething troubles were experienced but Chief Engineer Bernard McDonald on 
D279 kept us working. As always, the RRS Discovery was an excellent ship to 
work on and the crew were thoroughly professional. The 21 scientists were one 
of the most relaxed and enthusiastic groups it has been my privilege to lead. 
Thanks are also due in particular to Brian King, who travelled to the Bahamas 
to help with mobilisation and so allowed me a few days rest, confident that 
we would be ready to sail on time.


1.  INTRODUCTION

The 24.5°N transatlantic section between 69° 9'W and 23° 30'W has been 
occupied in 1957, 1981, 1992, 1998 and 2004 (reported here), with the western 
and eastern boundaries being closed at different latitudes (Table 1.1, Figure 
1.1). In 1957 and 1981 the western boundary was approached at 24.5°N while in 
1992 the boundary was closed perpendicular to the continental slope by a 
small adjustment to the zonal section. For occupations in 1998 and 2004 the 
western boundary is closed at 26.5°N, where long-term current meter arrays 
have measured the mean southward transport and variability of the Deep 
Western Boundary Current (DWBC) ([Lee et al., 1990], [Lee et al., 1996], 
[Fillenbaum et al., 1997], [Bryden et al., 2004]). In 1975 Spanish 
responsibilities for Western Sahara were transferred to the joint 
administration of Morocco and Mauritania. Subsequently there has been a 
territorial dispute between Morocco and the Polisario peoples of Western 
Sahara who are fighting to establish an independent state. Permission to work 
within the disputed territorial waters has not been sought, resulting in a 
northward excursion within Spanish and Moroccan water in 1981, 1998 and 2004.


Table 1.1: Hydrographic sections along 24.5°N.

              Year  Number of Stations  Reference
              ----  ------------------  ---------------------------
              1957          38          [Fuglister, 1960]
              1981          90          [Roemmich and Wunsch, 1985]
              1992         101          [Parilla et al., 1994]
              1998         130          [McTaggart et al., 1999]
              2004         125          [Cunningham, 2005]


The 1957 data differ most from the other occupations: the number of stations 
is much lower and temperature and salinity data were obtained from discrete 
samples at approximately 25 depths. From 1981 temperature and salinity 
profiles were obtained by CTD with discrete salinity samples being measured 
against standard sea-water. Using the linearity of the Eastern basin deep T/S 
relationship between 2 and 2.5°C ([Saunders, 1986], [Mantyla, 1994]) and 
assuming constant deep water characteristics the 1957 salinities are between 
0.004 to 0.006 higher than in subsequent years ([Bryden et al., 1996], [Arbic 
and Owens, 2001]).


Figure 1.1: CTD stations occupied during RRS Discovery Cruise 279 in 2004 
            (green plus), repeating the 1998 occupation (red circle) except 
            in the eastern basin where there were five fewer CTD stations in 
            2004. For these two occupations the western boundary is closed at 
            26.5°N, where long-term current meter arrays have measured the 
            mean southward transport and variability of the Deep Western 
            Boundary Current (DWBC) ([Lee et al., 1990], [Lee et al., 1996], 
            [Fillenbaum et al., 1997], [Bryden et al., 2004]). The 24.5°N 
            transatlantic section has been occupied five times between 69° 
            9'W and 23° 30'W, with the western and eastern boundaries being 
            closed at different latitudes. In 1957 (black circles) and 1981 
            (blue cross), the western boundary was approached at 24.5°N, 
            while in 1992 (pink plus) the boundary was closed perpendicular 
            to the continental slope by a small adjustment to the zonal 
            section. In 1975, Spanish responsibilities for Western Sahara 
            were transferred to the joint administration of Morocco and 
            Mauritania. Subsequently, there has been a territorial dispute 
            between the Polisario peoples of Western Sahara and Morocco, with 
            the Polisario seeking to establish an independent state. 
            Permission to work within the disputed territorial waters has not 
            been sought resulting in a northward excursion within Spanish and 
            Moroccan water in 1981, 1998 and 2004.



2. SCIENTIFIC BACKGROUND

In the North Atlantic the wind driven and thermohaline circulations combine 
in a meridional overturning circulation (MOC) that drives a northward heat 
transport reaching a maximum of 1.3PW at 24.5°N (~25% of the global net 
atmosphere-ocean heat flux) ([Bryden and Imawaki, 2001]). The ocean heat flux 
is effected by the temperature difference between a northward transport of 
very warm water in the Florida Current, cooler Intermediate water and very 
cold Antarctic Bottom Water (AABW), and the southward transport of warm 
thermocline and cold North Atlantic Deep Water (Figure 2.1) ([Hall and 
Bryden, 1982], [Roemmich and Wunsch, 1985], [Ganachaud and Wunsch, 2000], 
[Ganachaud, 2003]. As a consequence of the MOC northwest Europe enjoys a mild 
climate for its latitude: however abrupt rearrangement of the Atlantic 
Circulation has been shown in climate models and in paleoclimate records to 
be responsible for a cooling of European climate of between 5-10°C 
([Dansgaard, 1993], [Broecker and Denton, 1989], [Vellinga and Wood, 2002], 
[Rahmstorf and Ganopolski, 1999]).


Figure 2.1: CTD temperature (i) and salinity (ii) and from discrete samples 
            carbon tetrachloride (CCl4) (iii) at a nominal latitude of 24.5°N 
            measured during RRS Discovery Cruise 279, 4th April to 10th May 
            2004. The water mass distribution illustrates clearly our a 
            priori view of the circulation at 24.5°N ([Hall and Bryden, 
            1982], [Bryden and Imawaki, 2001]). In the upper 150dbar warm, 
            saline surface water is created by excess evaporation over 
            precipitation. The main thermocline between 9-22°C, with 
            isotherms sloping up to the east contains recently ventilated 
            late winter water, subducting southward under the surface water 
            as part of the Sverdrup circulation. Intermediate water between 4 
            to 8°C, with the 4°C isotherm sloping down to the east consists 
            of two water masses: in the western basin low salinity water due 
            to the northward penetration of Antarctic Intermediate Water and 
            in the east high salinities due to the southward and westward 
            spread of Mediterranean Overflow Water. Two cores of North 
            Atlantic Deep Water (NADW) are clearly shown in the CCl4 
            distribution, spreading south in the Deep Western Boundary 
            Current (DWBC). The upper NADW at a pressure of 1500dbar, with a 
            temperature and salinity of about 3.6°C and 34.99 respectively is 
            formed by deep winter mixing in the Labrador Sea. Lower NADW at 
            about 3500dbar has a core temperature and salinity of 2°C and 
            34.90 respectively has its source in the Greenland-Iceland-
            Norwegian Seas. Southward transport in the DWBC is confined to 
            within 200km of the continental slope and offshore 200km to 625km 
            (the eastward extent of existing current meter measurements) the 
            DWBC has a broad northward recirculation. The accumulated 
            transport eastward from the continental shelf deeper than 1000m 
            increases rapidly to a maximum of 34.9Sv southward 200km 
            offshore, gradually decreasing to less than 25Sv 625km offshore 
            ([Bryden et al., 2004]). Therefore, the CCl4 distribution is the 
            result of a relatively narrow and rapid transport southward close 
            to the continental slope with a broad interior recirculation and 
            isopycnal mixing by eddies, which from the upper NADW CCl4 
            distribution we conclude extends beyond the mid-Atlantic Ridge 
            (MAR). Northward flowing Antarctic Bottom Water with temperatures 
            less than 1.9°C is piled onto the western flank of the MAR. In 
            the eastern basin at depths below the intermediate waters the 
            NADW is thought to be the oldest and least varying water mass in 
            the North Atlantic, as it has no direct source and is a result of 
            mixing between AABW and NADW as the AABW flows north across a 
            series of sills. This results in a linear and stable relationship 
            between temperature and salinity, which can be used to compare 
            the quality of salinity measurements between cruises ([Saunders, 
            1986]).



3.  Objectives

This cruise is a contribution to the project "Monitoring the Atlantic 
Meridional Overturning Circulation at 26.5°N". In March and April 2004 22 
moorings were deployed across the Atlantic to continuously measure the size 
of the overturning [Cunningham, 2005]. A key objective of this cruise is to 
provide an independent estimate of the MOC to compare to the array.

• To measure the circulation across 24.5°N, for the first time including 
  direct top-to-bottom lowered ADP measurements at each station and 
  continuous current measurements in the top 1000m.
• To calculate the transport of heat, freshwater, oxygen, nutrients, CFCs and 
  carbon into the North Atlantic.
• To quantify the size and structure of the Atlantic MOC.



4. BASIC OBSERVATIONAL STRATEGY

Between 4th April and 10th May 2004125 full depth CTD/LADP stations were 
occupied across the Atlantic (Figure 1.1) at a nominal latitude of 24.5°N, 
including a section across the Florida Current. During two preceding cruises 
(D277 and D278) sections were also occupied across the Florida and Deep 
Western Boundary Currents and are reported here. Continuous underway 
observations were made of currents in the upper 1000m and of surface salinity 
and temperature. At each station up to 24 water samples were captured for the 
analysis of oxygen, salinity, nitrate, silicate, phosphate [Richard Sanders, 
Deacon Division SOC], CFC11, 12, 113 and CCl4 (carbon tetrachloride) [David 
Cooper, University of Miami], discrete total inorganic carbon (TCO2), discrete 
total alkalinity (TA) and, discrete partial pressure of CO2 (discrete pCO2) 
[Ute Schuster, University of East Anglia]. Direct, near real-time 
measurements of the air-sea turbulent fluxes of momentum and sensible and 
latent heat in addition to various mean meteorological parameters including 
testing of a new Licor sensor to determine its suitability for making direct 
measurements of the air-sea CO2 flux were also made [Margret Yelland, JRD 
SOC].


Figure 4.1: Bathymetry of the North Atlantic around 24.5°N. CTD stations 
            occupied during RRS Discovery Cruise 279 in 2004 are shown by 
            dots, repeating the 1998 occupation except in the eastern basin 
            where there are five fewer CTD stations in 2004. The 24.5°N 
            transatlantic section has been occupied five times between 
            69° 9'W and 23° 30'W with the western and eastern boundaries 
            being closed at different latitudes. In 1957 (stars) and 1981 
            (1981 as 1992 see below, including stations in the Florida Strait 
            at 26°N) the western boundary was approached at 24.5°N while in 
            1992 (pluses) the boundary was closed perpendicular to the 
            continental slope by a small adjustment to the zonal section. For 
            occupations in 1998 and 2004 the western boundary is closed at 
            26.5°N, where long-term current meter arrays have measured the 
            mean southward transport and variability of the Deep Western 
            Boundary Current (DWBC) ([Lee et al., 1990], [Lee et al., 1996], 
            [Fillenbaum et al., 1997], [Bryden et al., 2004]). In 1975 
            Spanish responsibilities for Western Sahara were transferred to 
            the joint administration of Morocco and Mauritania. Subsequently, 
            there has been a territorial dispute between the Polisario 
            peoples of Western Sahara and Morocco with the Polisario seeking 
            to establish an independent state. Permission to work within the 
            disputed territorial waters has not been sought resulting in a 
            northward excursion within Spanish and Moroccan water in 1981, 
            1998 and 2004. The 1957 data differ most from the other 
            occupations: the number of stations is much lower and temperature 
            and salinity data were obtained from discrete samples at 
            approximately 25 depths. From 1981 temperature and salinity 
            profiles were obtained by CTD with discrete salinity samples 
            being measured against standard sea-water. Using the linearity of 
            the Eastern basin deep T/S relationship between 2 and 2.5°C 
            ([Saunders, 1986], [Mantyla, 1994]) and assuming constant deep 
            water characteristics the 1957 salinities are between 0.004 to 
            0.006 higher than in subsequent years ([Bryden et al., 1996], 
            [Arbic and Owens, 2001]). [Arbic and Owens, 2001] show that this 
            systematic salinity error makes the comparison of salinities 
            below 2000dbar unreliably, but that for the intermediate and 
            thermocline water masses has no qualitative impact.


References

Arbic, B.K., and W.B. Owens, Climate warming of Atlantic Intermediate waters, 
    J. Clim., 14 (20), 4091-4108, 2001.

Broecker, W.S., and G.H. Denton, The role of ocean-atmosphere reorganizations 
    in glacial cycles, Geochim Cosmochim Acta, 53, 2465-2501, 1989.

Bryden, H.L., M.J. Griffiths, A.M. Lavin, R.C. Millard, G. Parrilla, and W.M. 
    Smethie, Decadal changes in water mass characteristics at 24°N in the 
    subtropical North Atlantic Ocean, Journal of Climate, 9 (12), 3162-3186, 
    1996.

Bryden, H.L., and S. Imawaki, Ocean Heat Transport, in Ocean Circulation & 
    Climate: Observing and Modelling the Global Ocean, edited by G. Siedler, 
    J. Church, and J. Gould, pp. 715, Academic Press, San Diego, San 
    Francisco, New York, Boston, London, Sydney, Tokyo, 2001.

Bryden, H.L., W.E. Johns, and P.M. Saunders, Deep Western Boundary Current 
    east of Abaco: Mean structure and transport, J. Mar. Res., submitted, 
    2004.

Cunningham, S.A., RRS Discovery Cruise 279, 04 APR - 10 MAY 2004: A 
    transatlantic hydrographic section at 24.5°N, pp. 150, Southampton 
    Oceanography Centre, Southampton, 2005a.

Cunningham, S.A., RRS Discovery Cruises 277 (26 MAR - 16 APR 2004) and 278 
    (19 MAR - 30 MAR 2004): Monitoring the Atlantic Meridional Overturning 
    Circulation at 26.5°N, pp. 150, Southampton Oceanography Centre, 
    Southamtpon, 2005b.

Dansgaard, W., Evidence for general instability of past climate from a 250-
    kyear ice-core record, Nature, 364, 218-220, 1993.

Fillenbaum, E.R., T.N. Lee, W.E. Johns, and R.J. Zantopp, Meridional heat 
    transport variability at 26.5°N in the North Atlantic, J. Phys. Oceanog., 
    27 (1), 153-174, 1997.

Fuglister, F.C., Atlantic Ocean atlas of temperature and salinity profiles 
    and data from the International Geophysical Year of 1957-1958, 209 pp., 
    Woods Hole Oceanographic Institution, Woods Hole, 1960.

Ganachaud, A., Large-scale mass transports, water mass formation, and 
    diffusivities estimated from World Ocean Circulation Experiment (WOCE) 
    hydrographic data, J. Geophys. Res., 108 (C7), 3213, doi: 
    10.1029/2002JC001565, 2003.

Ganachaud, A., and C. Wunsch, Improved estimates of global ocean circulation, 
    heat transport and mixing from hydrographic data, Nature, 408 (6811), 
    453-457, 2000.

Hall, M.H., and H.L. Bryden, Direct estimates and mechanisms of ocean heat 
    transport, DSR, 29 (3A), 339-359, 1982.

Lee, T.N., W. Johns, F. Schott, and R. Zantopp, Western boundary current 
    structure and variability east of Abaco, Bahamas at 26.5°N, J. Phys. 
    Oceanog., 20, 446-466, 1990.

Lee, T.N., W.E. Johns, R.J. Zantopp, and E.R. Fillenbaum, Moored observations 
    of western boundary current variability an thermohaline circulation at 
    26.5°N in the subtropical North Atlantic, J. Phys. Oceanog., 26, 962-983, 
    1996.

Mantyla, A.W., The treatment of inconsistencies in Atlantic deep water 
    salinity data, DSR, 41 (9), 1387-1405, 1994.

McTaggart, K.E., G.C. Johnson, C.I. Fleurant, and M.O. Baringer, CTD/O2 
    measurements collected on a Climate and Global Change cruise along 24°N 
    in the Atlantic Ocean (WOCE Section A6) during January-February 1998, 
    Pacific Marine Environmental Laboratory, Seattle, 1999.

Parilla, G., M. Garcia, H. Bryden, and R. Millard, Informe de la Campana HE06 
    (A-5, WOCE, 1992), pp. 110p, Inst. Esp. de Oceanog., Madrid, 1994.

Rahmstorf, S., and A. Ganopolski, Long-term global warming scenarios computed 
    with an efficient coupled climate model, Climatic Change, 43 (2), 353-
    367, 1999.

Roemmich, D., and C. Wunsch, Two transatlantic sections: meridional 
    circulation and heat flux in the subtropical North Atlantic Ocean, Deep 
    Sea Research, 32 (6), 619-664, 1985.

Saunders, P.M., The accuracy of measurement of salinity, oxygen and 
    temperature in the deep ocean, J. Phys. Oceanogr., 16, 189-195, 1986.

Vellinga, M., and R.A. Wood, Global climate impacts of a collapse of the 
    Atlantic thermohaline circulation, Climatic Change, 54 (3), 251-267, 
    2002.



5. ITINERARY

The main objective of this report is to document transatlantic hydrographic 
observations made during RRS Discovery Cruise 279 (125 CTD stations). Two 
previous cruises D277 and D278 also led by Stuart Cunningham were principally 
mooring deployment cruises with related scientific objectives. As part of the 
moorings deployments a limited number of hydrographic observations were made 
in the Florida Current and along the Abaco mooring array (12 and 16 CTD 
stations respectively). Instrumentation and calibration methods are the same 
for observations on all three cruises and so they are reported here. Moorings 
deployments on D277 and D278 are reported in {Cunningham, 2005 #1247}.






Table 5.1: Cruise timetable, ports of departure.

                                                     Days  No.   
                                                     at    CTD   
Cruise    Sail       Port       Dock    Port         sea   stns  Main science tasks
------  --------  ----------  --------  -----------  ----  ----  ---------------------------
 277    26/02/04  Santa Cruz  16/03/03  Freeport,     19    12   Moorings deployments,
                  de Tenerif            Grand                    Florida Current hydrography 
                                        Bahama                   and New Providence Channel 
                                                                 SADP section

 278    19/03/04  Freeport,   30/03/03  Freeport,     11    16   Moorings deployments,
                  Grand                 Grand                    Abaco mooring array 
                  Bahama                Bahama                   hydrography

 279    04/04/04  Freeport,   10/05/04  Santa Cruz    37   125   Florida Current and 
                  Grand                 de Tenerif               Transatlantic
                  Bahama                                         hydrography and chemistry
                 


5.1  D277 Hydrographic Observations of Note

1. Deep CTD station 277003 as test of new winch performance at 24° 25.44'N, 
   56° 1.38'W. Water depth 6454 m, CTD maximum depth 6419 m (6559 dbar).

2. Florida Current CTD section: CTD stations 277005 to 277012, from 14/3 2016 
   to 15/3 1222, occupied east to west.

3. Florida Current SADP section: 5 kn steam west to east along the CTD 
   section to obtain direct velocity measurements of the current from the 
   150kHz and 75kHz shipboard SADPs. The 75kHz obtained bottom track 
   velocities across the whole section. Dates: 15/3 1307 to 2145.

4. New Providence Channel SADP section: 5 kn steam across the channel in the 
   direction 024°T. Dates: 16/3 0554 to 1156.


5.2  D278 Hydrographic Observations of Note

1. CTD stations 278001 to 278016 occupied along the Abaco mooring array. The 
   stations were occupied around mooring operations and the east west station 
   grid is not monotonic in time.


5.3  D279 Hydrographic Observations of Note

1. Florida Current SADP section: 5 kn steam west to east along the CTD 
   section to obtain direct velocity measurements of the current from the 
   150kHz and 75kHz shipboard SADPs. The 75kHz obtained bottom track 
   velocities across the whole section. Dates: dd/mm hhmm to hhmm

2. Florida Current CTD section: . CTD stations 2 to 10, from 05/04 0634 to 
   06/04 0157, occupied east to west.

3. Transatlantic section: 26.5°N, lon1 to lon2 CTDnum to CTDnum; 26.5°N to 
   24.5°N, lon1 to lon2 CTDnum to CTDnum; 24.5°N to lat2, lon1 to lon2 CTDnum 
   to CTDnum; 24.5°N, lon1 to lon2 CTDnum to CTDnum.

4. Continuous underway observations were made of currents in the upper 1000m, 
   surface salinity and temperature. At each station up to 24 water samples 
   were captured for the analysis of oxygen, salinity, nitrate, silicate, 
   phosphate [R. Sanders, Deacon Division SOC], CFC11, 12, 113 and CCl4 
   (carbon tetrachloride) [D. Cooper, University of Miami], discrete total 
   inorganic carbon (TCO2), discrete total alkalinity (TA) and, discrete 
   partial pressure of CO2 (discrete pCO2) [U. Schuster, University of East 
   Anglia]. Direct, near real-time measurements of the air-sea turbulent 
   fluxes of momentum and sensible and latent heat in addition to various 
   mean meteorological parameters including testing of a new Licor sensor to 
   determine its suitability for making direct measurements of the air-sea CO2 
   flux were also made [M. Yelland, JRD SOC].



6. NARRATIVE

D279 Narrative ((Day of year), times in GMT, CTD station numbers given as 
D279 incremental number, five digit Discovery station number)

4th April (095): 0200 Clocks advanced one hour to GMT-4.1330 Muster stations.1500 
Sailing. 1630 CTD test station. 2030 Begin 5 kn steam east to west for SADP 
section across the Florida Current at a latitude of 27°N. Section slightly 
delayed due to heavy traffic. 5th (096): Begin working a planned 9 station CTD 
section west to east across the Florida Current. First CTD station at 
approximately 0630. Thereafter, stations worked through the day and night. A 
succession of problems have delayed the CTD operation: main logging PC is 
unreliable - keeps crashing. Options: swap with backup pc, reinstall software, 
get another computer - computers swapped, and there have since been no crashes; 
Secondary T seems not to be working - after three stations a faulty pump was 
replaced restoring the secondary temperature and oxygen; Oxygen sensor 
apparently not working - traced to the configuration file having zeros in ever 
entry; altimeters not working - altimeters swapped and cables. By 2400 we had 
started station 9 with 1 more station to complete. The estimated completion time 
was 1600 so we have lost about 12 hours completing this short section. 6th (097): 
Station 010, 15314, last on FC section completed at 0300. Steaming north about 
Grand Bahama and Abaco to start of main section. Arrived on station at 1800, 
found a suitable water depth of 300 m after running into 30 m deep water. As the 
CTD 11, 15315 was being recovered news came through that the agent had the 
followers in Freeport. Therefore, we are steaming back to collect them. Two of 
the scientific party had a reaction to the Scopoderm (hyoscine) patches for 
motion sickness. In one case this included severe side effects, of a loss of 
focus in one eye and abnormal retinal size in that eye. The patches were removed 
and the retinal size monitored with opthalmascope under advice from Haslar. An 
eye patch was worn to reduce eye strain. Over three days eye focus was recovered 
and retinal size returned to normal matching the unaffected eye. 7th (098): 
Arrived off Freeport and collected followers by off port transfer (OPT) at 0715. 
En-route back to start of CTD section. Arrived on station (12, 15316 at 2015 - a 
repeat of station 11 15315. Begin working CTD stations eastward along 26.5°N. 
Station spacing close, so CTD work very intensive. Time limiting factor is the 
LADP download between stations. 8th (099): Main event of the day was the failure 
of the winch scrolling gear on station 17, 15321, CTD o/b 1904. Due to the wear 
on the scrolling gear follower it was decided to replace the current follower 
with one of the new ones picked up in Freeport. On station 17 (at the foot of 
the continental slope in about 4800 m, 2 miles west of mooring WBH2 the follower 
sheared with the CTD 26 m off bottom. The depth shallowed and the CTD touched 
bottom, so we towed 135T to find deeper water to clear the CTD from the bottom 
and allow wire to be paid out. Richie Phipps, the ship's engineers and the 
Captain worked for three hours to replace the follower. This has now been done 
and we are at 3800 m hauling in at 30 m/min. The diagnosis of what happened is 
that as the old follower wore down it caused burrs to turn on the continuous 
screw. The new follower carriage seized on one of these and the knife/tooth of 
the follower sheared off. Fortunately the follower stuck solid in the middle of 
the screw rather than flying to one end and smashing into the gear case. The 
follower is under more tension in one dirn than the other because as the wire 
leads outboard from the follower it turns 90 degrees round a pully leading to 
the traction winch. CTD i/b 0300. 9th (100) to 12th (102): Continue working 
stations eastward across the Deep Western Boundary Current. On station 28, 15332 
the Work Horse battery pack was deployed with the air vent removed. The vent was 
spotted on the deck lab floor with the CTD at 2500 m, and we recovered the CTD, 
removed the flooded pack and started a new station 29, 15333. Deployments of 
styrene cups on the CTD were halted as one bottle at 2500 m on station 30, 15334 
had a dramatic CFC11 contamination. David Cooper suspected that the cups 
contravened the Montreal Protocol that bans the use of CFCs in such products. 
13th (103): A barbecue was held on the aft deck in celebration of three 
birthdays. Weather was splendid and we were on station 36, 15341 during most of 
the barbecue. 14th (104): Completed 040, 15344 last western boundary station on 
latitude 26.5°N at 1544. Turned south course 139°T. Weather has turned cooler 
and wet after the passage of a sharp front during the night. 17th (108): Murder 
game started at 0000. To try and recover some contingency we have relaxed the 
station positions to be within 0.5nm of the position. This allows the ship to 
approach at full speed, then come on station faster than coming on station to a 
precise position. 18th (109): Clock advance one hour to GMT-2. 22nd (113): 
Discovery 6 failed. Five hour interlude in data processing while the disks were 
mounted on Discovery2. 26th (117): Clocks advance one hour to GMT-1. We reached 
the MAR station today: station 079, 15381, completed at 1238. 27th (119): 
Workhorse slave unit removed from CTD frame prior to station 087, 15388. 29th 
(120): Deployed Richard Babb's trial Iridum argo float at 1515 at 24° 30.24'N, 
38° 32.07'W (24.50407°N, 38.53441°W) after station 090, 15391. The float is in a 
grey plastic case, is designed to float on the surface (no buoyancy control) to 
test the Iridum transmitter/receiver. 30th (121): A potential winch problem 
narrowly avoided. Just after the CTD was landed at the end of station 38, 15397 
the Chief Engineer heard the CTD traction winch gear box making an unusual 
noise. The problem was that the storage drum drive shaft and drive motor shafts 
had decoupled so that the storage drum was then stationery relative to the 
traction winch. The drive shaft decoupled because the shaft coupling joint came 
loose due to poor design. 2nd May (123): Clocks advanced tonight to GMT-0. 
Differential G12 receiver changed region from AM-SAT to EA-SAT at 1415. 6th 
(127): Electrical termination started to fail at the end of station 112, cast 
ended at 1912. After some diagnosis the work of retermination started at 2100. 
At start of 113 new termination failed as soon as the CTD was deployed. 
Therefore, a second termination was started. 7th (128): Second termination 
complete at 0715. Started station 113 at 0740. Time lost to termination problems 
about 10 hours. 8th (129): EB3 satellite buoy. This last reported position 
(26° 59.86'N, 16° 13.8'W) data from this buoy were received at 1930 on 30th March 
(090). Approach position from the south west along cruise track. Visibility and 
sea-state good for observations. The buoy could not be located so a box survey 
of length two cables was completed around this position, to no effect. Steamed 
for station 118, 6 nm away. Clocks advanced to GMT+1. 9th (130): Last station 
completed at 2100, station 125. Headed for Santa Cruz de Tenerife.



7.   D279 BRIDGE TIMETABLE OF EVENTS

Date      Time (UT)  Event

30/03/04  1500       Arrived Freeport - end of Cruise 278
03/04/04  2000       Familiarisation of newly joined non-RSU personnel
04/04/04  1330       Emergency and lifeboat muster
          1455       Pilot embarked
          1533       Vessel cleared berth
          1555       Pilot disembarked
          1600       Full away. Course 117 T
          1729       PES Fish cast outboard                        26 29.8N     079 00.2W
          1746-1842  Station 15305-CTD cast outboard               26 28.7N     079 00.6W
          1842       Set course 340 T
          2150       Altered course to 270 T onto ADP survey line  26 59.8N     079 11.4W
          2158-0617  Engaged in ADP Survey @ 5 knots               27 00.0N     079 11.8W
05/04/04  0617-46    Station 15306-CTD 46 cast outboard            27 00.3N     079 56.1W
          0801-53    Station 15307-CTD 47 cast outboard            27 01.0N     079 51.4W
          1004-49    Station 15308-CTD 48 cast outboard            27 01.1N     079 46.5W
          1244-1350  Station 15309-CTD 49 cast out to 525 m        27 01.0N     079 40.9W
          1540-1641  Station 15310-CTD 50 cast out to 635 m        27 01.0N     079 37.1W
          1834-1933  Station 15311-CTD 51 cast out to 760 m        27 00.9N     079 30.2W
          2109-2204  Station 15312-CTD 52 cast out to 670 m        27 00.9N     079 23.3W
          2321-0010  Station 15313-CTD 53 cast out to 605 m        27 00.0N     079 16.8W
06/04/04  0136-0220  Station 15314-CTD 54 cast out to 455 m        26 59.9N     079 11.6W
          0220       Set course 336 T full away
          0300       Altered course to 006 T                       27 05.0N     079 15.6W
          0447       Altered course to 090 T                       27 26.0N     079 12.0W
          0731       Altered course to 113 T                       27 26.0N     078 35.0W
          1237       Altered course to 129 T                       27 02.5N     077 30.2W
          1614       Altered course to 180 T                       26 36.8N     076 54.1W
          1734-1817  Station 15315-CTD 121 cast out to 340 m       26 30.4N     076 55.6W
          1836       PES inboard - proceeding to Freeport Roads    26 30.3N     076 55.0W
07/04/04  0600       Approaching Freeport Roads
          0726-33    Agents boat alongside - scroll followers transferred to ship
          0742       Full away to resume science
          1954       PES Fish outboard                             26 26.5N     076 55.0W
          2047-2121  Station 15316-CTD 121 cast out to 260 m       26 30.5N     076 55.6W
          2234-0040  Station 15317-CTD 120 cast outboard           26 32.0N     076 48.3W

08/04/04  0235-0502  Station 15318-CTD 119 cast out to 2350 m      26 30.7N     076 46.9W
          0700-1022  Station 15319-CTD 118 cast outboard           26 31.4N     076 44.3W
          1243-1701  Station 15320-CTD 117 cast out to 4440 m      26 30.5N     076 41.3W
          1904-0300  Station 15321-CTD 116 cast out to 4595 m      26 30.0N     076 37.6W
          2054       WINCH STOPPED - SCROLLING FAILURE
          2225       Attempting to tow CTD to deeper water for veering to scroll point
          2338       Scroll problem fixed - slow hauling and monitoring
  
09/04/04  0000       All aspects of winch handed back to lab and winch operator
          0300       CTD inboard                                   26 28.5N     076 34.2W
          0628-1103  Station 15322-CTD 115 cast outboard           26 29.1N     076 31.3W
          1325-1748  Station 15323-CTD 114 cast out to 4825 m      26 30.0N     076 25.8W
          1939-2330  Station 15324-CTD 113 cast out to 4825 m      26 29.5N     076 18.1W

10/04/04  0115-0501  Station 15325-CTD 112 cast out to 4805 m      26 29.2N     076 12.6W
          0727-1045  Station 15326-CTD 111 cast outboard           26 29.9N     076 05.6W
          1247-1605  Station 15327-CTD 110 cast out to 4700 m      26 30.1N     075 54.7W
          1750-2100  Station 15328-CTD 109 cast outboard           26 29.4N     075 42.3W
          2315-0240  Station 15329-CTD 108 cast out to 4685 m      26 28.9N     075 30.9W

11/04/04  0433-0745  Station 15330-CTD 107 cast out to 4630 m      26 29.5N 075 18.5W
          0955-1330  Station 15331-CTD 106 cast out to 4895 m      26 30.9N     075 04.7W
          1532-1704  Station 15332-CTD 105 cast but aborted due to battery problems
          1735-2038  Station 15333-CTD 105 cast out to 4525 m      26 30.6N     074 47.3W
          2332-0302  Station 15334-CTD 104 cast out to 4554 m      26 31.2N     074 29.8W

12/04/04  0439-0807  Station 15335-CTD 103 cast out to 4565 m      26 30.6N     074 14.1W
          0948-1330  Station 15336-CTD 102 cast out to 4750 m      26 30.1N     073 55.8W
          1531-1924  Station 15337-CTD 101 cast out to 4920 m      26 30.6N     073 33.8W
          2106-0100  Station 15338-CTD 100 cast out to 5080 m      26 30.0N     073 11.7W

13/04/04  0313-0701  Station 15339-CTD 99 cast out to 5124 m       26 30.1N     072 50.8W
          1005-1355  Station 15340-CTD 98 cast out to 5188 m       26 30.0N     072 29.1W
          1651-2053  Station 15341-CTD 97 cast out to 5274 m       26 29.3N     072 00.4W
          2255-0250  Station 15342-CTD 96 cast out to 5370 m       26 29.0N     071 45.1W

14/04/04  0539-0938  Station 15343-CTD 95 cast out to 5465 m       26 30.5N     071 20.6W
          1140-1544  Station 15344-CTD 94 cast out to 5495 m       26 29.4N     070 59.2W
          1832-2227  Station 15345-CTD 93 cast out to 5537 m       26 08.0N     070 36.1W


15/04/04  0115-0454  Station 15346-CTD 92 cast out to 5495 m       25 45.9N     070 14.3W
          0750-1208  Station 15347-CTD 91 cast out to 5504 m       25 22.8N     069 52.6W
          1458-1913  Station 15348-CTD 90 cast out to 5590 m       25 00.1N     069 30.4W
          2241-0230  Station 15349-CTD 89 cast out to 5670 m       24 29.6N     069 08.8W

16/04/04  0647-1050  Station 15350-CTD 88 cast out to 5740 m       24 30.5N     068 24.8W
          1455-1841  Station 15351-CTD 87 cast out to 5705 m       24 30.7N     067 40.2W
          2230-0220  Station 15352-CTD 86 cast out to 5730 m       24 29.2N     066 55.4W

17/04/04  0612-0950  Station 15353-CTD 85 cast out to 5260 m       24 30.2N     066 11.5W
          1335-1725  Station 15354-CTD 84 cast out to 5545 m       24 29.7N     065 27.8W
          2130-0130  Station 15355-CTD 83 cast out to 5600 m       24 30.6N     064 39.6W

18/04/04  0516-0905  Station 15356-CTD 82 cast out to 5755 m       24 29.9N     064 00.1W
          1327-1712  Station 15357-CTD 81 cast out to 5785 m       24 30.3N     063 16.1W
          2120-0115  Station 15358-CTD 80 cast out to 5850 m       24 30.2N     062 31.7W

19/04/04  0515-0905  Station 15359-CTD 79 cast out to 5686 m       24 30.5N     061 47.9W
          1300-1653  Station 15360-CTD 78 cast out to 5835 m       24 30.1N     061 03.8W
          2057-0105  Station 15361-CTD 77 cast out to 5880 m       24 30.7N     060 19.4W

20/04/04  0507-0907  Station 15362-CTD 76 cast out to 5820 m       24 30.9N     059 35.5W
          1315-1657  Station 15363-CTD 75 cast out to 5870 m       24 29.9N     058 51.5W
          2047-0045  Station 15364-CTD 74 cast out to 5800 m       24 30.0N     058 08.0W

