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CRUISE REPORT: I05       
(Updated JAN 2009)


A. HIGHLIGHTS

A.1. CRUISE SUMMARY INFORMATION

         Line/Section designation  I05
Expedition designation (ExpoCode)  74AB200203
                  Chief Scientist  Harry L. Bryden/SOC*
                            Dates  2002 MAR 01 - 2002 APR 15
                             Ship  RRS CHARLES DARWIN 
                    Ports of call  Durban, South Africa to Fremantle, Australia

                                              29° 23" S
    Station geographic boundaries  30° 20" E            115° 25" E
                                              34° 30" S

                         Stations  146 CTD/LADCP stations 
     Floats and drifters deployed  25 Argo floats launched 
   Moorings deployed or recovered  0

                              Contributing Authors
 H.L. Bryden,  S. Cunningham,    J. Benson,   L. Duncan,   M. Palmer,  J. Wynar,
 J. Benson,    V. Latham,        R. Sanders,  M. Álvarez,  A.F. Ríos,  M. Witt,
 M. Bridger,   D.P. Wisegarver,  K. McHugh,   L.M. Beal,   B. King,  


                                *Harry L. Bryden
           University Of Southampton • School of Ocean and Earth Science
                    Empress Dock • Southampton • SO14 3ZH • UK
                  Tel: 44-(0)23-80596437 • Fax: 44-(0)23-80596204
                         e-mail: h.bryden@soc.soton.ac.uk














                        SOUTHAMPTON  OCEANOGRAPHY  CENTRE
                               CRUISE REPORT No. 45
                          RRS CHARLES DARWIN CRUISE 139
                               01 MAR - 15 APR 2002

                  Trans-Indian Hydrographic Section across 32°S

                               Principal Scientist
                                   H L Bryden
                                      2003

School of Ocean and Earth Sciences              Tel:   +44 (0)23  8059 6437
Southampton Oceanography Centre                 Fax:   +44 (0)23  8059 6204
University of Southampton                   Email: H.Bryden@soc.soton.ac.uk
Waterfront Campus
European Way
Southampton
Hants  SO14 3ZH
UK



                              DOCUMENT DATA SHEET
                                     Author
                               BRYDEN, H L  et al
                                Publication Date
                                      2003


TITLE

          RRS Charles Darwin Cruise 139, 01 Mar-15 Apr 2002.  Trans-Indian
                        Hydrographic Section across 32°S.


REFERENCE

    Southampton Oceanography Centre Cruise Report, No. 45, 122pp.


ABSTRACT

A modern hydrographic section was made across the Indian Ocean at a latitude of 
about 32°S during a 46-day voyage from Durban to Fremantle aboard RRS Charles 
Darwin in March-April 2002. The principal goal of this work was to measure the 
flows of mass, heat, freshwater, inorganic and organic nutrients, and carbon 
dioxide across the southern boundary of the Indian Ocean in order to determine 
the meridional overturning circulation for the Indian Ocean, to define the heat, 
freshwater, nutrient and carbon transports across 32°S, and to produce overall 
physical and biogeochemical budgets for the Indian Ocean. A second goal was to 
examine the climate variability in ocean circulation from comparisons of these 
new measurements with previous surveys in 1936, 1965, 1987 and 1995. A total of 
146 hydrographic stations were made along this transoceanic section. At each 
station an instrument package consisting principally of a CTD, 3 Lowered ADCP's 
and 24 10-litre sampling bottles was lowered from the surface down to the ocean 
bottom to measure temperature, salinity, oxygen and eastward and northward 
current profiles throughout the water column. On the way back to the surface, 24 
water samples were collected at various depths and these samples were analysed 
on board ship for salinity and oxygen (to calibrate the continuous electronic 
profiles), for inorganic nutrients, constituents of the carbon system, and 
chlorofluorocarbons. Samples were also collected and stored for later, shore-
based analyses of helium, tritium, and organic nutrients. Throughout the cruise 
velocity data in the upper few hundred meters of the water column were provided 
by an ADCP mounted in the ship's hull, meteorological variables were monitored 
and samples of air and rainfall were periodically collected. In addition, 25 
Argo floats were launched along the section to provide continuing profiles over 
the next 5 years. This report describes the methods used to acquire and process 
the measurements on board ship during the cruise.

KEYWORDS

ADCP, AGULHAS CURRENT, ARGO FLOATS, BIOGEOCHEMICAL BUDGETS, CARBON CHEMISTRY, 
CFC, CHARLES DARWIN, CLIMATIC CHANGES, CRUISE 139 2002, CTD OBSERVATIONS, 
HELIUM-TRITIUM SAMPLES, HYDROGRAPHIC SECTION, INDIAN OCEAN, LADCP, LOWERED 
ACOUSTIC DOPPLER CURRENT PROFILER, MERIDIONAL OVERTURNING CIRCULATION, 
NUTRIENTS, OCEAN CIRCULATION, TRACER MEASUREMENTS, VESSEL MOUNTED ADCP

ISSUING ORGANISATION
     Southampton Oceanography Centre
     Empress Dock
     European Way
     Southampton  SO14 3ZH UK

Copies of this report are available from: 
     National Oceanographic Library, SOC  
     PRICE: £26.00

Tel:  +44(0)23 80596116  Fax:  +44(0)23 80596115  Email:  nol@soc.soton.ac.uk


CONTENTS

SCIENTIFIC PERSONNEL             
SHIPS PERSONNEL              
ITINERARY               
BACKGROUND AND OBJECTIVES            
  Chart of Hydrographic Station - Cruise Track for CD 139       
  Hydrographic Station positions and depths         
NARRATIVE             
CTD DATA PROCESSING AND CALIBRATION        
WATER SAMPLE SALINITY ANALYSIS         
DISSOLVED OXYGEN           
NUTRIENTS             
COˇ2 COMPONENTS            
CHLOROFLUOROCARBON (CFC) MEASUREMENTS       
SAMPLING FOR HELIUM AND TRITIUM         
LOWERED ACOUSTIC DOPPLER CURRENT PROFILER      
SHIPBOARD INSTRUMENTATION AND COMPUTING     
NAVIGATION          
VESSEL-MOUNTED ACOUSTIC DOPPLER CURRENT PROFILER (VMADCP)  
UNDERWAY METEOROLOGICAL MEASUREMENTS     
ATMOSPHERIC SAMPLING        
ARGO FLOATS          


SCIENTIFIC PERSONNEL
         _______________________________________________________________

          Name                  Role                     Affiliation
          --------------------  -----------------------  --------------
          Harry L. Bryden       Principal Scientist      SOES-SOC
          Brian  A. King        Watch Leader-LADCP       JRD-SOC
          Stuart A. Cunningham  Watch Leader-CTD         JRD-SOC
          Louise M. Duncan      Watch Leader-VMADCP      JRD-SOC
          Lisa M. Beal          LADCP                    SIO, San Diego
          Jeffrey R. Benson     CTD                      UKORS-SOC
          John B. Wynar         Instrumentation          UKORS-SOC
          Richard Sanders       Nutrients-Leader         GDD-SOC
          Valerie Latham        Nutrients                CSIRO, Hobart
          Angela Landolfi       Nutrients                SOES-SOC
          Aida Rios             COˇ2-Leader               IIM, Vigo
          Marta ¡lvarez         COˇ2                      IIM, Vigo
          David P. Wisegarver   CFC-Leader               PMEL, Seattle
          Kevin McHugh          CFC                      PMEL, Seattle
          W. Kevin Smith        Winch                    UKORS-SOC
          Steve Whittle         Winch                    UKORS-SOC
          Matthew D. Palmer     CTD                      SOES-SOC
          Melanie Witt          Atmosphere Trace Metals  UEA, Norwich
          Martin Bridger        Computing                UKORS-SOC
         _______________________________________________________________
          SOC    Southampton Oceanography Centre 
          PMEL   Pacific Marine Environmental Laboratory
          JRD    James Rennell Division  
          CSIRO  Commonwealth Scientific and Industrial Research Organisation
          SOES   School of Ocean and Earth Science 
          GDD    George Deacon Division
          UKORS  UK Ocean Research Services  
          IIM    Instituto de Investigacións Mariñas
          SIO    Scripps Institution of Oceanography 
          UEA    University of East Anglia
         _______________________________________________________________


SHIP'S PERSONNEL
                       _________________________________

                        Name             Rank
                        ---------------  --------------
                        LONG, G.M.       Master
                        NEWTON, P.W.     Chief Officer
                        OLDFIELD, P.T.   2nd Officer
                        HOOD, M.P.       2nd Officer
                        MOSS, S.A.       Chief Engineer
                        HOLT, J.M.       2nd Engineer
                        CLARK, J.R.C.    3rd Engineer
                        SLATER, G.       3rd Engineer
                        BAKER, J.G.L.    ETO
                        POOK, G.A.       CPO(D)
                        LUCKHURST, T.G.  PO(D)
                        ALLISON, P.      S1A
                        COOK, S.C.       S1A
                        CRABB, G.        S1A
                        MACLEAN, A.      S1A
                        HILLIER, L.J.    POMTR
                        BELL, R.         SCM
                        FAHEY, F.        Chef
                        KUJAWIAK, A.     M/S
                        MINGAY, G.M.     Steward
                       _________________________________


ITINERARY 

RRS Charles Darwin departed Durban, South Africa on Friday 1 March at 1500 local 
time to take a transindian hydrographic section along a nominal latitude of 32°S. 
We made 2 transects of the Agulhas Current and then began the coast-to-coast 
section just offshore of Port Edward 60 miles south of Durban. On Monday, 15 
April at 0800 local time RRS Charles Darwin arrived in Fremantle Australia after 
146 hydrographic stations over 46 days at sea (Figure 1).


BACKGROUND AND OBJECTIVES

The size and structure of the overturning circulation in the Indian Ocean is one 
of the foremost issues in observing the large-scale ocean circulation today. 
Taking advantage of the scheduling of a UK research vessel to work in the Indian 
Ocean in 2001/2002, we proposed a transindian hydrographic section across the 
southern boundary of the Indian Ocean at 32°S to measure this overturning 
circulation. Transoceanic hydrographic sections across the southern boundaries 
of the Atlantic Ocean at about 40°S and Pacific Ocean at about 32°S during the 
World Ocean Circulation Experiment (WOCE) have provided estimates of the basin-
scale meridional circulation and meridional heat, freshwater and biogeochemical 
fluxes that then define the ocean-scale heat, freshwater and biogeochemical 
budgets in effect defining the overall contribution of each ocean to the global 
heat, water and nutrient balances (Saunders and King, 1995a; Tsimplis, Bacon and 
Bryden, 1998; Wijffels, Toole and Davis, 2000). Unfortunately a hydrographic 
section across the southern boundary of the Indian Ocean was not carried out 
during WOCE.

There was a 1987 transindian section across 32°S of the Indian Ocean aboard RRS 
Charles Darwin (Toole and Warren, 1993), but that section consisted primarily of 
traditional hydrographic stations with CTD profiles and water sample analyses 
without the technological improvements that became standard during WOCE 
fieldwork. The technological improvements made during WOCE focussed on making 
velocity measurements with underway acoustic Doppler current profiler (ADCP) 
measurements combined with three-dimensional GPS navigation providing continuous 
velocity information in the upper 400 m (King, Alderson and Cromwell, 1996), on 
making full-depth Lowered ADCP (L-ADCP) measurements of velocity throughout the 
water column on each hydrographic station (King, Firing and Joyce, 2001), and on 
deploying neutrally buoyant floats to define the deep velocity field (Davis, 
1998). Each of these velocity techniques has proven useful for determining the 
reference level velocity for geostrophic velocity profiles (Saunders and King, 
1995b; Beal and Bryden, 1997; Wijffels, Toole and Davis, 2000). Without having 
these velocity techniques available, 10 analyses of the 1987 transindian 
hydrographic section have had to rely on traditional water mass analysis 
techniques to define the zero velocity surface for the geostrophic velocity 
profile for each station pair across the basin.

Another problem with the 1987 section across 32°S is that it took stations over 
the Broken Plateau for about 1300 km from 88°E to 101°E so that it 
preferentially sampled relatively shallow waters over the Plateau rather than 
the deeper waters to the north or south of the Plateau. Such sampling forces a 
shallow reference level for geostrophic velocity estimates in analyses using the 
1987 32°S section and this shallow reference level may compromise estimates of 
the meridional overturning circulation (Bryden and Beal, 2001).

Thus, the principal objective of the resulting RRS Charles Darwin cruise was to 
take a modern hydrographic section across 32°S in the Indian Ocean in order to 
measure the flows of mass, heat, freshwater, inorganic and organic nutrients, 
and carbon dioxide across the southern boundary of the Indian Ocean, to quantify 
the meridional overturning circulation for the Indian Ocean, and to produce 
overall physical and biogeochemical budgets for the Indian Ocean. The 2002 
section followed the track of the 1987 section out to 80°E but then, to avoid 
the problems of shallow reference levels, took a course to the south of Broken 
Plateau in order to take stations in deep water from 80°E to Australia. A 
second objective was to examine the climate variability in ocean circulation 
from comparisons of these new measurements with previous surveys along 32°S in 
1936, 1965 and 1987. Because changes in subantarctic mode water along this 
section have been suggested to be fingerprints of anthropogenic climate change 
based on Hadley Centre climate model runs (Banks and Wood, 2002; Banks and 
Bindoff, 2003), analysis of the actual changes is of much current interest. 
Since the 2002 track follows the track of the 1987 section from the coast of 
South Africa out to 80°E, climate changes can most easily be assessed in the 
western part of the section from 30°E to 80°E.

During the 46-day voyage (1 March to 15 April 2002) from Durban to Fremantle 
aboard RRS Charles Darwin across the southern boundary of the Indian Ocean, a 
total of 146 CTD/LADCP stations were taken along the 9000 km track (Figure 1, 
Table 1). On each station, continuous top-to-bottom profiles of temperature, 
salinity, oxygen and east and north velocities were made and up to 24 water 
samples were analysed for salinity, oxygen, nitrate, phosphate, silicate, CFC's 
and carbon system components alkalinity and pH. The CFC measurements were made 
by collaborating American scientists from PMEL in Seattle and the carbon system 
measurements were made by collaborating Spanish scientists from IIM in Vigo. In 
addition, 25 Argo floats were launched along the section to provide continuing 
profiles over the next 5 years, 385 paired water samples were collected for 
subsequent analysis of helium and tritium concentrations in the Noble Gas 
Laboratory in Southampton, and atmospheric trace metal measurements were made by 
a UEA scientist. 


REFERENCES

Banks, H. T. & Bindoff, N.L. 2003 Comparison of observed temperature and 
    salinity changes in the Indo-Pacific with results from the coupled 
    climate model HadCM3: Processes and mechanisms. Journal of Climate, 16, 
    156-166.

Banks, H. & Wood, R. 2002 Where to look for anthropogenic climate change in 
    the ocean. Journal of Climate, 15, 879-891.

Beal, L.M. & Bryden, H.L. 1997 Observations of an Agulhas Undercurrent. 
    Deep-Sea Research, I, 44, 1715-1724.

Bryden, H.L & Beal, L.M. 2001 Role of the Agulhas Current in Indian Ocean 
    circulation and associated heat and freshwater fluxes. Deep-Sea 
    Research, I, 48, 1821-1845.

Davis, R. 1998 Preliminary results from directly measuring mid-depth 
    circulation in the tropical and South Pacific. Journal of Geophysical 
    Research, 103, 24619-24640.

King, B.A., Alderson, S.G. & Cromwell, D. 1996 Enhancement of shipboard 
    ADCP data using DGPS position and GPS heading measurements. Deep-Sea 
    Research, I, 43, 937-947.

King, B.A., Firing, E. & Joyce, T.M. 2001 Shipboard observations during 
    WOCE. In Ocean Circulation and Climate, edited by G. Siedler, J. Church 
    and J. Gould, Academic Press, 99-122.

Saunders, P.M. & King, B.A. 1995a Oceanic fluxes on the WOCE A11 section. 
    Journal of Physical Oceanography, 25, 1942-1958.

Saunders, P.M. & King, B.A. 1995b Bottom currents derived from a shipborne 
    ADCP on WOCE cruise A11 in the South Atlantic. Journal of Physical 
    Oceanography, 25, 329-347.

Toole, J.M. & Warren, B.A. 1993 A hydrographic section across the 
    subtropical South Indian Ocean. Deep-Sea Research, I, 40, 1973-2019.


Tsimplis, M.N., Bacon, S. & Bryden, H.L. 1998 The circulation of the 
    subtropical South Pacific derived from hydrographic data. Journal of 
    Geophysical Research, 103 (10), 21443-21468.

Wijffels, S.E., Toole, J.M. & Davis, R. 2000 Revisiting the South Pacific 
    subtropical circulation: A synthesis of World Ocean Circulation 
    Experiment observations along 32°S. Journal of Geophysical Research, 
    106, 19481-19514. 
    

Table 1. Hydrographic station positions and depths.
         _____________________________________________________________________

          station     lat (°S)    lon (°E)  distance  depth  Notes
             #        deg min     deg min      km       m
          ---------  ---------    --------  --------  -----  ----------------
          Durban     -30 05.00    30 42.00      0        0   Depart 1Mar 1400
            1        -31 22.00    32 38.00    236     3410   Test station
            2        -30 37.00    33 24.00    347     3153 
            3        -30 28.00    33 11.00    373     2912 
            4        -30 19.50    32 59.00    398     2387 
            5        -30 11.00    32 47.00    423     1808   Winch stuck
            6        -30  3.50    32 36.00    445     1753 
            7        -29 56.00    32 25.00    468     1540 
            8        -29 48.00    32 14.00    491     1479 
            9        -29 41.00    32  4.00    512     1131 
           10        -29 37.00    31 58.00    524      868 
           11        -29 33.00    31 52.50    535      485 
           12        -29 29.00    31 47.00    547       99 
           13        -29 23.00    31 38.75    564       67 
           14        -31  0.89    30 19.97    785      213 
           15        -31  2.00    30 20.86    788      346 
           16        -31  2.90    30 22.10    790      549 
           17        -31  4.40    30 24.20    795      977 
           18        -31  5.80    30 25.40    798     1280 
           19        -31  7.30    30 28.30    803     1628   CTD Suspended
           20        -31  9.10    30 32.10    810     1877 
           21        -31 12.10    30 35.80    818     2387   He/Trit Samples
           22        -31 15.60    30 39.30    827     2904 
           23        -31 19.05    30 44.70    837     3295 
           24        -31 22.50    30 50.10    848     3304 
           25        -31 25.95    30 55.50    859     3257 
           26        -31 29.40    31  0.90    869     3206 
           27        -31 34.70    31  9.70    886     3338 
           28        -31 43.12    31 18.86    907     3198 
           29        -31 48.32    31 25.98    922     3380   He/Trit Samples
           30        -31 56.60    31 36.30    945     3647 
           31        -32  6.84    31 52.26    976     3582   Float deployment
           32        -32 18.57    32  8.75   1010     3408 
           33        -32 25.69    32 46.73   1071     3537   End of Week 1
           34        -32 32.80    33 24.70   1131     3551 
           35        -32 41.50    34 10.30   1204     2301 
           36        -32 54.00    35  0.10   1285     1640   He/Trit Samples
           37        -33  0.10    35 35.00   1341     1477 
           38        -32 59.40    36  4.70   1387     1862 
           39        -33  0.90    36 20.60   1412     2329   Float deployment
           40        -33  0.77    36 27.13   1422     3298 
           41        -33  0.70    36 30.90   1428     4265   He/Trit Samples
           42        -33  0.30    36 40.50   1443     4598 
           43        -32 59.70    37  4.80   1480     5105 
           44        -33  0.40    38  0.00   1566     4950 
           45        -33  0.00    39  0.00   1659     5173   He/Trit Samples
           46        -33  0.00    40  0.00   1752     5142   Float deployment
           47        -33  0.30    41  0.30   1846     5120 
           48        -33  0.00    42  0.00   1939     4430 
           49        -32 59.93    42 42.45   2005     4372 
           50        -32 59.92    42 50.18   2017     3371   Float deployment
           51        -32 59.90    43  2.50   2036     2270   He/Trit Samples
           52        -32 52.00    43 40.10   2094      891 
           53        -32 59.60    44 29.40   2171      958 
           54        -33  6.00    45 18.00   2247     1290 
           55        -33 12.40    46  4.80   2321     2172 
           56        -33 18.70    46 30.20   2362     2678 
           57        -33 22.80    46 55.00   2401     3039 
           58        -33 29.90    47 26.80   2452     3608   He/Trit Samples
                                                             End  of week 2
           59        -33 33.70    48 14.70   2526     3987   Float deployment
                                                             CTD stop at 300m
           60        -33 40.20    49 13.80   2618     4196   Reterminate wire
           61        -33 46.80    50 12.60   2709     4277   CTD stop at 550m
           62        -33 53.40    51 11.40   2801     4348   SIO LADCP install
                                                             Wire in block
           63        -33 59.50    52 10.60   2892     4414   Float deployment
           64        -33 59.90    52 44.70   2945     4638   He/Trit Samples
           65        -34  0.40    53 10.20   2984     4633 
           66        -34  0.40    53 36.90   3025     4302 
           67        -34  0.70    54  7.10   3071     3955 
           68        -34  0.13    54 54.99   3145     3610 
           69        -34  0.00    55 46.44   3224     3985 
           70        -33 59.66    56 15.09   3268     2725   Float deployment
           71        -33 59.33    56 26.80   3286     3847 
           72        -33 58.30    57  2.10   3340     4440   He/Trit Samples
           73        -33 59.70    57 29.10   3382     5083 
           74        -33 59.90    58 10.00   3444     4865 
           75        -33 59.70    58 53.60   3511     4169 
           76        -33 59.66    59 19.31   3551     5304   He/Trit Samples
           77        -33 59.60    59 57.00   3609     4841 
           78        -33 59.83    60 32.90   3664     5337   Float deployment
           79        -34  0.00    61  0.00   3705     4871   He/Trit Samples
           80        -33 59.40    61 59.70   3797     4846 
           81        -34  0.00    63  0.00   3890     4721 
           82        -33 59.50    63 59.90   3982     4599   He/Trit Samples
                                                             End  of week 3
           83        -34  0.00    65  0.00   4074     4567   Float deployment
           84        -33 59.80    66  0.20   4166     4581 
           85        -34  0.00    67  0.00   4258     4900   He/Trit Samples
           86        -34  0.10    67 59.90   4350     4489 
           87        -34  0.00    69  0.00   4442     4429   Float deployment
           88        -34  0.00    70  0.30   4535     4160   He/Trit Samples
                                                             Wire in block
           89        -34  0.00    71  0.00   4627     4605 
           90        -34  0.10    71 59.80   4718     4771   Reterminate wire
           91        -33 35.00    72 50.00   4809     4233   Float deployment
                                                             Snap on wire-kink
           92        -33 10.00    73 40.00   4899     4166 
           93        -32 45.00    74 30.00   4989     3668   He/Trit Samples
           94        -32 20.00    75 20.00   5080     3350 
           95        -31 55.00    76 10.00   5171     3199 
           96        -31 20.30    77 19.30   5298     3009   Wind/Swell 31 h
                                                             Position Revised
           97        -31  7.70    77 44.40   5344     3183   Float deployment
           98        -30 45.00    78 29.80   5427     3513   He/Trit Samples
                                                             End  of week 4
           99        -30 22.40    79 15.30   5511     3706   Evade cyclone
          100        -31 11.60    80  8.80   5636     3693   Float deployment
          101        -31 12.00    81  1.41   5719     4171 
          102        -31 12.00    81 54.02   5803     3688 
          103        -31 12.00    83 12.00   5926     3907   Float deployment
          104        -31 12.00    84 30.00   6050     3858   He/Trit Samples
          105        -31 20.88    85 30.00   6146     3627 
          106        -31 30.03    86 30.00   6242     3516 
          107        -31 36.13    87 10.00   6307     2109 
          108        -31 45.29    88 10.00   6403     2095   He/Trit Samples
          109        -31 48.34    88 30.00   6435     2917   Float deployment
          110        -31 52.91    89  0.00   6483     3305 
          111        -31 57.49    89 30.00   6530     3709 
          112        -32  2.07    90  0.00   6578     3887 
          113        -32 10.00    90 52.00   6661     3772   Float deployment
          114        -32 30.00    91 48.00   6756     4311 
          115        -32 50.00    92 44.00   6851     4402   He/Trit Samples
          116        -33 10.00    93 40.00   6946     4301 
          117        -33 30.00    94 36.00   7040     4381   Float Cluster
          118        -33 50.00    95 32.00   7134     4558   He/Trit Samples
                                                             End of Week 5
          119        -34 10.00    96 28.00   7227     4521   Wind delay 5h
          120        -34 30.00    97 24.00   7321     4512 
          121        -34 30.00    98 25.00   7414     4222   Float deployment
          122        -34 30.00    99 26.00   7507     4591 
          123        -34 30.00   100 27.00   7600     4337   He/Trit Samples
          124        -34 30.00   101 28.00   7693     4255 
          125        -34 30.00   102 29.00   7786     5343   Float deployment
          126        -34 30.00   103 30.00   7879     5732 
          127        -34  0.00   104 15.00   7968     5383 
          128        -33 30.00   105  0.00   8057     5332   He/Trit Samples
          129        -33  0.00   105 45.00   8146     5332 
          130        -32 30.00   106 30.00   8235     4355   Float deployment
                                                             Reterminate wire
          131        -32  0.00   107 15.00   8325     5125 
          132        -31 30.00   108  0.00   8415     5293 
          133        -31 30.00   108 55.00   8502     5327   He/Trit Samples
          134        -31 30.00   109 50.00   8589     5207   Float deployment
          135        -31 30.00   110 45.00   8676     5100 
          136        -31 30.00   111 19.00   8729     4924   End of Week 6 
          137        -31 30.00   112 14.00   8816     5444   Clearance delay7h
          138        -31 30.00   113  9.00   8903     5199   Float deployment
                                                             He/Trit Samples
          139        -31 30.00   114  4.00   8990     4447 
          140        -31 30.00   114 30.00   9031     3332 
          141        -31 30.00   114 35.82   9040     2292 
          142        -31 30.00   114 40.00   9047     1351 
          143        -31 30.00   114 50.00   9063      622 
          144        -31 30.00   114 56.00   9072      373 
          145        -31 30.00   115  2.00   9081      172 
          146        -31 30.00   115 25.00   9118        4   On deck 14Apr1600
          Fremantle  -32 04.80   115 42.00      0
         ______________________________________________________________________
          

NARRATIVE

Most of the scientists arrived in Durban on Monday, 25 February, and spent 
Tuesday, Wednesday and Thursday setting up the ship for the long hydrographic 
cruise. Networking the laboratory computers was an initial holdup, but was 
accomplished by noontime on Wednesday. The remainder of setup went steadily. We 
had a Safety Briefing for all scientists on Thursday afternoon and we were 
basically ready to sail Friday morning. One of the scientists, however, was ill 
and required a doctor's appointment Friday morning so we set a sailing time for 
1400. We actually left the pier at 1500 on 1 March 2002 and were out in open 
water by 1545. As usual, most of the scientists retired to their cabins to 
adjust and prepare for the station work ahead.

For this cruise, two changes were made to normal scientific manning for long 
hydrographic cruises. First, negotiations with UKORS and RVS resulted in taking 
2 UKORS mechanical technicians rather than the standard 3 to operate the winches 
for continuous 24-hour hydrographic station work, and entraining one RVS deckman 
(P. Allison) to operate the winch for 8 hours each day. Second, an additional 
scientist was berthed in the hospital for the duration of the cruise. These two 
changes allowed us to accommodate 2 additional scientists beyond Charles 
Darwin's normal capacity to carry out the CFC (chlorofluorocarbon) measurement 
programme. We very much appreciate RVS and UKORS cooperation in making these 
changes possible.

We sailed directly across the Agulhas Current to a test station in deep water 
(3410 m) at 0430 on 2 March. Wire tension seemed abnormally high and 
investigation found that improper calibration coefficients were being used, 
likely due to a system reset when the winches were started up. Installing the 
correct coefficients reduced the wire tension to normal levels, confirming that 
we would be able to do stations to 5500 m depth as required across the section.

Following the test station, we proceeded northeastward to begin a hydrographic 
section across the Agulhas Current (stations 2 to 13) at 1500 on 2 March. On 
station 5, the winch would not work and required repair for about 4 hours. We 
finished the northern Agulhas section in shallow water (67 m) at 1100 on 4 
March, and spent the remainder of the day steaming along the coast with the 
Agulhas Current in beautiful weather before beginning the southern Agulhas 
section (and the main hydrographic section) at 2100 on 4 March. On station 19, 

the winch stopped as the CTD was coming on deck and the package remained 
suspended above the deck for 3 hours while a fitting was rethreaded. On station 
21, we took our first set of helium-tritium samples and after station 31 on 7 
March we deployed our first Argo float. By the end of one week at sea we had 
accomplished 33 hydrographic stations.

Winds were persistently out of the east at about 20 to 25 knots, hampering our 
steaming eastward and sometimes forcing us to sample the rosette while hove to. 
The problem seemed to be related to Hurricane Hary travelling slowly 
southeastward from the coast of Madagascar. While our progress was slow, Brian 
King compared the EM log speed used by the Bridge with the GPS speed over ground 
for between-station steaming and found that the EM log displayed 1 knot faster 
than the actual ship speed. Because we feared that the Bridge Officers were 
aiming for a 10-knot EM log speed and blaming the 8.5 knot true speed on wind 
and swell, we decided to change the calibration coefficients for the EM log to 
reflect true speed. Nice weather set in following the change in coefficients, as 
Hurricane Hary decayed and moved away, but agreeably the EM log speed now 
matched the GPS speed over ground. By the end of Week 2 we had accomplished 58 
stations.

On station 59, the CTD signal ceased on the way down at 300m depth, always a 
scary moment. We brought the package back on board and found that the electrical 
connection at the wire termination had failed, so the wire was reterminated. 
Again at station 61, the CTD signal stopped at 550m on the way up. This time the 
problem was a fuse in the deck unit, most likely a power surge on the ship had 
blown the fuse. For station 62 we changed from the SOC Broadband LADCP to the 
SIO Broadband LADCP and, being happy with the SIO instrument performance, we 
continued with the SIO instrument for the remainder of the cruise. For these 
stations over the Southwest Indian Ridge, Elaine McDonagh had planned out 

station positions to be in the valleys between the series of mini-ridges based 
on the Smith and Sandwell bathymetry. As we steamed between stations over the 
mini-ridges that extended up to 2000 m depth, we were impressed that each of the 
planned station positions was indeed in the deepest part of the valleys at about 
5000 m. We had generally good weather from 14 to 22 March.

For 23 March we planned a barbecue on deck in the evening to mark the temporal 
mid-point of the cruise. As the barbecue started the rain began. Stuart 
Cunningham was heard to comment that it was perfectly acceptable Scottish 
barbecue weather, but spirits were dampened. The weather continued to 
deteriorate so we began to sample while hove to. There was a terrific roll in 
the early morning hours of 25 March followed by a terrific rain storm at 0600. 
Weather continued to be marginal but we pressed ahead with stations until 27 
March at 0700 when the Captain decided it was too rough to start station 96. 
After 30 hours of steaming slowly into the weather, we set out for the next 
station position which started at 1500 on 28 March. We then went back westward 
25 miles to do another station to help fill in the gap. As a consequence there 
is a sizeable separation between stations 95 and 96 and a small separation 
between 96 and 97. Stations 98 and 99 were accomplished in difficult wind and 
swell conditions. Before station 100, the Captain decided we must run 
southeastward to get away from tropical cyclone Ikeda. We had been following 
Ikeda on weather maps and it had been menacing us for nearly a week. It was a 
large system drawing in air from the east so the winds had been strongly against 
us. It appeared to wait for us at 20°S, 80°E and as we approached 80°E it 
moved south toward us. We diverted south then southeast as it circled around 
behind us and began to chase us.

As a result of avoiding Ikeda, we modified the section to head southeastward a 
bit earlier than planned. Wind and swell remained difficult for stations 100, 
101, 102 and 103 and steaming between stations was slow as Ikeda passed by us 
and dissipated. At the start of station 103, a kink in the wire was noticed and 
retermination was needed. Seriously worried now whether there would be enough 
time to finish the section into Australia, we opted to eliminate a station while 
we were reterminating. As a result there are larger than normal separations 
between stations 102 and 103 and between 103 and 104. Finally at station 105 on 
1 April, Easter Monday, the weather calmed and we began to work steadily for the 
first time in 10 days. At this point we estimated that we had just enough time 
to finish the section if there were no more problems with equipment or weather. 
On 5 April, we deployed a "cluster" of 4 floats near 95°E to study their 
dispersion over horizontal separations of 8 to 59 km. There was a freak squall 
during recovery of the CTD on the morning of 5 April that cut out the power to 
the bow thruster. Otherwise, for most of the remainder of the cruise, the wind 
came around behind us so that our steaming time between stations shortened 
considerably and we actually stored up some hours of time, enough to reterminate 
the wire after station 130 and to cover the 7-hour delay due to Australian 
clearance problems.

Slow progress due to adverse weather coloured the first 4 weeks of the cruise. 
We had not expected such adverse winds crossing the subtropical south Indian 
Ocean in late austral summer and I had never seen it rain so much at sea. 
Melanie Witt had come on the cruise hoping to fill a few small jars with 
rainwater and she posted a request in the Main Lab to awaken her if it rained. 
After being constantly awakened and filling all available containers by mid 
cruise, she removed the request. We were perhaps unlucky to encounter 2 tropical 
cyclones in Hary and Ikeda, neither of which hit us with much force but each of 
which created adverse winds for a week to ten days which slowed our progress.

About 1 April when we were about as far from land as possible, one of the COˇ2 
chemists became ill with first an earache (and a constant headache), then a sore 
throat, then a swollen left cheek. Initially she used eardrops and aspirin. 
After several days of worsening pain, the Captain put her on antibiotics and 
telephoned for medical advice. By 7 April, her condition seemed to stabilise and 
she started to work for a few hours each day. She was able to help with the COˇ2 
analysis (but not to sample on deck) but still complained of constant headache. 
When we docked in Fremantle, she went to the doctor for a diagnosis, which was 
that she had somehow contracted shingles out at sea. There was really no cure 
other than antibiotics and time, so the doctor prescribed antibiotics and 
patience pills for her subsequent holiday in Australia. Thus, the second major 
issue was a serious illness for one of the scientists over the last two weeks of 
the cruise. The scientific party stepped forward to do the necessary COˇ2 work, 
so there was no effect on the measurement programme. But the concern for her 
health and the worry about what we could do about it when we were so far from 
any port were all-consuming for about 10 days.

The final problem surprisingly was Australian diplomatic clearance to take 
stations within 200 miles of the coast of Australia. In planning the cruise we 
had expected such clearance to be a formality given the historically friendly 
relations between the United Kingdom and Australia. But in early March after 
departing Durban, the Captain mentioned that we did not yet have Australian 
clearance and in fact the clearance request had been 'lost' so that only in 
March had it been sent to Australia for consideration. Easter holidays from 24 
March to 7 April of course slowed progress on the clearance, so that about 5 
April I began emailing Australian colleagues for help with the clearance request 
while SOC called the Foreign Office in London each day. At noontime on Friday, 
12 April, we finished our last planned station outside the 200-mile Australian 
territorial waters and began our wait for clearance. Because it was already 
Friday afternoon and we did not expect much diplomatic activity over the weekend 
before docking on Monday, I made a contingency plan to connect our section to a 
line of WOCE stations into the Australian coast as a way of creating a coast-to-
coast transindian section for post-cruise analysis. We started this station plan 
late Friday afternoon (1600 local time) when it was already 1900 hours in 
Canberra where permission was being sought. Spirits around the ship were 
extremely glum: after 6 weeks at sea and 136 stations, it appeared that we would 
have no clearance to finish the last 10 stations before docking in Fremantle on 
Monday morning. Then at 1630 the Captain took a telephone call to say that 
clearance had been granted. We abandoned the contingency plan, recovered the CTD 
package and steamed off to do the final 10 stations. In 10 minutes the entire 
ship's party went from desolation to jubilation.

We finished the final hydrographic station at 1600 on 14 April, with just about 
12 hours to spare. We proceeded offshore and then alongshore to do a ground-
track calibration for the shipboard ADCP and then proceeded to Fremantle to tie 
up at the pier by 0800 on Monday, 15 April. The equipment was rapidly dismantled 
and packed away in shipping containers or in the hold for a subsequent cruise. 
By 1600, nearly all the scientific party had left the ship and only a short re-
visit by King and Bryden was required on 16 April to finalise the packing and 
shipping.

With completion of 146 stations over 46 days, worries about weather, illness and 
diplomatic clearance faded quickly. All of the equipment had worked extremely 
well; we had complete data sets for all components of the planned hydrographic 
section; and the scientific and ship's party had worked harmoniously for nearly 
7 weeks toward achieving the scientific and technical objectives of the cruise.

                                                                H.L. Bryden



CTD DATA PROCESSING AND CALIBRATION

CTD Package

The CTD package consists of a frame on which the CTD, fluoromenter, altimeter, 
LADCP's, battery packs and rosette system with 24 10-litre water samplers. The 
package also has 500 kg of weight strapped to the frame to improve its descent.

Instruments

A total of 146 CTD casts were undertaken on the cruise. The initial package 
configuration was as follows: 
 • Sea-Bird 9/11 plus CTD system 
 • 24 by 10L NOAA/PMEL CFC-Free water samplers 
 • Sea-Bird 43B Oxygen sensor 
 • Benthos PSA-916T Altimeter 
 • 10KHz beacon 
 • SOC RDI Broadband 150 KHz LADCP & battery pack 
 • Upward-Looking RDI Workhorse 300 KHz LADCP 
 • Downward-Looking RDI Workhorse 300 KHz LADCP 
 • Battery pack for both Workhorse LADCP's 

The Sea-Bird CTD configuration was as follows:
 • SBE 9 plus Underwater unit s/n 09P-19817-0528
 • Frequency 0-SBE 3P Temperature sensor s/n 03P-4107 (primary)
 • Frequency 1-SBE 4C Conductivity sensor s/n 03P-2573 (primary)
 • Frequency 2-Digiquartz temperature compensated pressure sensor s/n 73299
 • Frequency 3-SBE 3P Temperature sensor s/n 03P-4103 (secondary)
 • Frequency 4-SBE 4C Conductivity sensor s/n 03P-2580 (secondary)
 • SBE 5T submersible pump s/n 05T-3002
 • SBE 5T submersible pump s/n 05T-3195
 • SBE 32 Carousel 24 position pylon s/n 32-24680-0344
 • SBE 11 plus deck unit s/n 11P-19817-0495

The auxiliary A/D output channels were configured for casts 001 through 146 as 
follows:

   V0---SBE 43B Oxygen s/n 43B-0076
   V3---Benthos PSA-916T Altimeter s/n 874

After cast 013, Chelsea MKIII Aquatracka Fluorometer s/n 088243 was installed in 
V4. The cable was found to be defective and the fluorometer was removed for 
casts 022 through 034 whilst a replacement cable was spliced. The fluorometer 
was re-installed for casts 035 onwards.


Deployment Procedure

The package is lifted by the winch from the starboard deck with guidance ropes 
to keep the package from swinging. As the winch moves the package outboard and 
lowers it into the water, the ropes are retrieved. Because the SeaBird pumps 
start between 30 seconds and 1minute after the conductivity rises from zero, the 
package is inititally lowered to 5 m depth and held for 1 minute to allow the 
pumps to start. The package is then raised to the surface and then the station 
begins as the package descends. On several stations when there was significant 
ship roll as CTD was deployed and it was not considered safe to hold the package 
at 5 m depth, the package was sent immediately down. This resulted in lost or 
contaminated data in the top 20m while the pumps switched on during these 
stations. Therefore, the preferred deployment procedure should always include a 
1minute wait at a few meters depth and then a return to near surface before 
beginning the downcast.


Data Logging Setup

The signal from the SBE 9+ underwater unit is fed up the wire to the SBE 11+ 
deck unit and then to a PC with SBE software where the data is displayed and 
recorded to hard disk. For security of the basic data series, the acquisition PC 
is isolated from the shipboard computer network. After completing the station, 
the station data is put on a Zip Disk and carried to the processing system 
computer which is part of the shipboard computer network


CTD Data Processing

CTD data processing is now split between two software packages: Sea-Bird's 
proprietary software SEASOFT and the traditional PSTAR. Sea-Bird CTD's are new 
to UKORS and we describe in detail the Sea-Bird processing path and its 
interface to PSTAR.


Sea-Bird

Raw CTD data are returned up the seacable, translated by the deck unit and 
displayed as calibrated data in real time on dual logging PC's.

1. On completion of the CTD station copy the four CTD files to a zip disk. 
   The files have the extensions: ctdionnn.BL, .CON, .HDR, .dat. File 
   formats are described in Sea-Bird (2001b). Briefely, BL is created when 
   a bottle fire confirmation is received, and contains bottle sequence 
   number, position, date, time and beginning and end scan numbers; CON, 
   contains the instrument configuration and calibration coefficients; HDR, 
   header recorded when acquiring real time data; dat is the raw binary CTD 
   data.

2. sneakernet CTD files on zip disk to processing PC. Put files in a sub 
   folder of your cruise folder e.g. C:\CD139\data

3. Install the latest version of the Seabird-win32 processing software in 
   the directory C:\CD139. If you don't have a copy of this software it may 
   be found on the PC or can be downloaded prior to the cruise from the 
   Sea-Bird www site. Sea-Bird processing routines for windows can be 
   recognised from their name format, which appends "W" to each exe module. 
   E.g. DatCnvW.exe

4. The next step is to process the first CTD station by hand, storing 
   parameters in a .psu file. We can then create a batch processing routine 
   for all subsequent stations based on these psu files. Run the following 
   processing modules. This sequence below is recommended by Sea-Bird as 
   the standard processing of SBE 9/11 CTD data with a SBE-43 oxygen 
   sensor.

i. Data Conversion (DatCnv)

Converts raw data to calibrated data. Using the processing form, click the File 
tab. Make sure to select the station stored in C:\CD139\data and tick the box to 
match file name to configuration file. Write output file to the same directory. 
Now click the Data Setup tab. Tick process to end of file, scans to skip 0, 
output format: binary. Convert data from: upcast and downcast. Create: both 
bottle and data file. Source of scan range data Bottle log (.BL) file. Scan 
range offset 0, scan range duration 0.001. These last parameters ensure that the 
.ros file contains a single scan of all the CTD variables including the time of 
that scan at each bottle fire. Subsequently in PSTAR, we will merge a 10s 
average CTD profile onto this data to create the firing file for CTD versus 
bottle calibration. Now select output variables (Table C1).