21/04/04  0435-0835  Station 15365-CTD 73 cast out to 5870 m       24 30.1N     057 23.3W
          1232-1629  Station 15366-CTD 72 cast out to 5870 m       24 29.7N     056 40.0W
          2009-0017  Station 15367-CTD 71 cast out to 5890 m       24 31.1N     055 56.2W

22/04/04  0419-0800  Station 15368-CTD 70 cast out to 5865 m       24 30.3N     055 12.8W
          1210-1548  Station 15369-CTD 69 cast out to 5197 m       24 30.0N     054 28.4W
          1945-2345  Station 15370-CTD 68 cast out to 5870 m       24 29.6N     053 44.2W

23/04/04  0250-0648  Station 15371-CTD 67 cast out to 5325 m       24 29.9N     053 10.7W
          0940-1325  Station 15372-CTD 66 cast out to 5260 m       24 30.2N     052 38.2W
          1603-1926  Station 15373-CTD 65 cast out to 4909 m       24 30.0N     052 09.3W
          2300-0242  Station 15374-CTD 64 cast out to 5280 m       24 30.0N     051 32.3W

24/04/04  0554-0925  Station 15375-CTD 63 cast out to 5422 m       24 30.4N     050 59.8W
          1255-1611  Station 15376-CTD 62 cast out to 4703 m       24 30.3N     050 26.5W
          1915-2235  Station 15377-CTD 61 cast out to 4600 m       24 30.6N     049 52.4W
25/04/04  0142-0532  Station 15378-CTD 60 cast out to 5210 m       24 30.4N     049 20.0W
          0830-1150  Station 15379-CTD 59 cast out to 4400 m       24 29.8N     048 46.4W
          1602-1852  Station 15380-CTD 57 cast out to 3945 m       24 30.3N     047 57.8W
          2320-0205  Station 15381-CTD 56 cast out to 3485 m       24 29.9N     047 07.5W

26/04/04  0459-0740  Station 15382-CTD 55 cast out to 3300 m       24 29.7N     046 34.5W
          1025-1235  Station 15383-CTD 54 cast out to 2765 m       24 29.7N     046 02.1W
          1536-1817  Station 15384-CTD 53 cast out to 3415 m       24 30.3N     045 29.4W
          2117-2400  Station 15385-CTD 52 cast out to 3300 m       24 29.1N     044 56.7W
27/04/04  0323-0610  Station 15386-CTD 51 cast out to 3876 m       24 30.1N     044 23.7W
          0920-1207  Station 15387-CTD 50 cast out to 3770 m       24 30.0N     043 50.6W
          1614-1917  Station 15388-CTD 48 cast out to 4117 m       24 30.6N     043 00.5W
          2330-0253  Station 15389-CTD 47 cast out to 3965 m       24 29.9N     042 11.0W

28/04/04  0600-0910  Station 15390-CTD 46 cast out to 4610 m       24 30.5N     041 38.4W
          1225-1541  Station 15391-CTD 45 cast out to 5130 m       24 30.2N     041 05.5W
          2000-2317  Station 15392-CTD 43 cast out to 4852 m       24 30.7N     040 16.9W

29/04/04  0507-0823  Station 15393-CTD 42 cast out to 5150 m       24 29.9N     039 14.7W
          1230-1526  Station 15394-CTD 41 cast out to 4630 m       24 29.9N     038 31.4W
          1530       Float deployed by Pascal/Yelland              24 30.2N     038 32.1W
          1950-2330  Station 15395-CTD 40 cast out to 5500 m       24 29.9N     037 41.7W

30/04/04  0355-0710  Station 15396-CTD 39 cast out to 5300 m       24 29.4N     036 52.7W
          1130-1502  Station 15397-CTD 38 cast out to 5740 m       24 29.6N     036 02.8W
          1920-2242  Station 15398-CTD 37 cast out to 5040 m       24 30.3N     035 13.7W

01/05/04  0303-0610  Station 15399-CTD 36 cast out to 5030 m       24 29.7N     034 23.4W
          1015-1350  Station 15400-CTD 35 cast out to 5865 m       24 29.9N     033 34.4W
          1833-2209  Station 15401-CTD 34 cast out to 5870 m       24 30.6N     032 39.4W

02/05/04  0301-0637  Station 15402-CTD 33 cast out to 5635 m       24 30.0N     031 43.8W
          1117-1441  Station 15403-CTD 32 cast out to 5695 m       24 29.7N     030 48.7W
          1930-2305  Station 15404-CTD 31 cast out to 5710 m       24 30.1N     029 53.4W

03/05/04  0348-0715  Station 15405-CTD 30 cast out to 5658 m       24 30.5N     028 59.9W
          1200-1522  Station 15406-CTD 29 cast out to 5580 m       24 30.1N     028 04.1W
          2005-2335  Station 15407-CTD 28 cast out to 5531 m       24 30.7N     027 08.9W

04/05/04  0420-0738  Station 15408-CTD 27 cast out to 5370 m       24 29.9N     026 13.9W
          1210-1516  Station 15409-CTD 26 cast out to 5270 m       24 30.1N     025 19.1W
          2005-2328  Station 15410-CTD 25 cast out to 5136 m       24 29.7N     024 24.2W
05/05/04  0421-0735  Station 15411-CTD 22 cast out to 5050 m       24 30.8N     023 29.7W
          1130-1432  Station 15412-CTD 21 cast out to 4880 m       24 44.3N     022 49.3W
          1830-2135  Station 15413-CTD 20 cast out to 4740 m       24 59.1N     022 08.9W

06/05/04  0114-0427  Station 15414-CTD 19 cast out to 4565 m       25 13.3N     021 28.7W
          0815-1125  Station 15415-CTD 18 cast out to 4388 m       25 27.0N     020 48.3W
          1505-20    Station 15416-CTD 17 aborted due to depth     25 41.4N     020 09.1W
          1520-1610  Relocating vessel to desired depth
          1610-1900  Station 15416-CTD 17 cast out to 4180 m       25 39.0N     020 14.6W
          2236-0736  DOWN TIME for TERMINATION problems

07/05/04  0736-1020  Station 15417-CTD 16 cast out to 3772 m       25 55.2N     019 29.1W
          1332-1542  Station 15418-CTD 14 cast out to 3435 m       26 08.0N     018 54.6W
          1949-2223  Station 15419-CTD 13 cast out to 3635 m       26 23.1N     018 09.6W

08/05/04  0204-0436  Station 15420-CTD 12 cast out to 3640 m       26 35.8N     017 28.1W
          0815-1050  Station 15421-CTD 11 cast out to 3609 m       26 48.9N     016 47.1W  
          1345-1442  Search for telemetry mooring EB3 - No success after a thorough Box search.  
                     Mean position throughout                      26 59.9N     016 13.9W
          1528-1745  Station 15422-CTD 9 cast out to 3516 m        27 03.1N     016 07.5W
          2045-2255  Station 15423-CTD 8 cast out to 3130 m        27 14.0N     015 35.5W

09/05/04  0309-0500  Station 15424-CTD 7 cast out to 2594 m        27 26.0N     014 51.6W
          0825-1000  Station 15425-CTD 6 cast out to 2015 m        27 37.2N     014 13.7W
          1236-1445  Station 15426-CTD 5 cast out to 1545 m        27 49.7N     013 49.0W
          1514-1620  Station 15427-CTD 4 cast out to 1080 m        27 51.1N     013 33.0W
          1714-1755  Station 15428-CTD 3 cast out to  580 m        27 52.8N     013 25.2W
          1835-1905  Station 15429-CTD 1 cast out to  345 m        27 54.9N     013 22.5W
          1910       PES Fish inboard and secured
          1917       Commenced bathymetric survey                  27 55.0N     013 22.8W
          1930       Bathymetric survey completed - set course for Santa Cruz De Tenerife
                     Course 272 T                                  27 55.7N     013 21.6W

          END OF SCIENCE

10/05/04  0900       ETA Santa Cruz



8.  CTD OPERATIONS - D279

Dave Teare, Pete Keen, Martin Bridger

8.1  CTD Main Instrumentation

Sea-Bird 9/11 plus CTD system; Chelsea Mk III Aqua tracker Fluorometer; 
Chelsea MkII Aqua tracker transmissometer; Sea Tech Light Backscattering 
sensor; Benthos PSA-916T Altimeter; 150kHz Broadband ADP; 2 x 300kHz L-ADP; 
24 x 10L Water sampling bottles on a 24 position rosette; Sea-Bird SBE35 Deep 
ocean standards thermometer


8.2  Sea-Bird CTD Configuration

Frequency 0 -SBE 3P Temperature sensor (primary); Frequency 1 -SBE 4C 
Conductivity sensor (primary); Frequency 2 -Digiquartz temperature 
compensated pressure sensor; Frequency 3 - SBE 3P Temperature sensor 
(secondary); Frequency 4 - SBE 4C Conductivity sensor (secondary); SBE 5T 
submersible pump s/n 3607 or s/n 3195 (primary); SBE 5T submersible pump s/n 
3609 (secondary); SBE 32 Carousel 24 position pylon s/n 3231240-0243; SBE 11 
plus deck unit s/n 11P24680-0598; Break-out Box s/n B019108


8.3  Voltage Channels 
     V0  Oxygen, Current s/n 13055
     V1  Oxygen, Temperature s/n 130551
     V2  Fluorometer s/n 88-2360-108
     V3  Altimeter s/n 1040
     V4  Transmissometer s/n 161048
     V5  LSS s/n 400

Occasional changes were made to the original configuration. These are listed 
according to Cast number in Table 1.


8.4  Outboard Instrumentation
     150kHz BB ADP	s/n 1308
     300kHz ADP (downward looking - master)
     300kHz ADP (upward looking - slave)
     LADP Battery pack (tsn-1857-A, tsn-3726-A)
     BB Battery pack (s/n 002)
     


Table 8.1: List of changes to CTD configuration according to cast number.

Cast 
Nmbr  Configuration Change
----  -----------------------------------------------------------------------
002   Oxygen sensor disconnected
007   pump s/n 053607 swapped for s/n 053195
008   Oxygen sensor plugged back in
011   No 300kHz ADP
023   Fluorometer disconnected
025   Fluorometer, transmissometer and LSS disconnected
026   transmissometer and LSS disconnected
027   Fluorometer changed to V2, Altimeter to V4
035   Changed BB Battery pack
038   Temp/Conductivity sensors changed. 1o - T/C 2758/2450, 2o - T/C 
      2880/2637. 
042   BB Battery pack changed
047   Fluorometer s/n 108 changed to s/n 163
057   Oxygen calibration file error discovered. Voltage offset changed from -
      0.4187 to -0.4817
061   Fluorometer changed to V3
070   BB Battery pack changed
076   Small shrimp discovered lodged in 1o T/C intake, data reveals this 
      occurred at 3000m on the downcast.
088   300kHz slave (upward looking) ADP removed due to RSSI failure
094   1o Conductivity sensor changed to s/n 2407


Table 8.2: D277 CTD sensor serial numbers. Primary sensors are those reported 
           as the final data.

Stat     Primary  Primary  Secondary  Secondary
num      Temp     cond     temp       cond       press
-------  -------  -------  ---------  ---------  -----
001-012  2674     2231     4105       2571       78958


Table 8.3: D278 sensor serial numbers.

Stat     Primary  Primary  Secondary  Secondary
num      Temp     cond     temp       cond       press
-------  -------  -------  ---------  ---------  -----
001-009  2919     2407     4116       2840       78958
010-012  2758     2450     2880       2637       90573
013-016  2919     2407     4116       2840       78958


Table 8.4: D279 sensor serial numbers. Primary sensors are those reported as 
           the final data.

Stat     Primary  Primary  Secondary  Secondary
num      Temp     cond     temp       cond       press
-------  -------  -------  ---------  ---------  -----
001-037  2919     2407     4116       2840       78958
038-093  2880     2637     2758       2450       78958
094-108  2758     2407     2880       2637       78958
109-125  2758     2407     2880       2840       78958


8.5  CTD Temperature and Conductivity Sensor Calibration Coefficients 

Table 8.5: CTD temperature calibration coefficients. 2758 calibrated on 29th 
           January 2004, 2880 calibrated on 29th January 2004, 2919 calibrated 
           on 29th January 2004, 4116 calibrated on 29th January 2004, 2674 
           calibrate on 15th December 2003

Coeff       2674           4105           2758           2880           2919           4116
-----   -------------  -------------  -------------  -------------  -------------  -------------
  G     4.35677202e-3  4.39439791e-3  4.35397384e-3  2.37981443e-3  4.31706705e-3  4.42588002e-3
  H     6.42250609e-4  6.48223032e-4  6.37191919e-4  6.42919222e-4  6.44675270e-4  6.84231655e-4
  I     2.34570815e-5  2.34748617e-5  2.19294527e-5  2.33575674e-5  2.29910908e-5  2.43414204e-5
  J     2.29237427e-6  2.13130914e-6  2.05208215e-6  2.23078830e-6  2.17863836e-6  1.99246468e-6


Table 8.6: CTD conductivity calibration coefficients. 2450 calibrated on 29th 
           January 2004, 2637 calibrated on 29th January 2004, 2407 calibrated 
           on 29th January 2004, 2840 calibrated on 29th January 2004, 2231 
           calibrated on 12th December 2003

Coeff       2231            2571            2450            2637            2407            2840
-----  --------------  --------------  --------------  --------------  --------------  --------------  
  G    -1.02409209e+1  -1.02755424e+1  -1.05418122e+1  -1.02953467e+1  -1.02887317e+1  -1.00334576e+1
  H     1.613274421     1.59430177      1.67829897      1.44378557      1.49174063      1.37702479
  I    -3.29512721e-3   6.92468216e-6  -1.10832094e-3   9.41703627e-4   4.53878165e-4   5.80641988e-4
  J     3.42685450e-4   1.17144243e-4   2.03695233e-4   3.10647797e-5   5.42327985e-5   3.83582725e-5



Table 8.7: Pressure calibration coefficients for digiquartz pressure sensors 
           s/n 78958 calibrated on 17th June 2003 and s/n 90573 calibrated on 
           9th June 2002.


                  Coefficient    s/n 78958      s/n 90573
                  -----------  -------------  --------------
                      C1       -4.276843e+04  -4.666978e+04
                      C2       -1.236301e+00  -2.615846e-001
                      C3        1.090850e-02   1.373870e-002
                      D1        3.910900e-02   3.884300e-002
                      D2        0.000000e+00   0.000000e+00
                      T1        3.011212e+01   3.015158e+001
                      T2       -5.894647e+01  -3.442071e-004
                      T3        3.484130e-06   4.048350e-006
                      T4        3.687850e-09   2.094500e-009
                      T5        0.000000e+00   0.000000e+00


8.6  Oxygen

Table 8.8: Oxygen calibration coefficients. SBE 43 s/n 0619, calibrated on 
           26th February 2004.

                             Coefficient    Value
                             -----------  ----------
                               Soc         0.31220
                               Boc         0.0000
                               Voffset    -0.4187
                               Tcor        0.0015
                               Pcor        1.350e-04
                               Tau         0


8.7  Fluorometer

Table 8.9: Fluorometer calibration coefficients from laboratory calibrations 
           for s/n 88-2360-108 on 11 November 2002 and s/n 088163on the 13 
           November 2002. 108 D279 stations 1:37, 163 stations 38 to 125.


                     Coefficient                   88-2360-108  088163
      -------------------------------------------  -----------  ------
      V1 (1 ug chlorophyll per litre (of acetone)    2.0767     1.9807
      VB (Volt output - pure water)                  0.3674     0.3983
      Vace (Volt output - pure acetone)              0.2993     0.3078
      Volts for mechanically blanked detector        0.2791     0.3150


8.8  Post Cruise CTD Sensor Calibrations

At the end of D279 all CTD sensors were returned to Sea-Bird for calibration 
and servicing. A number of conductivity sensors and the oxygen sensor were 
broken or failed as noted in the tables below. Most temperature sensors 
performed well and no post cruise adjustments to temperature were performed.




Table 8.10: Post cruise conductivity sensor calibrations.

Cond 
Sensor                        Post 
s/n     Cruise  P/S  Statnum  Cruise Calibration        In Situ Calibration
------  ------  ---  -------  ------------------------  ------------------------------
 2231    277     P   001-012  Calibration satisfactory  
 2571    277     S   001-012  Calibration satisfactory  
 2407    278     P   001-009  End of conductivity cell 
                              broken, conductivity cell 
                              replaced    
 2407    278     P   013-016    
 2407    279     P   001-037    
 2407    279     P   094-125    
 2637    278     S   010-012  Conductivity cell failed, 
                              replaced  
 2637    279     P   038-093    
 2637    279     S   094-108    
 2840    278     S   001-009  Calibration satisfactory  
 2840    278     S   013-016    
 2840    279     S   001-037    
 2840    279     S   109-125    
 2450    278     P   010-012  Sensor cleaned and        Did not produce calibratable 
                              replatinized              data during cruise. Data  had
                                                        large pressure hysteresis that 
                                                        varied from station to station
 2450    279     S   038-093    


Table 8.11:  Post cruise temperature sensor calibrations.

 Temp 
Sensor                        Post Cruise Calibration (drift 
 s/n    Cruise  P/S  Statnum     since last calibration)       Action for Post Cruise Data
------  ------  ---  -------  -------------------------------  ----------------------------------
 2674    277     P   001-012          Drift +1.42m°C           none.  This T sensor had had a 
                                                               large positive drift - usually 
                                                               expect negative. FS current highly 
                                                               variable so T drift not critical 
                                                               here.

 4105    277     S   001-012          Drift -0.48m°C                        none
                              Drift -0.27m°C, 10/11 residuals

 2919    278     P   001-009  <0.06m°C, 1/11 0.13m°C at 15°C                none

 2919    278     P   013-016    

 2919    279     P   001-037    

 2758    278     P   010-012     Drift -0.18m°C, residuals                  none
                                        <0.08m°C  

 2758    279     S   038-093    

 2758    279     P   094-125    

 4116    278     S   001-009     Drift -0.08m°C, residuals                  none
                                        <0.08m°C  

 4116    278     S   013-016    

 4116    279     S   001-037    

 2880    278     S   010-012     Drift -0.34m°C, residuals                  none
                                        <0.08m°C  

 2880    279     S   094-125    


The SBE 43 dissolved oxygen sensor s/n 430619 had a torn oxygen membrane so 
post calibration of the sensor was not possible. Given the problems 
calibrating the oxygen data during the cruise the whole data set must be 
considered as suspect.


8.9  CTD Sensor Calibration Equations

The equations to convert raw sensor frequencies to calibrated data are;

Temperature

  Tcal(ITS-90)°C = 1/{g+h[ln(f/fo)]+i[ln2(f/fo)]+j[ln3(f/fo)]}-273.15
  ln             = the natural log
  f              = the output frequency in Hz
  fo             = 1000, an arbitary scaling for computational efficiency

Conductivity

Conductivity sensors are calibrated over a 0 - 60 mS/cm range using natural 
seawater. The calibration equation is,

  C(S/m) = (g+hf2+if3+jf4)/10(1+dt + ep)
  f is the instrument frequency (KHz)
  t is the temperature in degrees Celsius
  p is the pressure (db)
  d = -9.57 x 10-8 and is the bulk compressibility
  e = 3.25 x 10-6 and is the thermal coefficient of expansion for the 
      borosilicate glass

Pressure

Pressure is calibrated from,
  P = C(1-T2o/T2)(1-D(1-T2o/T2)
where T is pressure period (ms).
C, D, To are given by,
  C = C1 + C2U + C3U2
  D = D1 + D2U
  To = T1 + T2U + T3U2 + T4U3 + T5U4
where U is the temperature (°C).

Fluorimeter

Chlorophyll is calculated from voltage output,

          Chl a = (log10-1(VS)-log10-1(VB))/(log10-1(V1)-log10-1(VA))

where VS is the output voltage, VB is the output voltage in laboratory pure 
water, V1 is the output voltage for a 1ug/l Chlorophyll-a solution and VA is 
the output voltage for pure acetone.


8.10   Post Cruise Calibrations

CTD Deployment Procedure

The CTD section began on the western side of the Florida straight and 
continued eastward to the shoaling continental shelf of Africa. 125 casts 
were made from an original plan of 130. For each station the deployment 
procedure was identical and began with confirmation of being on station from 
the Bridge. On receiving this confirmation the CTD deck unit was switched on 
and data logging initiated on the master and slave computers. Once data 
acquisition was confirmed the winch operator was informed and the 
instrumentation package was deployed over the side and taken to 10 metres. 
The pack was held at 10 metres while sensors were thoroughly wetted and 
readings stabilized, typically 2-3 minutes. At this point the winch operator 
was asked to bring the package to just below the surface and then lower to a 
depth calculated to be approximately 50 metres above the bottom. Visual 
confirmation of height above the bottom was obtained using an acoustic pinger 
on the package in conjunction with the Simrad 500 echo sounder, this was in 
addition to altimeter readings. The package was then taken to approximately 
10 metres above the bottom marking the end of the downcast. At this point 
bottle sample #1 was taken and a 10 second wait initiated if the SBE35 
thermometer was present in order for this instrument to acquire its full 
compliment of data. The upcast was then continued to the next predetermined 
stop determined by the amount of wire out rather than an absolute depth. In 
the early part of the cruise casts were veered and hauled at 60 metres/minute 
which is the normal speed of deployment. Later, on instructions from the 
Principal Scientist, veering and hauling was accomplished at 70 metres/minute 
and, for approximately the last third of the casts, hauling was done at 80 
meters/minute while veering remained at 70.

Data acquisition was ceased once the instruments had been recovered and were 
on deck. SBE35 data was recovered using the SeaTerm package and all data 
files from the cast copied to a USB data key, or otherwise transferred, to a 
separate computer for data processing. CTD operators were not involved in 
data processing.

The early sections across the Florida Straight were beset by problems with 
some of the instruments which were subsequently swapped, or left, out. One 
major issue appeared to arise from an excessive power drain by the 
Fluorometer which caused the Altimeter to malfunction and give readings in 
the order of 6 metres once it made contact with the water. By separating 
these on to different channels readings from the Altimeter became more 
reliable. At another point, also early in the cruise, the slave computer 
malfunctioned and had to be swapped for an old spare. This gave rise to a 
slight increase in modulo error counts, probably as a result of the much 
slower processor speed of the replacement but in general it provided reliable 
service for the remainder of the trip.

Data Logging

The incoming signal from the CTD, via the sea cable, enters the rear of the 
SBE 11plus deck unit. NMEA data from the ships Global Positioning System is 
also fed to the deck unit. These data are distributed to the main PC, and a 
backup PC, via the SBE 11plus deckunits RS232 port. Data is logged on both 
PCs.



9.  CTD DATA PROCESSING AND CALIBRATION
    (Hannah Longworth and Stuart Cunningham)

Raw CTD data files from the logging PC are transferred to another PC on which 
modules from SEASOFT, the SeaBird CTD data processing package, are run 
manually since batch processing failed after the first station. Of the 
available SEASOFT routines, those employed are sequentially detailed below. 
Although the Filter option to smooth high frequency data is recommended by 
SeaBird, we omit this step. Output files are transferred onto the UNIX system 
by ftp and processing continued with PSTAR. 


9.1   Data Conversion (DatCnv)

Converts raw CTD data to calibrated data, creating one file containing the 
down and upcast CTD data and a rosette summary file.

Input Files: D279nnn.dat, D279nnn.BL

The .dat file contains uncalibrated engineering data output from the CTD, 
processed by the deck unit and logged to PC. The .BL file contains one record 
for each bottle fire: bottle number, date, time, scan number start, scan 
number end. When a bottle fire confirmation is received from the rosette the 
bottle confirmation bit is set for 1.5s or 36 scans, and these are the scan 
numbers recorded in the .BL file.

Output Files: D279nnn.cnv, D279nnn.ros

The .cnv file contains 24hz calibrated CTD data, with output variables 
determined by parameters set in the DatCnv specification file DatCnv.psu. 
Calibration data are read from the configuration file, which can be either a 
master file for the cruise or usually from a configuration file created for 
each station: D279nnn.CON. For D279 the output variables are given in 
Table 9.1. The .ros file is created from an option set in the DatCnv.psu file 
(create both bottle and data file). For D279 we specify the scan range offset 
to be 0s and the scan range duration to be 0.001s. This specification means 
only the first scan marked with the bottle confirmation bit recorded in the 
.BL file is recorded in the .ros output file. This can be confirmed by 
inspecting the scan number start in the .BL file and comparing it to the scan 
number in the .ros file. NB the .ros file contains only a single scan of CTD 
data at the time at which the first bottle confirmation bit is set.


Table 9.1: Calibrated CTD data output by SeaBird data conversion module 
           DatCnV.

Number  Parameter                                        Unit
------  -----------------------------------------------  -------------
  1     Pressure, Digiquartz                             db
  2     Temperature                                      ITS-90, deg C
  3     Conductivity                                     mS/cm
  4     Temperature, 2                                   ITS-90, deg C
  5     Conductivity, 2                                  mS/cm
  6     Altimeter                                        M
  7     Oxygen, SBE 43                                   umol/Kg
  8     Temperature Difference, 2 - 1                    ITS-90, deg C
  9     Conductivity Difference, 2 - 1                   mS/cm
 10     Pressure Temperature                             deg C
 11     Fluorescence, Chelsea Aqua 3 Chl Con             ug/l
 12     Beam Attenuation, Chelsea/Seatech/Wetlab CStar   1/m
 13     Beam Transmission, Chelsea/Seatech/Wetlab Cstar  %
 14     Time, Elapsed                                    seconds
 15     Julian Days          
 16     Latitude                                         deg
 17     Longitude                                        deg
 18     Flag          




9.2   Align CTD 

Aligns parameter data in time relative to pressure to reduce spiking or 
hysteresis.

Input and Output File: D279nnn.cnv

Coefficients for temperature and conductivity sensors are set to zero (the 
time response of the former is 0.06s and the required advancement for the 
latter of 1.75 scans is performed by the deck unit). Oxygen is advanced by 
+5s relative to pressure accounting for time delay of the sensor (5s at 0°C). 
The following are added to the data file header by the program: Alignctd_date 
- date and time the program was run; Alignctd_in - input .cnv file; 
Alignctd_adv - alignment times of relevant variables. 


9.3  Wild Edit

Input and Output File: D279nnn.cnv

The mean and standard deviation of each parameter are separately calculated 
for blocks of 500 cycles. Points that lie outside two times the standard 
deviation are temporarily excluded for recalculation of the standard 
deviation. Points outside ten times of the new value are replaced by a bad 
flag. 


9.4  Cell Thermal Mass

Input and Output File: D279nnn.cnv

Removes conductivity cell thermal mass effects with a recursive filter 
permitting salinity accuracy greater than 0.01 in regions of steep gradients. 
In such regions the correction may be of the order 0.005 but is otherwise 
negligible. The thermal anomaly amplitude (alpha) is 0.03 and the 
thermal anomaly time constant (1/beta) is 7.0. 

Cell Thermal Mass adds the following to the header: Celltm_date - date and 
time the program was run; Celltm_in - input .cnv file; Celltm_alpha - value 
of alpha; Celltm_tau - value of 1/beta; Celltm_temp_senso_use_for_cond - the 
temperature sensors used for the primary and secondary conductivity filters.


9.5   Translate (Trans)

Input and Output File: D279nnn.cnv

Creates an ASCII version of the binary .cnv file.


9.6   CTD Processing

Processing of CTD profiles beyond the .cnv files and assimilation of bottle 
sample data are performed by PSTAR routines. Only those that differ to those 
of previous cruises (Bryden, 2003) are described fully here. PSTAR execs 
ctd0, ctd1, ctd2, ctd3, fir0, sam0 and position_D279.exec create files 
ctd279{num}.24hz, ctd279{num}.1hz and ctd279{num}.10s, ctd279{num}.2db and 
ctd279{num}.ctu files, preliminary plots, fir279{num}, sam279{num} and 
{num}.position files respectively (the ctu file is equal to the 1hz file 
between the start of the downcast and the end of the upcast). Positions are 
obtained from the GPS file adnv2791. Instrument_serial_number.exec extracts 
the temperature, conductivity and pressure sensor serial numbers from the 
.cnv file and writes these into the header of the 24hz file. Adddepth.exec 
and Adddepth_D279.exec both write the water column depth at the times of the 
start, bottom and end of the CTD cast into the {num}.position file. The 
former uses the maximum depth from pressure and corresponding altimeter 
height from the 2db file. The latter extracts depths from the 5 minute 
averaged edited bathymetry file (sim279k1.ed5min) when altimeter data are not 
available or appear erroneous. This is the case for stations 1-24, 26, 61-63, 
66, 67 96, 97 and 110 (the altimeter was not working or disconnected for the 
first 24 stations and for some deep stations the maximum depth was out of its 
range). Linear interpolation of depth on time is used if bad data have been 
edited out of the bathymetry file on station. Processing routines involved in 
calibration are described in the relevant sections below. 


9.7  Calibration Introduction

All data processing for this cruise originates at the 24hz file (in contrast 
to the usual 1hz file). Conductivity and oxygen calibrations are applied to 
the 24hz version and worked through by reprocess1.exec that runs ctd1 and 
ctd2 then pastes the updated values into the firing and sample files. The 
final salinity offset however is applied to the 1hz and 10s files (see 
later). In retrospect use of the 24hz files is not ideal, creation of backup 
copies in calibration is slow and costly on disk space. 

Bottle sample data are entered onto a mac as text (tab delimited) files with 
names {parameter}279{num}.txt. The PSTAR exec {parameter}.exec transfers 
sample data onto the UNIX system and writes it into a PSTAR file 
{paramter}279{num}.bot. These values are pasted into the individual station 
sample files, sam279{num}, by pas{parameter}. Oxygen is an exception 
described later. The sam279{num}.calib files are created by 
botcond_D279.exec. Bottle conductivity is calculated from bottle salinity and 
(CTD - bottle) comparisons for conductivity, salinity and oxygen calculated. 
The sam279{num}.calib are appended by samappendcalib.exec to sam.append.calib 
with statistics in sam.append.calib.stat. 


9.8   CTD Conductivity Calibration

CTD conductivities are calibrated by comparing them to bottle conductivities 
derived from salinity samples obtained during the CTD upcast (see below for 
details). The CTD upcast is calibrated and applied to the downcast: the 
downcast and upcast must be free from hysteresis effects for this to be a 
valid procedure. 


9.9   Method

The correction applied to CTD conductivity is a slope correction to account 
for sensor drift (usually to lower values with time). This is equal to the 
station mean ratio of bottle to CTD conductivitiy

                                 K = <Cbot/CCTD>

Cbot is the bottle conductivity obtained from the salinity measured, CCTD the 
upcast CTD conductivity for the 10s around the bottle fire time (see below) 
and < > denotes the station mean. The corrected CTD conductivity (Ccorr) is 
given by 
                                 Ccorr = K*CCTD

Differences between Cbot and CCTD are not solely due to calibration effects 
particularly in the variable upper water column. To minimise the effect of 
the latter, differences between bottle and CTD conductivities are computed

                                Cdiff = Cbot-CCTD

Bottles with Cdiff outside the limits of Table 9.2 are rejected from the 
calibration dataset. For the remaining bottles, the mean (µ) and standard 
deviation (σ) are re-computed and K values outside µ ± 2σ are rejected. The 
station mean K is that of the remaining points. For shallow stations with few 
bottles (2 and 3) bottle selection is by eye. Station groups are identified 
and the value of K applied is, when possible, the mean of a station group or 
determined from a linear fit of K to station number. K values applied are in 
Table 9.3. 


Table 9.2:   Cdiff limits for pre-calibration bottle rejection.

First Station  Last Station  Upper limit of Cdiff  Lower limit of Cdiff 
-------------  ------------  --------------------  --------------------
      1             10             -0.015                 0.015
     12             37             -0.010                 0.010
     38             93             -0.015                 0.010
     94            125             -0.010                 0.010


Table 9.3: CTD conductivity and salinity calibration coefficients applied. 
           For coefficients of Pressure fit A and B see Table 9.4.

                   Pres.                                  Pres.         
    Stn     K      Fit      dsal           Stn     K      Fit      dsal 
    ---  --------  ----   -------          ---  --------  ----   -------
      1  1.000130  None    0.0004           61  0.999892          0.0000
      2  1.000100  None   -0.0001           62  0.999892          0.0002
      3  1.000070  None   -0.0001           63  0.999892          0.0006
      4  1.000030  None    0.0002           64  0.999879          0.0001
      5  1.000030  None    0.0001           65  0.999893          0.0002
      6  1.000030  None    0.0005           66  0.999907         -0.0001
      7  1.000030  None    0.0002           67  0.999889          0.0000
      8  1.000030  None    0.0008           68  0.999894          0.0003
      9  1.000030  None   -0.0007           69  0.999900          0.0004
     10  1.000030  None   -0.0009           70  0.999905         -0.0002
     11    NaN     NaN       NaN            71  0.999911          0.0001
     12  1.000058  None   -0.0003           72  0.999916          0.0000
     13  1.000046  None   -0.0002           73  0.999921          0.0002
     14  1.000033  None    0.0001           74  0.999927         -0.0007
     15  1.000021  None   -0.0002           75  0.999932         -0.0003
     16  1.000008  None    0.0001           76  0.999938         -0.0006
     17  0.999860  None    0.0003           77  0.999923          0.0002
     18  0.999860  None    0.0001           78  0.999923          0.0001
     19  0.999860  None    0.0005           79  0.999923          0.0003
     20  0.999860  None    0.0008           80  0.999923          0.0000
     21  0.999860  None    0.0001           81  0.999923         -0.0002
     22  0.999860  None   -0.0004           82  0.999893          0.0002
     23  0.999860  None    0.0007           83  0.999908          0.0002
     24  0.999860  None    0.0009           84  0.999908          0.0000
     25  0.999860  None   -0.0001           85  0.999932         -0.0001
     26  0.999860  None   -0.0003           86  0.999919          0.0004
     27  0.999860  None   -0.0002           87  0.999906          0.0002
     28    NaN     NaN       NaN            88  0.999893          0.0000
     29  0.999860  None    0.0000           89  0.999913         -0.0001
     30  0.999860  None    0.0001           90  0.999913          0.0001
     31  0.999700  None    0.0000           91  0.999913          0.0001
     32  0.999859  None    0.0001           92  0.999913          0.0003
     33  0.999873  None   -0.0004           93  0.999915          0.0001
     34  0.999889  None   -0.0003           94  0.999977  Fit B  -0.0003
     35  0.999860  None    0.0000           99  0.999964    _     0.0004
     36  0.999831  None    0.0000          100  0.999986         -0.0004
     37  0.999831  None    0.0001          101  0.999985         -0.0007
     38  0.999915  Fit A   0.0003          102  0.999985         -0.0001
     39  0.999915    _     0.0002          103  0.999985          0.0004
     40  0.999915         -0.0002          104  0.999985         -0.0002
     41  0.999915          0.0003          105  0.999985          0.0001
     42  0.999885          0.0000          106  0.999985         -0.0004
     43  0.999927          0.0003          107  0.999985          0.0001
     44  0.999915          0.0000          108  0.999985          0.0001
     45  0.999904          0.0001          109  0.999985         -0.0004
     46  0.999893          0.0006          110  0.999985         -0.0002
     47  0.999882         -0.0001          111  0.999985          0.0004

     48  0.999871          0.0002          112  0.999985         -0.0001
     49  0.999892         -0.0003          113  1.000015         -0.0002
     50  0.999892         -0.0001          114  0.999991          0.0000
     51  0.999892         -0.0003          115  0.999991          0.0001
     52  0.999892         -0.0004          116  0.999991         -0.0004
     53  0.999892          0.0002          117  1.000016         -0.0004
     54  0.999892         -0.0001          118  1.000016         -0.0002
     55  0.999892         -0.0001          119  1.000050          0.0000
     56  0.999892         -0.0001          120  0.999950         -0.0005
     57  0.999892          0.0000          121  0.999992  None    0.0005
     58  0.999892          0.0003          122  0.999992  None   -0.0003
     59  0.999892          0.0000          123  0.999992  None    0.0000
     60  0.999892         -0.0002          124  0.999992  None    0.0005
                                           125  0.999992  None   -0.0002


After the K value calibration station groups 38-93 and 94-120 still showed 
pressure dependence in Cdiff (note the sensor change at station 94). Correction 
by a pressure dependent offset added to conductivity of two forms were 
investigated: a linear temperature and pressure fit (docnd_1) and a quadratic 
pressure fit (dcond_2)

                           dcond_1 = -(a + b*P + c*T)
                            dcond_2 = d*P2 + e*P + f

P and T are the upcast CTD pressure and temperature at the bottle stop. 
Coefficients are the mean fit to a subset of Cdiff after first rejection of 
bottles with |Cdiff| > 0.01 and then rejection of those outside the recomputed 
µ ± 1.5σ. For stations 38-93 neither dcond_1, dcond_2 or a combination of both 
corrected the pressure dependence satisfactorily. The secondary temperature 
and conductivity sensors showed a reduced pressure effect and higher 
stability were preferred. The swap is made in the 24hz file and the primary 
(secondary) values renamed to secondary (primary). A pressure fit is still 
required, with best results achieved by dcond_1 in the upper water column and 
dcond_2 below, as is also the case for stations 94-120. The transition 
between corrections is at the pressure intersection between the two, pressure 
= Div in Table 9.4. 


Table 9.4:  Coefficients of dcond_1 and dcond_2 applied.

          A        b           c       Div (db)       e            f           g
-----  ------  ---------  -----------  --------  -----------  -----------  ----------
Fit A  -0.968  1.51x10-4  1.1562x10-1    2250    1.213x10-10  -9.358x10-7  1.731x10-3
Fit B  -0.482  2.97x10-4  -4.661x10-2    2050    1.399x10-10  -1.284x10-6  2.107x10-3

Note. Fit A is applied to stations 38-93, Fit B to 94-120 (see Table 9.3).


Finally a station by station salinity offset is added to CTD salinity

                              dsal = <Sbot - SCTD>
 
Notation follows that used above with S denoting salinity. The station mean 
dsal is computed after rejection of bottles with |Sbot - SCTD| > 0.002 (0.003 
for stations 12, 51 and 107 due to increased scatter), and subsequent 
rejection of those outside the recomputed µ ± 2σ. The statistics relating to 
this fit are in Table 9.5, with the final value applied in Table 9.3. The 
dsal correction is not applied to station 119 due to the large scatter in 
Cdiff for this station, the source of which has not been determined.


Table 9.5: Bottle-CTD salinity residual mean (µ) and standard deviation (σ). 
           N_tot is the total number of bottle samples and N those used to 
           compute the mean. % is the percent rejected.

    µ        σ      N   N_tot   %          Limits                  Notes
--------  ------  ----  -----  ----  ------------------  --------------------------
 0.0007   0.0003  2139  2626   18.5     ±0.002, ±2σ      Before application of dsal
 0.0001   0.0011  2338  2626   11.0      ±0.01, ±2σ      Final data set
-0.00006  0.0005  1274  1305    2.4  P > 1500db, ±0.002  Final data set


9.10 Calibration Application

Three calibration execs are used; ctdcondcal_D279.exec, 
ctdcondcal_D279.exec_press and reprocess.exec_final. The first applies the K 
value correction to the primary conductivity in the 24hz file and writes the 
K value into the header. The second applies the pressure dependant fit 
detailed above, also to the 24hz file. The third applies dsal to salinity in 
the 10s and 1hz files, computes conductivity from the corrected salinity and 
works these through to the ctu, 2db, fir and sam files.


Figure 9.1a: Bottle - CTD salinity versus i. station number, ii. pressure and 
             iii. bottle salinity. Selection limits are |Sbot - SCTD| < 0.01.

Figure 9.1b: Bottle - CTD salinity versus i. station number, ii. pressure and 
             iii. bottle salinity for pressure > 1500db. Selection limits are 
             |Sbot - SCTD| < 0.002 (refer to Table 9.5 for statistics of 
             bottles rejected).


9.11  D277 and D278

CTD data were calibrated in the manner described above. Residuals of bottle-
CTD conductivities are given in Table 9.7.  Station summaries are shown in 
Tables 9.8, 9.9 and 9.10.


Table 9.6: Conductivity slope and offset corrections.

                     Stn    D277     D277      D278      D277 
                     Nbr    Slope    Offset    Slope     Offset
                     ---  ---------  -------  ---------  ------
                      1   0.9999982   0.0     1.000012    0.0
                      2   0.9999982   0.0     1.000012    0.0
                      3   0.9999982   0.0     1.000012    0.0
                      4   0.9999982   0.0     1.000012    0.0
                      5   0.9999982   0.0     1.000012    0.0
                      6   0.9999982  -0.0023  1.000012    0.0
                      7   0.9999982   0.001   1.000012    0.0
                      8   0.9999982   0.001   1.000012    0.0
                      9   0.9999982   0.001   1.000012    0.0
                     10   0.9999982   0.001   0.999812    0.0
                     11   0.9999982   0.001   0.9998ty12  0.0
                     12   0.9999982   0.001   0.999812    0.0
                     13                       1.000012    0.0
                     14                       1.000012    0.0
                     15                       1.000012    0.0
                     16                       1.000012    0.0


Table 9.7: Bottle-CTD conductivity residuals.

                                       277        278
                         ---------  ---------  ---------
                         <btc-uc>   -0.00002   -0.00002
                         sd          0.0010     0.0006
                         n bottles   40/43      84/93
                         <btc/uc>    0.999995   0.999996
                         Sd          0.000031   0.000023
                         n bottles   39/43      86/93



Table 9.8: D277 CTD Station Summary. Florida Current section stations 5 to 12 
           occupied east to west.


                                                            depth   cor    cordepth-
sta      Date             latitude   longitude  pmin  pmax  _pmax  depth  depth_pmax
num  yyyy mm  dd  hhmmss  deg  min   deg   min  dbar  dbar    m      m         m
---  ---- --  --  ------  --- -----  ---  ----- ----  ----  -----  -----  -----------
001  2004  3   8  151558  24  28.82  -55  55.56   1   6341  6209   6131.6    -77.3
002  2004  3   8  205158  24  26.64  -56  02.03   1   5119  5026   6451.7   1425.5
003  2004  3   9  012353  24  25.44  -56  01.38   1   6559  6419   6454.2     35
004  2004  3  12  155834  26  31.38  -72  38.26   1   5065  4973   5186.5    213.5
005  2004  3  14  203608  27  00.26  -79  12.23   1    477   473    485.7     12.5
006  2004  3  14  232834  27  00.16  -79  17.14   1    611   606    617.5     11.6
007  2004  3  15  010703  27  00.55  -79  23.30   1    689   683    681.9     -1.2
008  2004  3  15  031006  27  00.08  -79  29.55   1    759   752    764       11.6
009  2004  3  15  052013  27  00.84  -79  37.44   1    623   618    631.9     14.1
010  2004  3  15  074250  27  00.66  -79  41.19   1    525   521    535.1     14.4
011  2004  3  15  091803  27  00.57  -79  46.72   1    387   384    400       16
012  2004  3  15  105048  26  59.97  -79  51.89   1    263   261    275       14


Table 9.9: D278 CTD Station Summary: Coherent CTD section east to west can be 
           made from stations: 1,2,3,4,15,14,13,12,11,10,9,8,7,6. Stations 4 
           and 16 are in the same position but station 4 makes a more 
           synoptic section with the inshore boundary stations 1,2,3. Station 
           5 is only to mid-depth.

                                                            depth   cor    cordepth-
sta      Date             latitude   longitude  pmin  pmax  _pmax  depth  depth_pmax
num  yyyy mm  dd  hhmmss  deg  min   deg   min  dbar  dbar    m      m         m
---  ---- --  --  ------  --- -----  ---  ----- ----  ----  -----  -----  -----------
001  2004  3  22  111601  26  30.37  -71  58.12  1  5395  5293.1  5297.9      4.8
002  2004  3  22  213729  26  30.11  -73  21.07  1  5121  5027.4  5033.6      6.2
003  2004  3  23  073346  26  29.67  -74  42.24  1  4513  4436.6  4464.9     28.3
004  2004  3  24  042000  26  30.01  -76  03.72  1  4863  4776.9  4796       19.1
005  2004  3  25  194433  26  31.29  -76  39.34  9  1005   995.8  4496.2   3500.4
006  2004  3  27  042107  26  31.90  -76  53.67  3    39    38.7    38.8      0.1
007  2004  3  27  063515  26  31.47  -76  49.00  9  1377  1363.2  1409.5     46.3
008  2004  3  27  102718  26  30.88  -76  47.07  7  2631  2597.4  2679       81.6
009  2004  3  27  152620  26  30.99  -76  45.40  7  3693  3637.1  3654.2     17.1
010  2004  3  28  042408  26  30.24  -76  39.96  7  4555  4477.4  4487.6     10.2
011  2004  3  28  091344  26  30.65  -76  38.31  7  4687  4605.8  4576.6    -29.2

012  2004  3  28  134609  26  30.44  -76  32.06  7  4881  4794.3  4846.2     51.9
013  2004  3  28  210426  26  30.40  -76  26.16  7  4895  4807.9  4848.5     40.6
014  2004  3  29  033638  26  29.62  -76  18.64  7  4907  4819.6  4831.7     12.1
015  2004  3  29  092333  26  30.19  -76  13.04  7  4895  4808    4818.7     10.7
016  2004  3  29  145059  26  29.64  -76  05.45  7  4881  4794.4  -999       -999


Table 9.10: D279 CTD Station Summary


                                                            depth    cor    cordepth-
sta      Date             latitude   longitude  pmin  pmax  _pmax   depth  depth_pmax   alt
num  yyyy mm  dd  hhmmss  deg  min   deg   min  dbar  dbar    m       m         m        m
---  ---- --  --  ------  --- -----  ---  ----- ----  ----  ------  -------  ---------  ---
002  2004 04  05  063352  027  0.86 -079  56.19  1.0   127   126.1   134.2      8.1     7.8
003  2004 04  05  084038  027  1.75 -079  51.75  1.0   255   253.1   269.7     16.6     8.3
004  2004 04  05  103021  027  1.04 -079  46.57  1.0   383   380.0   393.8     13.8     6.6
005  2004 04  05  130901  027  0.89 -079  40.95  3.0   525   520.7   532.2     11.5     6.6
006  2004 04  05  160717  027  0.94 -079  37.05  1.0   633   627.7   641.6     13.9     6.6
007  2004 04  05  185640  027  0.93 -079  30.21  1.0   763   756.4   755.1     -1.3     6.0
008  2004 04  05  213415  027  0.89 -079  23.28  1.0   677   671.2   665.6     -5.6     0.0
009  2004 04  05  234444  027  0.04 -079  16.84  1.0   605   600.0   606.6      6.6     0.0
010  2004 04  06  015718  026 59.92 -079  11.66  1.0   457   453.3   461.2      7.9     0.0
011  2004 04  06  175523  026 30.42 -076  55.64  1.0   343   340.4   305.5    -34.9     0.0
012  2004 04  07  210433  026 30.48 -076  55.64  1.0   263   261.0   248.7    -12.3     0.0
013  2004 04  07  232244  026 31.63 -076  48.38  1.0  1727  1708.4           1708.4     0.0
014  2004 04  08  033038  026 30.76 -076  46.91  3.0  2359  2330.3           2330.3     0.0
015  2004 04  08  081613  026 30.91 -076  44.73  1.0  3875  3814.8  3813.0     -1.8     0.0
016  2004 04  08  141534  026 30.52 -076  41.29  3.0  4501  4424.9  4357.8    -67.1     0.0
017  2004 04  08  204428  026 30.45 -076  38.25  1.0  4687  4605.8  4594.5    -11.3     0.0
018  2004 04  09  081118  026 29.95 -076  31.67  1.0  4907  4819.6  4835.7     16.1     6.2
019  2004 04  09  150154  026 30.03 -076  25.75  3.0  4913  4825.4  4833.4      8.0     0.0

020  2004 04  09  211812  026 29.55 -076  18.11  1.0  4919  4831.3  4829.0     -2.3     0.0
021  2004 04  10  024826  026 29.23 -076  12.59  3.0  4883  4796.3  4807.4     11.1     0.0
022  2004 04  10  085617  026 29.93 -076   5.74  1.0  4881  4794.4  4797.9      3.5     0.0
023  2004 04  10  140639  026 30.15 -075  54.62  3.0  4819  4734.1  4737.0      2.9     0.0
024  2004 04  10  191130  026 29.50 -075  42.22  1.0  4763  4679.7  4682.9      3.2     0.0
025  2004 04  11  003243  026 28.92 -075  30.87  1.0  4757  4673.9  4685.1     11.2     5.9
026  2004 04  11  055337  026 29.49 -075  18.46  1.0  4713  4631.1  4630.4     -0.7     0.0
027  2004 04  11  112156  026 30.93 -075   4.47  1.0  4675  4594.1  4603.8      9.7     6.4
028  2004 04  11  161900  026 30.63 -074  47.85  1.0  2829  2791.6  2846.6     55.0    14.6
029  2004 04  11  184935  026 30.57 -074  47.34  1.0  4601  4522.2  4532.5     10.3    10.3
030  2004 04  12  005450  026 31.20 -074  29.80  1.0  4551  4473.5  4487.3     13.8     7.7
031  2004 04  12  055538  026 30.58 -074  14.18  1.0  4593  4514.4  4528.7     14.3     8.8
032  2004 04  12  111717  026 30.07 -073  55.79  1.0  4737  4654.4  4665.6     11.2     7.2
033  2004 04  12  165524  026 30.63 -073  33.82  1.0  4953  4864.3  4872.4      8.1     6.0
034  2004 04  12  224252  026 29.97 -073  11.74  1.0  5131  5037.1  5048.1     11.0     6.3
035  2004 04  13  043711  026 30.13 -072  50.82  1.0  5223  5126.3  5136.2      9.9     6.0
036  2004 04  13  113152  026 29.98 -072  29.16  1.0  5291  5192.3  5204.2     11.9     5.9
037  2004 04  13  182505  026 29.29 -072   0.39  1.0  5381  5279.5  5287.2      7.7     6.5
038  2004 04  14  002334  026 28.98 -071  45.11  1.0  5465  5360.9  5373.3     12.4    10.5

039  2004 04  14  071010  026 30.48 -071  20.60  1.0  5579  5471.4  5482.9     11.5     6.3
040  2004 04  14  131758  026 29.40 -070  59.20  1.0  5583  5475.2  5487.7     12.5     6.2
041  2004 04  14  200529  026  8.03 -070  36.07  1.0  5597  5488.9  5500.4     11.5     6.1
042  2004 04  15  024035  025 45.91 -070  14.29  1.0  5607  5498.8  5510.5     11.7     6.7
043  2004 04  15  092831  025 22.82 -069  52.64  1.0  5615  5506.7  5516.7     10.0     6.5
044  2004 04  15  163108  025  0.05 -069  30.37  1.0  5705  5593.9  5604.8     10.9     6.6
045  2004 04  16  001844  024 29.65 -069   8.80  1.0  5741  5629.0  5638.4      9.4     6.3
046  2004 04  16  082202  024 30.53 -068  24.80  1.0  5815  5700.6  5710.3      9.7     8.2
047  2004 04  16  162927  024 30.65 -067  40.24  1.0  5819  5704.5  5713.1      8.6     5.5
048  2004 04  17  000841  024 29.24 -066  55.39  1.0  5839  5723.8  5732.9      9.1     6.6
049  2004 04  17  073836  024 30.17 -066  11.54  1.0  5367  5266.7  5276.4      9.7     8.8
050  2004 04  17  151325  024 29.75 -065  27.81  1.0  5663  5553.5  5563.4      9.9     9.9
051  2004 04  17  230648  024 30.55 -064  39.57  1.0  5803  5689.0  5696.5      7.5     7.0
052  2004 04  18  064953  024 29.87 -064   0.08  1.0  5881  5764.4  5774.3      9.9     8.0
053  2004 04  18  150313  024 30.30 -063  16.08  1.0  5901  5783.8  5791.8      8.0     6.4
054  2004 04  18  225903  024 30.24 -062  31.68  1.0  5995  5874.7  5890.3     15.6     7.1
055  2004 04  19  064743  024 30.45 -061  47.90  1.0  5793  5679.3  5692.2     12.9     6.8
056  2004 04  19  143709  024 30.07 -061   3.78  1.0  5963  5843.7  5850.1      6.4     6.2
057  2004 04  19  223811  024 30.71 -060  19.39  3.0  5955  5836.0  5859.9     23.9     8.1

058  2004 04  20  064117  024 30.92 -059  35.51  1.0  5903  5785.7  5796.7     11.0     7.4
059  2004 04  20  145036  024 29.89 -058  51.47  1.0  5997  5876.6  5914.9     38.3     6.5
060  2004 04  20  222259  024 29.97 -058   7.95  1.0  5927  5808.9  5822.4     13.5     8.2
061  2004 04  21  060806  024 30.13 -057  23.33  1.0  5989  5868.9  6274.7    405.8     6.0
062  2004 04  21  140223  024 29.71 -056  40.03  1.0  6003  5882.4  5985.2    102.8    12.6
063  2004 04  21  214934  024 31.02 -055  56.12  1.0  5959  5839.9  6462.4    622.5     6.6
064  2004 04  22  055315  024 30.27 -055  12.75  1.0  5993  5872.7  5884.5     11.8    11.8
065  2004 04  22  133440  024 29.98 -054  28.42  1.0  5297  5198.9  5209.4     10.5     6.1
066  2004 04  22  212402  024 29.66 -053  44.17  1.0  5999  5878.5  5965.8     87.3    11.3
067  2004 04  23  042216  024 29.86 -053  10.68  1.0  5437  5334.6  5433.5     98.9    10.1
068  2004 04  23  111544  024 30.27 -052  38.24  1.0  5367  5266.7  5278.8     12.1     6.8
069  2004 04  23  172610  024 29.96 -052   9.68  1.0  5005  4915.5  4922.6      7.1     5.5
070  2004 04  24  003548  024 29.99 -051  32.27  1.0  5389  5288.1  5300.3     12.2     7.7
071  2004 04  24  072418  024 30.46 -050  59.82  1.0  5525  5419.8  5429.2      9.4     8.9
072  2004 04  24  141849  024 29.97 -050  26.50  1.0  4793  4709.5  4717.1      7.6     7.6
073  2004 04  24  203450  024 30.61 -049  52.51  1.0  4643  4563.7  4579.9     16.2     9.8
074  2004 04  25  031400  024 30.43 -049  20.04  1.0  5315  5216.3  5228.9     12.6    10.8
075  2004 04  25  095755  024 29.84 -048  46.48  1.0  4487  4411.9  4426.2     14.3    14.3
076  2004 04  25  171051  024 30.33 -047  57.76  1.0  4013  3950.0  3958.5      8.5     8.1

077  2004 04  26  002410  024 29.93 -047   7.50  1.0  3539  3487.2  3498.8     11.6    11.6
078  2004 04  26  060434  024 29.75 -046  34.48  1.0  3331  3283.8  3295.9     12.1     6.9
079  2004 04  26  111506  024 29.73 -046   2.14  1.0  2795  2758.7  2764.1      5.4     5.4
080  2004 04  26  163918  024 30.29 -045  29.42  1.0  3467  3416.8  3426.6      9.8     5.8
081  2004 04  26  222743  024 29.15 -044  56.75  1.0  3653  3598.6  3605.2      6.6     6.6
082  2004 04  27  042956  024 30.12 -044  23.74  1.0  3933  3872.0  3884.0     12.0     6.8
083  2004 04  27  102807  024 30.01 -043  50.63  1.0  3831  3772.4  3781.8      9.4     9.4
084  2004 04  27  172542  024 30.58 -043   0.43  1.0  4171  4104.1  4111.8      7.7     7.7
085  2004 04  28  005257  024 29.94 -042  11.05  1.0  4031  3967.6  3980.2     12.6     7.6
086  2004 04  28  072045  024 30.52 -041  38.39  1.0  4687  4606.5  4618.8     12.3    10.0
087  2004 04  28  134951  024 30.19 -041   5.52  1.0  5215  5119.3  5129.1      9.8     9.8
088  2004 04  28  212726  024 30.71 -040  16.89  1.0  4931  4843.6  4853.9     10.3     8.8
089  2004 04  29  063628  024 29.87 -039  14.70  1.0  5257  5160.1  5172.3     12.2    12.2
090  2004 04  29  134617  024 29.94 -038  31.41  1.0  4699  4618.1  4626.8      8.7     8.7
091  2004 04  29  212907  024 29.95 -037  41.71  1.0  5621  5512.8  5531.9     19.1     6.9
092  2004 04  30  053129  024 29.36 -036  52.80  1.0  5385  5284.2  5296.1     11.9     6.0
093  2004 04  30  130329  024 29.56 -036   2.75  1.0  5837  5721.9  5730.9      9.0     9.0
094  2004 04  30  204555  024 30.27 -035  13.72  1.0  5131  5037.8  5047.1      9.3     6.1
095  2004 05  01  042410  024 29.75 -034  23.35  1.0  5123  5030.0  5045.7     15.7     6.2

096  2004 05  01  115048  024 29.95 -033  34.39  1.0  5993  5872.7  6213.5    340.8     9.5
097  2004 05  01  200457  024 30.58 -032  39.43  1.0  5991  5870.8  6263.0    392.2     7.8
098  2004 05  02  043300  024 29.97 -031  43.85  1.0  5757  5644.5  5652.0      7.5     7.5
099  2004 05  02  125009  024 29.71 -030  48.76  1.0  5819  5704.5  5720.2     15.7     8.9
100  2004 05  02  210608  024 30.09 -029  53.41  1.0  5829  5714.1  5722.3      8.2     8.2
101  2004 05  03  052018  024 30.17 -028  59.25  1.0  5779  5665.8  5677.3     11.5    11.5
102  2004 05  03  133005  024 30.08 -028   4.11  1.0  5699  5588.3  5598.4     10.1    10.1
103  2004 05  03  213847  024 30.71 -027   8.91  1.0  5621  5512.8  5523.9     11.1    11.1
104  2004 05  04  054953  024 29.94 -026  13.87  1.0  5481  5377.2  5390.1     12.9    10.9
105  2004 05  04  133241  024 30.07 -025  19.06  1.0  5379  5278.4  5285.3      6.9     6.9
106  2004 05  04  214116  024 29.72 -024  24.24  1.0  5235  5138.7  5150.9     12.2     8.2
107  2004 05  05  054902  024 30.81 -023  29.68  1.0  5095  5002.9  5015.3     12.4    12.4
108  2004 05  05  125135  024 44.29 -022  49.34  1.0  4977  4888.2  4895.1      6.9     7.0
109  2004 05  05  195445  024 59.10 -022   8.91  1.0  4843  4758.0  4768.0     10.0     6.1
110  2004 05  06  022701  025 13.30 -021  28.66  1.0  4601  4522.6  4576.7     54.1     7.5
111  2004 05  06  094020  025 27.01 -020  48.26  1.0  4497  4421.3  4434.0     12.7     7.4
112  2004 05  06  172535  025 38.99 -020  14.55  1.0  4259  4189.5  4199.4      9.9     6.4
113  2004 05  07  083840  025 55.22 -019  29.17  1.0  3833  3774.0  3786.8     12.8     5.9
114  2004 05  07  143050  026  8.01 -018  54.59  1.0  3489  3437.6  3445.8      8.2     5.9

115  2004 05  07  205726  026 23.13 -018   9.65  1.0  3665  3609.8  3621.7     11.9     6.1
116  2004 05  08  030508  026 35.79 -017  28.14  1.0  3693  3637.1  3648.4     11.3    11.3
117  2004 05  08  092313  026 48.87 -016  47.08  1.0  3667  3611.7  3621.7     10.0     6.3
118  2004 05  08  162727  027  2.59 -016   7.32  1.0  3523  3470.9  3483.7     12.8    10.8
119  2004 05  08  214035  027 14.01 -015  35.53  1.0  3175  3130.4  3141.7     11.3     7.4
120  2004 05  09  035906  027 26.00 -014  51.62  1.0  2615  2581.5  2592.1     10.6    10.6
121  2004 05  09  090906  027 37.24 -014  13.72  1.0  2039  2015.4  2026.1     10.7    10.7
122  2004 05  09  130459  027 49.75 -013  49.05  1.0  1557  1540.6  1548.1      7.5     2.2
123  2004 05  09  154237  027 51.14 -013  33.06  1.0  1091  1080.7  1090.3      9.6     9.6
124  2004 05  09  173214  027 52.80 -013  25.19  105   603   597.9   604.7      6.8     6.8
125  2004 05  09  184757  027 54.94 -013  22.44  1.0   347   344.3   355.0     10.7    10.8



10. SBE35 DEEP OCEAN STANDARDS THERMOMETER

The SBE35 is a highly accurate and stable laboratory standard deep ocean 
thermometer that can be used in fixed point calibration cells and at ocean 
depths up to 6800m and covers a temperature range from -5 to +35°C. It is 
unaffected by shocks and vibrations encountered in shipboard environments 
(Sea-Bird, 2004).


10.1 Measurement Method

An ultra stable aged thermistor with a drift rate of less than 0.001°C/year 
and reference resistances are excited by an AC current, and the outputs from 
these converted to sensor output in raw counts (n).

           Sensor Output (raw counts, n) = 1048576*(NT-NZ)/(NR-NZ)

Where NR is reference resistor output, NZ is zero ohms output, and NT is 
thermistor output. The measurement cycle takes 1.1sx8=8.8s. In a thermally 
quiet environment, temperature noise standard deviation is, 
0.000029xsqrt(8/ncycles)=0.29°mC.


10.2 Linearisation and Calibration

Temperature is calculated from the sensor output raw counts by,

            T90=(1.0/a0+a1ln(n)+a2ln2(n)+a3ln3(n)+a4ln4(n))-273.15

Temperature residuals are better than ±50_K. Coefficients a0 to a4 are 
determined by Sea-Bird in a low-gradient temperature bath and against ITS-90 
certified standard platinum resistance thermometers maintained at Sea-Bird's 
temperature metrology laboratory.

Finally the sensor measurements are certified in a triple water point cell at 
0.0100°C and a gallium cell at 29.7646°C and slow time drifts corrected using 
slope and offset adjustments as required,

                     T90=slopext90+offset [degC, ITS-90]


10.3   Specification

Table 10.1:  SBE 35 specification.

             Measurement Range    -5 to +35°C
             Initial Accuracy      0.001°C
             Typical Stability     0.001°C/year
             Resolution            0.000025°C
             Sensor Calibration   -1.5 to +32.5°C
             Data Storage          upto 170 samples
             Real-Time Clock       Watch-crystal type
             External Power        9-16VDC
             Current
             On Power (~1 minute)  140-160mA
             Operating             60-70mA
             Housing Materials     Aluminium, rated at 6800m
             Weight                0.5kg in water, 0.9kg in air


10.4  Instrument Calibrations

Table 10.2:  SBE35 Instrument calibration coefficients.

         Instrument s/n           0037                 0048
        Calibration Date        14/12/01             28/1/03
        ----------------  -------------------  -------------------
               A0          3.39029780x10(^-3)   4.21014933x10(^-3)
               A1         -8.90362832x10(^-4)  -1.12827756x10(^-3)
               A2          1.48133804x10(^-4)   1.74012910x10(^-4)
               a3         -8.46647755x10(^-6)  -9.73030909x10(^-6)
               a4          1.85819563x10(^-7)   2.09032576x10(^-7)


10.5  Temperature Measurement and Data Output Format for the SBE35

During D279 the SBE35 was set to average 8 (ncycles) temperature measurements 
at each bottle fire. Measurements occur when the SBE35 receives a valid 
bottle fire confirmation sequence (p24). At the end of each CTD station data 
are uploaded from the SBE35's EEPROM via a software interface and saved as an 
asc file in the following format:


Table 10.3:  SBE35 data output format.

Column                             Description
------  ---------------------------------------------------------------------
  1                               Sample number
  2     Date (DD MMM YYYY -day, month year). The month is a 3-character 
              alphabetic abbreviation; e.g., jan, feb, mar, etc).
  3                 Time (HH:MM:SS - hour, minute, second)
  4     Bn=bottle position number (bottle position number is 0 if sample was 
                              taken in response to TS)
  5     Diff=(maximum - minimum) raw thermistor reading during a measurement 
       (provides a measure of the amount of variation during the measurement)
  6     Val=average raw thermistor reading,corrected for zero and full scale 
                                reference readings
  7          T90=average corrected raw thermistor reading, converted to 
                            engineering units (°C[ITS-90])

NB: SBE35 time is stored in the real-time clock with a back-up lithium 
    battery. Time is kept when external power is removed. This time is not 
    from the same source as time recorded within the CTD raw data files.

    For comparison to the CTD 10s file the following time line was adopted 
    during D279.

    Time (s) ->
    1s CTD stop                 10s Bottle fire                    20s CTD up
                5s                            15s Average CTD data
                     10s         SBE35 record       18.8s


Therefore, the CTD 10s average file and SBE35 records do not correspond in 
time but overlap only for the last 5s of the 10s average CTD data. It is 
important that the CTD is not hauled in sooner than 10s after the bottle 
fire.



10.6   Gallium Cell (A Thermometric Fixed Point)

Temperature scales are defined be a series of fixed points along the scale. 
These fixed points are defined by the temperature at which pure materials 
have phase equilibrium between two or three states (solid, liquid, gas). The 
triple point of pure water has the assigned value of 0.01°C on the ITS 
(273.16K). Pure gallium has a solid-liquid equilibrum point temperature of 
29.7646±0.00026°C (ITS-90) and which within the range of normal ocean 
temperatures, and can be used as a reference standard for deep ocean 
thermometers. Isotech have produced a rugged, portable gallium cell that can 
be used aboard ship for periodic calibrations of the SBE35 deep ocean 
standards thermometer, and the cell is accompanied by a UK Accreditation 
Service certificate of traceability to the ITS-90 (Tavener, 2001).

For temperature measurements obtained from a CTD package the standard 
deviation of temperatures from pairs of deep ocean platinum resistance 
thermometers are normally limited by the size of the oceanic vertical 
temperature gradient, and thus accurate comparisons are limited to ocean 
depths below the permanent thermocline (deeper than 2000m say), where 98% of 
the ocean has temperatures colder than 4°C. Hence, precise temperature 
comparisons of CTD temperature and deep ocean standard thermometers are at 
temperatures typically 26° to 30°C colder than the transfer standard of the 
gallium triple point cell.

The gallium in the cell initially begins in the liquid phase, is first 
solidified and then the melting condition is established by holding the cell 
at a temperature just above the gallium melt temperature. The solid-liquid 
equilibrium temperature is unaffected by the temperature at which the cell is 
exposed but the duration of the constant temperature melt plateau is. 
Measurements of temperature are made by the SBE35 throughout: firstly the 
temperature rises as the gallium approaches its melt temperature; secondly 
the temperature remains constant until all the gallium has melted and; 
finally the end of the melt plateau corresponds to a rise in temperature. The 
total cycle time with the cell starting at 20°C is typically 32mins to reach 
the melt plateau then 16 to 20 hours on the plateau and a final 4 hours to 
refreeze the gallium.

The gallium melt point cell (s/n Ga369) was certified as a temperature 
reference point (certificate number 04-02-14, issued on the 13th February 2004 
by Isothermal Technology, Ltd.). The total uncertainty for Ga369 with respect 
to ITS-90 is ±0.26mK.

In the upper water column, differences between SBE35 and CTD temperatures may 
be attributed not only to sensor effects but also to spatial variability in 
the temperature field. 

  * Noting this, the mean µ± 2σ of the residuals after application of limit 1 
    is -0.001±0.006 ºC. With the exclusion of Group D (-0.003±0.012 ºC) this 
    is reduced to -0.0007±0.005 (Table 10.6). 

Both primary and secondary CTD temperature sensors appear to be biased 
towards warmer readings relative to the SBE35. In the deep water (> 2000 dbar 
and limits 2) the mean bias is -0.0006ºC, and is -0.0011ºC over the full 
water column (limits 1). 

In the deep water (pressures greater than 2000dbar) aspects of sensor 
performance may be deduced from the residuals

  * Figure 10.2 (ii) shows residuals up to -1.6x10(^-3) ºC at 6000dbar 
    between both the primary and secondary CTD sensors and SBE35 for stations 
    39-89. This is not apparent in Figure 10.2 (iii) when the same CTD 
    sensors are used but with SBE 0048, thus suggesting the large residuals 
    of the former to be associated with a pressure effect in SBE35 0037.

  * Agreement between CTD temperature sensors 2758 and 2880 and SBE35 00048 
    is good, µ± 2σ of the residuals are 0_0.0006ºC (Groups C and F, Table 
    10.6).

  * Higher variance in residuals of CTD temperature sensor 4116 (Group D), 
    especially noticeable in the deep water with σ = 7.1x10(^-4) ºC (while 
    that for other sensors ranges between 3.0 1x10(^-4) and 3.9x10(^-4) ºC), 
    but not in the 2919 (the corresponding primary) suggests a sensor problem 
    in 4116.

Are primary CTD temperatures more accurate than those from the secondary 
sensor?

Measuring performance of the CTD temperature sensors relative to the SBE35, 
at this stage of analysis it is not conclusive that the CTD primary yields a 
more accurate and consistent temperature reading than the secondary sensor. 
Variance of the secondary sensor residuals are approximately double those of 
the primary over the full water column for Groups A&D and C&F, and in deep 
water are on average 0.9x10(^-4) ºC lower for the primary compared to the 
secondary, although excluding sensor 4416 (for reasons noted above) the 
difference decreases to 0.2x10(^-4) ºC, supporting the assumption of better 
performance of the CTD primary relative to the secondary due to sensor 
positions. The bias between CTD and SBE35 temperature however may be larger 
in the primary sensor (as seen for Groups A&D and B&E in the deep water and 
B&E over full depth), contradicting the premise of improved accuracy of the 
CTD primary sensor relative to the secondary.  