Table C1: CTD variables calibrated and output from SEASOFT module DatCnv 
                ____________________________________________

                 Parameter                     Unit
                 ----------------------------  ------------
                 Pressure, digiquartz          dbar 
                 Temperature                   ITS-90, degC 
                 Conductivity                  mS/cm 
                 Temperature2                  ITS-90, degC 
                 Conductivity2                 mS/cm 
                 Pressure temperature          degC 
                 Altimeter                     m 
                 Oxygen, SBE 43                μmol/kg 
                 Temperature difference (2-1)  ITS-90, degC 
                 Time, Elapsed                 seconds 
                 Fluorimeter                   μg/l 
                ____________________________________________


ii. AlignCTD

Can be used to advance or retard any of the data streams to minimise spiking or 
hysteresis. To minimise oxygen hysteresis below 1000 dbar we advance oxygen 
relative to pressure by five seconds. For the 9/11 CTD, conductivity must be 
advanced relative to pressure; the default is to advance conductivity by 1.75 
scans. This is done in hardware by the deck unit for both primary and secondary 
conductivity.

iii. WildEdit

The SBE manual suggests this should not be required for 9/11 CTD systems but 
give it as part of the standard processing and so we have included this module 
without checks of its results. Standard deviations for pass one and two are 2 
and 10 respectively, applied to 500 scans/block and excluding scans marked bad 
for all variables.

iv. CellTM

Uses a recursive filter to remove conductivity cell thermal mass effects (Lueck 
(1990), Lueck and Pickelo (1990)) from the measured conductivity. In areas of 
steep temperature gradient the thermal mass correction is on the order 0.005 
PSU, and is negligible elsewhere. The algorithm used is: 

          dt = t(1)-t(-7)                                                 (1)
          c(t)tm = -1 x b x ctm(t-1)+a x dcdt x dt                        (2)
          Ccorr = C+ctm                                                   (3)
where

          a = 2α/(sample intervalxβ+2)
          b = 1-(2a/α)
          dcdt = 0.1x(1+0.006x(T-20))

Typical values are α=0.03 and 1/β=7.0 for a SBE 9/11 plus TC ducted 
conductivity cell (3000rpm pump).

v. Filter

Low pass filter pressure, τ = 0.15s

vi. RosSum

Writes out a summary of the bottle file .BL using the .ros file as input.

vii. Trans

Finally, create an ASCII version of the .CNV file.

Batch Processing

Having run through the SBE processing and set the required parameters in each 
.psu file (one psu file per programme), a DOS batch script can be used to 
automatically complete this processing on subsequent stations (assuming the 
instrument setup remains unchanged). The file below (called sbeproc.bat) should 
be placed in the CD139 folder. 

File:sbeproc.bat

DatCnv/cc:\CD139\data\ctdio%1.con/ic:\cd139\data\ctdio%1.dat/oc:\cd139\data/fctdio%1.cnv/pc:\CD139\DatCnv.psu
AlignCTD/ic:\cd139\data\ctdio%1.cnv/oc:\cd139\data/fctdio%1.cnv/pc:\CD139\AlignCTD.psu
WildEdit/ic:\cd139\data\ctdio%1.cnv/oc:\cd139\data/fctdio%1.cnv/pc:\CD139\WildEdit.psu
CellTM/ic:\cd139\data\ctdio%1.cnv/oc:\cd139\data/fctdio%1.cnv/pc:\CD139\CellTM.psu
Filter/ic:\cd139\data\ctdio%1.cnv/oc:\cd139\data/fctdio%1.cnv/pc:\CD139\Filter.psu
RosSum/cc:\cd139\data\ctdio%1.con/ic:\cd139\data\ctdio%1.ros/oc:\cd139\data/fctdio%1.btl/pc:\CD139\RosSum.psu
Trans/ic:\cd139\data\ctdio%1.cnv/oc:\cd139\data/fctdio%1.cnv/pc:\CD139\Trans.psu

This DOS batch file must be executed from a DOS window, and is the first 
argument to a SBE programme called sbebatch. In a DOS window, C:\CD139>sbebatch 
sbeproc.bat nnn. Station number is the argument %1 to sbeproc.bat.


CTD Sensor Calibrations

In DatCnv the following calibration equations convert raw sensor frequencies to 
calibrated data. 

Temperature
                                         1
 Tcal(ITS-90)°C = --------------------------------------------------      (4) 
                  {g+h[ln(f/fo)]+i[l^2n(f/fo)]+j[l^3n(f/fo)]}-273.15 

where ln is the natural log function, f is the output frequency in Hz, f0=1000 
is an arbitrary scaling used for computational efficiency. Throughout this 
report all temperatures and calibration equations are given on the ITS-90 
temperature scale. For equation of state calculations temperatures in ITS-90 are 
converted to ITS-68 using Saunders (1990), 

                             T68 =1.00024 x T90                           (5)

The temperature calibrations were performed on the 4th of December and 2nd of 
November 2001 for the primary and secondary sensors respectively. Fitted 
temperature residuals were less than ±0.00007°C for both sensors. The drift in 
temperature since the last calibrations (March 2001) was +0.00095°C/year for 
the primary and -0.00004°C/year for the secondary. See Table C2 for the 
calibration coefficients g, h, i & j.


Table C2: Temperature sensor calibration coefficients
          ______________________________________________________

           Coefficient        Primary            Secondary
           -----------  ------------------   ------------------
                g       4.40385186 x 10^-3   4.42352698 x 10^-3
                h       6.49254747 x 10^-4   6.47980623 x 10^-4
                i       2.35916338 x 10^-5   2.36589809 x 10^-5
                j       2.12472851 x 10^-6   2.16776478 x 10^-6
          ______________________________________________________


Conductivity

The conductivity sensors are calibrated over a range of 0 to 60 mS/cm using 
natural seawater; a water sample at each point is compared to IAPSO standard 
seawater using a Guildline AutoSal. The calibration equation is,

                                  g+hf^2+if^3+jf^4
                         C(S/m) = ----------------                        (6)
                                    10[1+δt+εp]       

where f is the instrument frequency (KHz), t is temperature (°C), p is pressure 
(db), δ = -9.57 x 10^-8 is the bulk compressibility and ε = 3.25 x 10^-6 is 
the thermal coefficient of expansion of the borosilicate cell.

The primary and secondary conductivity cells were calibrated on the 30th and 2nd 
of November 2001 respectively. Conductivity residuals were all less than ±0.00003 
S/m in a seven point calibration. Drift since last calibraion (6th and 20th 
March 2001) is 0.00000 psu/month for the primary and -0.00120 psu/month for the 
secondary. Calibration coefficients are given in Table C3.


Table C3: Conductivity calibration coefficients
         _________________________________________________________

          Coefficient  Primary (s/n 4107)   Secondary (s/n  4103)
          -----------  -----------------    ---------------------
               g      -1.05163057 x 10^1   -1.04988214 x 10^1
               h       1.63468814 x 10^0    1.54363454 x 10^0
               i      -1.02002185 x 10^-4   2.34998282 x 10^-4
               j       1.59143440 x 10^-4   7.50542098 x 10^-4
         _________________________________________________________


Pressure

Pressure is measured by a DIGIQUARTZ 410K-105 pressure transducer with quartz 
crystal pressure sensing and thermal compensation. Pressure is calibrated from, 

                             ⎛ Tˇo^2 ⎞ ⎛    ⎛   Tˇo^2 ⎞⎞
                     P = C 1-⎜ ----  ⎟ ⎜1-D ⎜1- ----- ⎟⎟               (7)
                             ⎝  T^2  ⎠ ⎝    ⎝    T^2  ⎠⎠

where T is pressure period (µs).  C,D,To are given by,

                          C = Cˇ1 + Cˇ2U + Cˇ3U^2                         (8)

                               D = Dˇ1 + Dˇ2U                             (9)

                 Tˇ0 = Tˇ1 + Tˇ2U + Tˇ3U^2 + Tˇ4U^3 +Tˇ5U^4              (10)

where U is temperature (°C) and the calibration coefficients are given in Table C4.


Table C4: Pressure sensor calibration coefficients.
                       _________________________________

                         Coefficient
                        -------------------------------
                             C1      -5.087539 x 10^-4
                             C2      -2.199664 x 10^2
                             C3       1.589010 x 10^-2
                             D1       3.721700 x 10^-2
                             D2       0
                             T1       3.011152 x 10^1
                             T2      -2.857091 x 10^-4
                             T3       4.528990 x 10^-6
                             T4      -5.48500  x 10^-11
                             T5       0
                       _________________________________


CTD Conductivity Calibration using Bottle Conductivities

The Sea-Bird conductivity sensor usually drifts by changing the slope of the 
conductivity calibration (referred to by Sea-Bird as the span), and changes are 
typically toward lower conductivity readings with time. Offset error in 
conductivity is normally due to electronics drift, and is usually less than ±
0.001 mS/cm/year. Offsets greater than ±0.002 mS/cm are symptomatic of sensor 
malfunction. Sea-Bird recommends that drift corrections to conductivity be made 
by assuming no offset error, unless there is strong evidence to the contrary 
Sea-Bird (2001a).

Therefore, compute,
                              K = <Cbot/Cctd>                            (11)

where Cbot is bottle conductivity = Fn(upcast press, upcast temp, botsal) and 
Cctd is upcast CTD conductivity at the time of the bottle sample and < > denotes 
the station average. The corrected CTD conductivity is given by,

                             Cctdcorr = KCctd                            (12)

Bottle samples are excluded where they are obviously bad and rejected data 
mainly occur in upper ocean.


CTD Oxygen Calibration

The Sea-Bird dissolved oxygen sensor (SBE43) is a Clark membrane polarographic 
oxygen detector. This sensor is similar in principle to the sensors we have used 
with the Neil Brown CTD, but has been redesigned with improved materials and 
electronics: the principal improvements are the elimination of hysteresis in the 
top 1000 m, continuous poloarization which eliminates the wait time for 
stabilization after power up and coupling to a pumped system so that the effects 
of flow rate variation are removed. The sensor and its operating principles are 
described in Sea-Bird Application note no. 64 and the product specification 
sheet for the sensor (both available on the Sea-Bird www site).

i. Sensor calibration

Voltage output in the range 0 to +5 volts is converted to oxygen concentration 
using a modified version of the algorithm by Owens and Millard (1985), 
     
         ⎛ ⎛      ⎛           ⎛      doc⎞⎞                 ⎞ ⎞ 
         ⎜ ⎜Sˇoc x⎜(v+offset)+⎜tau x ---⎟⎟+ Bˇoc x e^-0.03T⎟x⎟
   Oˇ2 = ⎜ ⎝      ⎝           ⎝      dT ⎠⎠                 ⎠ ⎟           (13)
         ⎜                                                       ⎟
         ⎝                 e^(Tˇcorr x T+Pˇcorr x p) x Oˇsat(T,S)⎠

Where, O2 is dissolved oxygen concentration (in the Sea-Bird routine datcnvW 
oxygen units may be specified - choose µmol/kg), T is water temperature (°C), p 
is pressure (dbar), S is salinity (psu), v is temperature compensated oxygen 
current (µamps), doc/dT is slope of oxygen current (µamps/sec), Soc is the 
oxygen current slope, Boc is oxygen current bias, Tcorr is residual temperature 
correction factor for membrane permeability, offset is the voltage produced for 
zero current, Pcorr is the pressure correction factor for membrane permeability, 
τ is the oxygen sensor response time and
                                                    
                ⎛  -173.4292+249.6339 x (100/T)+143.3483 x ln(100/T)+  ⎞
Osat(T,S) = exp ⎜                                                      ⎟   (14)
                ⎝ Sx[-0.033096+0.014259 x (100/T)-0.00170 x (T/100)^2] ⎠

is oxygen saturation Weiss (1970). The calibration coefficients are given in 
Table C5.


Table C5: Oxygen calibration coefficients for SBE43 dissolved oxygen sensor 
          s/n 0076
                       _____________________________________

                        Calibration Date 17 September  2001
                        -----------------------------------
                        Soc       0.36960
                        Boc       0.0212
                        Offset   -0.6308
                        Tcor      0.0020
                        Pcor      0.000134
                        τ        0.0
                       _____________________________________


ii.  Reconciliation of CTD to bottle oxygens

Bottle oxygens in µmol/l are first converted to units of µmol/kg and then the 
differences to CTD oxygens are calculated. The CTD oxygens are taken from the 
downcast because of hysteresis below 1000 dbar. Downcast datacycles were found 
by matching potential temperature on the upcast at each bottle stop to a 
potential temperature on the downcast. Bottle-CTD oxygen residuals from the 
first 91 stations gave a mean curve versus depth (Table C6). This correction was 
merged on pressure with the CTD data and oxycorr added to CTD oxygen. For 
stations after 91 the oxygen correction residual with pressure changed rapidly 
over groups of ten or so stations. The reasons for this are not clear but may be 
due to contamination or ageing of the oxygen sensor. 

For the first 91 stations the oxycorr values are constant between 125 and 1000 
dbar, increase linearly to 4500 dbar, and are constant below 4500 dbar (though 
not well determined because of rather few samples). This is similar to the 
specification of the sensor for no hysteresis at pressures less than 1000 dbar. 
A subtle effect shallower than 125 dbar is evident in the oxycorr values. 

Clearly, the oxycorr values increase towards the surface, from 4.9 to 7.1 
µmol/kg (near surface oxygen is about 250 µmol/kg). The near surface increase in 
oxycorr is not explained by any systematic differences between the down and up 
CTD oxygen profiles.


Table C6: oxycorr versus pressure, where oxycorr=<bto-uo> is the average of 
          the oxygen residuals in the pressure interval for stations in the 
          interval m-n.
          ______________________________________________________________________

           1-91          95-117         118-127        128-135        136-146
           pres oxycorr  pres oxycorr  pres oxycorr  pres oxycorr  pres oxycorr
           dbar µmol/kg  dbar µmol/kg  dbar µmol/kg  dbar µmol/kg  dbar µmol/kg
           ---- -------  ---- -------  ---- -------  ---- -------  ---- -------
            -10   7.1       0  21.3     -10  27.8     -10  27.8     -10  28.3
              0   7.1      25  21.3      25  27.8      25  27.8      25  28.3
             25   7.1      75  20.8      75  29.5      75  29.5      75  27.3
             75   6.2     125  20.3     125  27.1     125  27.1     125  26.2
            125   4.9     175  20.1     175  26.9     175  26.9     175  26.0
            175   4.7     250  17.7     250  26.7     250  26.7     250  23.9
            240   4.4     350  17.9     350  25.1     350  25.1     350  24.1
            340   4.1     450  17.6     450  23.8     450  23.8     450  23.9
            440   4.2     550  17.5     550  23.1     550  23.1     550  21.4
            540   4.3     650  17.4     650  23.1     650  23.1     650  18.3
            640   4.3     750  17.5     750  23.1     750  23.1     750  18.0
            740   4.3     850  16.3     850  21.0     850  21.0     850  15.1
            840   4.3     950  15.6     950  18.7     950  18.7     950  15.3
            940   4.3    1125  15.1    1125  17.2    1125  17.2    1125  12.7
           1040   4.8    1375  13.2    1375  16.0    1375  16.0    1375  11.5
           1250   5.9    1625  12.5    1625  13.5    1625  13.5    1625  13.8
           1750   6.7    1875  13.3    1875  14.4    1875  14.4    1875  14.3
           2250   7.9    2125  14.1    2125  15.1    2125  15.1    2125  14.1
           2750   8.4    2375  14.7    2375  17.1    2375  17.1    2375  13.1
           3250   8.8    2625  14.3    2625  16.9    2625  16.9    2625  15.1
           3750   9.7    2875  14.9    2875  18.1    2875  18.1    2875  14.8
           4250  10.6    3125  15.7    3125  17.8    3125  17.8    3125  15.2
           4750  10.7    3375  15.7    3375  17.5    3375  17.5    3375  16.0
           5250  10.5    3625  15.8    3625  17.0    3625  17.0    3625  16.0
           5750  10.4    3875  15.6    3875  16.5    3875  16.5    3875  14.6
           6000  10.4    4125  15.4    4125  16.8    4125  16.8    4125  15.1
                         4375  15.0    4375  16.2    4375  16.2    4375  14.5
                         4625  14.0    4625  17.6    4625  15.5    4625  16.5
                         6000  14.0    4875  17.5    4875  14.7    4875  16.4
                                       6000  17.5    6000  14.0    6000  15.2
          ______________________________________________________________________


Could the increase in oxycorr in the top 100dbar be explained by a problem with 
the bottle oxygens? We examined the percent saturation of the bottle oxygen 
values (Table C7). The bottle data suggest that the water column is 
supersaturated at 52 dbar, decreasing toward 100% saturation at the surface and 
also decreasing in saturation below 52 dbar. The supersaturation at 52 dbar 
corresponds to a peak in fluorescence and is probably caused by phytoplankton 
producing oxygen at this depth. An identical analysis for CTD oxygen has about 
3.2% less saturation at each depth than the values in Table C7. From this 
analysis of bottle oxygen saturations, we conclude that the bottle oxygens are 
probably accurate because it is expected that oxygen saturation is close to 100% 
near surface, and therefore the increase in oxycorr in the top 125 dbar is 
probably due to a reduction in the sensitivity of the CTD oxygen sensor near 
surface. These results have been passed to Sea-Bird and we await a response.


Table C7: Percent saturation of bottle oxygens (mean), where press is the 
          average pressure of the nbot samples, sd is standard deviation of 
          the mean and se is the standard error of the mean.
                       __________________________________

                        pres  nbot  mean %   sd     se
                        ----  ----  ------  -----  -----
                         11    95   1.004   0.014  0.001
                         42    21   1.008   0.016  0.003
                         52    30   1.013   0.016  0.003
                         77    22   0.982   0.035  0.007
                        100    32   0.927   0.052  0.009
                       __________________________________


After adding oxycorr to CTD oxygens, the residuals plotted against station 
number have a slowly changing low amplitude variation, which was removed as an 
offset on a station-by-station basis. This slow drift is broadly consistent with 
the sensor specification of 2% drift per 1000 hours of operation.

Figure C1 shows the distribution of oxygen residuals (bottle-CTD) versus bottle 
oxygen, station number and pressure. For points within ±2 standard deviations 
of the mean the mean±standard deviation oxygen residuals is 0.16±2.1 µmol/kg.


Figure C1: bottle-CTD oxygen versus i. bottle oxygen, ii. station number 
           (limits are for - 10<(btO2-O2)<10) and iii. Pressure.


Salinometry

Salts were drawn for analysis from every bottle. These were analysed by 
salinometer, and usually a standard sea water was measured at the beginning of 
each analysis and then every twenty four samples thereafter. A timeseries of the 
standard seawater (SSW) conductivity ratio divided by the stated conductivity of 
the SSW plotted against station number shows changes in the values of the 
measured SSW. Note that the standardisation of the salinometer was adjusted at 
station 022 so the timeseries must be considered in two parts. If the SSW 
conductivity is constant within the batch, then variability of the conductivity 
ratio of the SSW is due to variations of the salinometer or to variations in 
operator method. Between stations 022 and 048 the measured SSW conductivity 
ratio is extremely stable, varying by less than 0.00001, equivalent to 0.0003 
mS/cm at conductivity values around 32 mS/cm. If the salinometer is stable and 
the SSW varies sample to sample, then the variability of bottle conductivities 
will be apparent in the comparison of bottle-CTD conductivities if the CTD 
conductivity sensor is stable. We have compared the measured SSW values to the 
bottle-CTD conductivities and can see no evidence that the measured SSW 
conductivity variations are present. Either they are not present in the bottle-
CTD conductivities or are swamped by the typical variability of bottle-CTD 
conductivties of about 0.002 mS/cm. The best we can conclude is that the 
measurement of conductivity by the salinometer and standardisation against SSW 
introduces a conductivity error of about 0.0003 mS/cm, which is much smaller 
than the error due to variability in the bottle-CTD conductivities.


Post Cruise CTD Sensor Calibrations

The post cruise calibrations took place immediately after the cruise (Table C8) 
and we decided to implement corrections to the cruise data based on these 
calibrations. Pressure and temperature corrections are small and linear, and are 
a result of sensor changes either during the cruise or perhaps in transit. Here, 
we assume that changes occurred during the cruise and use the post-cruise 
calibrations to obtain the linear corrections to the cruise data. Conductivity 
residuals (bottle-CTD), were found to be quadratic with depth and linear with 
temperature. These were subsequently found to be due to an error in the 
calibration coefficients provided by SeaBird. After the post-cruise 
calibrations, dependent variables were recalculated. 