Table 10.4: Station groupings and sensor serial numbers for Table 10.5 and 
            Figures 10.1 and 10.2. Primary and Secondary refer to the 
            position of the CTD temperature sensor. For stations 38-93 this 
            is the reverse of Table 10.5 in CTD operations section since in 
            analysis of these stations the primary and secondary were swapped 
            in name. This convention is not followed here since we prefer to 
            compare sensors at the same position.

                               SBE35     CTD temperature  Primary /
          Group   Stations   serial No.     serial No.    Secondary
          -----  ----------  ----------  ---------------  ---------
            A    12-37         0048            2919        Primary
            B    39-89         0037            2758        Primary
            C    38, 90-125    0048            2758        Primary
            D    12-37         0048            4116       Secondary
            E    39-89         0037            2880       Secondary
            F    38, 90-125    0048            2880       Secondary


Table 10.5: SBE35 - CTD temperature residuals after application of limit 1 or 
            2. In limit 1, N is the number of residuals before selection, and 
            the number at pressures greater than 2000 dbar in limit 2. N(tot) 
            counts those remaining number after rejection of percent, % 
            reject. µ and σ are the mean and standard deviations of the N(tot) 
            residuals. Note change of scale between µ and σ columns for Limits 
            1 and 2.

                  Limit 1:                              Limit 2:
           ± 0.05ºC, ± 2σ, ± 2σ            P>2000 dbar, ± 0.005ºC, ± 2σ, ± 2σ
   -------------------------------------  ------------------------------------
                %      µ(ºC x    σ(º x                %      µ(ºC x    σ(ºC x 
Gp  N/N(tot)  reject  10(^-3))  10(^-3))  N/N(tot)  reject  10(^-4))  10(^-4))
-- ---------  ------  --------  --------  --------  ------  --------  --------
A  422/494     14.6     -0.4      2.1     194/208    6.7     -10.3      3.9
B  1026/1221   16.0     -1.4      2.3     549/589    6.8      -9.4      3.7
C  664/774     14.2     -0.2      2.5     302/331    8.8      -0.0      3.0
D  409/494     17.2     -3.0      5.8     191/208    8.2      -9.2      7.1
E  1055/1221   13.6     -0.3      2.1     552/589    6.3      -8.7      3.9
F  657/774     15.1     -1.1      4.4     306/331    7.6      -0.2      3.2
  

Figure 10.1: SBE35 - CTD temperature residual after application of limit 1(± 
             0.05ºC, ± 2σ, ± 2σ). (i) Primary CTD temperature sensors (Groups 
             A - C). (ii) secondary CTD temperature sensors (Groups D - F). 
             Station groups are (+) A or D, (∆) B or E and (o) C or F.

Figure 10.2: SBE35 - CTD temperature residual after application of limit 2 
             (pressure >2000 dbar, ± 0.005ºC, ± 2σ, ± 2σ). (i) Groups A (+) 
             and D (o), (ii) Groups B (+) and E (o), (iii) Groups C (+) and F 
             (o).



11.  WATER SAMPLE SALINITY ANALYSIS
     (Hannah Longworth, Rachel Hadfield, Amanda Simpson, Rhiannon Mather)


11.1  Equipment

All salinity sample analysis was performed on the UKORS Guildline 8400B 
Salinometer in the Constant Temperature (CT) laboratory. The water bath 
temperature was set to 24ºC and the laboratory temperature maintained between 
21.5ºC and 22.0ºC. The laboratory thermostat was adjusted on Day 100 
following a drop to 20.0ºC, analysis was suspended while the temperature 
stabilised. A leak in the salinometer between the external pump and the 
conductivity cell was repaired by replacement of a tubing section on Day 101, 
with effect from Station 20 onwards. On Day 121 the primary heater failed 
during analysis of Station 86, with no apparent effect on the results 
obtained. The heater was replaced before analysis of Station 87 and a delay 
of 19 hours resulted to allow stabilisation of the water bath temperature. On 
Day 130 the peristaltic pump tube split and was replaced. 10% Decon solution 
and distilled water were rinsed through the salinometer before analysis of 
Station 116. During this station wires connecting the pump and switch had to 
be resoldered. 

11.2   Sample Collection and Analysis

On each CTD cast (except stations 11 and 28 when no bottles were fired), one 
water sample was drawn per Niskin bottle for salinity analysis. A duplicate 
sample was taken from the deepest bottle when less than 24 were fired. 
Samples were taken in 200ml glass sample bottles, rinsed three times and 
sealed with disposable plastic stoppers and screw on caps after drying the 
neck. Samples were stored in the CT laboratory for a minimum of 24 hours 
before analysis to allow equilibration to the laboratory temperature, except 
for the last 4 stations (shallower than 2000m) for which the delay between 
sampling and analysis was reduced to 12 hours. Analysis followed the standard 
procedure. A sample of IAPSO Standard Seawater was run every 24 samples for 
salinometer calibration. Two Standard Seawater batches were used; P143 up to 
and including Station 7 and P144 subsequently. One bad standard in batch P144 
was identified and rejected. The standardisation dial was set to 724 and not 
changed during the cruise. Rachel Hadfield, Hannah Longworth and Amanda 
Simpson carried out the majority of analysis with Rhiannon Mather helping in 
the last week. The 12 duplicate water samples taken had a mean salinity 
difference of 0.0003 and standard deviation of 0.0003.

Stability of the salinometer during the cruise is indicated in Figure 11.1. 
Correction is the correction applied to the conductivity ratio measured by 
the salinometer (equal to the expected standard value minus the measured 
standard value). Correction has a range of -0.00019 to +0.00003, with a drift 
to increasingly negative corrections during the cruise. 

11.3   Data Processing

Raw conductivites from the salinometer are converted to salinities using an 
excel spreadsheet, accounting for salinometer calibration. Results are saved 
in a tab delimited text file with name sal279{num}.txt. After transfer to the 
UNIX system the PSTAR routine sal.exec creates a PSTAR version of the text 
file, sal279{num}.bot, with the same parameters. 

Figure 11.1: Correction applied to salinometer conductivity reading.



References

Bryden, H.L., RRS Charles Darwin Cruise 139, 01 MAR - 15 APR 2002, Trans-
    Indian Hydrographic Section across 32°S, pp. 122, Southampton 
    Oceanography Centre, Southampton, 2003.

Sea-Bird, SBE 35 Temperature Sensor, Deep Ocean Standards Thermometer, 
    Configuration and Calibration Manual, SEA-BIRD ELECTRONICS, INC., 
    Bellevue, Washington 98005, USA, 2004.

Tavener, J.P., Gallium Apparatus Model 17402B Includes Gallium Cell Model 
    17401, pp. 18, Isothermal Technology Limited, Southport, 2001.



12.  WINCHES

12.1  Standard CTD - Steel Armoured Electro-Optical Cable (Spare)

      Cable Specifications
      MBL:                    82.3kN or 8.39Te
      Diameter:               0.45" or ~11.43 mm
      Length:                 8000 metres
      Weight in Air:          505kg.km(^-1)
      Weight in Water:        417kg.km(^-1)
      Approved Manufacturer:  The Rochester Corporation
      Type Number:            A303418MW


12.2  Applications

Common applications for this cable include CTD and associated instrument 
deployments, water bottle rosette sampling, sound velocity profiling.

12.3  Handling

  • A traction winch with level wind is required for the handling of this 
    cable as it is essential that the cable is stored under low tension.
  • The storage drum shall be fitted with a Focal slip ring assembly. This 
    slip ring shall contain one FORJ (Fibre Optic Rotating Joint) for a 
    single mode fibre optimised at 1310/1550nm and two electrical passes each 
    rated at 3kV, 10A or better. 
  • D:d ratio shall be 40:1 or better throughout.
  • Pull capacity 5.0 Te.
  • Line speed 2.0 ms-1
  • Speed control continuously variable in increments of <0.03m/s between 
    zero and maximum throughout length.
  • An automatic render capability is required. This is to be capable of 
    manual adjustment for any tension between 20% and 60% of MBL.
  • Active heave compensation is required for this application.


Table 12.1: RSU CTD winch, 11.7mm electro-optical cable factors of safety, 
            where MBL is maximum breaking load, yield is for the electrical 
            conductor.

Load             Safety Ratio  Load (tonnes)  % of MBL        Notes
---------------  ------------  -------------  --------  ------------------
MBL                  5:1           8.39         100     Test haul required
Lloyds standard      3:1           1.67          20
Test haul           2.5:1          2.79          35
Average              2:1           3.35          40
Peak                               4.19          50        
Yield                              5.87          70
 

Analysis of winch data from two deployments with different packages and 
deployment profiles is given below.


Table 12.2:	Stations used in analysis of standard CTD cable tensions.

                                               Haul/Vee    Max    Maximum 
                                  Weight (T)     Rate    Wireout  Tension 
     File         Package Type    Air/Waterl   (m/min)     (m)      (T)
--------------  ----------------  -----------  --------  -------  -------
win27701_winch  Small frame with  0.410/0.370    ±50      3000      1.54
 trial1_noCTD    six pairs of 
                mooring releases.
  win279052     Full CTD package                 ±70      5755      3.09


12.4  Analysis Method

Each cast is split into down cast and upcast profiles including only data 
deeper than 500 m where the veer rate is constant. For the CTD station the 
upcast data are then further selected i. where the haul rate is 70 m/min and 
ii. where the haul rate is 0 m/min (i.e. package stopped to fire bottles). 
Each profile is fitted using a least squares fit of tension versus cableout.


Table 12.3: Least squares fit of tension versus cableout for downcast veer, 
            upcast haul and upcast stopped winch data for two stations with  
            different packages. The coefficients are for the equation:  
            Tension = C + M x cableout (km), where C is the weight of the  
            package and M is the rate of increase in tension with cableout.  
            Package and cable drag are estimated as the difference/2 of  
            downcast veer and upcast haul package weight values C and the  
            difference/2 of downcast veer and upcast haul rate of increase in  
            tension with cableout M respectively.

              Station                        27701                279052
      ------------------------  --------------------------------  ------
      C (down cast veer) T                   0.310                0.487
      M (down cast veer) T/km                0.356                0.356
      C (up cast haul) T                     0.381                0.819
      M (up cast haul) T/km                  0.392                0.387
      C (up cast stopped) T     0.345 (average of Cdown and Cup)  0.651
      M (up cast stopped) T/km  0.373 (average of Mdown and Mup)  0.373
      Package drag T                         0.04                 0.166
      Cable drag T/km                        0.018                0.016
	

On these two casts the package weights in water were 0.345T and 0.651T, and 
haul/veer rates were 50 and 70 m/min. From these two analyses the cable drag 
estimates are similar, approximately 0.017T/km, suggesting only weak 
dependence of cable drag on velocity. Estimates for the weight of cable in 
water are the same for both casts, and is 0.373T/km, and is inconsistent with 
the manufacturers specification of 0.417T/km: a difference of 0.044T/km.
For the large CTD package the model for estimating cable tensions as a 
function of cable out is:

   Tension(est)=0.651+0.373xcableout(km)±up/down(0.166+0.016xcableout(km))

From this equation the maximum average tension of 3.35T (safety factor 2.5:1 
or 40% of maximum breaking load), the maximum wire out would be 6512 m. For 
the manufactures weight of wire this reduces to 6074 m. 

A caveat to the above analysis is that no significant peak loads were 
observed due to the fine weather. Overall however, the performance of the new 
CTD cable is outstanding, easily achieving 6000 m depth.


13.  ADCP AND BATTERY PACK
     (Dave Teare)

Three SADPs and two battery packs were fitted to the CTD frame. One broad 
band 150Khz, in downward looking mode (serial no 1308), with its own battery 
pack, and two 300Khz workhorse narrow band units, one upward looking (serial 
no 1881) and one downward looking (serial no 3726), these two units had a 
shared battery pack. The 300kHz units were run in a master\slave mode, the 
150kHz was free running.

13.1   BB 150kHz Unit 

This ran without problem. The battery pack was changed on occasions when the 
charge rate was unable to keep up with the usage. 

13.2   Workhorse 300kHz Units

Several problems occurred to these units. On cast 28 the battery pack 
flooded, this was replaced and the flooded unit rebuilt and held as a spare. 
The upward looking unit started to exhibit data download problems around cast 
44, at cast 63 the unit failed to download. The problem was traced to a 
faulty cable on the CTD frame, which was replaced. Around cast 76 the upward 
looking unit started to lose meaningful data except at the surface and close 
to the bottom. Instrument receiver self tests were performed which indicated 
a loss of sensitivity in the receive circuits. The unit was remove from the 
frame, opened, and checked for loose/faulty connections. As there were no 
observable problems the unit was resealed. A second test revealed the same 
problem, the unit was left off for the rest of the cruise. The battery pack 
was changed on occasions when the charging could not keep up with the usage.


14.  LOWERED ACOUSTIC DOPPLER CURRENT PROFILER
     (Louise Duncan)

Instruments Used: BB 20 degree SOC 150Hz BB (unit S/N 1308); WH1 300kHz 
Workhorse LADP (unit S/N 1881); WH2 300kHz Workhorse LADP (unit S/N 3726) 

14.1   Difficulties During Cruise

During the first part of the cruise, crossing the western boundary section, 
battery power was a big concern. We initially experienced problems with the 
workhorse battery, which failed during the upcast of cast 15. They failed 
again on station 17, which was delayed at the bottom due to winch problems. 
The workhorse was not deployed for the next couple of stations and eventually 
was replaced on cast 22. On station 28 the both the BB and WH batteries were 
changed but the WH battery air vent was left open and the cast had to be 
aborted and the battery was returned flooded.

It was difficult during the cruise to determine the best charging rate to 
gain optimal performance. The BB has an intelligent charger, which regulates 
the amount of charge to that required. However, with the Workhorse charger it 
was hard to know the optimal charging rate. With the diode in place up to 
cast 62 it is more difficult to determine the voltage on the WH battery.

For stations 51 and 52, the master workhorse was setup with an incorrect time 
stamp resulting in a one hour error in the output times. This was noticed 
prior to cast 53 and corrected. However, for stations 51 and 52 it was 
necessary to use the RDI tools to extract the time from the raw binary files 
and replace with the correct time. Once corrected the binary files were ftp'd 
to unix and processed.

Communication With Slave WH

During the western boundary section, when stations were close together and 
deep the download times for the Broadband was slow and starting to hold up 
the start of the next station. To resolve this, the download rate was changed 
from a baud rate of 38400 to 115200.

14.2   Processing

Two processing schemes were used during the cruise. The older Firing scheme 
was primarily used to process the Broadband LADP and also used to process the 
Workhorse LADP's. After station 24, the primary processing for the Workhorses 
was the Visbeck method, in which the workhorses could be processed together. 
Outlines of the processing stages are provided below. For each instrument the 
initial raw binary file for a cast is downloaded from the instrument to PC 
and then FTP'd to UNIX.

14.3   Firing Method

The Firing processing scheme calculates absolute velocities by first 
calculating overlapping vertical shear profiles of horizontal velocity. These 
are averaged and combined to produce a full depth shear profile. This process 
removes any motion associated with the package. Integrating the shear profile 
obtains the baroclinic component of the water velocity. The barotropic part 
is then obtained from the unknown integration constant and is computed from 
the time-averaged, measured velocity and ship drift.

14.4   Visbeck Method

The Visbeck method calculates velocities using an inverse problem to remove 
package motion solved using a least squares technique. The problem is over 
determined and can be solved using sensible constraints (Visbeck 2002). This 
method of processing also allows the solution to be constrained by 
information from bottomtrack, ctd and SADP.

14.5   Processing Problems

Firing

Processing using the firing method went well. On a couple of stations, 25 and 
62, there were problems matching the LADP to CTD data. On station 25, the 
Broadband instrument was deployed as an upward looking ADP. It is unclear why 
the instrument changed from downlooking to upward looking for this one 
station. Command files sent to the instrument and station log files do not 
show any error by the user at the deployment stage.

During cast 62, there was a win explorer crash on the CTD PC during the 
upcast at wire out 3499m. It was unclear at the time whether any data loss 
had occurred for the CTD. However, a time gap was apparent on the first 
attempt to match the LADP to CTD data for this station. A new file was 
created specifically to use for matching CTD and LADP by filling in the time 
gap and linearly interpolating the salinity, temperature and pressure 
information. The new CTD file improved the match slightly, but remains quite 
poor.

Generally the firing method matched the CTD and LADP quite well 
automatically. There were less than twelve occasions where interactive 
editing was required.

Visbeck

Processing with the Visbeck method suffered a few more difficulties than the 
firing scheme. The smaller number of steps involved in the Visbeck scheme 
made it more attractive to use, although it uses more computer processor time 
than the Firing method. 

On occasions the CTD data was ignored by the Visbeck processing during run 
two. This occurred on four stations. Stations 25 and 62 have already been 
mentioned above and caused problems in the firing method. On station 13 the 
CTD data was rejected because the first ascii file contained a number of 
spikes. The Visbeck scheme returned warnings at the end of the second run 
indicating a time difference between the bottom times of the ADP and CTD of 
65 minutes! Once a new despiked CTD file was created, the CTD data was 
accepted and the processing ran without problems. (Note. Station 13 was rerun 
using the firing method when the new CTD was available.) Station 2 did not 
use the CTD data available, possibly due to the shallowness of the station 
(less than 200 metres).

For a number of casts, run2 of the Visbeck processing reported a bottom time 
difference between the CTD and LADP (Table 14.1). Unlike the Firing scheme 
the matching is performed within the processing automatically and does not 
allow external matching as an option. There was not enough time to 
investigate this error fully, however, some intervention maybe beneficial for 
the Visbeck scheme when using extra constraints. Time differences were 
usually about 1-2 minutes and occurred for both the broadband and workhorse 
LADP, but not necessarily on the same cast.



Table 14.1:  Visbeck and Firing processing parameters (key at end of table)

                VISBECK PROCESSING                       
       Broadband              Workhorse              FIRING PROCESSING
Stn  Run1    Run2         Run1         Run2          BB  Master  Slave  Comments
---  ------  -----------  -----------  ------------  --  ------  -----  --------------------------------------------------------------
  1  A       B            C1           ?             √     √       √    
  2  A       B X, td7     C1           D1 X, td6     √     √       √    
  3  A       B td8        C1           D1            √     √       √    
  4  A       B            C1           D1            √     √       √    
  5  A       B td2        C1           D1            √     √       √    
  6  A       B            C1           D1            √     √       √    
  7  A       B            C1           D1            √     √       √    
  8  A       B td1        C1           D1            √     √       √    
  9  A       B td1        C1           D1            √     √       √    
 10  A       B td2        C1           D1 td1        √     √       √    
 11  ND      ND           ND           ND            ND    ND      ND   Shallow station
 12  ND      ND           ND           ND            ND    ND      ND   Shallow station
 13  A       B            C1 nbot      D1 nbot       √     √       √    rerun - spikes in CTD data, caused CTD to be ignored first run
 14  A       B            C1 nbot      D1 nbot       √     √       √    
 15  A       B            C1 ie        D1            √     -       -    downcast only for wh - lack of battery power
 16  A       ?            ND           ND            √     ND      ND    
 17  -       -            -            -             √     -       -    winch problems - delay 4hrs at bottom, wh battery returned dead
 18  A       B            ND           ND            √     ND      ND    
 19  A       B td2        ND           ND            √     ND      ND    
 20  A       B td4        ND           ND            √     ND      ND    
 21  A       B            ND           ND            √     ND      ND   WH battery flat on recovery
 22  A       B            C1 ie        D1 td1        √     √       √    
 23  A       B td2        C1           D1 td1        √     √       √    
 24  A       B td1        C2           D2 td2        √     √       √    change wh cmd file to zero blank beyond transmit
 25  A       B X,?        C2           D2            √     √       √    Broadband deployed uplooking processed but bad match to CTD
 26  A       B            C2           D2            √     √       √    
 27  A       B td1        C2 ie        D2 td1        √     √       √    
 28  ND      ND           ND           ND            ND    ND      ND   new wh and bb battery, wh battery flooded
 29  A       B            ND           ND            √     ND      ND    
 30  A       B            C2 ie        D2            √     √       √    new wh battery 
 31  A       B            C2 ie        D2            √     √       √    
 32  A       B            C2 ie        D2            √     √       √    
 33  A       B            C2 ie        D2            √     √       √    
 34  A       B            C2 ie        D2            √     √       √    new bb battery
 35  A       B td3        C2 ie        D2 td3        √     √       √    
 36  A       B td2        C2 ie        D2 td2        √     √       √    
 37  A       B td2        C2 ie        D2 td2        √     √       √    
 38  A       B            C2 ie        D2            √     √       √    
 39  A       B            C2 ie        D2            √     √       √    
 40  A       B            C2 ie        D2 td2        √     √       √    
 41  A       B            CM2 ie       DM2           √     √       √    Slave not deployed - user error
 42  A       B td2        C2 ie        D2            √     √       √    new bb battery

                VISBECK PROCESSING                       
       Broadband              Workhorse              FIRING PROCESSING
Stn  Run1    Run2         Run1         Run2          BB  Master  Slave  Comments
---  ------  -----------  -----------  ------------  --  ------  -----  --------------------------------------------------------------
 43  A       B td1        C2 ie        D2 td2        √     √       √    
 44  A       B td1        C2 ie        D2 td1        √     √       √    
 45  A       B td1        C2 ie        D2            √     √       √    
 46  A       B td2        C2 ie        D2 td2        √     √       √    
 47  A       B td1        C2 ie        D2 td2        √     √       √    
 48  A       B td1        C2 ie        D2 td2        √     √       √    
 49  A       B td1        C2 ie        D2 td1        √     √       √    
 50  A       B td2        C2 ie        D2 td2        √     √       √    
 51  A       B            C2 ie        D2 td2        √     √       √    instrument time out by 1hour corrected prior to processing
 52  A       B            C2 ie        D2            √     √       √    instrument time out by 1hour corrected prior to processing
 53  A       B td3        C2 ie        D2 td3        √     √       √    
 54  A?      B td1, ??    C2 ie        D2 td2        √     √       √    
 55  A       B td2        C2 ie        D2            √     √       √    
 56  A       B td2        C2 ie        D2            √     √       √    
 57  A       B td1        C2 ie        D2            √     √       √    
 58  A       B            C2 ie        D2            √     √       √    
 59  A       B td1        C2 ie        D2 td1        √     √       √    
 60  A       B td2        C2 ie        D2 td1        √     √       √    
 61  A nbot  B nbot       C2 ie, nbot  D2 nbot       √     √       √    
 62  A       B X          CM2 ie, nbot DM2 X, nbot   √     √       ND   poor ctd match due to time jump in upcast ctd data
 63  A       B            C2 ie, nbot  D2 nbot       √     √       √    
 64  A       B            C2 ie        D2            √     √       √    
 65  A       B            C2 ie        D2            √     √       √    
 66  A       B            C2 ie        D2            √     √       √    
 67  A nbot  B nbot, td3  C2 ie,nbot   D2 nbot, td3  √     √       √    
 68  A       B            C2 ie        D2            √     √       √    
 69  A       B td1        C2 ie        D2 td1        √     √       √    
 70  Atrial  Btrial       C2 ie        D2            √     √       √    Broadband command file change to 20m bins
 71  A       B            C2 ie        D2 td1        √     √       √    
 72  A       B td2        C2 ie        D2 td2        √     √       √    
 73  A       B            C2 ie        D2            √     √       √    
 74  A       B            C2 ie        D2 td2        √     √       √    
 75  A       B td1        C2 ie        D2            √     √       √    
 76  A       B td1        C2 ie        D2 td1        √     √       √    
 77  A       B            C2 ie        D2 td2        √     √       √    
 78  A       B td1        CM2 ie       DM2 nbot, td1 √     √       -    slave returned with half cast good data
 79  A       B td1        CM2 ie       DM2 td1       √     √       -    slave stopped receiving data on up cast
 80  A       B td1        CM2 ie       DM2           √     √       -    No good data returned from slave
 81  A       B            CM2 ie       DM2           √     √       ND    
 82  A       B td1        CM2 ie       DM2           √     √       ND    
 83  A       B            CM2 ie       DM2           √     √       ND    
 84  A       B            CM2 ie       DM2           √     √       ND    

                VISBECK PROCESSING                       
       Broadband              Workhorse              FIRING PROCESSING
Stn  Run1    Run2         Run1         Run2          BB  Master  Slave  Comments
---  ------  -----------  -----------  ------------  --  ------  -----  --------------------------------------------------------------
 85  A       B td1        CM2 ie       DM2 td1       √     √       ND       
 86  A       B            CM2 ie       DM2 td1       √     √       ND    
 87  A       B td1        CM2 ie       DM2 td2       √     √       ND    
 88  A       B td1        CM2 ie       DM2 td2       √     √       ND    
 89  A       B            CM2 ie       DM2           √     √       ND       
 90  A       B            CM2 ie       DM2           √     √       ND    
 91  A       B td1        CM2 ie       DM2           √     √       ND    
 92  A       B            CM2 ie       DM2 td1       √     √       ND    
 93  A       B td2        CM2 ie       DM2 td2       √     √       ND    
 94  A       B            CM2 ie       DM2 td1       √     √       ND    
 95  A       B td1        CM2 ie       DM2 td3       √     √       ND    
 96  A nbot  B nbot       CM2 ie, nbot CM2 nbot      √     √       ND    
 97  A nbot  B nbot       CM2 ie, nbot CM2 nbot      √     √       ND    
 98  A       B            CM2 ie       DM2 td2       √     √       ND    
 99  A       B td2        CM2 ie       DM2 td2       √     √       ND    
100  A       B            CM2 ie       DM2 td1       √     √       ND    
101  A       B td1        CM2 ie       DM2 td1       √     √       ND    
102  A       B td1        CM2 ie       DM2 td2       √     √       ND    
103  A       B td2        CM2 ie       DM2           √     √       ND    
104  A       B            CM2 ie       DM2 td1       √     √       ND    
105  A       B            CM2 ie       DM2           √     √       ND    
106  A       B            CM2 ie       DM2           √     √       ND    
107  A       B            CM2 ie       DM2           √     √       ND    
108  A       B            CM2 ie       DM2 td1       √     √       ND    
109  A       B td1        CM2 ie       DM2 td1       √     √       ND    
110  A       B            CM2 ie       DM2           √     √       ND    
111  A       B td1        CM2 ie       DM2 td3       √     √       ND    
112  A       B td1        CM2 ie       DM2           √     √       ND    
113  A       B td2        CM2 ie       DM2 td2       √     √       ND    
114  A       B            CM2 ie       DM2           √     √       ND    
115  A       B            CM2 ie       DM2 td1       √     √       ND    
116  A       B td1        CM2          DM2 td1       √     √       ND    
117  A       B td1        CM2 ie       DM2 td1       √     √       ND    
118  A       B            CM2 ie       DM2 td1       √     √       ND    
119  A       B td1        CM2          DM2           √     √       ND    
120  A       B td1        CM2 ie       DM2           √     √       ND    
121  A       B            CM2          DM2           √     √       ND    
122  A       B td1        CM2          DM2           √     √       ND    
123  A       B            CM2          DM2           √     √       ND    
124  ND      ND           ND           ND            ND    ND      ND    
125  ND      ND           ND           ND            ND    ND      ND    
126  ND      ND           ND           ND            ND    ND      ND    

Key: A =      Broadband run 1 with ps.dz=16m and 0.5 weight on bin 1. NAV 
              constraint
     B =      Broadband run 2 with ps.dz=16m, 0.5 weight to bin1. NAV, CTD 
              constraints
     Atrial = Broadband run 1 with ps.dz=20m and 0.5 weight on bin 1. NAV 
              constraint
     Btrial = Broadband run 2 with ps.dz=20m and 0.5 weight on bin 1. NAV, 
              CTD constraints
     C1 =     Dual workhorse run1 with ps.dz=10m, 0.5 weight to bin1. NAV 
              constraint
     C2 =     Dual workhorse run1 with ps.dz=10m, 0 weight to bin1. NAV 
              constraint
     CM2 =    Dual workhorse run1 with ps.dz=10m, 0 weight to bin1 and master 
              only. NAV constraint
     D1 =     Dual workhorse run2 with ps.dz=10m, 0.5 weight to bin1. NAV, 
              CTD, BOT constraint
     D2 =     Dual workhorse run2 with ps.dz=10m, 0 weight to bin1. NAV, CTD, 
              BOT constraint
     DM2 =    Dual workhorse run2 with ps.dz=10m, 0 weight to bin1 and master 
              only. NAV, CTD, BOT constraint
     nbot =   No bottom track data available
     ie =     Increased error due to shear inverse difference
     tdn =    Bottom time difference between CTD and LADCP by n minutes
     X =      No CTD data
     ND =     Not Deployed
     ? =      Plotraw.m does not run in visbeck processing


For a large number of stations the first run of Visbeck processing for the 
workhorse returned a message stating an increase error because of shear - 
inverse difference. This message is displayed from the matlab script 
getshear2.m and is shown when uvds > mean(dr.uerr), where dr.uerr is the 
velocity error derived by solving the linear inverse method and uvds is

        sqrt((sd(dr.u-mean(dr.u)-ds.ur)2+(sd(dr.v-mean(dr.v)-ds.vr))2)

where dr.u and dr.v are velocities from the linear inverse problem and ds.ur 
and ds.vr are velocities derived by the older method of integrating average 
shear estimates from the bottom up.

14.6   Results

The Broadband LADP performed well during D279. For a large number of casts 
either side of and over the mid-Atlantic ridge the lack of scatterers in the 
water below approximately 2500m resulted in a lack of samples with which to 
determine sensible water velocities. Figure 14.1 shows the velocities from 
station 67 and the impact of lack of scatterers on the result. As soon as we 
reach stations towards the end of the cruise, full sensible looking profiles 
were retrieved once the number of samples increased.


Figure 14.1: LADP data from station 67 showing U and V velocities (panels a 
             and b) and the number of samples per bin (c) and the shear 
             standard deviation (d).


The master workhorse LADP performed well, but several problems were 
encountered during the cruise with the upward looking slave workhorse. 
Initially we had problems downloading and talking to the slave workhorse. 
This turned out to be a problem with the cable connection to the slave on the 
CTD frame itself. This cable was replaced prior to cast 64. No new problems 
with communication were experienced. On station 78 the slave workhorse 
returned with only half a cast (downcast) of good data available (as 
suggested by scan.prl in the firing processing). On station 79 the slave 
again, did not retrieve a full cast but collected its last good ensemble on 
the upcast at approximately 400 m depth. On station 80 the slave file gave a 
max depth of 0.3 and min/max depth of -517 using scan.prl. The three casts 
were examined on the deck laboratory PC using the RDI tools winADP. This 
allowed us to look at basic variables such as w at a glance. The files all 
contained some velocity information. For station 80, the only velocity data 
available seem to show the instrument tracking the surface, near the 
beginning of the cast and again near the end. RA tests were performed on the 
instrument. On cast 81 the instrument finally returned with no sensible data. 
In all stations 78 onwards, the slave returned with a file with similar 
magnitude to the master workhorse. However, the file was filled with absent 
data. 

14.7   Comparison of BB LADP and WH LADP With On-Station OS75 VM ADP

A comparison of the velocities from the Broadband using both processing 
schemes, the Workhorse using the Visbeck scheme and the vessel mounted OS75 
was performed during the cruise. Initially the velocities were compared 
visually using the script plot_topbot_uv.m. The comparison from station 23 is 
shown in Figure 14.1. In general both the shear profiles compare well 
although the broadband processed using the firing method would often show an 
offset from the visbeck processed broadband and OS75. For each cast 
velocities from the Broadband and Workhorse were interpolated onto the same 
depth bins as the OS75 using the script profstats.m. Table 14.2 shows the 
mean and standard deviation of the broadband from the OS75 using both the 
Visbeck and Firing processing.



Table 14.2:   Comparisons of BB LADP and WH LADP with on-station OS75 VM ADP

        Vessel Mounted OS75 - BB Firing  Vesssel Mounted OS75 - BB Visbeck
        -------------------------------  ---------------------------------
        mean u   sd u   mean v   sd v      mean u   sd u   mean v   sd v
   Stn  (cm/s)  (cm/s)  (cm/s)  (cm/s)     (cm/s)  (cm/s)  (cm/s)  (cm/s)
   ---  ------  ------  ------  ------     ------  ------  ------  ------
     1                  
     2                  
     3  -10.99   5.95   -49.40   3.44       4.02    4.53   11.78   11.54
     4   -1.80   4.59   -19.50   2.74       5.35    6.18   11.82   11.61
     5   -1.61   2.20    -8.87   7.43       1.16    2.20    5.57    7.80
     6   -2.91   2.49    -9.26   3.82      -1.35    4.58    8.40    4.60
     7   -2.10   1.63    -6.31   5.45      -1.14    2.43    4.67    5.70
     8   -3.64   1.87     1.14   2.18      -1.95    2.31    3.41    3.57
     9    0.75   2.57     3.79   3.90       4.14    3.12   -1.57    6.52
    10    0.11   3.25    -0.84   1.86       4.90    6.32  -10.59   11.15
    11                            
    12                            
    13   -1.35   1.95     0.04   0.96      -0.93    3.22    6.00    2.77
    14   -0.39   1.44    -1.62   1.15      -1.20    2.06    1.35    1.00
    15   -3.83   1.61    -2.65   1.58       0.15    2.05    2.29    4.40
    16                              
    17                             
    18   -8.38   1.14    10.37   0.89      -1.97    1.56   -0.02    1.10
    19   -2.12   1.31     1.89   1.39      -1.85    2.06    0.40    1.70
    20   -1.73   1.54     8.44   1.74      -0.21    1.27    0.19    1.64
    21    0.59   1.08    10.78   1.32      -1.67    3.79    0.86    2.87
    22    3.87   1.46    -8.83   1.63       0.35    2.11   -1.46    2.85
    23    7.89   0.97     0.35   1.45       0.74    2.16   -0.81    1.42
    24   -0.24   1.13     0.74   1.66       2.27    1.92   -1.10    5.34
    25                             
    26    1.34   1.47    -0.86   1.16       1.29    2.57   -2.43    3.60
    27   -2.25   1.26     0.24   0.92      -0.36    2.12   -2.50    0.96
    28                            
    29   -1.82   1.44     0.70   0.94       1.73    9.23   -2.78    3.50
    30   -1.52   1.02    -1.33   1.53       1.85    2.38    0.70    1.88
    31   -5.91   1.52     5.47   1.47       3.55    2.37   -1.25    2.12
    32   -1.98   1.27     5.15   1.48       1.19    3.21   -2.82    3.06
    33    3.08   1.57    -3.87   1.12       1.22    3.07    0.78    5.63
    34   -9.74   1.16     4.10   1.44       2.57    1.19   -1.32    1.13
    35   -1.15   1.43    -2.51   1.63      -1.24    1.25   -0.88    2.05
    36   11.71   1.21    -9.35   1.05      -0.64    1.38   -3.32    0.89
    37    3.27   1.88    -4.25   1.54      -0.60    1.58   -1.90    3.72
    38    7.23   1.39    -4.41   1.57       1.96    1.71   -0.93    3.20
    39   -6.06   1.47    -1.30   1.42      -1.68    2.72   -0.91    1.44
    40  -11.84   1.29     3.96   1.02       2.79    1.59   -2.76    1.45
    41  -13.82   1.34    14.70   0.96       3.47    2.03   -2.37    1.99
    42   -8.30   2.11    -3.39   2.28      -1.48    1.59   -0.51    1.43
    43    7.19   1.63    -8.86   1.03      -2.54    1.46   -0.63    1.52
    44    0.32   0.93     7.34   1.67      -2.59    2.48   -0.28    4.91
    45   32.75   1.46   -12.60   1.15      -3.88    2.24   -1.26    1.59
    46    1.02   1.00    -7.27   1.16      -3.70    2.01   -0.23    2.12
    47   17.42   1.55   -19.06   1.10       1.12    1.65   -1.63    4.60
    48    1.27   1.26    -4.55   1.25       1.19    1.65   -4.15    4.36
    49    6.88   1.38    -6.25   1.32       2.87    3.95   -3.42    2.19
    50    8.70   1.65   -12.87   2.20      -0.65    1.70   -2.66    2.52
    51   -1.92   1.40     8.16   2.03       0.34    2.97   -2.62    4.69
    52    6.00   1.46   -10.93   2.39      -0.16    1.50   -4.36    3.51
    53  -15.88   1.00     8.41   1.30       0.30    1.04   -1.79    2.33
    54    6.57   1.15     9.65   1.93       0.50    3.25    0.86    1.94
    55  -10.00   1.41    11.04   1.32       0.63    1.60   -1.42    1.15
    56   61.97   1.15   -49.22   1.57       0.06    1.89   -0.68    2.00
    57    5.92   1.17    20.13   1.45      -1.03    2.47   -1.64    1.33
    58   -5.26   0.87   -11.84   1.89       2.63    1.90   -3.54    1.60
    59  -27.70   1.45     4.10   1.19       2.91    2.16   -0.10    1.83
    60    2.42   1.71     2.93   1.17      -0.45    1.74    1.82    2.38
    61  -12.59   1.45     4.53   1.79       2.97    2.60   -3.26    2.24
    62                            
    63    6.35   1.16     3.68   1.41      -2.64    1.64   -2.52    1.27
    64   15.07   1.33   -30.71   2.89      -1.04    1.79   -3.77    3.40
    65   55.42   1.82    13.94   1.60      -1.40    2.44   -2.06    2.69
    66    4.79   0.95    -9.19   0.99       0.60    1.46   -1.88    2.70
    67  -41.71   1.28    30.31   1.61       0.48    3.75   -2.29    3.30
    68    1.32   0.93     5.69   2.43      -0.83    1.13   -0.91    2.64
    69   -4.90   1.43    -9.45   1.33      -1.38    2.15   -3.89    1.74
    70    1.15   1.99    -1.31   2.63      -3.64    4.92   -0.82    3.59
    71   17.75   1.70    -0.37   2.14      -0.97    2.83   -1.47    2.14
    72    5.21   1.75   -11.18   1.52      -2.33    4.94   -3.00    6.09
    73    1.76   1.13    -2.28   1.35      -0.06    2.14   -1.30    2.67
    74   11.74   2.10    -7.63   1.57      -1.62    3.11   -0.18    2.27
    75   -8.50   1.89     3.22   2.20      -1.18    2.26   -2.91    2.09
    76   -6.00   1.31    -1.97   1.32      -1.70    2.04   -0.39    1.66
    77   -9.73   1.00    -4.81   1.72      -0.55    0.76    0.16    1.95
    78    2.32   1.56     9.52   1.31       0.77    1.82   -0.82    1.83
    79   -3.86   1.58    -4.93   1.32       0.66    1.82   -0.03    2.86
    80    6.76   1.31    -7.90   1.53       0.75    2.07   -0.52    1.50
    81   -0.30   1.80    11.56   1.63      -0.79    1.75   -3.88    2.34
    82    7.31   1.29    -8.56   2.78      -0.51    1.52   -3.31    2.43
    83   -8.37   1.57    -1.47   1.60      -3.21    2.55   -1.96    3.10
    84   -8.45   1.09    14.10   2.01      -2.30    1.09    2.63    2.39
    85   15.04   1.88     8.13   1.21       0.49    1.53   -2.07    2.93
    86   11.43   1.78    -7.58   1.62      -6.88    3.25    4.06    2.66
    87    0.22   1.52    10.21   1.67      -3.47    1.33    0.69    1.69
    88   -0.49   1.50   -15.61   2.26      -4.45    1.93   -0.73    3.44
    89  -27.31   1.24    12.88   1.57      -0.07    1.69   -2.54    1.90
    90    3.41   1.27    -7.18   2.28      -0.50    1.29   -2.73    2.59
    91   -2.60   0.64   -16.81   1.50       1.99    1.84   -1.21    1.46
    92   14.31   1.76     5.35   1.63      -0.94    1.91   -3.60    2.04
    93   11.76   2.07   -10.82   1.81      -1.29    2.09   -2.05    3.54
    94   10.03   1.85   -16.12   0.85      -0.90    3.01   -0.50    1.95
    95   13.00   2.76    -8.39   1.49       3.26    2.90   -5.86    4.01
    96    4.21   1.58    -3.59   1.88       2.12    1.75   -0.05    1.51
    97   12.25   1.51    -6.06   1.31      -1.70    1.69   -1.64    1.25
    98   -7.70   1.24   -10.73   2.08      -2.47    2.25   -3.00    2.93
    99   12.18   1.42     1.86   1.03      -2.50    1.89   -2.43    1.51
   100   -9.96   1.78    -7.68   1.61      -1.64    1.74   -1.31    1.32
   101   12.64   0.97    -0.81   1.84      -3.40    2.66   -1.80    2.26
   102    6.67   1.03     6.55   1.17      -0.12    1.64   -2.55    1.27
   103   10.11   1.11    -8.90   2.00       0.87    1.74    3.10    2.67
   104   -9.88   1.77   -12.68   1.96      -1.32    2.19   -0.78    1.28
   105   16.19   2.08     6.46   0.96       2.15    2.05   -1.11    2.64
   106    1.62   1.29     2.92   1.20      -0.67    1.42   -2.21    2.30
   107   12.02   1.45    -8.25   1.70      -4.05    1.55    1.59    1.61
   108    8.96   2.33    -8.46   1.39       0.92    2.71    0.83    1.48
   109    1.17   1.32    -4.50   1.23      -0.43    1.76    0.35    1.90
   110   -9.02   1.20    -7.55   1.50       1.16    1.61   -0.38    2.15
   111    7.21   1.24     5.59   1.99      -1.10    1.88   -1.75    2.40
   112    2.88   1.11    -8.89   1.09       2.54    1.50   -1.38    1.74
   113   -5.43   1.55     5.02   1.05       3.30    9.84   -3.21    1.24
   114    1.13   1.15     2.87   1.07      -1.26    1.29    1.21    2.44
   115    0.43   1.06    -3.48   2.33      -0.30    2.60   -1.45    2.32
   116   -0.83   1.09     1.12   1.66      -0.08    1.66   -1.88    3.12
   117    5.16   1.06     2.01   1.26       0.28    1.50    0.49    6.53
   118   -1.67   1.30    -2.83   1.19      -1.46    1.77    1.21    1.36
   119    0.12   1.22     1.10   1.36      -1.05    1.27   -2.47    2.60
   120   -4.64   1.60    -0.22   1.59      -4.35    1.86   -2.65    3.41
   121    0.77   0.92    -1.88   0.85      -0.59    0.98   -1.31    0.82
   122    0.06   1.21    -0.50   1.58      -0.94    1.10   -1.93    1.65
   123   -0.12   1.25     0.08   1.28       0.27    1.81   -0.30    1.64
   
   
The velocity profiles were also compared visually to bottom track data from 
the master workhorse and broadband through the Visbeck processing.


Figure 14.2: Station 23. Broadband LADP velocities processed using the Firing 
             (U, V) and Visbeck (Ubbvis, Vbbvis) processing schemes, 
             Workhorse LADP profiles processed using the Visbeck scheme 
             (Udwh, Vdwh) and shipboard OS75 (Uadp, Vadp). Water track 
             velocities are shown in the left panel and bottom track 
             velocities on the right panel.

14.8   Command Files

BB cmd

CR1            Retrieve Factory Parameters
PS0            Show System parameters (Xdcr)
CY
CT 0           Turnkey = off
EZ 0011101     Sensor source (C;D;H;P;R;S;T)
EC 1500        Speed of sound
EX 11101       Coord Transform (Xform:Type;Tilts;3Bm;Map)
WD 111100000   Data Out (V;C;A;Pg;St;Vsum;Vsum^2)
WL 0,4         Water ref layer?
WP 00001       Ping per Ensemble
WN 016         Number of depth cells
WS 1600        Depth cell size
WF 1600        Blank after transmit
WM 1           Profiling mode
WB 1           Bandwidth Control (1=med)
WV 350         Ambiguity Velocity
WE 0150        Error Velocity Threshold
WC 056         Low Correlation Threshold
CP 255         Xmt Power
CL 0           Leapfrog = on
BP 000         Pings per ensemble
TP 000000      Time per ping
TB 00000200    Time per burst
TC 2           Ensembles per burst
TE 00000080    Time per ensemble
CF11101        Flow Control (Enscyc;Pngcyc;Binry;Ser;Rec)
&?
CS             Go (start pinging)
BB trial

CR1
PS0
CY
CT 0
EZ 0011101
EC 1500
EX 11101
WD 111100000
WL 0,4
WP 00001
WN 013
WS 2000
WF 2000
WM 1
WB 1
WV 350
WE 0150
WC 056
CP 255
CL 0
BP 000
TP 000000
TB 00000200
TC 2
TE 00000080
CF11101
&?
CS


WHM

PS0            Show Sys Parameters
CR1            Retrieve Factory Parameters
CF11101        Flow Ctrl (EnsCyc;PngCyc;Binry;Ser;Rec)
EA00000        Heading Alignment
EB00000        Heading Bias
ED00000        Transducer Depth
ES35           Salinity ppt
EX11111        Coord Transform (Xform:Type;Tilts;3Bm;Map)
EZ0111111      Sensor Source (C;D;H;P;R;S;T)
TE00:00:01.00  Time per Ensemble (hrs:min:sec.sec/100)
TP00:01.00     Time per ping (min:sec.sec/100)
LD111100000    Data Out (V;C;A;Pg;St;Vsum;Vsum^2)
LF0000         Blank After Transmit
LN016          Number of depth cells
LP00001        Pings per ensemble
LS1000         Depth cell size
LV250          Ambiguity Velocity
LJ1            Receiver gain select
LW1            Mode 1 pings before
LZ30,220
SM1
SA001
SW05000
CK             Keep parameters as user defaults
CS             Go (start pinging)

WHS

PS0            Show sys parameters
CR1            Retrieve factory parameters
CF11101        Flow Ctrl
EA00000        Heading alignment
EB00000        Heading Bias
ED00000        Trasnducer Depth
ES35           Salinity ppt
EX11111        Coord Transform
EZ0111111      Sensor Source
TE00:00:01.00  Time per Ensemble
TP00:01.00     Time per ping
LD111100000    Data out
LF0000         Blank After transmit
LN016          Number of depth cells
LP00001        Pings per ensemble
LS1000         Depth cell size
LV250          Ambiguity Velocity
LJ1            Receiver gain select (1=high)
LW1            Mode 1 pings before
LZ30,220
SM2
SA001
ST0
CK             Keep parameters as user defaults
CS             Go (start pinging)





15.  LOWERED ACOUSTIC DOPPLER CURRENT PROFILER DATA PROCESSING SOFTWARE TEST SUITE
     (Steven Alderson and Amanda Simpson)  

There are two sets of software available for analysis of LADP profiles, the 
Firing et al. software from the University of Hawaii (UH) and the Visbeck et 
al. software from LDEO. However, there are characteristics of the outputs 
from both methods that are not well understood and do not seem to relate to 
the oceanography when compared to shipboard measurements. It would be 
desirable to evaluate the performance of both methods and the effect of 
introducing certain types of error and bias on the calculated velocities.

The Firing software is more established but the Visbeck uses a more 
sophisticated method to estimate the velocities. It is also written entirely 
in Matlab whereas the Firing method uses both Perl and Matlab scripts. For 
these reasons, the Visbeck method would be preferred. However, there are 
occasions when the Visbeck method produces different results to Firing, when 
Firing is found to agree with shipboard ADP observations.

The aim of this project is to develop a program capable of generating test 
LADP output files for which the ocean velocity is known. This could then be 
used to test the two methods under different conditions, the aim being to 
determine which produces the best answers and when. This project was 
undertaken during cruise D279 although it was not the intention to take it to 
completion during that time period.

A report documenting this software is available from Steven Alderson.



16.  NAVIGATION AND SHIPBOARD ACOUSTIC DOPPLER CURRENT PROFILER
     (Steven Alderson and Amanda Simpson)

RRS Discovery has two SADPs mounted in the hull, the tried and tested 150kHz 
and the new Ocean Surveyor 75kHz. The 150kHz ADP is mounted 1.75m to port of 
the keel, 33m aft of the bow and at a depth of ~5m. The 75kHz ADP is 4.15m 
forward and 2.5m to starboard of the 150kHz instrument. This was the known 
state of affairs before the recent refit. The positioning of the 75kHz ADP 
that much further forward means that it is more prone to bubble contamination 
when the ship is pitching, therefore depth coverage and quality deteriorates 
noticeably in rough seas. To avoid echoes between the two instruments, 
synchronisation was necessary. They intention was to set up the instruments 
so that the 75kHz is the master.

High quality navigation data is crucial for obtaining accurate measurements 
of ocean currents using both vessel mounted and lowered ADPs. The following 
sections describe the operation and data processing paths for both ADPs as 
well as the navigation data, crucial for obtaining accurate ADP current 
measurements.

16.1   Navigation

There are four GPS receivers on RRS Discovery: the Trimble 4000 (gps_4000) 
which is a differential GPS; the Glonas (gps_glos) which uses a combination 
of Russian and American satellite networks; the Ashtech (gps_ash); and the 
GPS G12 (gps_g12). Data from all instruments were logged to the RVS Level A 
system before being transferred to RVS Level C system.

16.2   GPS and Bestnav

A standard PSTAR best navigation file was updated regularly throughout each 
cruise from datastream bestnav, using the script navexec0. The preferred 
input for bestnav is the Trimble 4000, as it has been found on previous 
cruises to give higher positional accuracy. If there were gaps in the Trimble 
4000 data, the bestnav process used other inputs as necessary in the order 
Glonass, Ashtech, G12.

From positions logged in port at the start of the cruise, the standard error 
in both lat and lon of the gps_4000 was found to be 0.000003 degrees (between 

0.3 and 0.4 m).

The gps_4000 coverage was extremely good during D278, with only one time-gap 

time gap : 04 084 04:42:19 to 04 084 04:43:24 (65 s)

Surprisingly, gaps were found in the bestnav datastream. It is unknown why 
these gaps occurred. This should be investigated.

            time gap : 04 078 20:00:10 to 04 078 20:01:00 (50 s); 
            time gap : 04 078 20:01:00 to 04 078 20:02:00 (60 s); 
            time gap : 04 078 22:01:10 to 04 078 22:02:10 (60 s); 
            time gap : 04 079 08:46:30 to 04 079 08:47:50 (80 s); 
            time gap : 04 080 07:25:40 to 04 080 07:26:50 (70 s); 
            time gap : 04 080 15:46:20 to 04 080 15:48:00 (100 s); 
            time gap : 04 081 10:42:50 to 04 081 10:44:40 (110 s); 
            time gap : 04 081 19:00:50 to 04 081 19:02:40 (110 s); 
            time gap : 04 083 02:27:50 to 04 083 02:29:20 (90 s); 
            time gap : 04 084 10:03:10 to 04 084 10:04:30 (80 s); 
            time gap : 04 085 02:43:40 to 04 085 02:44:20 (40 s); 
            time gap : 04 085 04:59:30 to 04 085 05:00:40 (70 s); 
            time gap : 04 086 04:15:20 to 04 086 04:17:10 (110 s); 
            time gap : 04 087 07:40:10 to 04 087 07:41:40 (90 s); 
            time gap : 04 087 18:16:40 to 04 087 18:17:40 (60 s); 
            time gap : 04 087 18:17:40 to 04 087 18:18:20 (40 s); 
            time gap : 04 087 20:07:30 to 04 087 20:08:10 (40 s); 
            time gap : 04 089 07:51:00 to 04 089 07:52:50 (110 s); 
            time gap : 04 089 16:08:20 to 04 089 16:09:10 (50 s)

These time gaps also occurred during D279, the longest being 110 seconds.

16.3  Ship's Gyrocompass

The ship's gyrocompass provides reliable (i.e. not dependent on transmissions 
external to the ship) estimate of the ship's heading. However, the instrument 
is subject to latitudinally dependent error, heading dependent error, and has 
an inherent oscillation following a change in heading.

Ship heading from the gyro was logged every second to the RVS level C. 
Processing consisted of regular acquisition of the gyro heading using PEXEC 
script gyroexec0. Data were edited for headings outside the 0-360 degree 
range, saved, and then appended to a separate master file for each cruise.

On cruise 279 a problem was noted with clock drift by the gyro Level A that 
affected all cruises to varying degrees. This is discussed further in the 
next section.



17. ASHTECH 3DF GPS ATTITUDE DETERMINATION

The Ashtech ADU2 (Attitude Detection Unit 2) GPS is a system comprising four 
satellite receiving antennae mounted on the bridge top. Every second, the 
Ashtech calculates ship attitude (heading, pitch and roll) by comparing phase 
differences between the four incoming signals. These data are used in post-
processing to correct ADP current measurements for 'heading error'. This 
post-processing is necessary because in real-time the ADP uses the less 
accurate but more continuous ship's gyro heading to resolve east and north 
components of current. In processing, small drifts and biases in the gyro 
headings are corrected using the Ashtech heading measurements.

Processing the Ashtech data was broken down into a number of execs and manual 
steps as follows.

    ashexec0  acquisition of raw data

    ashexec1  merge Ashtech and gyro data. The difference between the ashtech 
              and gyro headings are calculated (a-ghdg) and set in the range 
              between -180 and 180.

    ashexec2  quality control the data (ashexec2). This exec removes data 
              outside the limits for the following variables:

                             hdg        0         360
                             pitch     -5           5
                             roll      -7           7
                             attf      -0.5         0.5
                             a-ghdg    -7           7
                             mrms       0.00001     0.01
                             brms       0.00001     0.1

  • Manually edit out any remaining outliers in a-ghdg using plxyed with 
    ash.pdf. 
  • Interpolate a-ghdg and plot the resulting file.
  • Append data to a master file for each cruise.

Data coverage for all three cruises was good, with only minor gaps.

i) 277
         time gap: 04 060 06:55:04 to 04 060 06:56:37 (≈ 1.5 min)
         time gap: 04 060 06:57:02 to 04 060 06:58:50 (≈ 2 min)
         time gap: 04 065 12:04:36 to 04 065 12:05:39 (≈ 1 min)
         time gap: 04 069 21:29:17 to 04 069 21:33:49 (≈ 4 min)
ii) 278
         time gap : 04 080 21:17:05 to 04 080 21:18:46 (101 s)
         time gap : 04 084 03:59:04 to 04 084 04:00:07 (63 s)
         time gap : 04 085 23:51:38 to 04 085 23:52:42 (64 s)
iii) 279
         time gap : 04 104 07:00:20 to 04 104 07:02:49
         time gap : 04 120 07:36:13 to 04 120 07:37:19
         time gap : 04 122 20:00:16 to 04 122 20:09:54
         time gap : 04 123 22:00:27 to 04 123 22:02:00
         time gap : 04 129 05:17:47 to 04 129 05:18:50

However on 279 it was noted that the Ashtech-Gyro differences were 
increasingly noisy with time. At the start of day 120 the level A's for all 
navigation data streams were reset (because of a master clock jump). The 
differences for that day revealed almost no noise. On investigation it was 
found that instead of keeping in step with the master clock, the gyro level A 
timebase had been slowly drifting. Up to the time of the level A resets, it 
had become 19 seconds adrift. As a consequence, all gyro, Ashtech, 150kHz and 
75kHz ADP data was reprocessed from the beginning.




18.   OCEAN SURVEYOR 75KHZ SHIPBOARD ACOUSTIC DOPPLER CURRENT PROFILER

18.1   Configuration and Performance

The 75kHz ADP is a narrow band phased array with a 30degree beam angle. Data 
was logged on a PC, using RDI data acquisition software (version 1.3). The 
instrument was configured to sample over 120 second intervals, with 60 bins 
of 16m thickness, and a blank beyond transmit of 8 m. Data were then averaged 
into 2 minute averaged files (Short Term Averaging, file extension STA) and 
10 minute averaged files (Long Term Averaging, file extension LTA). The 
former were used for all data processing. The software logs the PC clock time 
and its offset from GPS time. This offset was applied to the data during 
processing, before merging with navigation. Gyro heading and GPS Ashtech 
heading, location and time were fed as NMEA messages into the software which 
was configured to use the gyro heading for coordinate transformation.

The method for calibration of this instrument (and of the 150kHz SADP) relies 
on the collection of bottom track data where the velocity of the bottom 
relative to the ship can be measured in water depths less than 1000m. This 
reduces the amount of data collected in the rest of the water column and 
therefore increases the noise in the measurements. Consequently the 
instrument is swapped into bottom track mode only when appropriate.

During D277 and D278 bottom tracking was switched on early in the cruise 
(until 081 1803) and at the end (from 086 2222hrs). 

A problem was encountered after a restart of the logging software at jday 080 
(0130 hrs), after which time the fully processed data appeared to be 
contaminated by the ship's motion. Since the processing routines still 
resulted in good data for earlier raw files, we came to the conclusion that 
it was a problem with the software or software / configuration file set up. 
The RDI logging software takes input firstly from the configuration file, in 
which certain parameters such as bindepth can be specified, and secondly from 
parameters set manually in the graphical user interface. In the GUI under 
'options', 'transforms', the heading correction, phi, was set to 60 degrees 
as required. For some unknown reason, it was not logged as such. To correct 
for this, 60 degrees was subtracted from the phi value in surexec3, giving Φ = 
-60.3694. To attempt to correct the problem, we completely rebooted the 
system, including turning the ADP deck unit itself off. We also tried 
switching configuration files. None of these changes worked.

At day 085, four configuration tests were carried out, varying the number of 
bins and switching between bottom tracking and water tracking modes. Details 
can be found by comparing parameters in

the raw output files from the instrument.

During D279 bottom tracking was employed on this cruise at the beginning, 
covering some of the same ground as in 277. From day 97 to the end of the 
cruise the instrument remained in water track mode. The configuration file 
for this is listed in Appendix 18.

18.2   Processing

i) D277, D278

Data were logged on the OS75 PC and transferred by ftp to a UNIX workstation 
for processing.

    surexec0:  read data into PSTAR format from RDI binary file; write water 
               track data into files of the form sur279nn.raw and equivalent, 
               where nn is a two character code; write bottom track data 
               where present into files of the form sbt279mm; scale 
               velocities to cm/s and amplitude by 0.45 to dB; correct time 
               variable by combining GPS and the PC times; set the depth of 
               each bin.

    surexec1:  edit data (status flag equal to 1 is bad data); edit on 
               percent good variable; move ensemble time to the end of its 
               interval.

    surexec2:  merge data with ashtech-gyro difference file (created by 
               ashexec2) and correct heading

    surexec3:  calibrate velocities by scaling by factor A and rotating by 
               angle phi.

    surexec4:  calculate absolute velocities by merging with navigation data 
               (bestnav) and removing the ship's velocity over the ground 
               from the ADP data.

ii) D279

On this cruise an additional script was introduced after surexec0.

    surexec0b: take a sequence of files created by surexec0, append them 
               together and extract data spanning a complete day.

This was intended to create files for the 75kHz instrument with similar names 
and data ranges as the corresponding 150kHz data files and each of the 
navigation files. Output files from surexec0 were given two character letter 
codes ('aa', 'ab', etc.) and those from surexec0b were assigned two digit 
numbers as usual.

18.3   Calibration

Calibration of the 75kHz ADP was undertaken using the following procedure:

  • run through the normal processing steps as described above, with A=1 and 
    phi=0 in surexec3.
  • convert bottomew/bottomns into speed and direction (botspd,botdirn using 
    pcmcal)
  • convert ve/vn into speed and direction (shipspd,shipdirn using pcmcal)
  • calculate A (=shipspd/botspd) and phi (=shipdirn-botdirn)
  • select a valid subset of data and calculate mean A and phi.

i) 277

On this cruise, the only part of the track suitable for bottom tracking was 
at the end. This meant that no calibration could be performed. The processing 
used an amplitude factor A = 1.0 and misalignment angle Φ = 0°.

ii) 278

The bottom track data available when the ship was close to the Bahamas on 
cruise D277 was worked up on this cruise. The method involved the additional 
steps:

  • data were first averaged into 20 minute bins (using pavrge) before 
    calculation of speeds and directions
  • after calculation of speeds and directions, the PSTAR file was saved in 
    matlab (using pmatlb)
  • matlab script ADP_Aphi_calib.m was run which undertook the following 
    steps: 
           - convert phi such that it lies between -180 and 180 degrees
           - remove data from Florida Strait CTD section
           - remove data where botspd < 200
           - remove data where change in ship direction > 30 degrees between 
             20 minute averages
           - remove outliers (A < 0.9, A > 1.1, phi < -5, phi > 5)
           - remove data that is over 2 standard deviations from the mean
           - calculate A and phi from mean values of A and phi

The calibration values obtained were A = 1.0017 (sd = 0.0103), phi = -0.2743 
(sd = 0.6106). As noted earlier, for raw data files from 080 (0131 hrs), we 
had to use phi = -60.2743.

iii) 279

For this cruise data were not averaged to 20 minutes, remaining as 2 minute 
ensembles.

Calculation of the mean A and phi from spot values was undertaken by visual 
inspection of the data values. Two extra parameters were calculated: the 
minimum range (from each of the four transducers) to the bottom and the 
absolute difference of the minimum and maximum ranges. Records of data were 
included in the averaging if they occurred in a consecutive sequence of 
records which involved stable heading, ashtech correction and ship's speed, 
and if the range difference was less than 15m. The selected data were then 
plotted, outliers removed and A and phi values averaged. The resulting 
calibration values were: A = 1.004 and phi = -60.12 with standard deviations 
0.007 and 0.44 respectively. Figure 18.1 shows the final distribution of data 
for these values.

With the luxury of more time on this cruise than on the previous cruises, a 
number of problems were corrected for the earlier data. Values of A and phi 
from the 150kHz instrument had been wrongly applied to the 75kHz during 278. 
These files were corrected with the above final calibration. Different files 
had been assigned different ranges of bin depths because of the wrong choice 
of a depth offset of the first bin. These were all adjusted to 21m for the 
first bin depth.


Figure 18.1: Scatter plot of amplitude correction A against angular 
             correction phi calculated from all suitable two minute averages 
             from D277 and D279.



19.  150KHZ SHIPBOARD ACOUSTIC DOPPLER CURRENT PROFILER

19.1  Configuration and Performance

The 150kHz ADP data was logged using the IBM DAS. It was configured to sample 
for 120 second intervals, with 64 bins of 8 m thickness, and a blank beyond 
transmit of 4 m. Where shallow water was encountered, the ADP was operated in 
bottom track (BT) mode, otherwise it was operated in water track (noBT) mode.

ii) 278

The ADP performed without malfunction for the entire cruise.

iii) 279

At the start of this cruise, considerable problems were encountered in 
starting the ADP. The PC software used to control the instrument repeatedly 
failed to connect to the deck unit. After many attempts with varying 
configurations, the ADP started. Unfortunately the slave synchronization 
instruction was omitted in this permutation. Rather than risk it failing to 
start again, the instrument was left with this configuration for the duration 
of the cruise. Bottom tracking was permanently on. It should be emphasised 
that the 75kHz instrument is not a perfect replacement for the 150kHz since 
the 75kHz performs less well when the ship is underway, and has lower 
resolution in order to improve the statistics of measurements in each bin.

19.2  Clock Correction

The ADP uses its own internal clock that drifts by a few seconds per day. To 
correct this to the ship's master clock, careful track was kept of the 
deviations between the two clocks (see clockdrift.dat).

ii) 278

A matlab program (clockdrift.m) was used to calculate the drift (assuming 
that it was linear) and correct the ADP times for it. As a result the ADP 
time is synchronized to the ship's master clock.

iii) 279

On this cruise data were processed in daily chunks and the clock corrections 
applied by linear intepolation from selected values spanning the day.

19.3  Processing

    adpexec0: read raw data into PSTAR format from the RVS level C; split 
              into gridded depth dependent and non-gridded depth independent 
              files; scale velocities to cm/s and amplitudes by 0.45 into dB; 
              perform nominal edits and adjust bin depths to correct levels.

    adpexec1: correct data timebase.

    adpexec2_clock: merge data with ashtech-gyro difference data and correct 
              headings

    adpexec3: apply calibration values to the velocities, scaling speed by A 
              and rotating directions by phi.

    adpexec4: calculate absolute velocities by merging with bestnav 
              navigation data and removing ship's speed over the ground.

19.4  Calibration

As for the 75kHz instrument, calibration of this ADP is necessary.

i) 276 and 277

During the transect between Glasgow and Santa Cruz de Tenerife (D276), the 
150Khz was set up in bottom tracking mode. The calibration was done using the 
data coming of the British shelf Removing the outliers and averaging over 15 
minutes, the following calibration values were obtained: A=1.0019±0.0022 and 
Φ=-0.232 ± 0.1270. The misalignment angle differs markedly from previous 
cruises (Φ=3.82 for D262 and Φ=3.814 during D253), suggesting that the ADP's 
alignment was changed during the recent dry dock refit at Viano Do Castelo. 
These values were used throughout these two cruises.

ii) 278

On previous cruise (D277) it was noticed that the ADP calibration might not 
be correct, and therefore a new calibration was undertaken for both SADPs.

Data was taken from the period when the ADP was in bottom track mode and the 
ship was close to the Bahamas. The steps undertaken to calibrate the ADP are 
the same as for the 75kHz. The calibration procedure produced values of 
A=1.0129±0.0135, Φ=-0.3694±0.5049.

iii) 279

It was noted on this cruise that plots of absolute velocity vectors against 
time for the 150kHz ADP showed clear differences between on and off station 
data. This was not true of the 75kHz. This is an indication of a poor 
calibration. Examination of all bottom track data assembled together produced 
inconsistent estimates for A and phi. Consequently because of the quality of 
the calibration for the 75kHz it was decided to use that instrument to 
calibrate the 150kHz.

Comparison of averaged relative velocities from the 150kHz and 75kHz ADP's 
lead to correction terms:

dA=0.985 (0.0142,104) and dΦ=0.0887 (0.17,94) and therefore an overall set of 
values of A=0.9977 and Φ=-0.2807.

Figure 19.1 shows a comparison of underway velocity profiles from both 
instruments after final calibration. Agreement between the two is remarkable.


Figure 19.1: Velocity profiles from the 75kHz (black) and 150kHz (red) ADCP's 
             averaged from underway data between each station pair. Each 
             profile is plotted on an axis of station number at the halfway 
             point at a scale of 50cm/s per station unit. A zero velocity 
             line is shown as a black dotted line for each profile. a) 
             Stations 2 - 32; b) Stations 32 - 64; c) Stations 64 - 96; d) 
             Stations 96 - 125.