Table C8: Timeline in days between pre and post cruise calibrations
                   ______________________________________

                    Event                     Time(days)
                    ------------------------  ----------
                    Pre-cruise calibrations        0
                    Cruise start                  90
                    Cruise end                   135
                    Post-cruise calibrations     157
                   ______________________________________


Pressure

Post-cruise the pressure sensor (s/n 73299) was tested against a stable 
reference pressure sensor on 8th May 2002: input pressures are generated using a 
Ruska model 5201 dead-weight tester, s/n 23330/380, and eleven calibration 
points were obtained between 0 and 7000 and back to 0 dbar. The pressure 
difference between pre and post cruise calibrations, is given by

                       Pcorr = -0.78+0.99989 x PCTD                      (15)

where PCTD is the pressure measurements during the cruise using the pre-cruise 
calibrations and Pcorr is corrected pressure. The standard deviation of pressure 
residuals corrected using (15) to the post-cruise calibration data is 0.1 dbar.


Temperature

The post-cruise temperature calibration coefficents are given in Table C9. The 
average temperature change±sd from pre to post cruise calibrations is 0.91±
0.26 m°C and 0.13±0.09 m°C for the primary and secondary sensors respectively, 
such that both sensors now read cold and these corrections could be added to 
temperatures measured during the cruise. These changes were calculated by 
applying the pre-cruise calibration coefficients to the post-cruise CTD 
calibration data and taking the difference to the post cruise calibration bath 
temperatures.

The primary sensor has a much larger offset and sd than the secondary sensor. 
This prompted us to look at these residuals as a function of temperature. For 
the primary sensor, the CTD reads cold by 0.66 m°C at -1.5°C and cold by -1.25 
m°C at 32.5°C, varying linearly between. Therefore, we corrected the cruise 
data using the following, 
   
                    Tcorr = 0.000569+1.00002214 x TCTD                   (16) 

where TCTD is the primary temperature measured during the cruise and Tcorr is 
corrected temperature. Secondary temperature has not been adjusted. 


Table C9: Temperature sensor calibration coefficients for post-cruise 
          calibrations on 07May2002
          ______________________________________________________

           Coefficient  Primary(s/n 4107)    Secondary(s/n 4103)
           -----------  ------------------   ------------------
                g       4.40361941 x 10^-3   4.42341950 x 10^-3
                h       6.48783845 x 10^-4   6.47681379 x 10^-4
                i       2.32699968 x 10^-5   2.34539360 x 10^-5
                j       2.05383746 x 10^-6   2.12200464 x 10^-6
          ______________________________________________________


Conductivity

Calibrated bottle-CTD conductivity residuals show an exponential shape with 
depth. Below 1500 m the conductivity difference is constant. Between 1500m and 
500m the conductivity difference increases by 0.001 mS/cm; shallower than 500 m 
the conductivity difference increases by 0.005 mS/cm. The bottle-CTD 
conductivity difference plotted against in situ temperature is linear; 
decreasing from 0.005 mS/cm at 25°C to 0 mS/cm at 0°C. Initially this was 
thought to be due to the vertical separation of the CTD and Niskin bottles in 
the CTD frame in the presence of large vertical conductivity gradients. However, 
this was incorrect and SeaBird after long and detailed inspection of our data 
and their calibration data discovered an egregious error in their calibration 
coefficients.

The CTD conductivity sensor is calibrated as follows. The sensor is immersed in 
a bath of seawater with an approximate salinity of 35 psu. The bath is heated 
from 0 to 35°C and readings of conductivity from the CTD are noted at eight 
precisely measured temperatures. The bath salinity is measured by Autosal using 
samples drawn from the bath at each calibration point and the bath conductivity 
is back calculated using bath temperature and pressure. i.e. Cˇbath 
=fn(P,TˇT68,S)ˇbath where Sbathis the bath salinity calculated from the 
conductivity ratio of water samples taken from the bath. The error made by Sea-
Bird in calculating Cbath was using bath temperatures measured on the ITS-90 
temperature scale and not converting them to ITS-68 temperatures and this error 
affects the calibration coefficients given in Table C3. The error in CTD 
conductivity Cerror (Table C10) closely matches the error observed during the 
cruise (Cˇbtc - CˇCTD), the mean±sd of 

           C∆=(Cˇbtc - CˇCTD)-Cerror is -0.0004±0.0002 mS/cm. 

Confident that the error introduced in CˇCTD during the cruise is correctly 
explained we corrected the CTD conductivities by, 

           Cˇcorr = CˇCTD - 0.000474+0.00025667*TinsituˇT90              (17) 

predicted from 2915 bottle samples taken during the cruise. The mean±sd of 
Cˇbtc - Cˇcorr is 0.0000±0.0009 mS/cm.


Table C10: Conductivity error Cˇerror = C(P,Tˇ68,S)ˇbath - C(P,Tˇ90,S)ˇbath 
           arising from T90 temperatures in the calculation of conductivity 
           instead of T68 temperatures (Cˇcorr = CˇCTD+Cˇerror). Cˇbtc is  
           bottle conductivity and CˇCTD is conductivity measured by the 
           CTD during the cruise, predicted from 2915 bottle samples taken 
           during the cruise 

           (Cˇbtc - CˇCTD) = 0.00025667*TinsituˇT90 - 0.000474, R^2 = 
           0.793. C∆ = (Cˇbtc - CˇCTD) - Cˇerror is the residual CTD 
           conductivity error after correction. 
           __________________________________________________________________

            Bath      Bath     Cˇbath=             Cˇerror   Cˇbtc-   C∆
            temp      temp     fn(P,TˇT68,S)ˇbath            CˇCTD
            T90(°C)    T68(°C)  mS/cm               mS/cm     mS/cm    mS/cm
            -------  --------  ------------------  -------  -------  -------
             0.01     0.01     29.03603            0        -0.0005  -0.0005
             2        2.00048  30.77615            0.00042   0.0000  -0.0004
             5        5.00120  33.45538            0.00109   0.0008  -0.0003
            10       10.0024   38.08971            0.00228   0.0021  -0.0002
            20       20.0048   47.91804            0.00487   0.0047  -0.0002
            24       24.00576  52.02918            0.00598   0.0057  -0.0003
            30       30.00720  58.35696            0.00769   0.0072  -0.0005
            35       35.00840  63.75694            0.00915   0.0085  -0.0006
           __________________________________________________________________


CTD Salinity Residuals

The distribution of bottle-CTD salinity versus bottle salinity, station number 
and pressure is given in Figure C2a, C2b and Table C11. The low scatter and 
small number of wild points is an indicator of the care with which bottle 
salinity samples were drawn and analysed. There are no trends in residuals 
plotted against either bottle salinity or pressure, confirming that the final 
conductivity corrections were sensible. 


Figure C2a: bottle-CTD salinity versus i. bottle salinity, ii. station 
            number  (limits are for -0.014<(bts-s)<0.014) and iii. 
            Pressure. 
Figure C2b: bottle-CTD salinity (for P>1500 dbar) versus i. bottle 
            salinity, ii. station number (limits are for -0.001<(bts-
            s)<0.001) and iii. Pressure.


Table C11:  Bottle-CTD salinity residual means (µ) and standard deviations 
            (σ). n number of points in mean and % is percentage of points 
            outside limits, limit is edit criteria applied to (bts-s) for 
            removal of data outliers before mean is calculated.
            ___________________________________________________________

               µ       σ         n        %          Limits
             ------  ------  ---------  ----  ------------------------
             0.003   0.0013  3018/3100   2.7  ±0.1,     ±2σ,  ±2σ
             0.001   0.0005  1093/1152   5.1  P>1500db, ±0.1, ±2σ, ±2σ
             0.0000  0.0005  1016/1152  11.8  P>1500db, ±0.1, ±0.001
            ___________________________________________________________


CTD and Sample Processing Paths

Sample Path

The object of the sample processing path is to gather the disparate sample data 
into one PSTAR file. Create ascii text sample files On the mac "gusto" there is 
a folder called "samples", and within this folder there are subfolders, one per 
sample type (e.g. cbn,cfc,nut,oxy,sal,sur). Within each sample folder there is a 
blank excel file to receive the sample data. Save sample file as text (tab) 
delimited and with the name format xxxionnn.txt where xxx is the sample type and 
nnn is the file number e.g salio001.txt. Read ascii text files to UNIX and 
create PSTAR files >xxx.exec, File in: xxxionnn.txt (from mac), File >out: 
xxxionnn.txt (ASCII) & xxxionnn.bot (PSTAR) Paste sample data into a master 
sample file >pasxxx, File in: xxxionnn.bot is pasted into samionnn.

Notes: sur is the file for thermosalinograph salinity samples; each sample file 
on the mac contains variables sampnum, statnum and botlnum. However, these are 
only pasted to the master sample file through the sal path; the master sample 
file (one per station) is created as part of the CTD processing (CTD Path step 
12). Use a tick sheet to keep track of which files have been processed and to 
which stage.

CTD Path

To obtain a fully calibrated 2db downcast CTD profile.

1.  Transfer Sea-Bird CTD files from logging PC to processing PC (zip disk)

2.  Sea-Bird processing. Process CTD data using Sea-Bird routines, as 
    described in detail in the cruise report

3.  ftp processed CTD data from PC to UNIX. PC ftp programme FTP Explorer 
    allows UNIX disk to be mounted on PC, so files can be ftp'd by drag and 
    drop.

4.  >ctd0: Read in 24hz ascii Sea-Bird file and output to PSTAR. A header 
    time is constructed from times within the Sea-Bird .cnv file. File in: 
    CD139nnn.cnv, File out: ctdionnn.24hz

5.  >ctd1: i. process 24hz data to 1hz (median despike, average on time to 
    1hz, interpolate pressure to remove any absent data). ii. Average 1hz 
    file to 10s for matching to bottle samples. iii. Note the datacycles in 
    the 1hz file of start downcast, maximum pressure and end upcast. File 
    in: ctdionnn.24hz, File out: ctdionnn.1hz & ctdionnn.10s.

6.  >ctd3: standard plots of CTD 1hz data; θ/s, deep θ/s and Oˇ2/pressure

7.  >fir0: i. read Sea-Bird rosette firing file into PSTAR. ii. Merge 
    firing file with 10s CTD file to produce file with the 10s averaged 
    upcast CTD variables at the time of bottle firing. iii. Read in winch 
    data using datapup. File in: CD139nnn.ros & ctdionnn.10s, File out: 
    firionnn & winionnn.

8.  >sam0: i. Create a blank sample file for station nnn from the master 
    sample file. At the beginning of the cruise create a master sample file 
    with all required variables set to absent. ii. paste firing file into 
    sample file. File in: sam.master & firionnn, File out: samionnn.

9.  >position.exec: i. creates a file with position at the three times from 
    the ctdionnn.1hz file corresponding to the datacycles noted in step 5 
    at start down, pmax and end up. ii. user is given the choice of adding 
    the position at the bottom of the downcast (nadir position) to the 1hz, 
    10s, fir, win and sam files. iii. Adds data cycles to ctd2.exec so that 
    datacycles do not have to be entered by hand a second time when 
    creating a ctd.2db file. File in: ctdionnn.1hz and 139gps01 (master gps 
    navigation file), File out: nnn.position & ctd2.exec.

10. >ctd2.exec: runs ctd2 but has a record of the datacycles at start down, 
    pmax and end up from step 9. File in: ctdionnn.1hz, File out: 
    ctdionnn.2db & ctdionnn.ctu (1 hz file for data cycles between start 
    down and end up).

11. >adddepth.exec: add corrected echo sounding depth to the position file. 
    File in: five minute averaged corrected depth, File out: position.nnn.

12. >pbotle.exec: warning this exec is a complete lash up - wouldn't trust 
    it, but it seemed to work on CD139. In principle: match potemp at 
    upcast bottle stops to downcast potemp and extract downcast oxygen to 
    match to upcast bottles. Writes the downcast CTD oxygen into variable 
    oxygen in the sam file. File in: ctdionnn.1hz & samionnn, File out: 
    pbtnnn, samionnn.

13. >sta.sum.exec: Produces a summary file of ctd station positions, times, 
    depths and bottles. File in: position.nnn & ctdionnn.1hz, File out: 
    stn_sum.ascii

Calibration

The two execs below calculate calibration variables, and can be run as often as 
required on any number of stations as set by the user. The principle is that 
whenever a CTD conductivity or oxygen calibration is done you will want to run 
these execs to recompute residuals.

1.  >botcond.exec: Calculate all derived variables required for CTD 
    conductivity and oxygen calibration. The following variables are 
    calculated: botcond=Fn(upcast temp, upcast press, botsal) where temp 
    and press are upcast CTD primary variables, botcond/cond & 
    botcond/cond2, btc-uc=botcond-cond, bts-us=botsal-salin, c2-c=cond2-
    cond and botoxyM(µmol/kg)=botoxy(µmol/l)/sigoxy(kg/l) where sigoxy is 
    potential density relative to 0 dbar at the fixing temperature of the 
    oxygen samples and finally calculate btouo=botoxyM(µmol/kg)-oxygen(ctd 
    downcast found by CTD path step 12, µmol/kg). File in: samionnn, File 
    out: samionnn.calib

2.  >sam.calib.append.exec: i. Appends samionnn.calib files and creates 
    some files where datacycles have been excluded using datpik on 
    press>1500db and -0.01<btc-uc<0.01. These datpik limits were chosen to 
    isolate deep bottles and to remove obvious outliers. The datpik files 
    were then averaged using pbins to provide some statistical estimates of 
    conductivity and oxygen residuals.

CTD Conductivity

1.  >ctdcondcal.exec: applies a conductivity correction Cctdcorr=KCctd to 
    the ctd.1hz file and reworks CTD processing to pass conductivity 
    correction through to the sam file. Dependant variables, salin, potemp 
    and sigma0 in the ctd.1hz file are also recalculated. The values of K 
    must be entered in an array and the exec is set for processing multiple 
    stations. File in: ctdionnn.1hz, File out: ctdionnn.10s, firionnn, 
    samionnn, ctdcondcal.version (record of the version codes changed).

2.  >resid.plot.exec: plots conductivity residuals with their means and 
    standard deviations: (btc-uc) versus i. botcond, ii. press, iii. 
    statnum and iv. K=botcond/cond versus statnum. Plots with all data 
    cycles or datpiked data cycles are possible.

CTD Oxygen

1.  >oxy.corr.exec: applies an oxygen correction curve versus pressure to 
    CTD oxygen in the .1hz file and the sam file. See cruise report for a 
    discussion of oxygen calibration. File in: ctdionnn.1hz & samionnn, 
    oxy.correction, File out: ctdionnn.1hz & samionnn, oxy.corr.version.

2.  >oxy.corr2.exec: applies a final station by station offset to oxygen. 
    File in: ctdionnn.1hz & samionnn, oxy.correction File out: ctdionnn.1hz 
    & samionnn, oxy.corr.version.

3.  >resid.oxy.plot.exec: plots oxygen residuals with their means and 
    standard deviations: (botoxyM-oxygen) versus i. pressure, ii. statnum.

Primary and secondary sensors

The UKORS Sea-Bird 911+ CTD's have separate dual conductivity and temperature 
sensors and these can be examined during the cruise for drift and/or jumps. A 
third independent measure would tell you which sensor had changed. Generally, 
only temperature is of relevance, as conductivity performance is monitored 
against standard seawater.


1.  >pbins.ct.exec: uses pbins to produce some statistics of variables t2-t 
    and c2-c. File in: sam.append.calib (see botcond.exec & sam.calib.append.exec)

2.  >ct.plot.exec: plot t2-t and c2-c versus statnum.

Others

1.  >osat.exec: uses a butchered version of oxygn3 to write out oxysat, and 
    then calculates percentage saturations of bottle and CTD oxygens.

2.  >salinom.exec: divides the measured SSW conductivities by the label 
    conductivity.

Units

1 S/m = 10 mmho/cm = 10 mS/cm


REFERENCES

Lueck, R. G. 1990 Thermal inertia of conductivity cells: theory. Journal of 
    Atmospheric and Oceanic Technology, 7, 741-755.

Lueck, R. G. & Pickelo, J. 1990 Thermal inertial of conductivity cells: 
    observations with a Sea-Bird cell. Journal of Atmospheric and. Oceanic 
    Technology, 7, 756-786.

Owens, W.B. & Millard, R.C. 1985 A new algorithm for CTD oxygen 
    calibration. Journal of Physical Oceanography, 15, 621-631.

Saunders, P.M. 1990 The International Temperature Scale, WOCE International 
    Newsletter, 10, 10.

Sea-Bird. 2001a Computing temperature and conductivity slope and offset 
    correction coefficients from laboratory calibrations and salinity 
    bottle samples. Sea-Bird Electronics, Inc.

Sea-Bird. 2001b CTD data acquisition software, SEASOFT, version 4.249. Sea-
    Bird Electronics, Inc.

Weiss, R.F. 1970 The solubility of nitrogen, oxygen and argon in seawater. 
    Deep-Sea Research, 17, 721-735.

                                          Stuart Cunningham and Jeff Benson



WATER SAMPLE SALINITY ANALYSIS

Laboratory Set-up

Two salinometers were set up in the constant temperature (CT) laboratory on RRS 
Charles Darwin. Both the JRD and UKORS salinometers were Guildline 8400B. 
Although both were set up, the JRD salinometer was the only one used during the 
cruise. Service and alignment of the JRD Autosal salinometer, s/n 60839, were 
performed just prior to the cruise. The temperature of the CT laboratory was set 
to 21 degrees and measurements of room temperature taken before the analysis of 
each crate indicate the temperature remained in the region 21 - 23°C. The 
salinometer water-bath was set to 24°C. No serious problems occurred with the 
salinometer. Only the peristaltic pump switch needed resoldering half way 
through the cruise. John Wynar performed the resoldering. Jeff Benson also 
repaired another peristaltic pump that needed a service.

Sampling and Analysis

Water samples for analysis were drawn from each Niskin into 200ml glass sample 
bottles which were then sealed with clean, dry, disposable plastic stoppers and 
screw on caps. The neck of the sample bottle is dried prior to insertion of the 
cap. Samples were then taken into the CT laboratory to equilibrate to room 
temperature for 24 hours before analysis. During the cruise, samples were also 
drawn from the non-toxic supply for TSG calibration approximately every four 
hours. Matt Palmer, John Wynar, and Jeff Benson performed most analyses, with a 
few carried out by Louise Duncan. On one occasion an untrained scientist 
performed analysis and the resulting salinity values from stations 52-54 are 
dubious. Usually a standard seawater sample, batch series P140, was run 
immediately before and after a crate. Initially the standard reset dial on the 
autosal was set to 493 but was changed to 490 at station 29. For this reason the 
CTD salinity calibration had to be considered separately before and after this 
change. In total 18 replica samples were drawn providing a mean salinity 
difference of 0.0004 with standard deviation 0.0004.

Processing

Following standard practise, the salinity values were obtained from the 
conductivity ratio measurements using an Excel spreadsheet, which corrects for 
offsets from standard readings. These results were transferred to Unix in the 
form of a tab-delimited ASCII file containing the variables statnum, sampnum, 
botnum, botsala, botsalb and botsal. No flag was used to indicate good and bad 
salinity readings, as in previous cruises. Bottle salinity values were combined 
with CTD data in samio{num} files.

Correction to the Guildline ratio obtained from the standards throughout the 
cruise is shown in Figure S1. The corrections range from -0.00002 to 0.00013, or 
0.0004 to 0.0026 Salinity Equivalent. Variability in the standards was very 
small (s.d. 0.00001) although a drift in standard readings can be seen over the 
cruise.


Figure S1. Analysis of Standard Seawater correction to the Guildline ratios 
           for SSW batch P140

                          Louise Duncan, Matt Palmer, John Wynar and Jeff Benson



CORRECTIONS ON THE CD139 DATA BASE 
(Marta Álvarez) 


Instituto de Investigaciones Marinas, C/ Eduardo Cabello, Nº6, Vigo, Spain. 
malvarez@iim.csic.es 

There are two kinds of checking or quality control when detecting and correcting 
dubious biogeochemical data (BioGeo Var) in a cruise data base: the intra 
station and the inter station variability. The intra station variability is 
somehow easier to detect, any sample breaking the trend of any biogeochemical 
variable against pressure, temperature, salinity, etc… would be considered 
suspicious and more thoroughly inspected. However, the interstation variability 
comprises the natural environmental variability, and any errors due to sampling 
and/or analytical procedures, therefore detecting these "errors" will be the 
result of a comprehensive and tricky work as we want to preserve the natural 
variability in the samples. 

Correction procedure followed. 

The first approximation to a data base searches for any bottle improperly fired 
and discards the data. Contrasting CTD salinity against salinometer salinity is 
the best way to trace these misleading bottles. 

The second step consists in checking the internal consistency of the data within 
each station. This is done taking advantage of the natural relationships between 
physical variables (considered as reference ones) and biogeochemical ones. 
Eventually, these relationships reflect the water mass properties. Additionally, 
nutrients, oxygen and carbon data apart of containing information about the 
water mass inner characteristics, are closely related as they are affected by 
biological activity, i.e., respiration and photosynthesis. Photosynthesis 
increases oxygen, reduces nutrients and Total Inorganic Carbon but increases pH, 
on the contrary, respiration reduces oxygen and pH, but increases nutrients and 
TIC. On the other side, alkalinity and silicate present a different dynamics as 
they are mostly affected by the hard pump, the dissolution and formation of hard 
tissue material. 

Taking this in mind, biogeochemical data from each station is carefully 
examined. A break in the trend of any BioGeo Var against a physical variable 
should be detected in the other BioGeoVar. Changes should be coherent. 