Appendix 19.A

Configuration file used for the OS75 SADP for D279 water track mode.
;----------------------------------------------------------------------------
-\
; ADP Command File for use with VmDas software.
; 
; ADP type: 75kHz Ocean Surveyor
; Setup name: default
; Setup type: Low resolution, long range profile(narrowband)
; 
; NOTE: Any line beginning with a semicolon in the first 
; column is treated as a comment and is ignored by 
; the VmDas software.
;
; NOTE: This file is best viewed with a fixed-point font (eg. courier).
;----------------------------------------------------------------------------
/

; Restore factory default settings in the ADP
cr1

; set the data collection baud rate to 115200 bps, 
; no parity, one stop bit, 8 data bits
; NOTE: VmDas sends baud rate change command after all other commands in 
; this file, so that it is not made permanent by a CK command.
cb811

; Set for narrowband profile mode, single-ping ensembles, 
; sixty 16m bins, 8m blanking distance, 390 mm/s ambiguity vel
NP001
NF800
NS1600
NN60


WP000

WF0800
WS1600
WN040

WV390

; Disable single-ping bottom track, 
; Set maximum bottom search depth to 1200 meters
BP000
BX12000

; output velocity, correlation, echo intensity, percent good
WD111100000

; Two seconds between bottom and water pings
TP000200

; Two seconds between ensembles
; Since VmDas uses manual pinging, TE is ignored by the ADP.
; You must set the time between ensemble in the VmDas Communication options
TE00000200

; Set to calculate speed-of-sound, no depth sensor, 
; external synchro heading sensor, use internal 
; transducer temperature sensor
EZ1020001

; Output beam data (rotations are done in software)
EX00000

; Set transducer depth to 5.3m
ED00053

; No synchro 
CX0,0

; save this setup to non-volatile memory in the ADP
CK




Appendix 19.B

Configuration file for the 150kHZ SADP used on all three cruises. The bottom 
track file is the same but with instruction BT 1 instead of BT 0.
AD,SI,HUNDREDTHS 120.00 Sampling interval
AD,NB,WHOLE  64 Number of Depth Bins
AD,BL,WHOLE  3 Bin Length
AD,PL,WHOLE  8 Pulse Length
AD,BK,TENTHS  4.0 Blank Beyond Transmit
AD,PE,WHOLE  1 Pings Per Ensemble
AD,PC,HUNDREDTHS 1.00 Pulse Cycle Time
AD,PG,WHOLE  25 Percent Pings Good Threshold
XX,OD2,WHOLE  5 [SYSTEM DEFAULT, OD2]
XX,TE,HUNDREDTHS 0.00 [SYSTEM DEFAULT, TE]
AD,US,BOOLE  YES Use Direct Commands on StartUp
DP,TR,BOOLE  NO Toggle roll compensation
DP,TP,BOOLE  NO Toggle Pitch compensation
DP,TH,BOOLE  YES Toggle Heading compensation
DP,VS,BOOLE  YES Calculate Sound Velocity from TEMP/Salinity
DP,UR,BOOLE  NO Use Reference Layer
DP,FR,WHOLE  6 First Bin for reference Layer
DP,LR,WHOLE  15 Last Bin for reference Layer
DP,BT,BOOLE  NO Use Bottom Track
DP,B3,BOOLE  NO Use 3 Beam Solutions
DP,EV,BOOLE  YES Use Error Velocity as Percent Good Criterion
DP,ME,TENTHS  150.0 Max. Error Velocity for Valid Data (cm/sec)
DR,RD,BOOLE  YES Recording on disk
DR,RX,BOOLE  YES Record N/S (FORE/AFT) Vel.
DR,RY,BOOLE  YES Record E/W (FORT/STBD) Vel.
DR,RZ,BOOLE  YES Record vertical vel.
DR,RE,BOOLE  YES Record error Good
DR,RB,BOOLE  NO Bytes of user prog. buffer
DR,RP,BOOLE  YES Record Percent good
DR,RA,BOOLE  YES Record average AGC/Bin
DR,RN,BOOLE  YES Record Ancillary data
DR,AP,BOOLE  YES Auto-ping on start-up
XX,LDR,TRI  4 [SYSTEM DEFAULT, LDR]
XX,RB2,WHOLE  192 [SYSTEM DEFAULT, RB2]
DR,RC,BOOLE  NO Record CTD data
XX,FB,WHOLE  1 [SYSTEM DEFAULT, FB]
XX,PU,BOOLE  NO [SYSTEM DEFAULT, PU]
GC,TG,TRI  1 DISPLAY (NO/GRAPH/TAB)
GC,ZV,WHOLE  1 ZERO VELOCITY REFERENCE (S/B/M/L)
GC,VL,WHOLE  -100 LOWEST VELOCITY ON GRAPH
CG,VH,WHOLE  100 HIGHEST VELOCITY ON GRAPH
GC,DL,WHOLE  0 LOWEST DEPTHS ON GRAPH

GC,DH,WHOLE  500 HIGHEST DEPTHS ON GRAPH
GC,SW,BOOLE  NO SET DEPTHS WINDOW TO INCLUDE ALL BINS
GC,MP,WHOLE  25 MINIMUM PERCENT GOOD TO PLOT
SG,PNS,BOOLE  YES PLOT NORTH/SOUTH VEL.
SG,PEW,BOOLE  YES PLOT EAST/WEST VEL.
SG,PVT,BOOLE  YES PLOT VERTICAL VEL.
SG,PEV,BOOLE  YES PLOT ERROR VEL.
SG,PPE,BOOLE  NO PLOT PERCENT ERROR
SG,PMD,BOOLE  NO PLOT MAG AND DIR
SG,PSW,BOOLE  NO PLOT AVERAGE SP. W.
SG,PAV,BOOLE  YES PLOT AVERAGE AGC.
SG,PPG,BOOLE  YES PLOT PERCENT GOOD
SG,PD1,BOOLE  NO PLOT DOPPLER 1
SG,PD2,BOOLE  NO PLOT DOPPLER 2
SG,PD3,BOOLE  NO PLOT DOPPLER 3
SG,PD4,BOOLE  NO PLOT DOPPLER 4
SG,PW1,BOOLE  NO PLOT SP. W. 1
SG,PW2,BOOLE  NO PLOT SP. W. 2
SG,PW3,BOOLE  NO PLOT SP. W. 3
SG,PW4,BOOLE  NO PLOT SP. W. 4
SG,PA1,BOOLE  NO PLOT AGC 1
SG,PA2,BOOLE  NO PLOT AGC 2
SG,PA3,BOOLE  NO PLOT AGC 3
SG,PA4,BOOLE  NO PLOT AGC 4
SG,PP3,BOOLE  NO PLOT 3-BEAM SOLUTION
SS,OD,WHOLE  5 OffSet for Depth
SS,OH,TENTHS  45.0 OffSet for Heading
SS,OP,TENTHS  0.0 OffSet for Pitch
SS,ZR,TENTHS  0.0 OffSet for Roll
SS,OT,HUNDREDTHS 45.00 OffSet FOR temp
SS,ST,HUNDREDTHS 50.00 Scale for Temp
SS,SL,HUNDREDTHS 35.00 Salinity (PPT)
SS,UD,BOOLE  YES Toggle UP/DOWN
SS,CV,BOOLE  NO Toggle concave/Convex transducerhead
SS,MA,TENTHS  30.0 Mounting angle for transducers.
SS,SS,HUNDREDTHS 1500.00 Speed of Sound (m/sec)
XX,GP,BOOLE  YES [SYSTEM DEFAULT, GP]
XX,DD,TENTHS  1.0 [SYSTEM DEFAULT, DD]
XX,PT,BOOLE  NO [SYSTEM DEFAULT, PT]
XX,TU,TRI  2 [SYSTEM DEFAULT, TU]
TB,FP,WHOLE  1 FIRST BINS TO PRINT
TB,LP,WHOLE  64 LAST BIN TO PRINT
TB,SK,WHOLE  6 SKIP INTERVAL BETWEEN BINS
TB,DT,BOOLE  YES DIAGNOSTIC TAB MODE
DU,TD,BOOLE  NO TOGGLE USE OF DUMMY DATA
XX,PN,WHOLE  0 [SYSTEM DEFAULT, PN]
DR,SD,WHOLE  4 Second recording drive
DR,PD,WHOLE  4 First recording drive (1=A:,2=B: ... )
DP,PX,BOOLE  NO Profiler does XYZE transform
SS,LC,TENTHS  5.0 Limit of Knots change
SS,NW,TENTHS  0.5 Weight of new knots of value
GC,GM,TRI  2 GRAPHICS CONTROL 0=LO RES, 1=HI RES, 2=ENHANCED
AD,PS,BOOLE  YES YES=SERIAL/NO=PARALLEL Profiler Link
XX,LNN,BOOLE  YES [SYSTEM DEFAULT, LNN]
XX,BM,BOOLE  YES [SYSTEM DEFAULT, BM]
XX,RSD,BOOLE  NO RECORD STANDARD DEVIATION OF VELOCITIES PER BIN
XX,DRV,WHOLE  4 [SYSTEM DEFAULT, DRV]
XX,PBD,WHOLE  3 [SYSTEM DEFAULT, PBD]
TB,RS,BOOLE  NO SHOW RHPT STATISTIC
UX,EE,BOOLE  NO ENABLE EXIT TO EXTERNAL PROGRAM
SS,VSC,TRI  0 Velocity scale adjustment
AD,DM,BOOLE  YES USE DMA
TB,SC,BOOLE  NO SHOW CTD DATA
AD,CW,BOOLE  NO Collect spectral width
DR,RW,BOOLE  NO Record average SP.W./Bin
DR,RRD,BOOLE  NO Record last raw dopplers
DR,RRA,BOOLE  NO Record last raw AGC
DR,RRW,BOOLE  NO Record last SP.W.
DR,R3,BOOLE  NO Record average 3-Beam solutions
DR,RBS,BOOLE  YES Record beam statistic
XX,STD,BOOLE  NO [SYSTEM DEFAULT, STD]
LR,HB,HUNDREDTHS 0.00 Heading Bias
SL,1,ARRAY5 1 1 8 NONE 19200 PROFILER
SL,2,ARRAY5 0 1 8 NONE 1200 LORAN RECEIVER
SL,3,ARRAY5 0 1 8 NONE 4800 REMOTE DISPLAY
SL,4,ARRAY5 2 1 8 NONE 9600 ENSEMBLE OUTPUT
SL,5,ARRAY5 0 1 8 NONE 1200 AUX 1
SL,6,ARRAY5 0 1 8 NONE 1200 AUX 2
DU,1,ARRAY6 100.00 100.00 60.00 0.00 0.00 YES D1
DU,2,ARRAY6 -100.00 -100.00 60.00 0.00 0.00 YES D2
DU,3,ARRAY6 200.00 200.00 60.00 0.00 0.00 YES D3
DU,4,ARRAY6 -200.00 -200.00 60.00 0.00 0.00 YES D4
DU,5,ARRAY6 200.00 19.00 60.00 0.00 0.00 YES AGC
DU,6,ARRAY6 0.00 0.00 60.00 0.00 0.00 NO SP. W.
DU,7,ARRAY6 0.00 0.00 60.00 0.00 0.00 NO ROLL
DU,8,ARRAY6 0.00 0.00 60.00 0.00 0.00 NO PITCH
DU,9,ARRAY6 0.00 0.00 60.00 0.00 0.00 NO HEADING
DU,10,ARRAY6 0.00 0.00 60.00 0.00 0.00 NO TEMPERATURE
DC,1,SPECIAL "FH00004" MACRO 1
DC,2,SPECIAL "DA24" MACRO 2
CI,1,SPECIAL "D277" CRUISE ID GOES HERE 
LR,1,SPECIAL " " LORAN FILE NAME GOES HERE

The bottom track configuration file is the same except for the following 
exchanges:

DP,BT,BOOLE   NO Use Bottom Track -> DP,BT,BOOLE   YES Use Bottom Track
SS,OD,WHOLE   5 OffSet for Depth  -> SS,OD,WHOLE   13 OffSet for Depth
DC,1,SPECIAL  "FH00004" MACRO 1   -> DC,1,SPECIAL  "FH00001" MACRO 1


20.  MEASUREMENT OF DISSOLVED OXYGEN
     (Rhiannon Mather, Angela Landolfi, Richard Sanders)

Dissolved oxygen samples were drawn from Niskin bottles on each CTD cast 
following the collection of samples for CFC analysis, and analysed using the 
Winkler whole bottle titration method. Between one and six duplicate samples 
were drawn on most casts from various Niskin bottles.

Samples were drawn through short pieces of silicone tubing into clear, pre-
calibrated (approximately 100ml) wide-necked glass bottles. The temperature 
of each sample was taken using a handheld temperature probe immediately prior 
to fixing on deck with 1ml manganous chloride and 1ml sodium hydroxide. These 
chemicals were dispensed using Anachem dispensers, which were periodically 
rinsed throughout the cruise. The temperature at fixing of each of the 
samples was later used to calculate any temperature dependent changes in the 
volume of the sample bottles. After fixing, the lid of the sample bottles was 
inserted, taking care to ensure that no air bubbles were introduced, and the 
bottles shaken thoroughly. The samples were then taken to the CT (controlled 
temperature) laboratory, whereupon they were shaken once more, and then 
stored for later analysis. All reagents were prepared after Dickson (1984).

Analysis of the samples in the CT laboratory started at a minimum of one hour 
after the collection of the samples. The SIS Winkler whole bottle titration 
method with spectrophotometric end-point was used for analysis. Immediately 
prior to titration, each sample was acidified with 1ml of sulphuric acid 
(using an Anachem dispenser) in order to dissolve the precipitate and release 
the iodate ions, and stirred with a magnetic stir bar set at a constant spin. 
Movement of the ship may have disturbed the magnetic stirrer bar, possibly 
resulting in less effective stirring, which would lead to a longer titration 
time, but it is unlikely that this would have affected the accuracy of the 
end-point determination.

The user variable parameters in the SIS supplied software, (parameters screen 
in the options menu), were determined by trial and error at the start of the 
cruise and applied throughout. The following values were used: Stepsize 10, 
Wait time, 10, Fast delay, 3, Slow delay 3, Fast factor 0.5. This parameter 
set resulted in titration times of less than four minutes.

Several batches of sodium thiosulphate solution (25gL-1) were made up during 
the cruise to titrate against the seawater samples. As the thiosulphate 
solution is unstable, it was standardised by titrating it against 5ml of 
certified standard 0.01N solution of potassium iodate. This was done every 
two to three days; the volume of thiosulphate required to titrate 5ml of this 
standard was then used in calculations of oxygen concentration in an MS Excel 
spreadsheet following the equations of Dickson (1994). Batch 3 of the 
thiosulphate solutions was very unstable (see Figure 20.1); the volume 
required to titrate 5mls of potassium iodate increased rapidly over a couple 
of days. Following this discovery, a new batch of sodium thiosulphate 
solution was made up. To monitor the breakdown of the new solution more 
carefully and without using up the certified standards, a batch of potassium 
iodate solution was made up by dissolving 0.3567g of potassium iodate in 1L 
Milli-Q water. This new batch was relatively stable (see fig. 1), and results 
from the stations titrated using batch 3 were discarded. The reagent blank 
was evaluated at the start of the cruise and was found to be 1.0 x10-3 ml for 
the single batches of reagents used during the cruise. This value was applied 
to all calculations undertaken.

The duplicate samples drawn at each station were compared and the percentage 
difference between them is shown in Figure 20.2, for a sample size of 77 
pairs of duplicates. When obvious outliers are removed, the mean percentage 
difference between duplicate samples is 0.62% (standard deviation = 0.5487). 
Percentage differences greater than 3% accounted for 11.5 % of the samples.


Figure 20.1: Volume of sodium thiosulphate used to titrate 5mls of certified 
             standard of potassium iodate the duration of the cruise.

Figure 20.2: Percentage difference of oxygen concentration between duplicate 
             samples.


20.1  Problems

In the time taken to sample the complete rosette of Niskin bottles, some of 
the later bottles may have warmed slightly in the sun. The handheld 
temperature probes are subject to a certain amount of variability, and in 
several cases it was difficult to obtain reliable temperatures. Over the 
length of the cruise, several different thermometers were used. In total, 
2699 samples were analysed using the SIS Winkler apparatus. During the 
cruise, there were 57 approximation failures (2.11% of samples). Other 
failures accounted for 0.74% of samples. 




21.  MEASUREMENT OF NUTRIENTS
     (Richard Sanders)

Analysis for nitrate + nitrite (hereinafter nitrate), phosphate and silicate 
was undertaken on a skalar sanplus autoanalyser following methods described 
by Kirkwood  (1994) with the exception that the pump rates through the 
phosphate line are increased by a factor of 1.5 which improves 
reproducability and peak shape. Samples were drawn from niskin bottles into 
25ml sterilin coulter counter vials and kept refrigerated at 4 C until 
analysis which commenced within 24 hours. Stations were run in batches of 2-6 
with most runs containing 3 or 4 stations. Overall 34 runs were undertaken. 
An artificial seawater matrix (ASW) of 40 g/l sodium chloride was used as the 
intersample wash and standard matrix. The nutrient free status of this 
solution was checked by running Ocean Scientific International (OSI) nutrient 
free seawater on every run. In a departure from our previous methodology a 
single set of mixed standards were made up at the start of the cruise and 
used throughout the cruise. These were made by diluting 5 mM solutions made 
from weighed dried salts in 1 l of ASW into plastic 1l volumetric flasks that 
had been cleaned by soaking for 6 weeks in MQ water. This was in an effort to 
minimise the run to run variability in concentrations observed on previous 
cruises. OSI nutrient standard solutions were used sporadically during the 
cruise to monitor the degradation of these standards. Data was transferred to 
another computer initially using a zip disk and then after station 66 by 
means of a memory stick. The zip disk transfer route was unreliable and 
resulted in a delay between sample analysis and data work up of 8-10 
stations. After station 66 data was worked up immediately. This delay has the 
effect that the problems with the nitrate line described below could not be 
evaluated in close to real time. Data processing was undertaken using Skalar 
proprietary software. Generally this was straightforward however a detailed 
examination of nitrate data from stations 20-60 was needed to achieve 
acceptable calibrations and bulk nutrient values. The wash time and sample 
time were 90 seconds, the lines were washed daily with 0.25M NaOH (P) and 10% 
Decon (N, Si). Time series of baseline, bulk standard concentration, 
instrument sensitivity, calibration curve correlation coefficient, nitrate 
reduction efficiency and duplicate difference were compiled and updated on a 
daily basis.

21.1  Performance of the Analyser

1) In the early part of the cruise the phosphate baseline on runs 1-3 
   (stations 2-21) suffered frequent catastrophic baseline degradations. All 
   the samples were rerun however duplicates could not be run as the 
   available duplicate time was use to reanalyse samples. This was alleviated 
   mid run by removing the flow cell and shaking it vigorously and a 
   eliminated over the longer term by refitting some elements of the line and 
   reducing the pull through rate. Stations 49-52 were also affected by this 
   problem and no P data is available for stations 51 and 52. Stations 71-74 
   were compromised by a failure of the temperature water bath. These 
   stations were reanalysed 24 hours later using samples from salinity 
   bottles.

2) The nitrate line was very noisy between stations 22 and 60. Initially this 
   was suspected to be due to a fault with the reagents which were renewed 
   several times however after this failed to rectify the situation the 
   cadmium column was repacked on two occasions. This also failed to rectify 
   the situation and a new cadmium column was therefore fitted which gave no 
   problems during the rest of the cruise. Stations 22-60 were reprocessed to 
   give bulk nutrient values in line with those from the remainder of the 
   stations. The effect of this on data quality has yet to be systematically 
   evaluated.

21.2  Analyser Performance

The performance of the autoanalyser is monitored via the following 
parameters: baseline value, calibration curve slope, regression coefficient 
of the calibration curve, nitrate reduction efficiency. Time series of these 
parameters are shown below in Figures 21.1 to 21.3.


Figure 21.1: Autoanalyser sensitivity.


The instrument sensitivity for nitrate varied widely and unpredictably during 
the cruise by up to 40%. Phosphate and silicate sensitivity behaved much more 
reproducibly with these parameters varying by about 10% over the 5 week 
period of observations.


Figure 21.2: Calibration curve regression coefficients and reduction 
             efficiency.


The quality of the calibration curves was generally good with 95% having 
regression coefficients of better than 0.999. The reduction efficiency of the 
cadmium column was <100% during the early part of the cruise. This increased 
to better than 100% after station 66 at which point when we changed the 
column. Then the efficiency increased to approximately 100%.


Figure 21.3: Baseline values.

The baseline value of the instrument barely changed through the cruise, with 
the exception of phosphate which declined after the first run from 6300 to 
about 5900.



21.3 Data Quality

Precision of measurements: The short term precision of the measurements was 
evaluated by running one or two duplicate samples per station (thus 3-6 per 
run). Figure 21.4 shows time series of the percentage difference between the 
duplicates for a) silicate, b) nitrate and c) phosphate together with five 
point running means through the data. The mean differences for Si, N and P 
were 0.67, 1.63 and 2.04%. However this conceals substantial variability in 
both N and P precision during the cruise. A group of stations from 
approximately 25 - 60 have poor N precision and the precision of the 
phosphate analyses improved over the course of the cruise from about 5% to 
about 1%.


Figure 21.4: Percentage difference between duplicates for: a - nitrate, b - 
             silicate, and c - phosphate.

Internal consistency of measurements: This was evaluated by using a deep 
water sample taken on station 1. This was run on every station. The 
concentrations of nitrate, phosphate and silicate in this sample over time 
are shown in Figure 21.5.


Figure 21.5: Concentrations of nitrate, phosphate and silicate with time.


Nitrate concentration appeared to be invariant whereas the P and Si 
concentrations declined markedly over the cruise. The variability of bulk 
nutrient concentration from the mean is indicative of the internal 
consistency of the dataset. For nitrate this is simple to evaluate (Figure 
21.6) as the concentration appeared to be invariant. The residual 
concentration appears to be normally distributed and shows no significant 
trend over time. The absolute average residual value was 0.27 micromoles per 
litre or 1.2%.


Figure 21.6: Nitrate residuals.


For phosphate and silicate a linear function was fitted which predicted 
concentration as a function of elapsed day. This regression was used to 
generate values for P and Si for each day and the residual difference 
calculated (Figures 21.7 and 21.8).


Figure 21.7: Phosphate residuals.

Figure 21.8: Silicate residuals.


Both P and Si residuals appear to be normally distributed with Si (and to a 
lesser extent P) residuals displaying a sinusoidal pattern with time for 
unknown reasons. The mean residual values are 0.12 micromoles per litre or 
1.17% for Si and 0.03 micromoles per litre or 2.1% for P.

21.4  Accuracy of Measurements

The accuracy was monitored by use of OSI nutrient standard solutions which 
need to be diluted by the user. The analysis of these standards gave values 
of P 1.01 +/- 0.02 micromoles per litre for a nominally 1 micromolar 
solution, N 10.9 +/- 0.13 for a nominally 10 micromolar solution and Si 21.4 
+/- 0.1 micromoles per litre for a nominally 20 micromolar solution. These 
imply that the N and Si results are too low by about 10 and 5% respectively. 
The standards used on this cruise have been retained for further 
investigation and a comparison with historical data will also be used to 
address this issue.



22.  AUTOFLUX - THE AUTONOMOUS AIR-SEA INTERACTION SYSTEM
     (Margaret Yelland and Robin Pascal)

AutoFlux is an autonomous, stand-alone system that obtains direct, near real-
time (2hr) measurements of the air-sea turbulent fluxes of momentum and 
sensible and latent heat in addition to various mean meteorological 
parameters. The two main aims of the present deployment were 1) testing of a 
new Licor sensor to determine its suitability for making direct measurements 
of the air-sea CO2 flux, and 2) system development (detailed below). The 
AutoFlux system was mobilised in Govan in February 2004 prior to the start of 
cruise D276 and left to run autonomously until the beginning of D279. JRD and 
OED staff then joined the ship to install the new sensors and develop the 
system during D279. The system was then left to run autonomously during the 
return passage from Tenerife to Govan and was demobilised in Govan at the 
beginning of June.

Until this cruise, the system obtained flux measurements using the inertial 
dissipation (ID) method that relies on good sensor response at frequencies up 
to 10 Hz. The ID method has the advantage that the flux results a) are 
insensitive to the motion of the ship and b) can be corrected for the effects 
of the presence of the ship distorting the air flow to the sensors. Momentum 
and latent heat flux measurements have been successfully made using this 
method for a number of years. Sensible heat and CO2 flux measurements are made 
more difficult by the lack of sensors with the required high frequency 
response. For these fluxes the eddy correlation (EC) method provides an 
alternative. This method requires good sensor response up to only about 2 to 
3 Hz, but is a) very sensitive to ship motion and b) the fluxes can not be 
directly corrected for the effect of air flow distortion. The development 
work on this cruise entailed testing and integration of a MotionPak sensor in 
order to measure the ship motion and thus make EC measurements of all the 
fluxes. Once EC fluxes are obtained they can be corrected for flow distortion 
effects by comparison with the corrected ID fluxes where available. Since the 
scalar fluxes (sensible and latent heat and CO2) are all affected by flow 
distortion in the same fashion, only one ID scalar flux is required in order 
to quantify the effects of flow distortion on EC scalar fluxes. If the new CO2 
sensor performs adequately at low frequencies, direct measurements of the 
air-sea CO2 flux will thus be obtained. In collaboration with the UEA carbon 
team, any successful CO2 flux measurements will be used to improve the 
parameterisation of the CO2 transfer velocity.

This report describes the AutoFlux instrumentation (Section 22.1). A brief 
discussion of the performance of the mean meteorological sensors is given in 
Section 22.2, where comparisons are made between the ship's instruments with 
those of AutoFlux where possible. As part of a separate project visual 
observation of the cloud cover were made and related to the downwelling long 
wave radiation measurements obtained from the AutoFlux system. These are also 
discussed in Section 22.2. Initial flux results are described in Section 
22.3. Appendix A lists significant events such as periods when data logging 
was stopped, and Appendix B contains figures showing time series of the mean 
meteorological data. All times refer to GMT.

More information on air-sea fluxes and the AutoFlux project in particular can 
be found under http://www.soc.soton.ac.uk/JRD/MET/AUTOFLUX.


22.1  Instrumentation

The SOC Meteorology Team instrumented the RRS Discovery with a variety of 
meteorological sensors. The mean meteorological sensors (Table 22.1) measured 
air temperature and humidity, wind speed and direction, and incoming longwave 
(4-50 micron) radiation. The Windsonic is a new 2-D anemometer on loan for 
trials from the manufacturers, Gill Instruments Ltd. The surface fluxes of 
momentum, heat, moisture and CO2 were obtained using the fast-response 
instruments in Table 22.2. The HS and R3 sonic anemometers provided mean wind 
speed and direction data in addition to the momentum and sensible heat flux 
estimates. A new sensor based on a fast response thermistor was also trialed 
for the first time during D279. The data from the thermistor was logged via 
the analogue input of the R3.

To obtain EC fluxes, ship motion data from the MotionPak system has to be 
synchronised with those from the other fast response sensors. In order to 
achieve this the MotionPak output was logged via the analogue input channel 
of the HS anemometer. In addition, a timer circuit was added in to the HS 
sonic interface unit. This circuit generated a square wave sync signal which 
was input to the analogue channel of the Licor and to the PRT input to the 
HS. Once allowance was made for the 0.185-second delay in the H2O and CO2 
output from the Licor, this enabled synchronisation of all fast response data 
except those from the R3. The period of the sync signal was increased from 
2.34 seconds (47 samples) to 8.6 seconds (172 samples) on day 111 at 2200 in 
order to remove any ambiguity when synchronising the data streams 
automatically.

Navigation data were logged in real time at 2-second intervals, using the 
ship's data stream rather than the separate AutoFlux GPS and compass. These 
data are used to convert the relative (measured) wind speed and direction to 
true wind speed and direction. The ship's mean meteorological data were also 
logged in real time at 2-second intervals. The details of the ship's 
meteorological instruments are given in Table 22.3.

All data were acquired continuously, using a 58 minute sampling period every 
hour (the remaining 2 minutes being used for initial data processing), and 
logged on "nimbus", a SunBlade 100 workstation. Processing of all data and 
calculation of the ID fluxes was performed automatically on "nimbus" during 
the following hour. Program monitoring software monitored all acquisition and 
processing programs and automatically restarted those that crashed. A time 
sync program was used to keep the workstation time synchronised with the GPS 
time stamp contained in the navigation data. Both "nimbus" and all the 
AutoFlux sensors were powered via a UPS. The EC flux processing was developed 
during the cruise and performed on a second SunBlade 100 ("cirrus") but was 
not integrated in to the automatic processing.

All of the instruments were mounted on the ship's foremast (Figure 22.1) in 
order to obtain the best exposure. The psychrometers and the fast response 
sensors were located on the foremast platform and the radiation sensors were 
mounted on a platform installed at the top of the foremast extension. The 
heights of the instruments above the foremast platform were: HS sonic 
anemometer, 2.11 m; R3 sonic anemometer 2.81 m; psychrometers 1.85 m; 
thermistor sensor 1.80 m; Licor H2O / CO2 sensor 1.21 m; Windsonic anemometer 
2.11 m.

22.2   Mean Meteorological Parameters

Air Temperature and Humidity

Two wet- and dry-bulb psychrometers were installed on the foremast and 
performed well until the end of day 117 when the starboard wet bulb stopped 
wicking. This did not cause any problems since the automatic processing 
chooses the lowest of the two wet bulb temperatures. The wicking problem was 
corrected on day 127. Excluding this period, 1 minute averaged data from the 
two psychrometers showed that the mean difference between the wet bulb 
temperatures was 0.05º (standard deviation of 0.07º), which is within the 
sensor specification. The difference between the dry bulb temperatures was 
only 0.005º (s.d. 0.15): the standard deviation was larger due to occasional 
drips from the wet bulbs falling on the dry bulbs. Again the problem was 
circumvented by the automatic processing which selects the higher of the two 
temperatures. A comparison between the ship's air temperature sensor and the 
best psychrometer data showed that the former is biased high by 0.18º (s.d. 
0.12º). This could be due to the effects of solar heating since the ship's 
sensor is only ventilated rather than aspirated.

Relative humidity was calculated from the psychrometer data and compared to 
the ship's humidity sensor. The ship's sensor read high by 4.6 % (s.d 1%). 
Only 1% or less of this can be attributed to the automatic processing 
selecting the lowest wet bulb and the highest dry bulb, thus tending to bias 
the psychrometer humidities slightly low.

Wind Speed and Direction

There were four anemometers mounted on the foremast platform (Figure 22.1). 
On the port side were the ship's propeller anemometer and vane plus the 2-D 
Windsonic on trial from Gill Instruments Ltd. On the starboard side were two 
fast response Solent sonic anemometers, an HS and an R3. Both measured all 
three components of wind speed and both are calibrated on a regular basis. 
The HS anemometer was the best exposed and will be used as the reference 
instrument in the following comparison. The measured wind speeds (uncorrected 
for ship speed) from each anemometer are compared to those from the HS in 
Figure 22.2, which shows the wind speed ratio (measured / HS measured) 
against relative wind direction for each anemometer. A wind blowing directly 
on to the bows is at a relative wind direction of 180 degrees. For a bow-on 
wind, the R3 sonic and the ship anemometer read high by about 5% and the 
Windsonic was high by nearly 15%. Some of the biases will be due to flow 
distortion. Accurate flow distortion corrections have yet to be determined 
for the precise anemometer locations, but previous work (Yelland et al. 2002) 
has shown that the bias at the Windsonic and HS anemometer sites should be 
between -1 and +2%. The 15 % bias in the Windsonic data is much greater than 
that expected due to flow distortion effects. Furthermore, the wind sonic and 
ship's anemometer were mounted close together, suggesting that the Windsonic 
is biased high by at least 10%. Figure 22.2 also clearly shows that the 
effects for flow distortion are, as expected, very sensitive to the relative 
wind direction. Since the HS and R3 sonics were located on the opposite side 
of the foremast extension to the other two anemometers, roughly 50% of the 
trend in wind speed error seen in the latter is actually due to the variation 
in flow distortion with wind direction at the HS anemometer site. The large 
dips in the speed ratios at 90 and 270 degrees are due to the HS/R3 and 
Windsonic/ship anemometers being in the wake of the foremast extension for 
winds from the port and starboard beams respectively. Figure 22.3 shows the 
difference in relative wind direction as measured by each anemometer compared 
to that from the HS. For bow-on winds the HS, R3 and ship's anemometers agree 
to with 4 degrees but the Windsonic appears to be mis-aligned by 10 degrees. 

TIR and PAR Sensors

The ship carried two total irradiance sensors, one (Ptir) on the port side of 
the foremast platform and the other (Stir) on the starboard. These measure 
downwelling radiation in the wavelength ranges given in Table 22.3. Ptir 
functioned well throughout but Stir intermittently gave very noisy values for 
periods of up to a few days at a time. Figure 22.4 gives an example of this. 
It can be seen that from day 115 to day 118 the Stir values were very noisy 
even at night when zero W/m2 should be measured. It was thought that the 
problem may lie in the cabling between the junction box on the foremast and 
the acquisition PC in the main laboratory. However, when the two sensors were 
plugged into each other's connector in the foremast junction box the original 
Stir continued to be at fault, showing that the problem lies in the sensor 
itself or in the cable between sensor and junction box. The periods of noisy 
data seemed to occur during and after rain or times of high humidity, 
suggesting that moisture ingress may be the problem.

Mounted alongside each TIR sensor is a "PAR" (photosynthetically active 
radiation) sensor. Early examination of the data from these revealed a number 
of problems. The port sensor (Ppar) serial number was correct in the 
"surfmet" acquisition software and the correct calibration was applied in the 
data output from the surfmet PC to the AutoFlux system. However, the sensor 
is actually a solarimeter rather than a PAR sensor and measures radiation in 
a different wavelength range (Table 22.3). In contrast, the starboard (Spar) 
sensor was indeed a PAR sensor but its serial number was illegible. The 
Surfmet sensor handbook contained calibrations for two possible sensors, and 
both of these were included in the "smtexec" processing scripts. However, in 
the scripts both calibrations were commented out. Matters were confused 
further when it was discovered that the calibration applied by the 
acquisition PC agreed with neither of those in the handbook. Determination of 
the correct calibration was not possible since there were no data from a 
second PAR sensor for comparison.

A complete overhaul of all TIR and "PAR" sensors is required.

Long Wave Radiation

As part of the AutoFlux instrumentation, two Epply pyrgeometers were 
installed on top of the foremast extension. These sensors measure incoming 
long wave (LW) radiation. Following the procedure of Pascal and Josey (2000) 
three outputs from each sensor were recorded and a correction made for short-
wave leakage. The Ptir data were used for this purpose. From 1 minute 
averages of the resulting LW data, the mean difference between the two 
sensors was 5.6 (s.d. 2.3) W/m2, with sensor 31170 reading relatively high. 
Although this is within the expected accuracy of the sensors the difference 
between the two was seen to depend on shortwave radiation. Figure 22.5 shows 
the difference vs. Ptir. It can be seen that the difference is 5 W/m2 or less 
for low levels of shortwave radiation, but increases with shortwave to a 
maximum of over 8 W/m2. This suggests that the short-wave leakage term for 
sensor 31170 is too small.

Visual Cloud Observations

During D279, visual cloud observations were made every hour by the scientific 
watch according to the classifications given in the Met. Office guide "Cloud 
types for observers". Since visual observations are rather subjective it is 
usual to obtain a second independent set of observations wherever possible.

The observations of the scientific staff will be used to parameterise the 
downwelling longwave radiation in terms of cloud cover and type (Josey et al, 
2002). The parameterisation will allow calculation of the LW radiation to be 
made from the visual observations routinely obtained by the 7000-strong 
Voluntary Observing Ship fleet, thus ultimately improving the accuracy of 
weather forecast models. 

Sea Surface Temperature

Sea surface temperature (SST) data from the thermosalinograph (TSG) was 
logged on the AutoFlux acquisition workstation as part of the "surfmet" data 
stream. A comparison of the TSG SST data with those obtained from the CTD at 
10 m depth showed that the TSG was biased high by about 0.08 degrees (s.d. 
0.15). Some of this bias may be due to the TSG intake being at a depth of 
about 5 m rather than 10.

Ship Borne Wave Recorder (SBWR)

The SBWR was switched on prior to the ship leaving Govan. On arrival at the 
ship for the start of D279 it was seen that the starboard accelerometer was 
permanently registering full scale. The logging PC and deck unit, both 
located in the main lab, were checked and found to be working correctly. The 
fault seems to lie with the starboard accelerometer itself, or with the 
cabling from the sensor (located in the winch room) to the deck unit. Repairs 
to the SBWR are required.

22.3  Initial Flux Results

Inertial Dissipation (ID) Flux Measurements

The ID momentum flux obtained from the HS sonic anemometer is shown in Figure 
22.6 where the drag (transfer) coefficient is shown against the true wind 
speed corrected to a height of 10 m and neutral atmospheric stability. The 
drag coefficient is defined as (103 * momentum flux / wind speed2)

The mean drag to wind speed relationship from previous cruises (Yelland et 
al., 1998) is also shown. The drag coefficient is about 10% lower than that 
found during previous cruises. About half of this difference is due to the 
ship's draught being 1 m less than shown on the general arrangement plans, 
since the ID flux calculation depends on the height of the anemometer above 
the water. Although flow distortion corrections have not yet been determined 
for the exact HS anemometer position, it has been shown that the vertical 
displacement of the flow varies little with anemometer position or relative 
wind direction (Yelland et al. 2002). In contrast, the mean bias in the 
measured wind speed is sensitive to both these factors. The remaining 5% bias 
in the drag coefficient would be explained by a bias in the measured wind 
speed of only 1 to 2%, possibly due to a combination of calibration error 
and/or the effect of flow distortion on the mean wind speed. All the 
anemometers will be re-calibrated after the cruise, and accurate flow 
distortion corrections applied.

Figure 22.7 shows the ID latent heat flux obtained from the Licor H2O data. 
The agreement with results from previous experiments is good.

Figure 22.8 shows the ID sensible heat flux obtained from the sonic 
anemometer temperature data. In this case the measured fluxes are biased 
high. This is due to high frequency noise contaminating the temperature 
spectra at all frequencies above about 2 Hz. The temperature spectra obtained 
from the thermistor were likewise not suitable for the calculation of the 
heat flux via the ID method due to poor high frequency response. 

Eddy Correlation (EC) Flux Measurements

This section shows "quick look" EC results for the small proportion of data 
processed by the end of the cruise: a proper analysis of the results will 
take place after the cruise.

Figure 22.9 shows the EC momentum flux obtained from the HS sonic against the 
10 m wind speed. The ID fluxes are also shown for comparison. For EC fluxes, 
a sampling period of 30 minutes or more is usually required, but the data 
shown in Figure 22.9 were obtained from periods of only 12.8 minutes for 
processing and initial quality-control reasons. The data were obtained for 
relative wind direction within 10 degrees of the bow, and grouped according 
to whether the ship was on station (deploying the CTD) or on passage between 
stations. It can be seen that a) the EC momentum flux is somewhat larger than 
the ID flux and b) the scatter in the EC flux may be less when the ship is on 
passage. The increase in scatter when the ship is on station could be due to 
the small changes in ship speed and heading required for deployment of the 
CTD. When the ship is on passage its speed and direction are much more likely 
to be constant. Figure 22.10 shows the EC fluxes binned against ID fluxes for 
various relative wind directions. The ID fluxes have been corrected for the 
vertical displacement of the flow at each direction (maximum correction of 
3%), whereas those from the EC method can not be corrected. The 5% low bias 
in the ID flux due to the change in the ship's draught has not been removed 
from these data. From this it can be seen that the EC fluxes are biased high 
by about 10-20% for winds blowing on to the bow (relative wind direction of 
180 degrees). For wind directions up to 30 degrees to starboard of the bow 
this bias may reduce somewhat, but for directions up to 30 degrees to port of 
the bow the bias is increased to about 40-50%. This asymmetry is a result of 
the HS sonic being located at the starboard edge of the foremast platform.

Figure 22.8 shows the EC and ID sensible heat flux results from the HS 
anemometer, obtained when the wind was within 10 degrees of the bow. The ID 
results are clearly very poor and consistently overestimate the flux compared 
to a bulk formula. However, the EC sensible heat flux is in good agreement 
with the bulk estimate, and does not seem to show the bias seen in the EC 
momentum flux data. The EC sensible heat flux data were too scatted to 
identify any dependence of the EC flux on relative wind direction.

Figure 22.7 shows the EC and ID latent heat fluxes from the Licor H2O data 
when the wind was within 10 degrees of the bow. The measured fluxes are 
displayed against a bulk formula estimate of the flux. Again it can be seen 
that the EC data are more scattered than the ID except when the ship is on 
passage. As for the EC sensible heat flux data, the EC latent heat flux does 
not seem to be significantly biased compared to the ID results. There were 
not enough data available to examine the dependence of the EC latent heat 
flux on relative wind direction since the data processed to date were 
selected to coincide with periods where the Licor was shrouded.

In summary, the initial results from the EC flux calculations are very 
encouraging. The excellent ID and EC latent heat flux results mean that the 
effects of flow distortion on all the scalar fluxes (sensible heat, latent 
heat and CO2) is quantifiable for the first time.

CO2 Flux Measurements.

The major difficulty with measuring the CO2 flux is that it is usually very 
small, about two orders of magnitude smaller than the latent heat flux. There 
are additional practical difficulties such as; 

1) the "dilution effect" whereby the measured CO2 flux is affected by both 
   sensible and latent heat fluxes. The magnitude of this effect is similar 
   to that of the CO2 flux itself. 

2) the Licor sensor head is not completely rigid. During pre-cruise trials of 
   the sensor it was found that changing the angle of the head to the 
   vertical resulted in a significant shift in the CO2 signal. During the 
   cruise the Licor head was periodically shrouded using an empty water 
   bottle. Data from these periods were examined in conjunction with data 
   from the MotionPak in an attempt to quantify and remove the effect of the 
   distortion to the sensor head. 

The analysis performed during the cruise was encouraging in that the small 
sample of calculated CO2 fluxes were of a reasonable magnitude and were steady 
over periods of a few hours or more. A full analysis requires more detailed 
examination of the periods when the instrument was shrouded in order to 
determine the best correction for the angle of the head from the vertical. 
Since the magnitude of the CO2 flux depends on both the wind speed and the 
air-sea CO2 concentration difference, it will only be possible to judge the 
quality of the results once ∆p CO2 data from the UEA carbon team are 
available.

22.4 Summary

Significant progress was made in the development of the AutoFlux system;

a) The new Licor and MotionPak sensors were fully integrated in to the 
   automatic data acquisition system.

b) The H2O data from the Licor were processed in near real time to produce 
   inertial dissipation estimates of the latent heat flux.

c) Software was written to produce eddy correlation calculations of all the 
   fluxes. The main reason for not integrating this into the automatic 
   processing was lack of disk space for the large hourly files produced.

The relatively small sample of EC flux results produced during of the cruise 
were very encouraging. As expected, the EC momentum fluxes were shown to be 
more sensitive to flow distortion than those from the ID method. The EC 
scalar fluxes of latent and sensible heat agreed well with bulk and/or ID 
data, but determination of their sensitivity to flow distortion will not be 
possible until the entire data set is processed. The Licor sensor produced 
excellent latent heat fluxes via both methods: this will allow the effects of 
flow distortion on any of the scalar fluxes to be quantified for the first 
time. Finally, preliminary examination of the performance of the Licor in 
obtaining CO2 fluxes is encouraging.



Acknowledgements

The AutoFlux system was developed under MAST project MAS3-CT97-0108 (AutoFlux 
Group, 1996)). The developments described in this report were funded under a 
SOC TIF project (Yelland and Pascal, 2003). Thanks are due to Rachel Hadfield 
and Amanda Simpson for helping with the visual cloud observations.



References

AutoFlux group, 1996: AutoFlux - an autonomous system for monitoring air-sea 
    fluxes using the inertial dissipation method and ship mounted 
    instrumentation. Proposal to MAST research area C - Marine Technology, 38 
    pp. + appendices

Josey, S. A., R. W. Pascal, P. K. Taylor and M. J. Yelland, 2002: A new 
    formula for determining the atmospheric longwave flux at the ocean 
    surface at mid-high latitudes. In press JGR-Oceans.

Pascal, R. W. and S. A. Josey, 2000: Accurate radiometric measurement of the 
    atmospheric longwave flux at the sea surface. J. Atmos. Oceanic Technol., 
    Vol. 17, No. 9, pp. 1271-1282. 

Smith, S. D., 1988: Coefficients for Sea Surface Wind Stress, Heat Flux and 
    Wind Profiles as a Function of Wind Speed and Temperature. J. Geophys., 
    Res., 93, 15467-15474.

Yelland, M. J., B. I. Moat, P. K. Taylor, R. W. Pascal, J. Hutchings and V. 
    C. Cornell, 1998: Wind stress measurements from the open ocean corrected 
    for airflow disturbance by the ship. J. Phys. Oceanogr., 28, 1511 - 1526.

Yelland, M. J., B. I. Moat, R. W. Pascal and D. I. Berry, 2002: CFD model 
    estimates of the airflow distortion over research ships and the impact on 
    momentum flux measurements. . J. Atmos. Oceanic Technol. 19, 1477-1499.

Yelland M. J. and R. W. Pascal, 2003: Measurement and parameterisation of the 
    air-sea fluxes of CO2 and H2O. Proposal to the Southampton Oceanography 
    Ccentre Techmology Innovation Fund.


Table 22.1: The mean meteorological sensors. Front left to right the columns 
            show; sensor type, channel number, rhopoint address, serial 
            number of instrument, calibration applied, position on ship and 
            the parameter measured.

              Channel,                   Calibration Y =
              variable           Serial  C0 + C1*X +       Sensor       Parameter
Sensor        name      Address  No.     C2*X2 + C3*X3      position    (accuracy)
------------  --------  -------  ------  ----------------  -----------  ------------
Psychrometer  1         $ARD     IO2002  C0 -10.744746     Port side    Wet and dry
     1        pdp1               DRY     C1 4.0231547E-2   of foremast  bulb air
                                         C2 -7.5710697E-7  platform     temperatures 
                                         C3 1.2482544E-9                and humidity
                                                                        (0.05°C)

Psychrometer  2         $BRD     IO2002  C0 -10.432580
     1        pwp1               WET     C1 4.0010589-2
                                         C2 -2.3751235-7
                                         C3 9.3405703E-10

Psychrometer  3         $CRD     IO2001  C0 -10.439874     Port side    Wet and dry
     2        pds2               DRY     C1 3.9174703-2    of foremast  bulb air
                                         C2 7.6768407E-7   platform     temperatures 
                                         C3 5.7930693-10                and humidity 
                                                                        (0.05°C)

Psychrometer  4         $DRD     IO2001  C0 -1.443511
     2        pws2               WET     C1 4.0045908E-2
                                         C2 -3.6063794E-7
                                         C3 1.0917947-9

Epply LW      6         $3RD     31170   C1 1              Top of       Incoming 
dome temp     Tdl                                          foremast     longwave 
                                                           platform,    radiation 
Body temp     7         $KRD     31170   C1 1              port         (10 W/m2)
              Tsl                                          position

Thermopile    8         $LRD     31170   C1 1
              El

Epply LW      9         $MRD     31172   C1 1              Top of       Incoming 
dome temp     Td2                                          foremast     longwave 
                                                           platform,    radiation 
Body temp     10        $NRD     31172   C1 1              stbd         (10 W/m2)
              Ts2                                          position  

Thermopile    11        $ORD     31172   C1 1
              E2 

Wind Sonic    WSU       ?Q       025127  C1 1              Port side    Windspeed
U component                                                of platform  

Wind Sonic    WSV       ?Q       025127  C1 1              Port side    Windspeed
V component                                                of platform  


Table 22.2:  The fast response sensors.

                                            Data Rate  Derived flux/
         Sensor       Program   Location      (Hz)       parameter
         ----------   -------  -----------  ---------  -------------
         Gill HS      gillhsd  stbd side    20 Hz      momentum and
         Research              of foremast             sensible heat
         Ultrasonic            platform  
         Anemometer 
         serial no. 
         000027     
         
         Licor-7500   licor3   90 cm        20 Hz      latent heat
         CO2/H2O               directly                and CO2
         sensor                beneath HS
         serial no. 
         75H0614 
         
         Gill R3      gillr3d  94 cm to     20 /       momentum and
         Research              port of HS   100 Hz     sensible heat
         Ultrasonic 
         Anemometer 
         serial no. 
         000227  
         
         MotionPak    via      114 cm       20 Hz      EC motion
         ship motion  gillhsd  directly                correction
         sensor                aft of HS
         serial no. 
         0682 
         
         Thermistor   via      100 cm       20 Hz      heat
         sensor       gillr3d  below R3
         

Table 22.3: The ship's meteorological sensors. All logged by Vaisala QLI50 
            (R381005).

                                             Serial    
Name              Sensor           Type        No.     Sensitivity       Cal
----------  ------------------  -----------  -------  -------------  ------------
STIR        Kipp & Zonen CM6B   Pyranometer  973135   11.88µV/W/m2   8.688097E4
             (335 - 2200 nm)
PTIR        Kipp & Zonen CM6B   Pyranometer  99433    10.27µV/W/m2   9.737098E4
             (335 - 2200 nm)
PPAR        ELE DRS-5           Solarimeter  1843B-   10.05µV/W/m2   9.9502488E4
             (0.35 to 1.10 µm)               1-35901
SPAR        ELE DRP-5           PAR?         30470    7.18µV/W/m2    1.39275766E5
             (0.35 to 0.70 µm)               30471    8.20µV/W/m2    1.21951219E5
                                             unknown  6.48µV/W/m2    1.5432099E5
Pressure    Vaisala PTB100A     Barometric   S361     800-1060 mbar
                                             0008
Wind speed  Vaisala WAA151      Anemometer   P50421   0.4-75 m/s
Wind Dir    Vaisala WAV151      Wind Vane    S21208   -360 deg 
Air temp    Vaisala HMP44L      Temp         U 185    -20-60 deg C
                                             0012
Humidity    Vaisala HMP44L      Humidity     U 185    0-100%
                                             0012
TSG         See section 24



Figure 22.1: Schematic plan view of the foremast platform, showing the 
             positions of the sensors.

Figure 22.2: Measured wind speed/wind speed from the HS sonic for the R3 sonic, 
             the Windsonic and the ship's anemometer each binned against 
             relative wind direction. Error bars indicate the standard deviation 
             of the mean. A relative wind direction of 180 degrees indicates a 
             flow directly on to the bow of the ship. R3 sonic - black, 
             windsonic - blue, ship's anemometer - red.

Figure 22.3: As Figure 22.2 but showing the difference (measured - HS) in the 
             relative wind direction from the three anemometers. R3 sonic - 
             black, windsonic - blue, ship's anemometer - red.

Figure 22.4: Time series of downwelling short wave radiation from the Ptir 
             (solid line) and the Stir (dashed). The data have been averaged 
             over periods of one hour.

Figure 22.5: Difference between the two longwave sensor data binned against 
             short wave radiation from the Ptir sensor. Error bars show the 
             standard deviation of the mean.

Figure 22.6: Fifteen minute averaged values of the measured ID drag 
             coefficient (dots), plus the mean results (solid line) binned 
             against the 10 m neutral wind speed. The Yelland et al. (1998) 
             relationship is shown by the dashed line.

Figure 22.7: Direct measurements of the kinematic latent heat flux from the 
             ID method (solid circles) and the EC method shown against a flux 
             estimated from a bulk formula (Smith, 1988). The EC data are 
             separated according to whether the ship was on station (crosses) 
             or on passage (open squares).

Figure 22.8: Direct measurements of the kinematic sensible heat flux from the 
             ID method (solid circles) and the EC method shown against a flux 
             estimated from a bulk formula (Smith, 1988). The EC data are 
             separated according to whether the ship was on station (crosses) 
             or on passage (open squares).

Figure 22.9: Momentum flux measurements from the ID method (solid circles) 
             and the EC method against the 10 m wind speed. The EC results 
             are shown for periods when the ship is on station (crosses) and 
             on passage (open squares).

Figure 22.10: EC momentum flux binned against ID momentum flux data. The data 
             have been grouped according to the relative wind direction as 
             shown by the key in the figure. A bow-on wind is at a direction 
             of 180 degrees, winds to port of the bow by the blue lines and 
             to starboard by the red and yellow lines.



Appendix 22.A - List of significant events

Day 044 One day after sailing from Govan, a LW rhopoint blew and took out the 
power supply for the mean meteorological data stream. LW sensors unplugged at 
the end of D278. Data from Govan to the end of D277 were reprocessed using 
the surfment data instead of AutoFlux mean met data; Day 062 HS and R3 data 
stopped logging at 14:00 and did not restart until the workstation was 
rebooted on day 074 at 03:00. Logging probably stopped while staff on the 
ship tried to diagnose the problem with the meant met data stream; Day 094 
Prior to start of D279, RC filter on MotionPak output changed from a cutoff 
frequency of 4.79 Hz to 30 Hz; Day 111 Period of time sync signal changed 
from 47 samples (2.3 seconds) to 172 (8.6 seconds). This allows unambiguous 
automatic syncing of data streams; Day 115 Stopped logging R3 sonic 
anemometer to Nimbus. Started logging R3 to Cirrus at 100 Hz; Day 116 Swapped 
Ptir and Stir at foremast junction box at 18:30; Day 117 Ptir and Stir 
swapped back again at 17:30. Reprocessed data in AutoFlux 1 minute master 
files so that Ptir and Stir in correct channels; Day 117 Starboard 
psychrometer wet bulb stopped wicking. Corrected on day 127; Day 122 Nimbus 
stopped for backups at 0100. Restarted ready for 0500; Day 122 Nimbus system 
administration error caused data loss from 1400 to end of 1700.


Table 22.A.1: Periods during which the Licor was shrouded using an empty 
              water bottle. NOTE: on day 128, used the Licor calibration tube 
              as well as the water bottle and covered the outside of the 
              latter with foil. Removed the foil (only) just before 128 
              22:00, then removed the rest aon day 129 at 16:58.

Shroud   099  17:20  109  16:30  114 16:55  120 14:58  124 14:50  128  13:45
Removed  100  01:15  110  00:50  114 23:57  120 20:55  124 20:58  129  16:58


Table 22.A.2:  Day and time when sensors were cleaned.

           Licor cleaned  TIR sensors cleaned  LW sensors cleaned
           -------------  -------------------  ------------------
             095 12:00         095 12:00           095 12:00
             100 1015               -                   -
             105 18:40         105 18:40           105 18:40
             108 21:58         108 21:40           108 21:40
             110 00:50              -                   -
                 -                  -              114 16:35
             124 13:30         124 13:30                -
             127 1700          127 1700            127 17:00


Appendix 22.B - Time series of mean meteorological and air-sea flux data

The following Figures show time series of 1 minute averages of the mean 
meteorological data. Only basic quality control criteria have been applied to 
these data. Each page contains four plots showing different variables over a 
seven day period. 

    Top panel:   the best wet (pwUSE) and dry (pdUSE) bulb temperatures from 
                 the two psychrometers plus sea surface temperature (sst) 
                 from the TSG. 

    Upper middle panel:  downwelling radiation from the two shortwave TIR 
                 sensors and the two longwave sensors, all in W/m2.

    Lower middle panel:  relative wind direction (reldd = 180 degrees for a 
                 wind on the bow) and true wind direction (TRUdd) from the HS 
                 anemometer. The ship's true heading is also shown.

    Bottom panel:  relative (spdENV) and true wind (TRUspd) speeds in m/s 
                 from the HS anemometer. The ship's speed over the ground is 
                 also shown in m/s. When the relative wind direction was to 
                 port of the bow the significant flow distortion is apparent 
                 as steps in the true wind speed.


Figure 22.B.1: Mean meteorological data for days 095 to 102.

Figure 22.B.2: Mean meteorological data for days 102 to 109.

Figure 22.B.3: Mean meteorological data for days 109 to 116.

Figure 22.B.4: Mean meteorological data for days 116 to 123.

Figure 22.B.5: Mean meteorological data for days 123 to 130.


23. SURFACE MET DATA
    (Rachel Hadfield, Margaret Yelland, Robin Pascal)

The meteorological data was processed by the following execs:

    Smtexec0   transfers the underway surfmet data from RVS to PSTAR format. 

    Smtexec1a  changes surfmet absent data values of 99999 to -999, computes 
               the surface salinity and merges in bestnav positions. 

    Smtexec1b  merges the underway data with the heading files, gyro and ash-
               gyro.

    Smtexec2   computes vessel speed and subtracts this from relative winds 
               to get true wind speed and direction.

    Pikexec    copies the time in seconds and converts it to a jday time 
               variable.

    Multiplot  produces daily and weekly plots of the data.

For cruise 279, this processing was done on a daily basis, while data from 
cruises 277 and 278 was processed in one go at the start of cruise 279. 
During cruise 279, there were problems with the starboard incoming radiation 
sensor, with large spikes evident in the data, even during night time. On day 
116, the cables for the port and starboard sensors were switched to check if 
the problem was due to the sensor malfunctioning or the cable. After the 
switch the starboard sensor continued to give poor data, indicating that the 
problem was with the sensor itself and on jday 117, the cables were swapped 
back again.


23.1 Surfmet Sensor Information

The Surfmet sensor information, which remained unchanged for cruises 277 
through 279 is shown in the table below. All sensors, with the exception of 
the conductivity sensor are calibrated.

 
Table 23.1:  Surfmet sensor information.

            Manufacturer  Sensor              Serial No  Remarks
            ------------  ------------------  ---------  -------
            FSI           OTM (Temperature)   1340       Housing
            FSI           OTM (Temperature)   1348       Remote
            WetLabs       Fluorometer         W53S-248  
            SeaTech       Transmissometer     CST-113R  
            FSI           OCM (conductivity)  1376  



24.  SALINITY CALIBRATION OF UNDERWAY DATA
     (Rachel Hadfield) 

For calibration of underway salinity data, bottle salinities were collected 
from the uncontaminated water supply at roughly four hour intervals. 
Throughout cruise 277, sampling frequency was typically much less than this, 
with an average of one sample roughly every 10 hours. However whilst crossing 
the Florida Straits, samples were taken every 1-2 hours. During cruise 279, 
samples were drawn from the contaminated water supply, due to low water 
pressure in the uncontaminated supply, with sample frequency varying between 
2 and 8 hours.

The collected bottle salinities were analysed in the usual way and the 
results were entered into excel CSV files, ftp'd onto the unix system and 
converted into PSTAR format. To remove any heat dependence bottle salinities 
were converted to conductivity using the PSTAR routine peos83. The bottle 
conductivities were then merged with 5 minute binned underway data. The 
merged file was exported into Matlab where a 6 point running mean of the 
conductivity offset was calculated. This running mean was then applied as a 
calibration curve to the original 2-minute averaged underway data file. The 
first and last points of the calibration curve were taken to be the first and 
last conductivity offsets. Where the end points appeared to be an outlier 
from the mean trend, the mean trend was extrapolated to provide start and end 
points. This analysis was carried out using four main execs - time.exec, 
merg.exec, condsur.exec and smtcornnn.exec (where nnn is the cruise number). 
Table 24.1 below shows the processing sequence.


Table 24.1:  Processing sequence

            Process                        File(s) In      File(s) Out
---------------------------------------  ---------------  --------------
time.exec - converts csv to pstar and    surnnn001.csv    surnnn001.time
            calcs time in seconds

papend -    appends all bottle           surnnn001.time…  surnnn.time
            salinity files together      surnnn002.time,
            

Pavrge -    bins underway data into      smtnnn99.met     smtnnn99.bin
            5 min bins

merg.exec - merges bottle salinity       smtnnn99.bin     smtnnn99.bin.pik
            files with underway data     surnnn.time      surnnn.dif
            files, and calculates                         smtnnn_bin.mat
            offset between the 2.

Condsur.exec - calculates bottle         surnnn.dif       surnnn_bin.mat
            conductivities and offsets 
            between underway and bottle 
            conductivity

Smtnnn.m -  a matlab file which          surnnn_bin.mat   cornnn.mat
            calculates the correction    smtnnn_bin.mat   cor_curve.ps
            curve

pmatlb -    converts matlab file to      cornnn.mat       cornnn.p
            pstar  

smtcornnn.exec - applies the correction  cornnn.p         smtnnn99.cor
            and outputs file with        smtnnn99.pik
            calibrated salinities

merg.exec2 - calculates the difference   smtnnn99.cor     surnnn_cor.mat
            between calibrated and       surnnn.time
            bottle salinities


Table 24.2: The mean offset between calibrated and uncalibrated salinities 
            (i.e. calibrated minus uncalibrated) and the standard deviation 
            of corrected salinities against bottle salinities

                    Cruise  MeanOffset  Standard Deviation
                    ------  ----------  ------------------
                     277     -0.13648         0.009
                     278     -0.07080         0.021
                     279     -0.11361         0.009
 
The standard deviation for cruise 278 is quite high due to a couple of spikes 
remaining in the underway data despite binning of the data into 5 minute time 
periods.

The calibrated underway salinities were also compared to the gridded 10m CTD 
station salinities (Figure 24.1). Mean differences between the CTD and 
underway salinities were -0.003, 0.009 and 0.002 with standard deviations of 
0.009, 0.010 and 0.012 for cruises 277, 278 and 279 respectively.


Figure 24.1: Surface (TSG) and 10m (CTD) readings of (a) salinity across the 
             Florida Current, (b) temperature across the Florida Current, (c) 
             salinity, cruise D278, (d) temperature, cruise D278, (e) salinity, 
             cruise D279 and (f) temperature, cruise D279.


25.  BATHYMETRY
     (Amanda Simpson)

The RRS Discovery is equipped with a Hull mounted transducer, Precision 
Echosounding (PES) 'fish' transducer and Simrad EA500 Hydrographic 
Echosounder. The PES fish transducer was deployed shortly after leaving 
Freeport and was used in preference to the hull transducer for the duration 
of the cruise. During the cruise, the Simrad Echosounder was used 
continuously for bottom detection.

The depth of the 'fish' transducer is approximately 5m below the water 
surface. However, it was noticed at the end of the cruise that the transducer 
depth on the SIMRAD control setting had been set to 0.0m. The intended set up 
was for 5m and so it is not clear when this was altered. **This will need 
investigating in post-cruise processing.

The SIMRAD control screen and monitor showed a visual display of the return 
echo. A secondary monitor and control screen was slaved to the main system 
and positioned at the back of the main lab for use when on station. A hard 
copy output of the screen's display was also produced using a colour HP paint 
jet printer. This paper output was marked with the position of the stations 
and filed. Watchkeepers were required to check on an hourly basis that the 
echosounder was functioning correctly, that the visual display was set to a 
sensible range and that the printer was working normally.

The depth values logged by the echosounder were passed via a RVS level A 
interface to the level C system for processing. A constant sound speed of 
1500 ms-1 was used by the echosounder throughout the cruise. The first level of 
processing was to correct the raw data for variations in the speed of sound. 
This was done using Carter tables by RVS level C stream prodep.

Data were then converted from RVS format into PSTAR files using simexec0, 
which prompts the user to enter the start and end times of the data to be 
processed. This was done daily, producing the PSTAR file sim279nn.cal (nn 
refers to the number of the file) which contains the time, uncorrected depth, 
corrected depth and the carter table area at intervals of around 6s. Simexec1 
was then run, which uses pintrp to interpolate for missing data and then 
pmerg2 to merge the bathymetry data with the navigational data (abnv27901). 
The main output file used is sim279nn.nav which contains the fields: time, 
latitude, longitude, uncorrected depth, corrected depth, carter table area, 
distance and speed made good. A 5 minute averaged file is also produced at 
this stage containing the same fields (sim279nn.5min).

It was then necessary to edit the corrected depth variable for spikes and 
erroneous data, especially on station. The merged sim279nn.nav file was 
copied to file sim279nn.naved, in preparation for editing. This was done 
using the pstar routine plxyed, which allows the user to manually select and 
remove data from an interactive plot. The speed made good was also displayed 
on the plot, to facilitate identification of station sections.

There appeared to be substantial interference between the CTD pinger and the 
echosounder transducer. Also, on a few occasions the loss of accurate bottom 
detection was apparent whilst steaming and where obvious, this was also 
removed.

After editing, the output file sim279nn.naved was then averaged into 5 minute 
intervals using pavrge, to generate the file sim279nn.ed5min.

Four master files were created from the daily files. These were: 

sim279il.nav      This is the appended file of all the daily .nav files and 
                  contains the unedited corrected depth data.

sim279j1.naved    This is the appended file of all the daily .naved files for 
                  which the corrected depth has been edited to remove spikes and 
                  anomalous on station data.

sim279k1.ed5min   This is the appended file containing the edited data 
                  averaged into 5 minute intervals.

sim279m1.int5min  Finally, the corrected depth in sim279k1.ed5min was interpolated 
                  to provide a continuous estimate of depth along the cruise 
                  track.

As the intended cruise tracks for D279 and D277 were identical, it was 
interesting to compare the echosounder data for the two cruises. In order to 
do this, the 5 minute average files for both cruises were first sorted in 
terms of longitude and then the two files were merged using pmerg2. On 
merging, the D277 depths were interpolated onto the longitude data of D279. 
The difference between the two depth estimates was then calculated for each 
longitude using parith.

The top plot in Figure 25.1 shows the bathymetry for D279 and D279 and the 
bottom plot shows the difference between the two depth estimates.

Some of the discrepancy can be accounted for by differences in latitude 
between the two cruise tracks. This accounts for the large differences seen 
at the start of D279, when a return trip to Freeport was taken over a 
different route from the main cruise track.

Away from the Mid-Atlantic ridge and ignoring the beginning and end sections 
where the cruise tracks diverge, the mean absolute difference between the two 
estimates is 15.3 m with a standard deviation of 10.8 m. This increases to a 
mean of 97.2 m and standard deviation of 173.29 m across the ridge. The 
echosounder may find it difficult getting accurate estimates of depth over 
such steep bottom topography, accounting for the greater variation. 
Variations in latitude also have a greater impact on the depth recorded over 
the rough Mid-Atlantic ridge section.

There is significant divergence between the two estimates around 38W, which 
did not relate to a large latitude difference. When investigated on the hard 
copy output from D279, the strongest echoes do not relate to the bottom 
output on file. Although not obvious in editing, the bottom detection 
algorithm was unable to provide an accurate estimate of depth at this point.

Towards the end of D279, the D277 and D279 cruise tracks diverge in latitude 
and so the bathymetry also differs. The large spikes seen in the D279 
bathymetry at this point were identified as seamounts.


Figure 25.1:  D277 and D279 bathymetry.


26.  SHIPBOARD INSTRUMENTATION AND COMPUTING

26.1  Data Logging

Data were collected using the Level ABC data logging system.

          Data       Grabber                   Instrument
          --------   -----------------------   -----------------
          GPS_4000   Trimble GPS 4000          MkII Level A
          GPS_ASH    Ashtec ADU                MkII Level A
          GPS_GLOS   Glonass GPS               MkII Level A
          GPS_G12    SeaStar G12 (DGPS)        MkII Level A
          SURFMET    On board surfmet system   Direct to Level B
          ADP        150Khz ADP                Direct to Level C
          WINCH      CLAM system               Direct to Level B
          LOG_CHF    Chernikeef Log            MkII Level A
          GYRONMEA   Ships Gyro                MkII Level A

26.2  Logging Parameters

    Fromlevb -t20 | parse -L &
    FromADP -d /dev/ttya -t 180s | ADPin ADP &

The grabbers log these data files in /rvs/raw_data in files with the same 
name.

26.3  Level C Data Files

In addition to the above data files, which are called raw data, there are 
processed data files, which are stored in /rvs/pro_data and referred to as 
pro data. These are:

    Rawdep  an intermediate file created with the copyit command directly 
            from ea500d1, and avoids problems with bad data and backward 
            times.

    Pro_dep Depth corrected to Carter Area, using the prodep program.

    Relmov  Required by bestnav, stands for relative motion, and uses 
            gyronmea and log_chf to calculate the relative motion 

    Bestnav & bestdrf  are generated by the bestnav program, and use up to 3 
            gps input files, in this case gps_4000 (1), gps_g12 (2), and 
            gps_glos (3), in order of their priority. It also takes in the 
            relmov data, and outputs a 10 second 'best of what's available 
            from navigation'. It automatically calculates position in case of 
            gps failure. 

    Pro_wind  Absolute wind direction and speed calculated using the windcalc 
            command, takes in bestnav and surfmet data streams. 

26.4   Master Clock Jump

Occurred at midnight on day 120, time offsets were observed between gps_ash, 
and gyronmea. After the level As were reset, these offsets vanished. Prior to 
the master clock jump, the offset was in the region of 16 seconds. Further 
investigation showed that the gyronmea level A was not syncronising with the 
external clock correctly, and running on the internal clock only. The 
internal clock is drifting by about 0.5 seconds per day, it was agreed to 
manually reset the level A, meaning the maximum error would be less than 1 
second. A record of manual resets was kept and passed to Steve Alderson. 

26.5   Level B

No problems were experienced with the Level B data logger throughout the 
cruise.

26.6   ADP

The 150kHz ADP was logged directly to the Level C workstation. The ADP data 
files were accessed directly by the scientific party using datapup.


26.7   GPS Systems

GPS positioning was logged from a variety of receivers. Ashtec 4000 
(gps_4000) is the main receiver, Ashtec G12 being the secondary receiver. 
Both these receivers were fed differential corrections from the Fugro Seastar 
differential receiver from the AM-SAT. For a few hours, these differential 
corrections were not being received, the effect was temporary and was not 
caused by being outside the AM-SAT satellite footprint. During the cruise, 
and before we reached the limit of the AM-SAT footprint, the Seastar receiver 
was allowed to autoscan to the EA-SAT. Once it was tuned, and checked to 
ensure correct operation, the autoscan option was disabled, effectively 
locking the receiver to the EA-SAT.

26.8  Processed Data Fields

The data files were processed during the cruise bestnav (using gps_4000), 
prodep, protsg and pro_wind. The raw data file (rawdep) used for prodep was 
not edited for bad data during the cruise at the request of the Principal 
Scientific Officer, as on the previous cruise. However it was processed for 
carter area correction, and the wind was processed, resulting in absolute 
values for direction and speed. 

26.9  Winch

Winch data were logged directly to the Level B, and as long as the CLAM 
system was not powered down totally and the Stop Logging button was pressed 
on the screen to return the wire settings menu. On several occasions near the 
start of the cruise, the CLAM system stopped logging several times to the 
Level B after the a write error message appeared. This was resolved by 
pressing the "Continue" button on the error message box, which started 
logging again.

26.10  General Computing

Several computers were attached to the ships network during the cruise. At 
the moment, there is no DHCP service on board and so IP numbers were issued 
as normal, entries were made in /etc/hosts on Discovery2. The wireless 
network at the moment gives full coverage to all laboratories on the main 
working deck, with a limited signal quality to the port accommodation, 
however, it was not used to great effect at this point due to the lack of 
wireless capable computers onboard.

26.11  CTD Processing and Data Archiving

CTD cast data were transferred to the Black Translation PC in the computer 
room, either by zip (this proved unreliable), or memory stick (slightly more 
reliable) and via the network, (quick and easy). Seabird processing was 
carried out on the Translation PC, and processed files stored locally, with 
an archive on Discovery 5 /data51/rvsD279/.

/data51/rvsD279/RAW contained *.CON, *.DAT, *.BL, *.HDR, and ASCII digital 
thermometer files

/data51/rvsD279/Processed/ contained the *.cnv and *.ros files (binary data 
conversion and rosette) 

Further CTD processing was performed by the scientists using pstar/pexec 
suite.

26.12  Email

A similar email schedule to the previous cruise was adopted, to best coincide 
with working hours in the UK, and US. As the cruise progressed the schedule 
was altered to allow for the advancing ships clock. Between the days 114-116 
the HSD system suffered with problems obtaining and maintaining a reliable 
connection with SOC. This was wholly due to the satellite antenna being 
obscured by the main mast. The combination of constant easterly heading, and 
I would guess a low elevation of satellite position and angle, at that 
particular location in the ocean, lead to this temporary problem. As soon as 
the ship turned or we left the area, comms were back to normal. 

26.13  Backup Options

Backup to CD, DVD, and DLT were available for final archiving. Daily backups 
were made to DLT on a 2-day odd/even rotation using the following command 
from Discovery 2.

Cd /

Tar cvf /dev/rmt/3 ./data51 ./rvs/raw_data ./rvs/pro_data ./rvs/def7/control

26.14  Level B Tape Archive

echo reading.. ; cat /dev/rmt/0 > tape_`jday` ; echo compressing.. ; compress 
tape_`jday`

echo lb_tape_ini-ing.. ; lb_tape_ini -b4 -f /dev/rmt/0 -v ; echo checking 
inititalisation.. ; cat /dev/rmt/0 ; echo All Done

As level B tapes last longer than 24 hours, it was possible to have automatic 
daily naming of tapes. Archive of Level B tapes is for internal use only, and 
is only used to restore lost data in case of a catastrophic loss of level C 
data and backups.

This would be done by decompressing the data files

Uncompress tape112.Z

Then 'cat'ing' the tape into the parse command to rebuild the rvs data files.

Cat tape112 | parse &

26.15   CTD Computing Facilities

The two CTD logging computers were ,in my opinion, not a suitable choice for 
use in such a critical job as Seabird logging. The Windows 98 equipped 
desktop machines were, at best, just about satisfactory, and at worst, 
unsuitable. After only a few days, one broke down and refused to work any 
more, requiring an older CTD computer to substitute it, which was just about 
OK, and only crashed a few times. Careful nursing was required to avoid loss 
of important cast data.