Usually we first calculate the conservative parameters NO (=O2 + RN·NO3) and PO 
(=O2 + Rp·PO4), using Redfield ratios. The distribution of these parameters 
against potential temperature (Tpot) is studied. Then PO against NO, any dubious 
sample must be examined either in the oxygen or in the nutrient distribution. 
Then, pH is checked against Tpot and NO3 and finally silicate (SiO4) with Tpot, 
and then Normalised Alkalinity ( NTA = TA·35/Sal) with SiO4. 

Suspicious data are flagged and interpolated. 

Once each station is coherent itself we proceed to check the interstation 
variability. As previously said any changes in a BioGeoVar should be accordingly 
reflected in the others. In order to avoid areas with a high biogeochemical 
variability and detect the "errors" we preferentially study deep waters where 
biological activity is supposed to be low, and the variability in the BioGeoVars 
should be mostly related to the inner characteristics of the water masses. 

The influence of several water masses is detected in the data distribution along 
the CD 139 cruise track. This fact is clearly detected in the complex 
relationship between Tpot and NO, for example. 


Figure 1: Final Data: NO against potential temperature for the whole CD 139 data 
          set. 

With the aim of detecting offsets in the BioGeoVars we calculated a multilinear 
regression between every BioGeo Var and the following physical variables: 
pressure, Tpot and salinity for waters below 5ºC. 


Then, we calculated the residual of these regressions: ResBioGeoVar = BioGeoVar 
calculated - BioGeoVar measured. 

The residuals should contain information about the biological aging of the water 
plus any additional offset in the data due to analytical standardisations. 

We calculated the residuals for the following BioGeo Var: NO3, PO4, SiO4, pH, 
NTA, SiO4 and O2. 

O2 and pH residuals should be positively correlated, while they should be 
negatively correlated to NO3 and PO4 residuals. NO3 and PO4 residuals should be 
positively correlated and their magnitude should practically equal the Redfield 
ratio (about 16). 

Residuals of SiO4 and NTA should be positively correlated. 

Additionally we calculated the mean salinity (34.66) and Tpot (2.2) of the 
samples below 5ºC and then the mean of the following: (Tpot - 2.2) and (Sal - 
34.66) quantities in each station. Both give us information about the 
thermohaline variability between stations. 

All these information put together will allow us to detect spurious variations 
and correct the biogeochemical data. 

a) O2 and pH residuals. Figure 2. 
   The following figure shows the variation of the O2 and pH residuals along the 
   cruise track. Res pH is multiplied by 400 to be compared with the O2 Res. It 
   also shows the variation of 10·(Tpot-2.2) along the section. 

   Although a bit difficult to see, changes in RespH are correlated with ResO2 
   and Tpot-2.2. These distributions helped to detect offsets in the pH values 
   of several stations (70, 71, 98, 101, 111, 133, 134) which are corrected. 

b) NO3 and PO4 residuals. Figure 3. 
   This figure shows the distribution of the NO3 raw and the PO4 residuals 
   values multiplied by 16 (mean Redfield ratio) so to get quantities of the 
   same order of magnitude. This figure tells you that there are some suspicious 
   uncorrelated changes in the NO3 and PO4 residuals, and that sharp changes in 
   their magnitude are not reflected in the pH and O2 plot. 



Figure 2. Initial Data: along station variability of the pH and O2 residuals 
          (Calculated- Measured) and mean value of (Tpot-2.2) for waters <5ºC. 
Figure 3. Initial Data: along station variability of the NO3 and PO4 residuals 
          multiplied by 16 (Calculated-Measured) (µmol/kg) for waters <5ºC. 


c) SiO4 and NTA residuals. Figure 4. 
   This figure shows the distribution of the SiO4 and NTA residuals along the CD 
   139 section. In a first approximation these residuals are mainly well 
   correlated in sign and size and follow the trend in the temperature changes. 
   However a closer look is still needed. 


Figure 4. Initial Data: along station variability of the SiO4 and NTA residuals 
          (Calculated- Measured) (both in µmol/kg) and mean value of (Tpot-2.2) 
          for waters <5ºC. 


d) Correlations between residuals. Figures 5 and 6. 
   Figure 5 shows the correlation between O2 residuals and NO3, PO4 (multiplied 
   by 16) and pH (multiplied by 400) residuals. This figure points to the high 
   correlation among the residuals indicating that biological activity or aging 
   is the main reason for this correlation. However, some points (stations) need 
   further investigation. 



Figure 5. Initial Data: correlation between O2 residuals and NO3, PO4 
          (multiplied by 16) and pH residuals (multiplied by 400). NO3 and PO4 
          residuals are in µmol/kg. 
Figure 6. Initial Data: correlation between PO4 and NO3 residuals (µmol/kg). 


Figure 6 indicates that the relationship between NO3 and PO4 residuals is low 
compared to the Redfield value (about 16) and therefore that some stations need 
more investigation. 


Figure 7. Initial Data: correlation between SiO4 and NTA residuals (µmol/kg). 


Figure 7 shows the good correlation between SiO4 and NTA residuals and helps 
to identify some dubious points. 

The next step in the correction procedure was to check the trends of the 
residuals means along the CD 139 track. A group of about 10 stations was 
selected and all the residuals and Tpot and Sal means plotted. O2 and pH Res are 
firstly inspected, if they do not have a coherent distribution a closer look to 
the corresponding station is done. Usually was pH the variable corrected, pH is 
corrected with an offset added or subtracted to the whole water column data for 
the corresponding station. 

Next, NO3 and PO4 residuals are inspected. In this case if any anomaly detected 
a factor is calculated by eye to force the mean value of the residuals to follow 
the O2 and pH trends. PO4 residuals are allowed to be higher than the NO3 ones. 
I mean, I do not force the PO4 Res to equal the NO3 as in most of the stations 
the PO4 residuals (multiplied by 16) are higher than the NO3. The water column 
data is multiplied by this factor. 

Any correction applied over the data is then checked. The new data is plotted, 
Tpot vs. pH, NO3, PO4, SiO4, NTA; and Tpot vs. NO, PO; pH vs. NO3, PO4; NO3 vs. 
PO4; NO vs. PO; SiO4 vs. NTA. 

Corrections applied. 

The following plots show the absolute corrections applied to the data. 


Figure  8. Corrections added to the NO3 and PO4 initial data base in µmol/kg. 
Figure  9. Corrections added to the pH and TA initial data base, pH changes are 
           multiplied by 50, TA is in µmol/kg. 
Figure 10. Corrections added to the O2 and SiO4 initial data base, both in 
           µmol/kg. 


New data set. The following figures compare the distribution of the BioGeo Var 
in the initial and final data base. 


Figure 11. NO (µmol/kg) distribution against potential temperature for the 
           initial and final data base. 
Figure 12. PO (µmol/kg) distribution against potential temperature for the 
           initial and final data base. 
Figure 13. Relationship between NO3 and PO4 (µmol/kg) for the initial and final 
           data base. 
Figure 14. Relationship between SiO4 and NTA (both in µmol/kg) for the initial 
           and final data base. 
Figure 15. Relationship between NO3 (µmol/kg) and pH25T for the initial and 
           final data base. 




DISSOLVED OXYGEN

Acquisition

Dissolved oxygen samples were drawn directly from the Niskin bottles into 100 ml 
volume, calibrated oxygen bottles, their temperature measured and then fixed 
immediately using alkaline iodide and manganous chloride solutions prepared 
following Dickson (1994). The dispensers used to fix the samples were thoroughly 

cleaned in hot water at the start of the cruise and whenever they became sticky. 
Samples were shaken twice, once on deck and a second time shortly afterwards in 
the lab and then titrated in the lab within 12 hours.

Analysis

Dissolved oxygen was measured on all bottles from all CTD casts using a semi-
automated whole-bottle Winkler titration unit with spectrophotometric end-point 
detection manufactured by SIS. Acidification was performed using a 1ml Finn 
pipette. The user variable parameters in the SIS supplied software are in the 
parameters screen accessed through the options menu. The following values were 
determined by trial and error at the start of the cruise and applied throughout: 
Stepsize 15, Wait time 10, Fast delay 5, Slow delay 5, Fast factor 0.5. This 
parameter set resulted in titration times of less than three minutes.

One litre batches of sodium thiosulphate (25g/l) were prepared as required 
during the cruise. This strength solution results in titration volumes of about 
1.00 ml. The thiosulphate solution was standardised at the start and end of the 
batch using a commercially available 0.01N Potassium iodate standard (Ocean 
Scientific International, Petersfield, Hants). Between these points the 
thiosulphate breakdown was regularly (every few days) monitored using an in-
house solution of Potassium iodate prepared on board by dissolving 0.3567 g 
reagent grade KIO3 in 1 litre Milli-Q water. The average volume of thiosulphate 
required to titrate 5 ml aliquots of the OSI standard to an agreement better 
than 0.002 ml was used in the calculation of oxygen concentration which was 
performed on an excel spreadsheet following the equations supplied by Dickson 
(1994). The reagent blank was evaluated at the start of the cruise and found to 
be 0.0011 ml and this value was applied to all calculations undertaken. The 
thiosulphate solution was found to be extremely stable. A minimum of one bottle 
on each cast was sampled twice to gain an estimate of the analytical precision. 
The mean difference in calculated oxygen concentration between all the duplicate 
pairs sampled was 0.38%.


REFERENCE

Dickson, A.G. 1994 Determination of dissolved oxygen in seawater by Winkler 
    titration. WOCE operations manual, WOCE Report 68/91 Revision 1 
    November 1994.
                                                                      Val Latham



NUTRIENTS

Background

Water samples for inorganic nutrient analysis analysis were drawn from each 
Niskin bottle on every station into 40ml polystyrene coulter counter vials after 
pH, alkalinity, oxygen, CFCs and He/Tr but before salinity. Inorganic nutrient 
concentrations were measured using a Skalar San Plus autoanalyser purchased by 
SOC in November 2000. This instrument was last used on RRS Discovery cruise D258 
(Marine Productivity I). On D258 it was configured according to the 
manufacturers specifications (Kirkwood, 1995) with the exception that the flow 
rates through the phosphate line were changed from 0.8 ml/min sample, 0.1 ml/min 
ascorbic acid, 0.1 ml/min ammonium molybdate solution to 2 ml/min sample, 0.23 
ml/min ascorbic acid, 0.23 ml/min ammonium molybdate solution to improve peak 
reproducibility and definition relative to the results obtained on RRS Discovery 
cruise D253 (FISHES). However, whilst addressing the phosphate peak shape and 
reproducibility, this change during D253 had the effect of causing frequent 
(occurring on around 50% of runs) catastrophic deterioration in the phosphate 
baseline which rendered data from that run unusable.

In an effort to counter this problem for use on RRS Charles Darwin cruise D139 
the instrument was configured in Durban with a compromise configuration for 
phosphate consisting of 0.16 ml/min for each reagent and 1.4 ml/min for the 
sample. In addition large sections of the line, which had previously been made 
of polypropylene tube were replaced with glass and acidflex pump tubing. These 
precautions produced an acceptable peak shape and eliminated baseline failures; 
however, the reproducibility of the measurements was not as good as desired and 
the matrix effect observed at the interface of samples and the Artificial 
Seawater (ASW) wash solution was larger than desirable. After a mid-cruise 
review of the phosphate data, it was decided to revert to the pump tube sizes 
used on D258 and these were employed for the remainder of this cruise after 
station 78. This improved the sample resolution, reduced the matrix effect and 
resulted in only two of the remaining runs suffering catastrophic baseline 
failure. Thus the modifications to the reaction line undertaken at the start of 
the cruise must have been effective. The effects of the changes in sample and 
reagent flow rates on the quality of the P data are discussed later.

Acquisition

Initially we were equipped with two lap-top PCs, one to run the autoanalyser and 
one to run the dissolved oxygen analyser. In the past the autoanalyser has been 
known to abruptly and without warning cease communications with the computer 
operating it. Often this failure has been associated

with processing data from previous runs. We therefore took the precaution of 
loading the software for both instruments onto both computers. The autoanalyser 
stopped communications on three separate occasions, only once in the middle of a 
run. Fortunately on each occasion we were able to switch immediately to the 
other machine and reconfigure the offending machine, a process which takes at 
least two hours. Attempts to write a cd-rom with ready-configured software 
failed for unknown reasons (but maybe because the software modifies one of the 
files in the windows directory as well as installing itself into the 
c:/flowaccess directory). Raw datafiles were processed on laptop PC's and backed 
up onto zip disks, following compression using winzip and transfer to the PC 
interfaced to the zipdrive. This procedure was not 100% successful as some of 
the raw datafiles were too large to be transferred in this manner, and therefore 
were not backed up. Unfortunately the PC on which they were acquired stopped 
functioning after station 33 and the raw datafiles for stations 22-32 will have 
to be recovered from the hard drive of this machine at SOC. Fortunately the raw 
data had been processed from these stations and results files created; however, 
the quality control parameters from two of these runs were not recorded. A 
reserve computer supplied by UKORS was used to acquire the oxygen data following 
this problem and we thank them for the loan of this instrument.

Quality Control

Under the nutrients system currently in use at SOC the samples are run 
interspersed with an intersample wash solution consisting of 40 g/l analar 
sodium chloride in MilliQ (MQ) water, this solution (called artificial seawater, 
ASW) is also used as the standard matrix. Generally we find that this solution 
is free of nitrate, phosphate and silicate, although this is checked on each run 
using a nutrient-free seawater. On this cruise however a large and batch-
dependent phosphate contamination was observed in the various batches of ASW 
made up, ranging from zero to 0.3 about station 54 and had serious effects on 
the phosphate data from station 54 to the end of the cruise. Every run from that 
point onwards (with the exception of the final run) had to be manually processed 
(or reprocessed) in Excel to account for this. This manual recalculation 
involved combining the computer generated corrected peak heights (which take 
account of instrument sensitivity and baseline drift) with an additional 
component corresponding to the contamination in the baseline relative to 
phosphate-free seawater and then calculating the phosphate concentration 
equivalent to the combined peak height using the phosphate standards as a 
standard additions curve. Phosphate concentrations calculated on a station with 
no phosphate contamination via this method appear to be within 2% of those 
calculated via the software working alone. It is possible that this phosphate 
contamination resulted from a fault with the MQ water system on the ship. This 
appears unlikely given that the conductivity of the MQ water remained constant 
and that no nitrate or silicate contamination was observed. A further 
consequence of this problem was that checking the runfiles became a time-
consuming business that had to be undertaken at the same time as acquiring data 
from the analyser. Fortunately no loss of data resulted from this procedure.

Overall approximately 3250 samples were analysed in 67 separate runs. The 
performance of the analyser is monitored via two parameters: the baseline value 
(in Digital Units, DU) and the gradient of the calibration curve (in DU/ 
baseline for all three nutrients moved over the course of the cruise in the 
manner shown in Figure N1.


Figure N1: Baseline values for phosphate, silicate and nitrate versus station.


The baseline for all three nutrients varied. Silicate and phosphate both drifted 
up over the course of the cruise, this may be related to changes in the 
intensity of the light source which the two methods share. The nitrate baseline 
decreased over the course of the cruise with a sawtooth pattern imposed on this 
general decline. This decrease is associated with reagent deterioration.

The gradient of the calibration curve is shown in Figure N2. Of the three 
nutrients the silicate gain is by far the most stable with only two stations 
showing deviations from a value of about DU/ Durban. Note that the silicate time 
series is only plotted from station 9. The high silicate concentrations 
encountered on this cruise necessitated the construction of a dilution loop in 
which the sample was diluted with an equivalent volume of silicate free ASW. 
This was built in port but could not be tested until sailing. It proved to be 
inadequate and was modified such that it diluted the sample with twice its own 
volume of ASW. Thus silicate data from stations 1-8 were processed using a 
second order calibration curve. Further examination of this data in SOC may be 
required. The nitrate gain value drifted up steadily over the course of the 
cruise. Again, data from the early part of the cruise are not presented. Some of 
the early nitrate runs required calibration with a second order polynomial.


Figure N2: Gain values for nitrate, phosphate and silicate versus station.


This problem appeared to resolve itself as the cadmium column bedded in (a 
single column was used over the course of the cruise, the efficiency of which 
was 100 +/- 3%) and was not directly addressed. Further examination of this data 
in SOC may be required.

Duplicates

Two samples per station were run in duplicate. The mean differences between the 
pairs of samples expressed as a percentage of the top standard were nitrate, 
1.1%, phosphate, 0.9%, silicate, 0.43%. When the phosphate data is split into 
two groups comprising those samples analysed before and after the change in 
methodology which took place after station 78 the mean differences are 0.4% 
after the change and 1.3% before.

The time variability of the differences between duplicate phosphate samples is 
shown in Figure N3. Clearly the modifications to the phosphate methodology 
undertaken in mid cruise were beneficial in terms of reducing the difference 
between pairs of duplicate measurements. 


Figure N3: Absolute difference between duplicate phosphate samples versus station.


We investigated the reasons for these differences in duplicate concentrations by 
evaluating whether or not the second measurement of nutrient concentration was 
systematically larger or smaller than the first determination. If the error is 
random then we expect the average difference between the two determinations to 
be zero. If the error is systematic then we expect the average difference 
between determinations to be non zero. The average differences for the entire 
datasets were N, 0.03%, P, 0.43%, Si 0.46%. When this parameter as evaluated for 
the phosphate data before and after station 78 its value was 0.8% in the early 
part of the cruise and 0.1% in the latter part of the cruise. A comparison of 
these values with the mean differences set out earlier suggests that the error 
in the determination of nitrate concentration is almost entirely random, whereas 
the error in silicate and phosphate concentrations are substantially systematic 
(that is replicate 1 is consistently higher than replicate 2 or vice versa), 
accounting for approximately 70% of the difference between replicate silicate 
determinations and 50% of the difference between replicate phosphate 
determinations. This is almost certainly a consequence of carryover of water 
from one sample to the next and is the first direct evidence we have that this 
is an issue that should be addressed. Interestingly the modifications to the 
phosphate line reduced the proportion of the error attributable to systematic 
causes from approximately 60% to about 20%. In light of this consideration 
should be given to increasing the flow rate through the silicate line.

The concentration of a bulk nutrient sample collected on WOCE cruise A23 was 
determined on each run to provide some measure of the internal consistency of 
the dataset. The results of these determinations are shown in Figure N4 together 
with the deep N/P ratio. The results of these determinations were Nitrate 34.98 
+/- 0.6 mM, Phosphate 2.46 +/- 0.07 mM, Silicate 129.9 +/- 1.9 mM. These are 
equivalent to errors of 1.63, 1.47 and 2.81% respectively. When the phosphate 
data is broken into to groups before and after station 78, the errors are 3.8 
and 1.8% for the early and late part of the cruise respectively.

Some difficulty was encountered in sampling the bulk seawater standard in a 
clean manner, particularly for phosphate. Obviously erroneous determinations 
have been excluded from the errors calculated above, however these errors 
represent upper limits. As a further internal consistency measurement we 
evaluated the deep N/P ratio throughout the cruise, plotted in Figure N4. This 
showed a high degree of uniformity. The standard deviations of the points used 
to evaluate this ratio were Nitrate 2.4% and Phosphate 2.56%. This suggests that 
the internal consistency of the phosphate data is broadly comparable to that of 
the nitrate data.

Accuracy

In the absence of a certified reference material an evaluation of accuracy is 
dependent on a comparison with historical data. This will be undertaken at SOC.


Figure N4: Bulk nutrient concentrations and deep nitrate/phosphate ratio 
           versus station.


Organic Nutrients

Dissolved organic nutrient samples were drawn from 10 bottles per station into 
pyrex glass bottles with teflon-lined lids and frozen immediately. A separate 
set of approximately 400 samples were collected in 40ml sterilin sample pots and 
also frozen. Chlorophyll samples were taken on one station per day. For these 

samples 5l of water were filtered through a glass-fibre filter (GFF) and the 
filter frozen for subsequent analysis back at SOC using HPLC (High Pressure 
Liquid Chromatography).


REFERENCE

Kirkwood, D.S. 1995 Nutrients: Practical notes on their determination in 
    seawater. ICES Techniques in Marine Environmental Sciences report 17, 
    International Council for the Exploration of the Seas, Copenhagen. 25p. 
    ISSN 0903-2606.
                                                                 Richard Sanders



COˇ2 COMPONENTS

During the Charles Darwin 139 cruise along 32°S in the Indian Ocean, carbon 
system components pH and alkalinity were sampled and analysed. As well, samples 
for total inorganic carbon were taken and stored to be analysed on land. Table 
O1 shows the stations where samples were taken for the different COˇ2 
parameters.


pH analysis

pH was measured spectrophotometrically following techniques described by Clayton 
and Byrne (1993). Roughly, this method consists of adding a dye solution to the 
seawater sample, so that the ratio between two absorbances at two different 
wavelengths is proportional to the sample pH.

i. Sampling and analytical methods.

Seawater samples for pH were collected after oxygen samples using cylindrical 
optical glass 10-cm pathlength cells which were filled to overflowing and 
immediately stoppered. Seawater pH was measured using a double-wavelength 
spectrophotometric procedure (Byrne, 1987). The indicator was a 1 mM solution of 
Kodak m-cresol purple sodium salt (C21H17O5Na) prepared in seawater. After 
sampling all the samples were stabilised at 25°C. The absorbance measurements 
were obtained in a thermostatted (25±0.1) cell compartment of a CECIL 3041 
spectrophotometer.

After blanking with the sampled seawater without dye, 100 to each sample using 
an adjustable repeater pipette. The absorbance was measured at three different 
fixed wavelenghts (434, 578 and 730 nm). pH, on the total hydrogen ion 
concentration scale, is calculated using the following formula (Clayton and 
Byrne, 1993): 

pH(T)=1245.69/T+3.8275+(2.11.10-3)(35-S)+log((R-0.0069)/(2.222-R*0.133))   (1) 

where R is the ratio of the absorbances of the acidic and basic forms of the 
indicator corrected for baseline absorbance at 730 nm (R=A578/A434), T is 
temperature in °Kelvin and S is salinity. Therefore pH values are given on the 
total scale and referred to 25°C (pH25T).

ii. Quality control.

In order to check the precision of the pH measurements, samples of COˇ2 
Certified Reference Material (CRM, batch 55, distributed by Dr. A.G. Dickson 
from the Scripps Institution of Oceanography) were analysed during the cruise 
(Figure O1). The mean value for the set of CRM measurements was 7.909±0.003. 
The overall precision of the pH measurements during the cruise was obtained from 
the analysis of duplicate samples (usually 9 cells) drawn from the same bottle. 
The mean standard deviation of the series of replicates was ±0.0007.


Figure O1: Spectrophotometric pH25T measurements on the CRM batch 55 during 
           the cruise. Each batch consists of 8 measurements from the same 
           CRM bottle.


Alkalinity Analysis

i. Sampling and analytical methods.

Seawater samples for alkalinity were collected after pH samples in 600 ml glass 
bottles. Samples were filled to overflowing and immediately stoppered. Total 
alkalinity was measured using an automatic potentiometric titrator "Titrino 
Metrohm", with a Metrohm 6.0233.100 combination glass electrode and a Pt-100 
probe to check the temperature. Potentiometric titrations were carried out with 
hydrochloric acid ([HCl] = 0.1 M) to a final pH of 4.44 and 4.40 (Pérez and 
Fraga, 1987). The electrode was standardised using a 4.4 buffer made in COˇ2-
free seawater (Pérez et al., 2000). Concentrations are given in µmol/kg-sw.

ii. Quality control.

Determinations of alkalinity on COˇ2 Certified Reference Material (CRM, batch 
55) were made during the cruise to monitor the Titrino performance (Figure O2).

As well, in order to obtain a more precise determination of alkalinity for each 
sample, each was analysed twice, a mean and standard deviation were then 
calculated. 75% of the double determinations had a standard deviation lower than 
1 µmol/kg and a further 20% between 1 and 2 µmol/kg. In the test station No 1, 
the whole set of bottles were fired at the same depth. The standard deviation of 
a total of 24 analyses over 12 bottle samples collected for alkalinity was 1.04 
µmol/kg.


Total Inorganic Carbon Sampling

Samples for Total Inorganic Carbon to be analysed at the land laboratory were 
collected at crossover stations where previous cruises in the Indian Ocean had 
sampled. Emptied Certified Reference Material bottles were rinsed twice and 
filled from the bottom, overflowing half a volume while taking care not to 
entrain any bubbles. Then 0.2 ml of saturated mercuric chloride solution was 
added to the sample as a preservative and the bottle was sealed with glass 
stoppers covered with

Apiezon-L grease and stored in the dark at room temperature. Samples for 
Inorganic Carbon were taken at stations 48, 100, 117 and 134.


Figure O2: Alkalinity measurements on the CRM batch 55 during the cruise.


REFERENCES

Byrne, R.H. 1987 Standardization of standard buffers by visible 
    spectrometry. Analytical Chemistry, 59, 1479-1481.

Clayton, T.D. & Byrne, R.H. (1993). Spectrophotometric seawater pH 
    measurements: total hydrogen ion concentration scale concentration 
    scale calibration of m-cresol purple and at-sea results. Deep-Sea 
    Research I, 40, 10, 2115-2129.

Pérez, F.F. & Fraga, F. 1987 A precise and rapid analytical procedure for 
    alkalinity determination. Marine Chemistry, 21, 169-182.

Pérez, F.F., Ríos, A.F., Rellán, T. & Álvarez, M. 2000 Improvements in a 
    fast potentiometric seawater alkalinity determination. Ciencias 
    Marinas, 26, 463-478.
                                                  Marta Álvarez and Aida F. Ríos



Table O1: List of sampled stations for pH, alkalinity (TA) and total 
          Inorganic carbon (TIC).
          ____________________________________________________________

           St.  pH  TA  TIC      St.  pH  TA  TIC    St.  pH  TA  TIC
           ---  --  --  ---      ---  --  --  ---    ---  --  --  ---
             1   +   +           50   +   +           99   +
             2   +   +           51   +              100   +   +   +
             3   +               52   +   +          101   +
             4   +   +           53   +              102   +   +
             5   +   +           54   +   +          103   +
             6   +               55   +              104   +   +
             7   +   +           56   +   +          105   +
             8   +               57   +              106   +   +
             9   +   +           58   +   +          107   +
            10   +               59   +              108   +   +
            11   +   +           60   +   +          109   +
            12   +   +           61   +              110   +   +
            13   +   +           62   +   +          111   +
            14   +   +           63   +              112   +   +
            15   +               64   +   +          113   +
            16   +               65   +              114   +   +
            17   +   +           66   +   +          115   +
            18   +               67   +              116   +   +
            19   +   +           68   +   +          117   +   +   +
            20   +               69   +              118   +
            21   +   +           70   +   +          119   +
            22   +               71   +              120   +   +
            23   +   +           72   +   +          121   +
            24   +               73   +              122   +   +
            25   +   +           74   +   +          123   +
            26   +               75   +              124   +   +
            27   +   +           76   +   +          125   +
            28   +               77   +              126   +   +
            29   +   +           78   +   +          127   +
            30   +               79   +              128   +   +
            31   +   +           80   +   +          129   +
            32   +   +           81   +              130   +   +
            33   +               82   +   +          131   +
            34   +   +           83   +              132   +   +
            35   +               84   +   +          133   +
            36   +   +           85   +              134   +   +   +
            37   +               86   +   +          135   +
            38   +   +           87   +              136   +   +
            39   +               88   +   +          137   +
            40   +               89   +              138   +   +
            41   +   +           90   +   +          139   +
            42   +               91   +              140   +   +
            43   +   +           92   +   +          141   +
            44   +   +           93   +              142   +   +
            45   +               94   +   +          143   +
            46   +   +           95   +              144   +   +
            47   +               96   +   +          145   +   +
            48   +   +   +       97   +   +          146   +   +
            49   +               98   +   +
          ____________________________________________________________


CHLOROFLUOROCARBON (CFC) MEASUREMENTS

Samples for the analysis of dissolved CFC-11 and CFC-12 were drawn from ~2100 of 
the 3500 water samples collected during the expedition. Samples for carbon 
tetrachloride (CCL4) analysis were drawn from ~540 samples. Specially designed 
10 liter water sample bottles were used on the cruise to reduce CFC 
contamination. These bottles have the same outer dimensions as standard 10 liter 
Niskin bottles, but use a modified end-cap design to minimize the contact of the 
water sample with the end-cap O-rings after closing. The O-rings used in these 
water sample bottles were vacuum-baked prior to the first station. Stainless 
steel springs covered with a nylon powder coat were substituted for the internal 
elastic tubing provided with standard Niskin bottles. When taken, water samples 
for CFC and carbon tetrachloride analysis were usually the first samples drawn 
from the 10 liter bottles. Care was taken to co-ordinate the sampling of CFCs 
with other samples to minimize the time between the initial opening of each 
bottle and the completion of sample drawing. In most cases, dissolved oxygen, 
alkalinity and pH samples were collected within several minutes of the initial 
opening of each bottle. To minimize contact with air, the CFC samples were drawn 
directly through the stopcocks of the 10 liter bottles into 100 ml precision 
glass syringes equipped with 2 way metal stopcocks. The syringes were immersed 
in a holding tank of clean surface seawater until analysed. To reduce the 
possibility of contamination from high levels of CFCs frequently present in the 
air inside research vessels, the CFC extraction/analysis system and syringe 
holding tank were housed in a modified 20' laboratory van on the aft deck of the 
ship.

For air sampling, a 100 meter length of 3/8" OD Dekaron tubing was run from the 
CFC lab van to the bow of the ship. A flow of air was drawn through this line 
into the CFC van using an Air Cadet pump. The air was compressed in the pump, 
with the downstream pressure held at ~1.5 atm. using a back-pressure regulator. 
A tee allowed a flow (100 ml min-1) of the compressed air to be directed to the 
gas sample valves, while the bulk flow of the air (>7 l min-1) was vented 
through the back pressure regulator. Air samples were only analysed when the 
relative wind direction was within 60 degrees of the bow of the ship to reduce 
the possibility of shipboard contamination. The Air Cadet pump was run for at 
least 60 minutes prior to analysing each batch of air samples to insure that the 
air inlet lines and pump were thoroughly flushed.

Concentrations of CFC-11 and CFC-12 in air samples, seawater and gas standards 
were measured by shipboard electron capture gas chromatography (EC-GC) using 
techniques similar to those described by Bullister and Weiss (1988). For 
seawater analyses, a 30 ml aliquot of seawater from the glass syringe was 
transferred into the glass sparging chamber. The dissolved CFCs in the seawater 
sample were extracted by passing a supply of CFC-free purge gas through the 
sparging chamber for a period of 4 minutes at 70 ml min-1. Water vapour was 
removed from the purge gas during passage through an 18 cm long, 3/8" diameter 
glass tube packed with the desiccant magnesium perchlorate. The sample gases 
were concentrated on a cold-trap consisting of a 1/8" OD stainless steel tube 
with a ~7 cm section packed tightly with Porapak N (60-80 mesh). To cool the 
trap, isopropanol cooled by a Neslab Cryocool refrigeration system was forced 
from a reservoir beneath the trap to a level above the packing with a stream of 
compressed nitrogen. After quickly bringing the isopropanol to the top of the 
trap, a low flow of nitrogen was bubbled through the bath to reduce gradients 
and maintain a temperature of -20°C. After 4 minutes of purging the seawater 
sample, the sparging chamber was closed and the trap was held open for an 
additional 1 minute to allow nitrous oxide (N20) to pass through the trap and 
thereby minimize its interference with CFC-12. The trap was isolated, the cold 
isopropanol in the bath was drained, and the trap was heated electrically to 
125°C. The sample gases held in the trap were then injected onto a precolumn 
(~50 cm of 1/8" O.D. stainless steel tubing packed with 80-100 mesh Porasil C, 
held at 90°C) for the initial separation of the CFCs and other rapidly eluting 
gases from the more slowly eluting compounds. The CFCs then passed into the main 
analytical column (~183 cm of 1/8" OD stainless steel tubing packed with 
Carbograph 1AC, 80-100 mesh, held at 90°C) for final separation, and into the 
EC detector for quantification.

The analysis of carbon tetrachloride was made on a separate, but similar 
apparatus to the EC-GC system used in the analysis of CFC-11 and CFC-12. Samples 
were drawn in the same type of syringes used for the CFC analysis. In the CCL4 
system, the sample injection port was flushed with 30-40 ml of sample before 
injecting sample into a calibrated loop (~30 ml). After filling, an additional 
30 ml of water was pushed through the loop and allowed to overflow. For 
analysis, a valve was switched and the water sample held in the loop was pushed 
into the stripper with the same CCL4 free nitrogen that was used to strip the 
sample. The gases removed from the sample were dried while passing through an 
~18 cm x 3/8" OD tube of magnesium perchlorate and concentrated on a trap packed 
with 10 cm of Porapak N and held at -30°C during trapping. At the conclusion of 
stripping, the trap was heated electrically and the contents swept onto the 
precolumn (0.53mm I. D. x 30 meters, DB624 capillary column held at 45°C) with 
clean nitrogen. The desired gases passed on to the main analytical column 
(0.53mm I. D. x 30 meters, DB624 capillary column, 45°C) before the precolumn 
vented the later peaks. All other aspects of the analysis were the same as for 
the CFC analysis.

Both of the analytical systems were calibrated frequently using a standard gas 
of known CFC composition. Gas sample loops of known volume were thoroughly 
flushed with standard gas and injected into the system. The temperature and 
pressure was recorded so that the amount of gas injected could be calculated. 
The procedures used to transfer the standard gas to the trap, precolumn, main 
chromatographic column and EC detector were similar to those used for analysing 
water samples. Two sizes of gas sample loops were present in the CFC analytical 
system, while four calibrated sample loops were used in the CCL4 system. 
Multiple injections of these loop volumes could be made to allow the system to 
be calibrated over a relatively wide range of concentrations. Air samples and 
system blanks (injections of loops of CFC-free gas) were injected and analysed 
in a similar manner. The typical analysis time for seawater, air, standard or 
blank samples was 12 minutes on the CFC system and 20 minutes on the CCL4 
system.

Concentrations of the CFCs and CCL4 in air, seawater samples and gas standards 
are reported relative to the SIO98 calibration scale (Cunnold, et. al., 2000). 
Concentrations in air and standard gas are reported in units of mole fraction 
CFC in dry gas, and are typically in the parts-per-trillion (ppt) range. 
Dissolved CFC and CCL4 concentrations are given in units of picomoles per 
kilogram seawater (pmol kg-1). CFC and CCL4 concentrations in air and seawater 
samples were determined by fitting their chromatographic peak areas to multi-
point calibration curves, generated by injecting multiple sample loops of gas 
from a working standard (PMEL cylinder 33780 for CFC-11, CFC-12, CFC-113 and 
CCL4) into the analytical instrument. Full range calibration curves were run at 
intervals of ~3 days during the cruise. Single injections of a fixed volume of 
standard gas at one atmosphere were run much more frequently (at intervals of 1 
to 2 hours) to monitor short term changes in detector sensitivity.

Extremely low CFC-11 and CFC-12 concentrations (<0.01 pmol kg-1) and carbon 
tetrachloride concentrations (0.01-0.02 pmol kg-1) were measured in waters 
between 2800-3200 meters depth along the section east of ~89°E. Based on the 
median of concentration measurements in these regions, which is believed to be 
nearly CFC-free, blank corrections of 0.007 pmol kg-1 for CFC-11, 0.004 pmol kg-1 
for CFC-12 and 0.007 pmol kg-1 for carbon tetrachloride have been applied to 
the data set. If the measured CFC concentration for a sample is very low, these 
blank corrections can result in a very small negative concentration being 
reported. On this expedition, based on the analysis of duplicate samples, we 
estimate precisions (1 standard deviation) of 1% or 0.005 pmol kg-1 (whichever 
is greater) for dissolved CFC-11 and CFC-12 measurements and 1.4% or 0.006 pmol 
kg-1 for CCL4.measuremnents.

A very small number of water samples had anomalously high CFC or CCL4 
concentrations relative to adjacent samples. These samples occurred sporadically 
during the cruise and were not clearly associated with other features in the 
water column (e.g. anomalous dissolved oxygen, salinity or temperature 
features). This suggests that these samples were probably contaminated with CFCs 
or CCL4 during the sampling or analysis processes. Measured concentrations for 
these anomalous samples are included in this report, but are given a quality 
flag value of either 3 (questionable measurement) or 4 (bad measurement). A 
total of 11 analyses of CFC-11, 36 analyses of CFC-12 and 7 analyses of CCL4 
were assigned a quality flag of 3. A total of 13 analyses of CFC-11, 17 analyses 
of CFC-12 and 6 analyses of CCL4 were assigned a quality flag of 4.


REFERENCES

Bullister, J.L. & Weiss, R.F. 1988. Determination of CC13F and CC12F2 
    seawater and air. Deep-Sea Research, 25, 839-853.

Prinn, R. G., Weiss, R.F., Fraser, P.J., Simmonds, P.G., Cunnold, D.M., 
    Alyea, F.N., O'Doherty, S., Salameh, P., Miller, B.R., Huang, J., Wang, 
    R.H.J., Hartley, D.E., Harth, C., Steele, L.P., Sturrock, G., Midgley, 
    P.M. & McCulloch, A., 2000. A history of chemically and radiatively 
    important gases in air deduced from ALE/GAGE/AGAGE. Journal of 
    Geophysical Research, 105, 17751-17792.

                                            David P. Wisegarver and Kevin McHugh



SAMPLING FOR HELIUM AND TRITIUM

Background

In December 2001, following a discussion with Bill Jenkins and Clare 
Postlethwaite, we decided to attempt sampling for Helium and Tritium during the 
transindian hydrographic section across 32°S beginning in March 2002. The 
section (WOCE I5) had been sparsely sampled at the eastern and western 
boundaries during WOCE and the central region had not previously been sampled at 
all for Helium and Tritium. Because there was no space for an additional 
scientist to participate on the cruise to do tracer sampling, the physical 
oceanographers on the cruise took on the commitment to acquire the samples. The 
idea was to draw samples in copper tubes for Helium and in one-litre bottles for 
Tritium for later shore-based analysis at the Noble Gas Laboratory at 
Southampton Oceanography Centre. It was envisioned that it would be possible to 
sample about one station each day outside the densely sampled eastern and 
western boundary regions.

Clare Postlethwaite prepared the materials for surface shipment in early January 
2002 and provided about 2 hours training to Louise Duncan and Brian King on how 
to take and preserve the samples and to maintain the equipment.

Sampling

For Helium sampling, 68 cm pieces of copper tube are cut from 20m reels of 
copper tube and are labelled as to station, bottle, and with a unique 
identification number. Each tube is dented in 2 places, + and - 14 cm from the 
centre of the tube. During sampling (which occurs directly after CFC's) water is 
syphoned through tygon tubing into the bottom of a copper tube and out of the 
top draining through more tygon tubing. All bubbles in the water are beaten out 
of the tubing and copper with a wooden bat; when all bubbles are gone, the 
tubing is clamped below, then above, the copper tube. Holding the tygon tubing 
firmly onto both ends of the copper tube, the tube is then sealed with a 
hydraulic cutter powered by compressed air at one end, then in the middle of the 
tube, and finally at the other end. In effect the tube ends are sealed by a cold 
weld. The result is a pair of duplicate samples from each bottle. Re-rounding 
each tube creates a vacuum inside; if the seal is tight, a sharp flick of the 
tube creates a click which verifies the integrity of the sample. The copper 
tubes are later wrapped in bubble wrap and labeled with the unique 
identification number on the outside of the bubble wrap.

For Tritium sampling, which is the last water sample to be drawn from each 
bottle, a small piece of tygon tubing is attached to the Niskin bottle, rinsed 
and used to dribble water down the sides of a one-litre bottle which had been 
baked under an argon atmosphere and sealed at Southampton Oceanography Centre in 
January. Each bottle has a unique bar code which is recorded versus station and 
Niskin bottle number on the log sheet; at the same time the station and Niskin 
bottle numbers are written on the label of the sample bottle. The bottles once 
filled are then sealed with electrical tape to prevent movement of the cap 
during storage and shipment back to Southampton. A tritium sample was drawn from 
each Niskin bottle for which helium samples were drawn.

Sampling for Helium and Tritium was principally done during the 0800-1600 watch 
period. Principal samplers were Louise Duncan, Melanie Witt, Brian King and 
Harry Bryden. During the cruise, 24 stations were sampled for Helium and 
Tritium, slightly less than anticipated due to other commitments. As the cruise 
developed, the goal evolved to sample approximately every 3 degrees of longitude 
across the width of the Indian Ocean. A total of 375 duplicate copper tube 
samples for Helium and 375 one-litre bottle samples for Tritium were acquired 
and shipped back to Southampton Oceanography Centre at the end of the cruise. 
Details of the sampling are presented in Table H1.

                                           Harry L. Bryden  and Louise M. Duncan



Table H1: Sampling for Helium and Tritium
          RRS Charles Darwin 139, March-April 2002.
          ________________________________________________

           Station Latitude    Longitude   Depth  Samples
           ------- ---------   ---------   -----  -------
              21   -31 13.10   030 35.10   2705     18
              29   -31 48.20   031 25.50   3315     15
              36   -32 53.70   035 00.50   1602     15
              41   -33 01.00   036 31.40   4839     18
              45   -32 59.60   038 59.70   5091     18
              51   -33 00.00   043 02.20   2321     14
              58   -33 29.30   047 27.20   3570     14
              64   -34 00.30   052 44.70   4478     16
              72   -33 58.00   057 02.10   4997     17
              76   -33 59.10   059 19.60   5551     17
              79   -34 00.20   060 59.60   4946     16
              82   -33 59.00   063 59.90   4666     14
              85   -34 00.00   067 00.00   4681     16
              88   -33 59.70   070 00.90   4219     16
              93   -32 45.20   074 29.40   3850     16
              98   -30 45.00   078 30.00   3454     15
             104   -31 13.40   084 30.40   4068     15
             108   -31 44.80   088 09.50   1932     12
             115   -32 10.20   090 52.20   4444     15
             118   -33 50.00   095 32.00   4558     15
             123   -34 30.00   100 27.00   4337     15
             128   -33 30.00   105 00.00   5332     16
             133   -31 30.00   108 55.00   5327     16
             138   -31 30.00   113 09.00   5199     16
          ________________________________________________



LOWERED ACOUSTIC DOPPLER CURRENT PROFILER

Summary

During the trans-Indian Ocean section across 32 S(RRS Charles Darwin cruise 139) 
three Lowered Acoustic Doppler Current Profilers (LADCPs) were deployed 
simultaneously on a specially adapted frame. The intention was to combine the 
new RDI 300kHz Dual Workhorse configuration of one upward-looking and one 
downward-looking LADCP, with the more established downward-looking 150kHz 
Broadband LADCP, to produce an outstanding, comprehensive (and comparable) 
dataset of direct velocities.