27.   CARBON PARAMETERS (CBN)

Ute Schuster, Gareth Lee, Maria Nielsdottir

The CO2 parameter analytical equipment was set up in the seagoing laboratory 
container of the Laboratory for Global Marine and Atmospheric Chemistry 
(LGMAC), University of East Anglia (UEA), Norwich, UK. Four instruments were 
set up, for the analysis of discrete total inorganic carbon (TCO2), discrete 
total alkalinity (TA), discrete partial pressure of CO2 (discrete pCO2) and, 
continuous partial pressure of CO2 (continuous pCO2) and oxygen. The discrete 
instrumentation was used to analyse seawater samples collected from the 
Niskin bottles of the CTD, the continuous pCO2 was analysing sea surface pCO2 
and oxygen continuously in the non-toxic seawater supply. Due to the length 
of time needed for the analyses, particularly the TIC (30 min per sample), 
every second station was sampled for the three discrete analyses, apart from 
the beginning of the cruise (Florida Straight), were almost every station was 
sampled. TA could not be analysed at the beginning of the cruise due to the 
instrument not being operational. It was a new system and delivered one week 
before transport to the cruise, hence setting up this system took until 
station 15; samples sampled prior to that had been fixed and stored, and run 
later during the cruise.

Discrete seawater samples were taken according to Standard Operating 
Procedure (SOP) 1 outlined in DOE (1994). Reagent bottles of 250ml volume 
were used for TCO2 and TA samples, and 500ml volumetric flasks were used for 
discrete pCO2. They were drawn from the Niskin bottles immediately after the 
oxygen samples were taken. All seawater samples were taken with Tygon tubing 
into pre-cleaned bottles and flasks. They were rinsed once, filled from the 
bottom, and overflown once. Bottles and flasks were stoppered without any gas 
bubbles entrapped. The samples were fixed by creating a headspace and adding 
saturated mercuric (II) chloride (HgCl2) solution according to DOE (1994). 
Samples were fixed and stored at room temperature and run within 16 hours of 
sampling, except for those TCO2 samples which were stored at 12°C until post-
cruise analysis back at the UEA laboratory. 

Replicates samples were taken for all discrete analyses from random Niskin 
bottles at several stations, and run on board for all TA and discrete pCO2. 
TIC replicates of Niskin bottles were analysed on board or stored for 
analysis back at UEA. Additional replicates were taken from the ship's non-
toxic seawater supply and analysed on board. 

Table 27.1 lists number of samples taken and analysed on board from either 
CTD Niskins or the ship's non-toxic seawater supply, including replicates. A 
total of 4672 samples were taken, 1623 for pCO2, 1526 for TA, and 1523 for 
TCO2. A total of 4280 samples were analysed on board, 1563 for pCO2, 1501 for 
TA, and 1216 for TCO2. A total of 297 fixed TCO2 samples were stored for 
analysis back at UEA.

27.1  Discrete Total Inorganic Carbon (TCO2)

Total inorganic carbon was analysed by coulometry. The instrument consisted 
of a coulometer (model 5100, UIC Inc, USA), and an CO2 extraction unit based 
on the Single Operator Multiparameter Metabolic Analyzer (SOMMA), developed 
by Kenneth Johnson (Johnson et al. 1985, 1987, 1993; Johnson 1992), and 
modified at UEA.

In this system, all inorganic carbonate is converted to CO2 (gas) by addition 
of excess phosphoric acid (1 M, 8.5%) to a calibrated volume of seawater 
sample. OfN nitrogen gas passed through soda lime to remove any traces of CO2, 
is used to carry the evolving CO2 to the coulometer cell. In the coulometer 
cell, all CO2 is quantitatively absorbed forming an acid, which is 
coulometrically titrated. The coulometer is set to integrate the titration as 
counts (CTS), and titration endpoint is set to within 25 CTS per 60 min.

The accuracy of the analysis on board was determined regularly by measuring 
certified reference material (CRM), supplied by Dr. A. Dickson of Scripps 
Institution of Oceanography (SIO), Batch #62 (certified TCO2 value: 
2126.46±0.56_mol/kg). A total of 66 CRMs were run, Figure 27.1. The cruise-
length average of CRM analyses was 2126.65±2.3_mol/kg.

Standard deviation of replicate TCO2 analysis is plotted in Figure 27.2 
(station 1 was a test station, and station 11 was repeated as station 12, 
hence used for replicate analysis). The cruise-length standard deviation of 
Niskin replicate analyses was ±0.5_mol/kg (n=33) and for replicates of the 
nontoxic supply was ±1.1_mol/kg (n=23).

Post-cruise work will involve the analysis of the stored samples, which could 
not be analysed on board. A post-cruise calibration of the temperature sensor 
and the pipette volume will also be done, and the sample results recalculated 
if necessary.

27.2  Discrete Total Alkalinity (TA)

Total alkalinity was determined by the titration of a calibrated volume of 
seawater, equilibrated to 25ºC, with a strong acid (HCl). The s-shaped 
titration curve produced by potential of a proton sensitive electrode shows 
two inflection points, characterizing the protonation of carbonate and 
bicarbonate, respectively. The acid consumption up to the second point is 
equal to the titration alkalinity. From this value, the carbonate alkalinity 
is calculated by subtracting the contributions of other ions present in the 
seawater. These concentrations can be derived from the pH and salinity of the 
sample.

For this analysis, the VINDTA (Versatile INstrument for the Determination of 
Titration Alkalinity, Marianda, Kiel, Germany) was used. It is an open cell 
titration system, with sample delivery via a thermostated calibrated pipette. 
Sample handling and titration is program controlled. The titration is carried 
out using a Titrino (Model 719 S, Metrohm, Switzerland). The results are 
calculated using a non-linear curve fitting approach, comparing a calculated 
curve to the data points and making use of the best-fit coefficients for 
alkalinity calculation. 

A 0.1M solution of hydrochloric acid was made up for the titrations. This 
acid was made up on board and a sub-sample taken for post-cruise analysis to 
determine the exact concentration. The correct concentration will then be 
used to recalculate the results.

The accuracy of the analysis was determined twice daily by measuring 
Certified Reference Materials (CRM), supplied by Dr. A. Dickson of Scripps 
Institution of Oceanography (SIO), Batch #62 (certified TA value: 
2338.2±0.46µmol/kg). A total of 43 CRMs were run, Figure 27.3. The cruise-
length average of CRM analyses was 2337.8±1.8µmol/kg.

Alkalinity data was calibrated with CRMs. However, the calculation method is 
dependent on a realistically estimated ratio of acid factor and pipette 
calibration, since the same calibration factor can also be obtained with 
various combinations of these two parameters, but the quality of the curve 
fit will be different. Therefore a re-calibration of the pipette and exact 
calculation of the acid factor will be processed post cruise. Changes that 
would exceed the mean standard deviation of the method are not likely. A 
number of early stations were analysed using an inaccurate acid factor. These 
stations have an incorrect concentration at the end of the cruise. 
Recalculation is required post cruise to enter the correct acid factor and 
thus obtain a corrected result. The nutrient and salinity data will also be 
included in the post cruise processing, together with back calculation of 
rejected samples.

Analysis of replicates taken from Niskin bottles or the ship's non-toxic 
supply have a standard deviation of ±1.1µmol/kg and ±1.5µmol/kg respectively.

For the calculation of carbon alkalinity from total alkalinity, the phosphate 
and silicate alkalinity has to be known. This can be done using the 
separately determined nutrient concentrations. However, the contribution is 
low, for phosphate about equal to the phosphate concentration (i.e. 0-
3µmol/kg for open ocean waters), a factor of 10 lower for silicate. Nutrient 
data was not available immediately during this cruise and therefore not 
included in the calculations. This will be part of the post-cruise 
recalculation.

A problem of system blockages was encountered during the mid phase of the 
cruise. This resulted in pipette emptying problems and incorrect sample 
volumes. Tubing was renewed to overcome the problem, but a number of stations 
were affected and the samples were rejected. Stations rejected were 73, 75, 
77, 79, 81, 83, 85, and 87. Although these samples have been rejected, back 
calculation is possible from the values of pCO2 and TCO2. This will be carried 
out in post-cruise reprocessing.

27.3  Discrete Partial Pressure of CO2 (Discrete pCO2)

The partial pressure of CO2 in seawater was determined by infrared absorption 
of CO2 in a gas stream that was equilibrated with CO2 in a seawater sample at 
15°C. The system was built new at UEA prior to this cruise, its design based 
on the one described by Waninkhof & Thoning (1993).

A headspace was created in the 500ml volumetric flasks by replacing a volume 
of seawater with a gas of a CO2 concentration close to that of the seawater. 
Six gas standards (10 litre, BOC, UK) were available with different CO2 
concentrations: 267.43ppm, 357.35ppm, 479.27ppm, 696.49ppm, 890.54ppm, and 
1150.11ppm, which had been calibrated against primary NOAA gas standards 
prior to the cruise. Headspace volumes created in sample flasks ranged from 
62 to 84ml, and were measured for each sample. The headspace gas was 
circulated through the seawater sample and the IR detector (LiCor model 6262, 
LiCor, Inc., USA) until equilibrium was reached, generally after 20 min, 
whilst maintaining close to atmospheric pressure within the loop.

The system has two loops, which were used alternatively, saving analysis time 
by equilibrating one sample, whilst preparing the next. On 02 May 2004, loop 
2 failed, and remaining samples were analysed only on loop 1.

All gas standards were run after each 12 to 15 samples, in order to calibrate 
the LiCor detector. The precision of the analysis was determined by running 
replicate samples, taken either from Niskin bottles or the ship's non-toxic 
seawater supply.

27.4   Continuous Partial Pressure of CO2 (Continuous pCO2)

The partial pressure of CO2 in surface seawater was determined by infrared 
absorption of CO2 in a gas stream being continuously equilibrated with the CO2 
of surface seawater. The system used was built new at UEA prior to this 
cruise, its design based on the one described by Cooper et al (1998).

Seawater from the continuous non-toxic supply of RRS Discovery was tee-ed off 
from a high flow (>50 litres/min) bypass, passed through a strainer and 
housing containing an oxygen/temperature sensor (Aanderaa model 3930, 
Aanderaa Instruments AS, Norway), and into a perculator type equilibrator at 
5 litres/min. A coulterflow of air was continuously circulated through the 
equilibrator and the detector (LiCor model 6262, LiCor, Inc., USA). At least 
once per hour, the system analysed CO2 in air, pumped in from the foremast.

Gas standards of 267.43ppm, 357.35ppm, and 479.27ppm CO2 in air were measured 
throughout the cruise, in order to calibrate the LiCor detector.

Under controlled conditions in the laboratory, and during a pool side 
international intercomparison in Japan in 2003, the type of instrument used 
for this cruise gave a precision of ± 0.7ppm CO2.


Figure 27.1:  Results of the TIC analysis of CRM batch 62 throughout the 
              cruise.

Figure 27.2:  Standard deviation of TIC analysis of replicate samples 
              taken from Niskin bottles or the non-toxic seawater supply.

Figure 27.3:  Results of the TA analysis of CRM batch 62 from 18 April 
              2004 onwards. Prior to 18 April, the acid factor used was not 
              correct, and CRM as well as sample values need to be recalculated.

Figure 27.4:  Standard deviation of TA analysis of replicate samples 
              taken from Niskin bottles or the non-toxic seawater supply.


Table 27.1: Number of samples taken and analysed during the cruise for the 
            three discrete carbon parameters pCO2, TA, and TIC, from either 
            CTD Niskins or the RRS Discovery's non-toxic seawater supply. 
            Numbers sampled include replicates. TIC samples not analysed were 
            stored to be analysed back at UEA.

      Samples taken
Stn        from                 pCO2                TA                TIC
---  -----------------  -----------------  -----------------  -----------------
       CTD    non-tox.           Analysed           Analysed           Analysed
     Niskins  supply    Sampled  on board  Sampled  on board  Sampled  on board
     -------  -------   -------  --------  -------  --------  -------  --------
  1    24                 20        8                            20       13
  2     3                  3        3         3         2         3        0
  3     4                  4        4         4         2         4        4
  4     5                  5        5         5         5         5        5
  5     6                  6        6         6         5         6        6
  6     6                  6        6         6         6         6        5
  7     7                  8        8         7         7         8        8
  8     7                  7        7         7         7         7        7
  9     6                  6        6         6         6         6        6
 10     5                  5        5         5         5         5        5
 11    12                 12       12                            12       10
 12     5                  5        5         5         5         5        5
 13    14                 14       14        14        14        14       14
 14    16                 16       16        16        16        16       16
 15    20                 20       19        20         0        20       20
 16    22                 22       22        22        22        22       22
 17    23                 23       22                            23        0
 18    24                 24       23        24        24        24       24
 19    24                 24        0                            24        0
 20    24                 24       24        24        24        24       24
 22    24                 24       24        24        24        24       24
 24    24                 24       24        24        24        24       24
 26    22                 22       22        22        22        22        0
 29              X         6        6
 29    24                 24       24        24        24        24       
                                                                          24
 31    23                 23       23        23        23        23       23
 33              X         6        6
 33    24                 24       24        24        24        24        0
 35    23                 23       22        25        25        23       23
 37              X         6        6
 37    24                 24       24        24        24        24       24
 39              X         6        6
 39    24                 24       24        24        24        24       24
 41    24                 24       24        24        24        24       24
 43              X         6        6       
 43    24                 24       23        24        24        24       24
 45              X        12       10        10         9
 45    24                 24       24        24        24        24       24
 47              X         6        6         5         5
 47    24                 24       24        24        24        24       24
 49              X         6        6
 49    24                 24       24        24        24        24       24
 51              X         6        6        10        10
 51    24                 24       24        24        24        24       24
 53              X         6        6         8         8
 53    24                 24       24        24        24        24       24
 54              X                           15        15
 55              X         6        6
 55    24                 24       24        24        24        24       24
 57              X                           15        15
 57    24                 24       23        24        24        24       24
 58              X         6        6
 58     1                  1        1
 59    23                          23        22        23        23       23
                                                                          23
 60              X         6        6
 60    1                   1        1
 61              X                                                4        4
 61    24                 24       24        28        28        28       26
 62              X         6        6
 63    24                 24       24        24        24        24       24
 65              X         6        6         6         6
 65    24                 24       24        24        24        24       24
 66              X         6        6
 66    1                   1        1
 67    24                 24       23        24        24        24       24
 69    24                 24       23        24        24        24       24
 71    24                 24       23        24        24        24       24
 72              X                                               10       10
 73    24                 24       23        24        24        24       24
 75    24                 24       24        24        24        24       24
 77    24                 24       24        24        24        24        0
 79    24                 29       29        29        29        24       24
 81    24                 24       23        24        24        24        0
 83    24                 24       24        24        24        24       24
 85    24                 24       24        24        24        24        0
 87    24                 24       24        24        24        24       24
 89              X         2        2         2         2         2        2
 89    24                 26       26        26        26        26       26
 90              X         5        4         4         4         4        4
 91    24                 24       24        24        24        24       24
 93              X         5        3         5         5
 93    24                 26       26        26        26        26       26
 95              X                            5         5         5        3
 95    24                 26       26        26        26        26        0
 97    24                 26       26        26        26        26       24
 99    24                 26       25        26        26        26       26
101              X        10        9        10        10
101    24                 26       25        26        26        26       26
103    24                 26       26        26        26        26       25
105              X                           10        10        10       10
105    24                 26       26        26        26        27       26
107    24                 26       25        26        26        26       25
109    24                 26       26        26        26        26        2
111    24                 26       26        26        26        26       26
113              X        10       10        10        10
113    24                 26       26        27        27        26        0
115    20                 22       20        22        22        22       20
117    21                 23       23        21        21        23       22
119    19                 21       21        21        21        22       20
121    15                 17       16        17        17        17        0
123    12                 13       13        13        13        14        0
125     7                  8        8         8         8         8        0
----------------------------------------------------------------------------
Total                   1623     1563      1526      1501      1523     1216
----------------------------------------------------------------------------



REFERENCES

Cooper, D.J., Watson, A.J., Ling, R.D. (1998) Variation of pCO2 along a North 
    Atlantic shipping route (UK to the Caribbean): A year of automated 
    observations. Marine Chemistry 60, 147-164.

DOE (1994) Handbook of methods for the analysis of the various parameters of 
    carbon dioxide system in sea water; version 2, A.G. Dickson & C. Goyet, eds., 
    ORNL/CDIAC-74.

Johnson K.M., King, A.E., Sieburth, J.M. (1985) Coulometric TCO2 analyses for 
    marine studies; an introduction. Marine Chemistry 16, 61-82.

Johnson, K.M., Williams, P.J.leB., Brändström, L., Sieburth, J.M. (1987) 
    Coulometric TCO2 analysis for marine studies: automation and calibration. 
    Marine Chemistry 21, 117-133.

Johnson, K.M., Wills, K.D., Butler, D.B., Johnson W.K., Wong, C.S. (1993) 
    Coulometric total carbon dioxide analysis for marine studies: maximising the 
    performance of an automated continuous gas extraction system and coulometric 
    detector. Marine Chemistry 44, 167-187.

Wanninkhof, R., Thoning, K. (1993) Measurement of fugacity of CO2 in surface 
    water using continuous and discrete methods. Marine Chemistry 44, 189-204.



28.  HALOCARBONS
     (David Cooper and Charlene Grail)

Cruise D279 presents an excellent opportunity to measure concentrations of 
CFC-12, CFC-11, CFC-113, and carbon tetrachloride (CCl4) from the WOCE 
reoccupation transect 26-24.5ºN (A05). The objective is to provide a high 
quality data set, and make them available nearly immediately to the community 
as required by the Global Repeat program. The program is in support of CLIVAR 
and the Carbon Science Programs, and is a component of a global observing 
system for the physical climate/CO2 system. The data will contribute to 
documenting and understanding how ventilation and ocean carbon change over 
time. A number of alternative, although still indirect, means of estimating 
anthropogenic CO2 use CFC data. These will contribute to quantifying the 
inventory and flux of anthropogenic CO2 in the oceans, and to understanding 
its variability. The 26-24.5º N CFC data from this cruise occupation will 
fill a zonal gap in a region where CFC inventories are relatively large, and 
in the west increasing rapidly throughout the water column. Our intention was 
to sample as extensively as possible.


28.1   Sample Collection

Samples were collected from 10 litre Niskin bottles attached to a 24 bottle 
rosette. The Niskin bottles were refitted with o-rings specially made without 
grease or solvents to avoid any chance of halocarbon contamination. A water 
sample was collected directly from the Niskin bottle petcock using a 100ml 
ground glass syringe which was fitted with a three-way stopcock that allowed 
flushing without removing the syringe from the petcock. The syringes were 
stored in a flow-through seawater bath and analyzed within 8 -10 hours after 
collection.


28.2   Analysis

Halocarbon analyses were performed on a gas chromatograph (GC) equipped with 
an electron capture detector (ECD). Samples are introduced into the GC-EDC 
via a purge and dual trap system. The samples are purged with nitrogen and 
the compounds of interest are trapped on a main Porapack N trap held at ~ -
20°C with a Vortec Tube cooler. After the sample has been purged and trapped 
for several minutes at high flow, the gas stream is stripped of any water 
vapor via a magnesium perchlorate trap prior to transfer to the main trap. 
The main trap is isolated and heated by direct resistance to 140°C. The 
desorbed contents of the main trap are backflushed and transferred, with 
helium gas, over a short period of time, to a small volume focus trap in 
order to improve chromatographic peak shape. The focus trap is also Porapak N 
and is held at ~ -20°C with a Vortec Tube cooler. The focus trap is flash 
heated by direct resistance to 155°C to release the compounds of interest 
onto the analytical pre-column. The analytical pre-column is held in-line 
with the main analytical column for the first 3 minutes of the 
chromatographic run. After 3 minutes, all of the compounds of interest are on 
the main column and the pre-column is switched out of line and backflushed 
with a relatively high flow of nitrogen gas. This prevents later eluting 
compounds from building up on the analytical column, eventually eluting and 
causing the detector baseline signal to increase.

In total, measurements were made on 129 stations, most of which contained 24 
samples, plus one duplicate taken randomly. Every ten measurements were 
followed by a purge blank and a standard, gas2.09ml. Time permitting, the 
surface sample was held after measurement and was sent through the process in 
order to "restrip" it to determine the efficiency of the purging process. In 
all cases, the restripped sample contained no more concentration of targeted 
halocarbons than the purge blanks.


28.3   Calibration and Precision

For accuracy, the standard, S43, was cross-calibrated to the SIO-98 absolute 
calibration scale. A 19 point calibration curve was run every 7-10 days for 
all four halocarbons. Estimated accuracy is ±2%. Precision for CFC-12, CFC-11 
and CFC-113 is less than 1%; precision for CCl4 was approximately 1-2%.


28.4   Final Comments

In large part, sample collection and measurement were very successful. The 
three-way stopcock on the syringes made sample collection a simple and rapid 
procedure. The integration of the computer software with the GC-EDC system 
hardware made the procedure almost completely automated. A few problems were 
encountered initially. The analytical column had to be replaced with the 
spare due to some unknown source of contamination. The focus trap failed and 
was replaced by a spare trap. The humidity and temperature were a little high 
in the chemistry lab, thus necessitating daily replacement of the magnesium 
perchlorate trap which removed any water vapour from the nitrogen gas stream 
after purging.


29.  ATMOSPHERIC SAMPLING
     (Rhiannon Mather)

29.1   Aerosol Collection

During this cruise aerosol samples were collected over roughly a 24-hour 
period using a high volume aerosol sampler, placed on the monkey island of 
the ship. Filters were changed during the morning, usually between the hours 
of 8 and 9:30 ship time (ST), corresponding with between 11:00 and 14:00 GMT. 
The sampler was generally left to run continuously, as the ship was 
positioned head to wind when on station, therefore reducing the risk of 
contamination from the chimney stack.

The sampler was switched off each morning for the changing of the filter 
paper. The filter paper was changed in the fume cupboard of the chemistry 
lab, as no laminar flow hood was available on the ship. The fume cupboard was 
rarely used for any other purposes. Filter papers were changed wearing 
plastic gloves to avoid the risk of sample contamination. Once removed from 
the cartridge, the filter paper was sealed in a zip lock bag, which was 
subsequently placed in two further plastic bags (one other sealed) in the 
freezer. These were stored at -25ºC for the remainder of the cruise. 
Transport of the filter papers between the monkey island and the fume 
cupboard, was carried out in the sampler cartridge covered with an aluminium 
plate, and subsequently placed into a large plastic zip lock bag. Samples 
were collected on to Whatman 41 filters.

At the start and end of each sample, the time, position, date, air 
temperature, pressure, wind direction, wind speed, ship direction, and ship 
speed were all noted down (Table 29.1). A counter reading within the sampler 
was unable to be recorded as this failed to work for the entire cruise. As a 
back up, circular chart recorders were also used. Samples failed to be taken 
at the start of the cruise on the 5th and 6th of April. On these days the 
aerosol sampler failed to work due to an electrical problem within the 
instrument. This problem was resolved to commence sampling on the 7th April.
Two blanks were also run during the cruise; a cassette blank and an exposure 
blank. The cassette blank was performed whilst docked in Freeport, Grand 
Bahama. For this a filter paper was loaded into the sampler cartridge with 
the aluminium cover in place, and subsequently placed in a large zip lock bag 
for 24 hours. This sample was performed in the chemistry lab of the ship. The 
exposure blank was treated in exactly the same manner as the running of 
normal samples, with the exception that the sampler was not switched on for 
the 24 hour duration within which the sample was loaded. The exposure blank 
was performed on the 4th of April on the first leg out of Freeport.


29.2   Sample Analysis

Aerosol samples collected throughout this cruise will be delivered to the 
University of East Anglia (UEA) Environmental Sciences department for 
analysis. The samples are expected to be analysed for a number of nutrients, 
including nitrate, ammonia, silica, phosphate, and sulphate. The 
concentrations of trace metals such as lead, copper, zinc, nickel, cobalt and 
cadmium will also be investigated with graphite furnace atomic absorbance 
spectrometry (GFAAS). This technique has the low detection limits that are 
required to measure the expected low concentrations. The filter papers are 
finally to be analysed for the presence of chloride. This is likely to have 
originated from sea spray, and the potential contamination of the paper can 
therefore be assessed.


D279 DISCOVERY CRUISE
04 APRIL 2004 - 10 MAY 2004

AEROSOL DEPOSITION SAMPLES
NB:  Wind direction here is written as the direction that the wind is blowing

                                     SAMPLING START
SAMPLE NAME       SAMPLE NUMBER    DATE    START TIME  LATITUDE
                                              GMT         N
----------------  -------------  --------  ----------  --------
Cassette Blank 1   DI04MI CB1    03/04/04    22:09        -
Exposure Blank     DI04MI EB1    04/04/04    21:25     26 54.08




30.  TRIAL FLOAT DEPLOYMENT
     (Robin Pascal)

Instruments on Argo floats are severely limited by the low data capacity of 
the standard Argos satellite link. The advent of the Iridium and Orbcomm 
systems based on low orbit satellite constellations offer the possibility of 
increasing the data capacity by several orders of magnitude. There is also 
some interest in recoverable Argo floats; the chances of successfully 
recovering these would be greatly enhanced by an on board GPS receiver with a 
near real time data link to the mother ship.

The float deployed on this cruise is intended to investigate the behaviour of 
GPS and Iridium on the far from ideal platform of an Argo float using a newly 
developed marinised and pressure resistant antenna assembly. The float has a 
plastic body designed to mimic the dynamic behaviour of a surfaced Argo float 
but cannot dive; the latter restriction enables a very large battery capacity 
sufficient for many months of transmission every four hours. Initial 
indications are that the Iridium transmitter is performing well but the GPS 
much less so, probably because the GPS is unable to receive digital data with 
sufficient continuity.


30.1  Deployment Details

The float was deployed immediately following a CTD cast with the ship 
steaming slowly forwards. No problems were expereinced during the deployment 
and the float appeared to be floating at the expected level just below the 
end cap. Deployed on Day 120 at 15:30 hrs GMT, 24° 30' N, 38° 32' W.


31.  DISSOLVED OXYGEN MICROELECTRODE SENSOR
     (Robin Pascal)

A new dissolved oxygen sensor is being developed within OED. The sensor is 
based on a platinum microdisc (25 _m diameter) working electrode and a copper 
counter electrode. The advantage of this type of sensor compared to those 
commercially available is that it has the potential to have a very fast 
response time (fractions of a second) and should not suffer from hysteresis 
due to temperature and pressure effects.

Previous experience with the sensor has shown that it is sensitive to 
fluctuations in the flow across the head. A new head arrangement has been 
designed so that the electrode sits within a chamber through which water is 
pumped periodically. Oxygen measurements are made while there is no flow. Due 
to the pumps construction it is mounted in a separate oil filled pressure 
balanced housing. A major objective of the current trial was to ascertain 
that the new flow head and pump arrangement was robust enough to work under 
pressure and to withstand depths down to 5000 m. If so, it was hoped that the 
new arrangement would reduce the noise in the data caused by the motion of 
the CTD through the water.


31.1  CTD Deployments

The sensor was installed within the CTD frame prior to cast 93. Unfortunately 
on power-up it became clear that it had been incorrectly wired. This resulted 
in the pump circuit being damaged, which resulted in only 2 pumps per cycle 
rather than the usual 5 being performed from then on. With the wiring 
corrected subsequent tests on deck showed the sensor to be working correctly 
and that data was being successfully acquired by the Seabird CTD. However, as 
soon as the CTD entered the water the sensor output went full scale and 
stayed there for the entire profile. Different sensor setups and gains were 
tried but with little improvement. It was concluded that the various metals 
(e.g. zinc) contained in the CTD frame and in the other instruments were 
pulling the oxygen sensor's measurement potential away from its correct 
setting. Adjustments were made for this and significant improvements were 
seen. The sensor was removed from the CTD frame for the deep stations 
(greater then 5000 m) and was later re-installed on CTD cast 109. For this 
and subsequent casts the sensor was mounted on the fin, rather than within 
the frame, to try to minimise unwanted electropotential effects. This 
resulted in significant improvement but the measurement potentials still 
needed to be shifted significantly from their design settings. Despite this, 
after some minor modifications to the inlet the sensor performed very well 
and produced encouraging profiles (Figure 31.1). The calibration for the 
sensor was based on the bottle sample data (below). The profiles in Figure 
31.2 have been adjusted to allow for an approximate 2 minute delay in the 
sensor response. This delay may be partly due to the reduced number of 
pumping cycles not completely flushing the flow head in one cycle. 


31.2  Bottle Sample Measurements

During the deep stations when deployment of the sensor on the CTD was not 
possible a second sensor was used to measure the dissolved oxygen levels in 
the water bottle samples. A suitable head was chosen which could be fully 
inserted into a standard oxygen water sample jar. Samples from the CTD 
bottles were then measured and the results compared to those of the 
independent oxygen titrations. Initially the oxygen results were calculated 
using the temperatures recorded for the titrations. However, these 
temperatures proved rather inaccurate and the errors in temperature resulted 
in large apparent errors in the calculated oxygen values. A thermometer was 
therefore obtained in order to make direct measurements: this significantly 
improved the quality of the oxygen results.

The main aim of performing the bottle sample measurements was to detect any 
drift in the sensor calibration. In 3 out of 12 of the casts sampled the 
sensor showed temporary calibration jumps. The reason for this is not yet 
known but intermittent use of the sensor in this fashion is far from ideal. 
Despite this, the results were generally in very good agreement with the 
oxygen titration results (Figure 32.2) and no calibration drift was detected 
between casts.
 

Figure 31.1: Three up casts from the microelectrode oxygen sensor 
             plotted with oxygen titration values. The same calibration is 
             applied to all three profiles.. Black cast 115 (offset -50 
             µmoles). Blue cast 116. Red Cast 117 ( offset +50 µmoles).

Figure 31.2: The average of 5 profiles (blue) made up from discrete 
             samples taken from the CTD water bottles are plotted with 
             the average of the same 5 profiles of oxygen titrations
             (pink). Error bars indicate the standard deviation of the data.



DATA PROCESSING NOTES

2010-06-04  Bartolocci  BTL         Data files edited, online 
            2010.06.04 DBK
            Reformatting notes for carina cruise a05_74DI200404 bottle file, 
            submitted by Bob Key on 2009.01.27
            Following edits were made to exchange bottle file units header:
            • Edited DEGC to DEG C
            • Edited DBARS to DBAR
            • Edited PPM to UATM (for PCO2, as per Bob Key)
            Merged TIME (as zero) into bottle file using 
              merge_exchange_bot.rb.
            Created WOCE format and netcdf files from exchange file. 
            Checked file with JOA. Exchange file would not load into JOA, no 
              error message given or reason found. NetCDF files opened and 
              plotted with no errors.
            Created directory and linked files. Sent notes to Jerry. 

2008-05-12  Key         CFCs        1 extra sample 
            This is a clean data set, but note when you merge that for sta 27 
            Debra's file has one more sample (deepest) than in the version of 
            the bottle file I have. 

2008-04-28  Willey      CFCs        revision of 2005 cfc file 
            This is a re-submittal of the CFC data for the D279 2004 cruise. 
            Some revisions have been made since the original April 2005 data 
            submission. 

2007-03-13  Willey      BTL         CSV file 
            Hydro: Who - H. Longworth; Status - final; S Plus - up to date
                  Notes: See Cunningham 2004a,b
                  Many apparent mistrips
            Nuts/O2: Who - R. Sanders; Status - final; S Plus - up to date
                  Notes:
            TCO2: Who - U. Schuster; Status - final; S Plus - up to date
                  Notes: CRM Batch 62; 66 analyses with mean of
                        2126.65+/-2.3umol/kg with certified value of
                        2126.46+/-0.56umol/kg. On-board replicates implied 
                        precision of 1.1umol/kg
                  Carbon data from U. Schuster 11/2/06 
            TA: Who - U. Schuster; Status - final; S Plus - up to date
                  Notes: RM Batch 62; 43 analyses with mean of
                        2337.8±1.8µmol/kg with certified value of
                        2338.2±0.46µmol/kg. On-board replicates implied 
                        precision of 1.1-1.5umol/kg
                  Due to analytical problems results from stations
                        73, 75, 77, 79, 81, 83, 85, and 87 rejected.
            pCO2: Who - U. Schuster; Status - final; S Plus - up to date
                  Notes: reported @15C
                  Underway data also collected
            pH25: Who - ; Status - not measured; S Plus - 
                  Notes: 
            CFC: Who - D. Cooper; Status - no data in file; S Plus - 
                  Notes: includes also CFC-113 and CCl4
                  Estimated accuracy of 2%
            C-14: Who - ; Status - not measured; S Plus - 
                  Notes: 
            C-13: Who - ; Status - not measured; S Plus - 
                  Notes: 
            H-3/He-3: Who - ; Status - not measured; S Plus - 
                  Notes: 
            Other: LADP
            REFERENCES:
            Cunningham, S.A., RRS Discovery Cruise 279, 04 APR - 10 MAY 2004: 
                A transatlantic hydrographic section at 24.5°N, pp. 150, 
                Southampton Oceanography Centre, Southampton, 2005a.
            Cunningham, S.A., RRS Discovery Cruises 277 (26 MAR - 16 APR 2004) 
                and 278 (19 MAR - 30 MAR 2004): Monitoring the Atlantic Meridional 
                Overturning Circulation at 26.5°N, pp. 150, Southampton 
                Oceanography Centre, Southamtpon, 2005b. 

2005-04-05  Willey      CFCs        no hyd file yet to merge into 
            From http@odf.UCSD.EDU Tue Apr 5 11:28:22 2005
            Date: Tue, 5 Apr 2005 08:26:03 -0700 (PDT)
            From: WHPO Website 
            To: dwilley@rsmas.miami.edu, jrweir@odf.UCSD.EDU, whpo@ucsd.edu
            Subject: WHPO DATA D279: BOT from WILLEY
            This is information regarding line: D279
            ExpoCode: Cruise Date: 2004/04/04 - 2004/05/09
            From: WILLEY, DEBRA
            Email address: dwilley@rsmas.miami.edu
            Institution: UNIVERSITY
            Country: USA
            The file: D279_24N_2004_CFCs.csv - 120964 bytes has been saved as: 
            20050405.082602_WILLEY_D279_D279_24N_2004_CFCs.csv in the 
            directory: 20050405.082602_WILLEY_D279
            The data disposition is: Public
            The bottle file has the following parameters: CFC-11, CFC-12, CFC-
            113, CCL4
            The file format is: WHP Exchange
            The archive type is: NONE - Individual File
            The data type(s) is: Bottle Data (hyd)
            The file contains these water sample identifiers: Cast Number 
            (CASTNO) Station Number (STATNO) Bottle Number (BTLNBR)
            WILLEY, DEBRA would like the following action(s) taken on the 
            data: Merge Data, Place Data Online
            Any additional notes are: I don't know the line number nor the 
            expo code for this cruise.  The cruise was on the Discovery, in 
            the Atlantic, along 24N. 