The Dual system was deployed throughout the cruise, except on station 3, with a 
ping cycle of 1.54 s. Two 150kHz instruments were brought on the cruise: the SOC 
instrument, and a backup loaned by Teri Chereskin at the Scripps Insititution of 
Oceanography (SIO). Both instruments were deployed with a staggered ping cycle 
(0.8 s/1.2 s) to eliminate the bottom interference layer. The SIO LADCP has 30 
degree beam angles, compared to SOC's 20 degrees, and thus produces horizontal 
velocities of consistently 20% lower standard deviation.

Interference between the instruments was a concern. The dual system was designed 
for simultaneous deployment and therefore able to asynchronise pings and avoid 
interference with one another, but the 150kHz LADCP has no such capability. The 
150kHz instrument was deployed alone during one cast and its beam amplitudes 
from this and another cast examined to assess the effect of interference. 
Interference from the 300kHz pings was found to effect about 4% of its returns. 
This reduced the number of good samples collected, but did not appear to have a 
detrimental effect on the measured velocity profile, which compared favourably 
to both shipboard ADCP profiles and bottom-tracked velocities. Thus, it was 
concluded that the instrument was flagging the interference correctly as bad 
data and thus not introducing errors, except via the slight reduction of good 
samples.

Comparisons between the instrument measurements revealed that the 150kHz LADCP 
out- performed the 300kHz LADCPs in most respects. In waters deeper than about 
1500 m, where scatterers are few, the higher frequency instruments often did not 
obtain enough return samples to produce a realistic ocean velocity profile. In 
contrast the 150kHz LADCP always maintained a return sample number of over 50 
(more often over 100) per depth bin. In addition the shear standard deviation of 
the returns in deep water was generally 34% larger for the 300kHz instruments. 
Processing the upward and downward-looking 300kHz data simultaneously, and 
thereby doubling the number of return samples per depth bin, did little to 
improve the erroneous deep velocities. We conclude that the Dual Workhorse 
system did not perform well during this cruise, perhaps because of the clear, 
unproductive Southern Indian Ocean water. This was disappointing, because the 
same instruments produced good data in the Drake Passage in November 2001.

Comparisons were also made between the established Firing processing technique, 
with which we had many cruises of experience, and the Visbeck technique which 
was relatively new to us. In Firing's method a differentiation of velocities 
into noisier shears is required, whereas in Visbeck's method this is no longer 
necessary. Therefore, in theory the new technique has an advantage and should 
produce cleaner velocity profiles. However, on comparing a station of 150kHz 
data processed using each technique it was found that the Visbeck method 
underestimated top-to-bottom (first baroclinic mode) shear and created more 
disparate up-down profiles (causing the classic X-profile). In addition, the 
reader should be advised that using the Visbeck method with the added constraint 
of bottom-tracked data, as Visbeck intended, should be conducted cautiously. On 
deep stations, where it was clear that the 300 kHz data was erroneous due to 
unrealistically strong deep shears and large bottom velocities, a plausible 
profile is created using the bottom-tracked velocity constraint, since it 
prevents the profile from blowing up. However, the resulting velocity profile is 
quite wrong. During the cruise Visbeck released a modified version of his 
software which was set up, tested and used on board. Results were much more 
encouraging, with the obvious under-estimate of the shear no longer apparent. 
The technique holds promise for the future.

In summary, the 150kHz LADCP data is good quality, comparing well with surface 
velocities from shipboard ADCP and with bottom-tracked velocities from the 
downward-looking 300kHz instrument. In fact the data is an improvement over 
measurements collected during ACE, because of the staggered ping deployment. 
Further improvement of the data is possible through subjective use of the 
bottom-tracked and on-station shipboard ADCP velocities to adjust the top-to-
bottom (first baroclinic mode) shear.

Configuration, Deployment, and Recovery 

Two RD Instruments 300 kHz Workhorse (WH) Lowered Acoustic Doppler Current 
Profilers (LADCPs) and one RD Instruments 150kHz Broadband (BB) LADCP were 
secured to a modified CTD frame for simultaneous deployment throughout the 
cruise. An additional 150kHz Broadband instrument, loaned by Teri Chereskin at 
the Scripps Institution of Oceanography (SIO), was available as backup. The two 
150kHz instruments were identical except for their beam angles. The SOC 
instrument has a beam angle of 20, while the SIO instrument has a beam angle of 
30°. The 150kHz LADCP was mounted at the centre of the frame, below the rosette 
mechanism, with a separate battery pack mounted horizontally at the level of the 
CTD. One of the 300kHz instruments was mounted off-centre at the bottom of the 
frame, as the down-looker or master Workhorse (MWH).  The other was mounted to 
the side of the rosette at the top of the frame, as the up-looker or slave 
Workhorse (SWH). The uplooker was protected by an arc segment of frame built on 
the side of the main frame. The battery pack for both Workhorses was also 
mounted horizontally at the level of the CTD. To avoid confusion over the 
different LADCPs, hereafter the Dual Workhorse (DWH) system, consisting of both 
300kHz instruments, will be referred to as DWH, while singularly the up-looker 
will be referenced as SWH and the down-looker as MWH. Finally the 150kHz LADCP 
will be referred to as BB (for Broadband).

The workhorse instruments were deployed in master/slave mode, with the master 
telling the slave when to ping, therefore avoiding interference between the 
instruments. Otherwise, each instrument was set up identically having ping 
intervals of 1 s with a 0.5 s snych delay after the slave ping, sixteen bins 
each of length 10 m, a 5 m blank after transmit, and an ambiguity velocity of 
2.5 m s^-1. Copies of the deployment command files, WHM.CMD and WHS.CMD can be 
found in the appendix. The workhorses have RDI firmware that obtains bottom-
tracked velocities from water-tracking pings (in beam coordinates), thus giving 
good 'truth' data at the bottom of each cast.

The BB setup during CD 139 was one not previously used by SOC scientists. In 
previous experiments (such as ACE) the interference layer, which results from 
the previous ping reflecting off the bottom, has caused a data gap in the BB 
LADCP profile, causing an uncertain velocity offset of several cm s^-1 between 
the parts of the profile on either side of the gap. It is possible to set a long 
ping interval to reduce this problem. For example, a 2 s interval will place the 
interference layer about 1500 m off the bottom, therefore reducing the strength 
of the interference signal to insignificance. However, with this approach one 
loses at least 50% of possible measurements, thus increasing the variance of the 
resultant velocity profile. Instead, during CD 139 the BB was deployed with a 
staggered ping. By setting an ensemble time of 0.8 s, with two ensembles per 
burst of 2 s duration, one achieves a PING PING WAIT pattern, resulting in 
intervals of 0.8 s and 1.2 s between pings. Thus, one set of pings causes an 
interference layer about 600 m off, the other about 900 m off, but in neither 
case is the entire data set contaminated and there is no data gap. Other 
significant settings for the BB were: sixteen times 16 m bins, a 16 m blank 
after transmit, and an ambiguity velocity of 3.5m s^-1. A copy of the deployment 
command file for the BB, BB13901.CMD can also be found in the appendix.

Examples of the log sheets, deployment and recovery instructions for LADCP 
watchkeepers can be found in the appendix. The logsheet was modified to 
accommodate 'start-pinging' times etc of both instruments (the master and slave) 
for a DWH cast. The slave entries were left blank in the case of a BB cast. 
Separate logsheets (of the same format) were used for the DWH cast and the BB 
cast on each station.

Interference 

In deploying the DWH and BB LADCP systems simultaneously there was concern that 
interference from the pings of one in the returns of the other would cause data 
degradation. It was clear after the test cast (station 1) however, that the BB 
produced good velocity profiles during a DWH deployment. As a result both 
systems were used on each station throughout the cruise, except station 3 when 
the DWH were not deployed, and stations 97/98 when the SWH was not deployed. 
These latter stations offered the chance for a more careful examination of 
interference by comparing BB data from casts with and without simultaneous 
workhorse deployments.

The beam amplitudes from stations 3 (BB) and 2 (BB + DWH) are shown in Figures 
L1, L2, plotted as a function of ping number (equivalent to seconds) and bin 
number. All beams are shown for each bin, so that there are 16 bins each with 
four beams, making a total of 64 on the y-axis. The large regions of high 
returns at the beginning and end of each cast represent the subsurface scatter 
maximum in the water column. Below the scatter maximum the trend from higher to 
lower amplitudes with distance from the instrument becomes more apparent. In 
addition to this background gradient there are intermittent high return signals 
throughout the record, evident in white and pale grey. Figures L3, L4 show a 
deep region of each cast (approximately 2500-2800 m) in more detail. There are 
short high-amplitude signals, over only one bin of one ensemble present in 
station 2 and not in station 3. These are interference from the DWH pings. When 
the first and second BB pings are separated out (lower plots in Figure L4) we 
can distinguish a diagonal pattern of these interference signals, as they march 
through the BB bins at a constant but different rate for each ping interval.

We can estimate the number of BB bins that are contaminated in two ways. First, 
by adding them up over the 300 pings shown in Figure L3, assuming it is a 
representative time segment.  This indicates that 3.3% of the BB bins contain 
interference from the DWH pings. Second, by considering the relative ping rates 
and listening times of the instruments. The BB pings on average once per second 
and is set to sample 16 bins of 16 m each with a 16 m blank after transmit. 

Therefore it 'looks out' over 272 m which, taking the speed of sound as 1500 m 
s^-1, will require a travel (or listening)-time of 0.36 s. Meanwhile, the DWH 
has a ping rate of 0.77 s, since each workhorse pings every 1.54 s. Thus, over a 
period of 300 s the BB will collect 300 16 bins of data and listen for s, during 
which time the DWH will ping 142 times, leading to an estimate of 3.0% 
contamination. This is smaller than the estimate above taken from the data, 
because some pings contaminate more than one bin.

Station 97 has no SWH (up-looker) data. A detail of the beam amplitudes over 300 
pings is shown in Figure L5. The data shows that contamination from MWH pings 
alone is about 2.1%, or two thirds the contamination from both workhorses. 


PROCESSING 

Firing Method

The LADCP provides a full-depth profile of ocean current. However, to obtain the 
ocean current the unknown package motion must be removed during processing. In 
the Firing method, overlapping profiles of the vertical shear of horizontal 
velocity are averaged and gridded, to form a full-depth shear profile. By 
differentiating individual profiles the constant velocity of the package has 
dropped out. The full-depth shear profile is then integrated vertically to 
obtain the baroclinic ocean velocity, and the resulting unknown integration 
constant is the barotropic (depth-averaged) velocity. 


FigureL1: SoloBBdeployment: BeamAmplitudes
FigureL2: CombinedBBandDWHdeployment: BeamAmplitudes
FigureL3: SoloBBdeployment: DetailofBeamAmplitudes
FigureL4: CombinedBBandDWHdeployment: DetailofBeamAmplitudes
FigureL5: CombinationBBandMWHdeployment: DetailofBeamAmplitudes


This barotropic component is computed as the sum of the time-averaged, measured 
velocity and the ship drift (minus a small correction, less than 1 cm s^-1, to 
account for a nonconstant fall rate) (Fischer and Visbeck, 1993; Firing, 1998).

Errors in the baroclinic profile accumulate as ∑std/√(N) where N is the number 
of ensembles (Firing and Gordon, 1990). This error translates to the lowest 
baroclinic mode and, for a cast of 2500 m depth, it is about 2.4 cm s^-1 (Beal 
and Bryden, 1999). The barotropic component is inherently more accurate, because 
the errors result from navigational inaccuracies alone. These are quite small 
with DGPS, about 1 cm s^-1 (2 to 4 cm s^-1 without). Thus, the errors in LADCP 
velocities are of the order of the expected oceanic variability, 3-5 cm s^-1 
(Send, 1994), which is due primarily to high frequency internal waves.

The Firing software was routinely used during CD 139 as the primary technique 
for obtaining final velocities. This is both because it is well established and 
because results from the new Visbeck technique were disappointing (see the next 
section). GPS and CTD data are required to produce final LADCP velocities and 
therefore Firing's software was slightly adapted by Brian King (BAK) to 
accommodate pstar data streams. The Firing software directory tree was set up 
under /data/ladbbuh.

A copy of the step-by-step, first-pass processing sheet, as followed by LADCP 
watchkeepers during the cruise, can be found in the appendix. Typical BB 
profiles as output from Firing's method are shown in Figures L6, L7. The first 
figure shows down, up and mean velocity profiles in the east (U) and north (V) 
directions. The second shows the same for vertical velocity (W), plus plots of 
the number of shear samples and the ping standard deviation (of U and V shears) 
as a function of depth. Looking at vertical velocity is a useful proxy for the 
quality of the full-depth profile: if W is small (as we would expect for the 
ocean) then data quality is good. The standard deviation indicates the quality 
of the individual ping returns, which in the case of the BB are almost constant 
with depth.

A few of the processing steps used during CD139 were a little out of the 
ordinary and are described here. Bottom interference appeared at approximately 
600 and 900 m off the bottom, affecting half the data in each case (at two 
depths because of the staggered ping). Therefore, a clip margin of 15 was set in 
mergeb 1.cnt to cut out the affected data. Water (bottom) depth is used during 
Firing processing to predict the cut off depth of the full-depth velocity 
profile. It is initially estimated from the integral of vertical velocity, when 
scan.prl is run on the raw BB cast data, and output to file proc.dat. For final 
data during CD139, however, the absolute water depth was obtained from MWH 
height off plus CTD depth. Height off is one of the parameters of RDI bottom-
tracked data, part of the data download from the MWH. The absolute water depth 
is output by Visbeck processing and, together with bottom-tracked velocities, 
saved in file C(stn)(run name).bot under the Visbeck directory tree. This depth 
is used to update proc.dat for a final processing run (rerun domerge.prl and do 
abs.m). Final velocity data can be found under Firing's proc directory in 
/matprof/h/*.mat. MWH bottom velocities are also saved here in matlab format.


FigureL6: BB eastward and northward velocity profiles processed using 
          Firing method
FigureL7: BB vertical velocity, number of samples and standard deviation 
          Output from Firing method


We are very grateful to Firing who, immediately prior to the cruise worked on a 
modification to his software to enable merging of SWH and MWH data. The script, 
merge_ud.m, together with required modified versions of two other mfiles, can be 
found under Firing's proc directory in /dual. To combine up- and down-looker 
data, 'dual_system' and 'dual_method' were set to 1 in matlab, and do_abs was 
rerun calling the new scripts (by setting addpath('dual')). Unfortunately, due 
to the disappointing quality of the DWH data, little use was made of this.

Visbeck Method

The Visbeck processing method has a theoretical advantage over Firing's method, 
because it does not calculate shear in order to remove the package motion. Thus, 
there is not the introduction of noise that the shear calculation inevitably 
causes. Nor is there a random-walk error associated with building up a full-
depth shear profile. Instead, Visbeck poses an inverse problem to solve for the 
package motion using a least squares technique (Visbeck, 2002). The resulting 
problem is overdetermined and as a result should produce robust velocities, 
provided the weights (or covariances) are considered carefully. Another 
advantage of the inverse method is that it is possible to add constraints, such 
as bottom-tracked data and shipboard ADCP data. Visbeck routinely uses RDI 
bottom-tracked velocities in addition to navigation data to constrain full-depth 
velocity profiles. Finally, the method allows processing of the Workhorse up- 
and down-looker data simultaneously.

The Visbeck software directory tree was set up under /data/ladbbvis and all 
processing steps were carried out from the vis_ship/pro directory. Originally, 
Visbeck intended demo.m to be hand modified with position, time, data paths, 
control settings etc for each station and then run to carry out all the 
processing steps. In this case some front-end programs were written by BAK to 
pull in various data streams automatically. Time and position information is 
fetched from Firing's *.scn files and from the RVS GPS datastream respectively, 
using shell script scanexec. Pstar CTD data is modified so that the timestamp 
has origin at the beginning of the year and then written out in ascii format 
using ctd_timadj.exec. Then, the Visbeck processing is run in matlab by calling 
run laproc(stn), where stn is station number. This script was written by Lisa 
Beal and processes BB and DWH data, both with and without a bottom-tracked-
velocities constraint. It calls some more front end (BAK) scripts which load the 
peripheral data, set paths and control parameters and then runs the Visbeck 
processing proper. An example of the full-depth velocity profiles output from 
the Visbeck method is shown in Figures L8, L9. The first figure (from a run with 
bottom-tracked velocity constraint) is output directly after processing and 
shows up/down/mean U and V profiles, plus number of samples, velocity error, 
target strength (like beam amplitude) and the ship drift on station. The latter 
figure (from a run without bottom-tracked velocity constraint) shows U and V in 
the same format as the Firing output to allow a direct comparison.


Figure L8: BB velocity profiles, data quality, and ship drift processed 
           Using Visbeck method
Figure L9: BB eastward and northward velocity profiles processed using 
           Visbeck method


The MWH collects RDI bottom-tracked velocities (processed internally from water-
tracked pings)which are extracted and cleaned during Visbeck processing. Ifno 
RDI bottom-tracked velocities are available, as is the case for BB data, then 
they are estimated during processing, by examining the beam amplitudes to find 
the bottom returns. It was perceived (although not rigorously tested) that the 
RDI bottom-tracked velocities were more accurate than those processed from BB.

In practice the Visbeck method was not found to be an improvement over Firing's 
processing. BB data was processed using both methods, with each setup in a 
similar manner for a comparison (GPS and CTD data were used, but not the 
additional bottom-tracked velocities in the Visbeck case). The Visbeck method 
routinely under-estimated the top-to-bottom shear of the ocean velocity profile, 
often by more than 10 cm s^-1. Moreover, it produced dissimilar up and down 
profiles which, when constrained to a single barotropic current from the 
navigation, results in the classic 'X-profile'. When produced from the Firing 
method such profiles are taken as an indication of uncertain velocities.

A new release of Visbeck's software was received via email about half way 
through the cruise. It has a number of modifications and bug-fixes which result 
in top-to-bottom BB shears which are much better matched to those from the 
Firing method. There are also some internal changes to the software which make 
it incompatable with old data files. As a result we implemented the new version 
in a new directory tree (/vis_ship) and began processing all the station data 
from scratch. There was not time to properly assess the performance of the 
upgraded software, but it is apparent that it is much improved and now provides 
a viable alternative to Firing's software.

The DWH data was processed together using Visbeck's method, but the results were 
disappointing due to poor data quality below 1500 m or so (see next section), 
where profiles tended to blow up to unrealistic bottom velocities. However, the 
DWH profiles were better handled by Visbeck's (modified) method than by 
Firing's. On a cautionary note, the Visbeck method can produce plausible looking 
velocity profiles (with totally manufactured shears) from bad data when the 
bottom-tracked velocity constraint is employed. We strongly recommend that 
processing is always run with this constraint off (botfac=0) as a first pass, so 
that bad data will not slip by unnoticed.

In conclusion, we are indebted to Eric Firing and Martin Visbeck who worked on 
additions and improvements to their software in time for this cruise, in 
response to feedback from BAK after taking the new DWH system to Drake Passage 
in November 2001. This report summarises achievements during CD139, but the 
software issue is by no means closed and discussions will continue subsequently. 


DATA QUALITY

During the cruise there were a number of deployments made with unusual 
configurations in order to test (or try to improve) data quality. Some of these 
have been described above in the section on interference. Station 003 was 
deployed with BB alone (no DWH) to compare BB data with and without DWH 
interference. Stations 097 and 098 have no SWH (up-looker) deployment, allowing 
an assessment of its interference with the BB. For station 117 the DWH were 
configured with a 0.95 s ping rate, so that they were pinging at twice the rate 
of the BB. On station 134 DWH was deployed in a broader band mode, giving better 
quality pings but reduced range. Tests were also conducted on DWH compass error, 
because the poor DWH profiles appear to be dominated by biased errors, rather 
than random noise. Each workhorse was rotated in turn through 360 in steps of 90 
per cast in order to untangle heading related errors. The BB configuration was 
not altered during the cruise (except for swapping from SOC to SIO instruments 
at station 062), since it was considered optimum.

Results from the compass tests and from stations 117 and 134 are described in 
the DWH section below, beginning with a summary of the instruments' general 
performance. Following this the BB is assessed by comparing its velocity 
profiles to on-station shipboard ADCP and to bottom-tracked velocities. Finally 
the two systems, BB and DWH, are compared quantitatively for range and ping 
quality.

Dual Workhorse

In general the workhorses performed very poorly. DWH data from the Agulhas 
Current was the best quality, with most profiles resembling their BB 
counterparts. This is because the stations were relatively shallow. There was no 
evidence that the DWH provided better data than the BB, however. Elsewhere, DWH 
velocity profiles blew up in deep water, exhibiting unrealistically strong, 
unidirectional shears and large bottom velocities. For example, Figures L10, L11 
show a typical DWH profile as processed by the Firing dual method. The 
workhorses were not getting enough returns (samples) below about 1500 m to 
maintain a good full-depth velocity profile from the Firing shear technique. 
There is some improvement using Visbeck's inverse technique (Figure L12), 
probably because strong shears are penalised, but still the profiles compare 
unfavourably with the BB profile. Note that the Visbeck solution should be 
treated with caution when implementing the bottom-tracked velocity constraint. 
By pulling in the blown up deep velocities the constraint can make a bad profile 
look plausible. This is dangerous because, as Figure L13 shows, the deep shears 
are manufactured.

There seems to be two issues. The first is that the WHs suffer from a much 
greater loss of ping returns in the deep water than does the BB. Often the 
number of DWH (both 300 kHz instruments) returns per 5 m depth bin (of the full-
depth profile) drops to less than 50 below 1500 m (the up-looker always performs 
worse), whilst the BB collects 100 or more. Evidently, the higher frequency WH 
signal does not scatter as well from deep marine particles as the lower 
frequency BB. The second is that the individual WH pings are of lower quality in 
the deep water (about 34% higher standard deviation) than the BB pings. As a 
result we would require more returns (twice as many) to obtain a full-depth 
profile of the same quality as the BB, whereas we are actually obtaining far 
fewer. This second issue could perhaps be alleviated by choosing a higher ping 
rate and/or smaller bins. However, the fact that the quality and number of the 
DWH returns is compromised in deep water to a much greater extent than those of 
the BB must be based on the physics of deep marine scatterers and is therefore 
insuperable.


FigureL10: DWH eastward and northward velocity profiles processed using the 
           Firing method
FigureL11: DWH vertical velocity, number of samples, and variance processed 
           using Firing method
FigureL12: DWH velocity, data quality and ship drift processed using 
           Visbeck method without bottom-tracked velocity constraint
FigureL13: DWH velocity, data quality and ship drift processed using 
           Visbeck method WITH bottom tracked velocity constraint


Fast ping deployment

The motivation for a fast ping deployment of the DWH was to even out the mean 
standard deviation statistics of the 5 m shears with those from the BB. It was 
noted that the deep shear standard deviation (per ping) of the DWH was about 4.7 
x 10^-3 s^-1, while that for the BB was 3.5 x 10^-3s^-1. By dividing the square 
of these terms, this implies that the number of DWH samples required to obtain 
data of equal quality to the BB is 1.8 times the number of BB samples collected. 
Therefore the DWH were set to ping every 0.95 S, providing more than twice the 
number of BB pings. This was accomplished by re-setting the ping interval (TP) 
in the command file to zero and reducing the wait time (SW) of the asynchronous 
ping to 0.3 s.

The results from station 117 were disappointingly similar to previous casts. 
Qualitatively there did appear to be some improvement, with more realistic fine 
scale shears, but there is still a bias, in this case in the V component, which 
dominates the data and blows up the deep velocities. The bias could be related 
to a mean package tilt.

Broader bandwidth deployment

There are two modes of deployment for the workhorses: mode 0 (LW0) is the 
default broad bandwidth configuration and mode 1 (LW1) is a narrower bandwidth 
pulse with a greater range, but increased standard deviation. When using the DWH 
as a lowered system mode 1 is recommended (Visbeck, 2001), and this is how the 
instruments were deployed in the main. On station 134 the DWH was switched to 
mode 0. The motivation was that since the DWH were losing so much range at 
depth, is it not better to have better quality pings at the expense of more 
range? The answer is emphatically, no. Below 2000 m depth the DWH in this mode 
collected no good samples and there was complete data drop out. This was 
surprising, since it implies that even those data in bins right next to the 
instruments were flagged bad.

Dual Workhorse heading related compass errors 

An investigation was carried out into the magnetic compasses of the WHs. The 
motivation is that heading related and relative compass errors of the two 
instruments play a large part in resulting velocity profile errors.

From the analysis that follows, we expected to be able to determine the 
instruments compass errors. Unfortunately, the results are puzzling, as will be 
described. The experiment consisted of comparing differences of reported heading 
between the two instruments, with the instruments being rotated in their clamps 
between casts.

The instrument headings returned by the compasses are subject to errors from two 
sources.  First, distortion of the local magnetic field by the CTD frame and 
possibly by the instrument itself, and second, instrumental error whereby it 
fails to measure the local field perfectly. Let the local field error, presumed 
to be caused chiefly by the influence of the frame, be denoted by F. Let the 
instrument error be I and the measured heading be H. Then at some instant, the 
true heading T of the underwater package (e.g. the direction in which the fin 
was pointing) is given by 

                                T = H+O+F+I                               (1)

where O is the offset between beam 3 of the instrument and the nominal true 
package heading. The sense of F and I is that they are corrections that must be 
applied. All elements of (1) are dependent on time t, except for O. We assume 
that F is a function of T. That is to say, whenever the package points in the 
same direction, F has the same value. We also assume that I is a function of H: 
whenever the instrument measures a heading of, say 90°, it will be subject to a 
reproducible error. Thus, in full,

                       T(t) = H(t)+O+F(H(t))+I(H(t))                      (2)

Now (2) applies for both uplooker (subscript 1) and downlooker (subscript 2) 
instruments, 

           T = Hˇ1+Oˇ1+Fˇ1(T)+Iˇ1(Hˇ1)T = Hˇ2+Oˇ2+Fˇ2(T)+Iˇ2(Hˇ2)

Taking the difference of the two equations, and noting that the true package 
heading is the same for both instruments, gives

                        Hˇ1Hˇ2 = Oˇ2Oˇ1+Fˇ2Fˇ1+Iˇ2Iˇ1                     (3)

Suppose that Hˇ1-Hˇ2 has been measured for a complete range of headings, with 
instrument positions we will denote by subscript A. (Note on many casts, the 
package completes one or more complete rotations, but on some casts this was not 
the case.) Thus, Hˇ1-Hˇ2 is considered to be known as a function of T. Now 
suppose that one of the instruments is rotated on the frame, and the new 
geometry is denoted by B. To preserve generality, we will suppose that each 
instrument is rotated by an amount δ counterclockwise viewed from above. Of 
course, for any adjustment we chose to keep either δˇ1 or δˇ1 as zero, rotating 
just one instrument. Thus, on cast A 

                       T = Hˇ1+Oˇ1A+Fˇ1(T)+Iˇ1(Hˇ1),

and on cast B 

                       T = Hˇ1+Oˇ1B+Fˇ1(T)+Iˇ1(Hˇ1), 

where Oˇ1B and Oˇ1A+δˇ1 similarly, Oˇ2B = Oˇ2A+δˇ2.

Consider (3) for two casts before and after a rotation. At some true package 
heading (estimated from the uplooker, for instance, by assuming that and are 
small), 

          Hˇ1A-Hˇ2A = Oˇ2AOˇ1A+Fˇ2A(T)Fˇ1A(T)+Iˇ2A(Hˇ2A)Iˇ1A(Hˇ1A)

          Hˇ1B-Hˇ2B = Oˇ2BOˇ1B+Fˇ2B(T)Fˇ1B(T)+Iˇ2B(Hˇ2B)Iˇ1B(Hˇ1B)

Subtract these two equations to discover the change in Hˇ1- Hˇ2. Assuming that 
the error terms are small, we can write, for example, H~TO, so I(H)~I(T-O), 

                    (Hˇ1B-Hˇ2B)(Hˇ1A-Hˇ2A) =
                      + {(Oˇ2B-Oˇ2A)(Oˇ1B-Oˇ1A)}
                      + {(Fˇ2B(T)-Fˇ2A(T))-(Fˇ1B(T)-Fˇ1A(T))}
                      + {Iˇ2B(T-Oˇ2B)Iˇ2A(T-Oˇ2A)}
                      - {Iˇ1B(T-Oˇ1B)Iˇ1A(T-Oˇ1A)}. 

Now assume Fˇ1B(T) = Fˇ1A(T)and Fˇ2B(T) = Fˇ2A(T), i.e. the frame induced error 
is assumed to be unchanged by rotation of the instrument in the frame, then 

                    (Hˇ1B-Hˇ2B)(Hˇ1A-Hˇ2A) =
                      + {δˇ2δˇ1}+ 0
                      + {Iˇ2B(T-Oˇ2A-δˇ2)Iˇ2A(T-Oˇ2A)}
                      + {Iˇ1B(T-Oˇ1A-δˇ1)I1A(T-Oˇ1A)}.

Now, we also assume that the functional form of I(H) has not changed, so Iˇ1 and 
Iˇ2 do not need subscript A or B. Finally if δˇ1, for example is zero, then the 
last line of the above equation is zero, so 

            (Hˇ1B-Hˇ2B)(Hˇ1A-Hˇ2A)=δˇ2+{Iˇ2(T-Oˇ2A-δˇ2)Iˇ2(T-Oˇ2A)}       (4) 

Thus the double difference (change in heading differences) resulting from the 
rotation of an instrument in the frame has a mean offset equal to the rotation 
of the instrument, and a functional form (as a function of T) that arises from a 
phase shift of Iˇ2.

Next, we observe that the left hand side (LHS) of (4), is found to be roughly 
sinusoidal in shape, with amplitudes up to 5 degrees either side of the mean. If 
I=sin(H), then LHS should be described by a sine curve, however this did not fit 
the results satisfactorily. Therefore assume, 

                        I(H)=Aˇ1sin(H+φˇ1)+Aˇ2sin(2H+φˇ2).

In principle, the four coefficients Aˇ1, Aˇ2, φˇ1, φˇ2 can be determined from a 
single rotation of amount δˇ2. Indeed, it was found that this functional form 
fitted the measurements very well. The residuals of LHS after fitting were 
invariably less than 1°. Now, 

                       sin(H-δ)sin(H)=2cos(H-δ/2)sin(-δ/2)

and (4) becomes,

  LHS-δˇ2 =
    2Aˇ1cos(T-Oˇ2A+φˇ1-δˇ2/2)sin(-δˇ2/2)+2Aˇ2cos(2(T-Oˇ2A)+φˇ2-δˇ2)sin(-δˇ2).


Table L1: Rotations and switches of Workhorse LADCPs during CD 139
          ______________________________________________________________________

           Orien-  Station  H1-H2    O1     O2    δˇ1    δˇ2    Comments
           tation   range   (degs) (degs) (degs) (degs) (degs) 
           ------  -------  ------ ------ ------ ------ ------  ---------------
             A     001-028   183     39    222     39      0    M 1855, S 1881
             B     029-076   222      0    222      0      0    S CW*
             C     077-079   320      0    320      0     98    M 90° CCW
             D     080-084    34      0     34      0    172    M 90° CCW
             E     085-106   125      0    125      0    263    M 90° CCW
             F     107-112    34     91    125     89    263    S 90° CCW
             G     113-126   128     91    219     91    357    M 90° CCW†
             H     127-131    37    182    219    182    357    S 90° CCW
             I     132-135   305    274    219    274    357    S 90° CCW
             J     136-141   307    272    219    272    357    M 1881, S 1855§
             K     142-146    37    272    182    272    357    S 90° CW
          ______________________________________________________________________

          Table notes: M is master workhorse, S is slave. Instruments are COˇ2 
          COˇ2 identified by serial numbers 1881 and 1855. All rotations, are 
          given relative to configuration B. *SWH turned to put CTD wire between 
          beams. †MWH back to its original position. §Instruments switched 
          top-to-bottom. (Values of δˇ1 and δˇ2 in orientation J were 
          determined by comparing offsets between MWH and BB on stations 135-
          141.)


The unknown coefficients and phases were determined from the lowest two modes of 
an FFT of (LHS-δˇ2) in Matlab. Note that if δˇ2 is exactly 180°, the cos(2H) 
term cannot be determined.

A series of adjustments to the WH positions was made, as summarised in the 
table, to attempt to solve for the unknown amplitudes and phases of the 
instrument error.

If all our assumptions were correct, any move of the MWH should enable us to 
determine the SAME A and φ coefficients for Iˇ2. However, we don't find this is 
to be the case. Instead different coefficients are found for different 
orientations (A to J) of the two instruments. One or more of the assumptions 
must be wrong. At present, we consider the most likely difficulty to be the 
assumption that when the master is rotated,Fˇ2(T) is unchanged. We also need to 
consider that the problem may arise from comparing Hˇ1(T+Oˇ1)with Hˇ2(T+Oˇ2), 
when in fact it should be H(T+O+F+E), although we expect this effect to be 
small.

The goals of this piece of work have not been achieved as of the end of the 
cruise. However, the experimentation with instrument orientation, and the 
mathematical description of the problem described here has laid the groundwork 
to be able to solve for instrument compass errors back at SOC.

Broadband

The broadband data, in comparison to the DWH, is very good. However, there may 
be large errors, especially on deep casts, and these are highlighted by 
comparing the BB full-depth profile with independent observations at the surface 
and at the bottom. These comparisons have been done qualitatively (see Figure 
L14), but a more thorough post-cruise statistical analysis is required. On-
station ADCP velocities were, almost without exception, well matched (within 4 
cm s^-1) to the BB profiles. At the bottom, both RDI bottom-tracked velocities 
from the MWH and processed bottom-tracked velocities from the BB were used to 
compare to the BB full-depth profile. About 45% of the profiles matched to 
bottom-tracked velocities within 5 cm s^-1. The deeper the cast, the larger the 
W velocities at the bottom, and the worse the match appears (although this is 
not always the case). Deep stations suffer from increases in velocity error not 
only because of the random walk of the single ping standard deviation when 
ensembles are strung together for the full-depth profile (see processing 
section), but also because the standard deviation itself increases with depth 
and the range decreases.

As outlined in the processing section above, the dominant errors in the Firing-
processed BB data propagate into the first baroclinic mode. The barotropic 
velocity is known really quite well, since it is dominated by ship drift which 
is determined by GPS positioning and not by the BB. Therefore, we strongly 
advise that BB profiles be adjusted to better match ADCP and bottom-tracked data 
using constant shear and not constant velocity.

It is worth mentioning here again that the Visbeck processing method will not 
suffer from errors introduced by the calculation of shear, or by the random walk 
described above. The LADCP community is in agreement that the inverse method is 
an advance from the Firing shear method. A few bugs were apparent in the 
original version of Visbecks software however, which caused a large 
underestimate of the shears, as described above. A modified version of the 
software was received half way through the cruise, so that by the time the new 
version was set up, tested, and station processing got up to date (Visbeck's 
processing is significantly slower than Firing's) there was not sufficient time 
to investigate the quality of the profiles. It is clear that the profiles are 
much improved and may provide a better estimate of the ocean velocity, 
particularly on deep stations. A comparison of Visbeck profiles to SADCP and 
bottom-tracked velocities is needed, as done for the Firing profiles during the 
cruise.

Performance statistics (range and variance) of BB and DWH pings The W shear 
variance and number of samples are good proxies for the data quality of a 
lowered velocity profile. The latter is closely correlated with the range of the 
instrument. In order to assess the performance of the BB and MWH at depth these 
two parameters were studied in the downcast (to avoid bottle stops) at 200 m and 
at 2000 m, well below the 'scatter-cline'. The results are shown


Figure L14: BB velocity profile (Firing processed) compared to on-station ADCP
            and MWH bottom-tracked velocities
Figure L15: Performance statistics of BB and MWH


The results are shown in Figure L15, where the left hand plots give the ratio of 
the instruments' performance at 200 m to that at 2000 m. On average (for all 
stations up to 115) the Wshear variance ratio is 0.96 for the BB, and 0.71 for 
the MWH. In other words, the quality of BB pings is hardly effected, while the 
MWH pings decrease in quality by over 40%. As for the range, the cruise sample 
ratio (samples at 200 m / samples at 2000 m) is 2.88 for the BB and 4.24 for the 
MWH. So the range loss is quite dramatically worse for the MWH. There is a 
possibility that the BB could see farther at 200 m than the 256 m that the 
instrument is configured for. This would bias the BB sample ratio low. To test 
this the samples at 1000 m were compared to those at 3000 m and the resulting 
ratios were found to be not significantly different. The blue water of the 
Southern Indian Ocean is attenuating the 150kHz signal to less than 250 m 
penetration even at 200 m. The relatively poor performance of the higher 
frequency MWH appears to be real. The only factor that can explain the poor 
performance of the MWH compared to the BB is the physics of deep marine 
scatterers, which must backscatter the 150kHz signal in preference to the 300kHz 
signal.


REFERENCES

Beal, L. M., and H. L. Bryden, 1999, The velocity and vorticity structure of 
    the Agulhas Current at 32 S, J. of Geophys. Res., 104, 5151-5176

Firing, E. F. and R. Gordon, 1990, Deep ocean acoustic Doppler current 
    profiling, Proceedings of the IEEE Fourth International Working Conference 
    on Current Measurements, Clinton, MD, Current Measurement Technology 
    Committee of the Ocean Engineering Society, 192-201

Firing, E., 1998, Lowered ADCP development and use in WOCE, WOCE NOTES, 30, 
    10-14 

Firing, E., Erratum, 1998, Intl. WOCE Newsletter, 31, 20

Fischer, J. and M. Visbeck, 1993, Deep velocity profiling with self-
    contained ADCPs, J. Atmos. and Oceanic Tech., 10, 764-773

Visbeck, M., 2002, Deep velocity profiling using lowered acoustic Doppler 
    current profiler: Bottom track and inverse solutions, J. Atmos. Oceanic 
    Technology, 19, 794-807

Send, U., 1994, The accuracy of current profile measurements - effect of 
    tropical and mid-latitude internal waves, J. Geophys. Res., 99, 16229-16236



___________________________________________________________________________________________________________ 
___________________________________________________________________________________________________________


                                   APPENDIX

                              LADCP Command Files

Down-looker Workhorse Configuration

WHM.CMD
  PS0 CR1 CF11101 EA00000 EB00000 ED00000 ES35 EX11111 EZ0111111 TE00:00:01.00
  TP00:01.00 LD111100000 LF0500 LN016 LP00001 LS1000 LV250 LJ1 LW1 LZ30,220 SM1
  SA001 SW05000 CK CS

Up-looker Workhorse Configuration

WHS.CMD
  PS0 CR1 CF11101 EA00000 EB00000 ED00000 ES35 EX11111 EZ0111111 TE00:00:01.00
  TP00:01.00 LD111100000 LF0500 LN016 LP00001 LS1000 LV250 LJ1 LW1 LZ30,220 SM2
  SA001 ST0 CK CS

Broadband Configuration

BB13901.CMD
  CR1 PS0 CY CT 0 EZ 0011101 EC 1500 EX 11101 WD 111100000 WL 0,4 WP 00001 WN
  016 WS 1600 WF 1600 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 &?


Processing instructions

Instructions to Watchkeepers as at Jday 67.

Now that things are settling down, it is worth asking watchkeepers to push the 
LADCP processing a bit further after each cast. It is important to see that the 
instruments, particularly the BB, are producing complete and plausible casts 
after each station.

1) After download, check the log sheets have been completed, and the file names 
   are right. Please complete 'bottom of cast' details on BOTH logsheets. Check 
   the three data file names have been changed correctly. 

   CnnnB.000
   CnnnW.000
   CnnnS.000

These now all reside in one directory on unix.

2) On the laptop:
   start / run / ftp darwin2
   lcd ladcp'bb
   cd /data33/bbraw
   binary
   put CnnnB.000

3) on the WH PC:
   a) Copy 000 files to ZIP; insert ZIP in 'walknet' PC.
   b) Open FTP explorer window
   c) select unix directory 'bbraw'; doubleclick. This brings up the contents of 
      bbraw in the right hand half of the window.
   d) drag and drop files from ZIP into right hand half of FTP explorer window.
   e) return zip disk to zip drive of WH PC.

4) On unix: log on to sohydro6 as pstar

5) start a new terminal window

6) cd /data33/ladbbuh

7) source LADall

8) cd proc

9) cd Rlad

You should now be in the directory where all the raw ADCP data sit. In order to 
process all data together, the three instruments are referred to as casts 01, 
02, 03 for B, M, S data. Firing's data handles multiple casts more gracefully 
than multiple instruments.

10) Check the raw data file names.

11) l.exec nnn [this makes links from the file names that Firing requires, such 
    as c027 01, to the raw files.

12) cd proc
                                                     Lisa M. Beal and Brian King



SHIPBOARD INSTRUMENTATION AND COMPUTING

Data logged to LevelC

SURFMET   PC
ADCP      PC
WINCH     PC
EA500 D1  MKII LevelA
GPS_4000  MKII LevelA
LOG_CHF   MKII LevelA
GYRONMEA  MKII LevelA
GPS_ASH   MKII LevelA
GPS_G12   MKII LevelA
GPS_NMEA  MKII LevelA


Ashtec ADU

The Ashtec ADU2 is the most precise GPS-based three-dimensional position and 
attitude determination system available, providing real-time heading, pitch, and 
roll measurements. The technology is based on differential carrier phase 
measurements between 4 antennas connected to the receiver. The ADU2 employs a 4 
channel/12 channel configuration with the ability to select the best eight of 
twelve channels to use in Position and Dilution of Precision (PDOP)- based 
satellite searching and tracking. This improves solution integrity, allowing 
close to 100% attitude availability, providing two meter position accuracy and 
attitude angles can be as accurate as 1 milliradian (0.057°) or better in real-
time at a 2 Hz update rate.

Before the start of the cruise it was recognised that the quality of data 
obtained by the ADU2 installed on the RRS Charles Darwin was not up to 
specifications. After thorough research it was decided that the only way to 
improve the performance was to replace the antenna cables. The cables installed 
initially were within the specifications, but were inferior to available 
alternatives. Four cables were prepared at SOC and brought out to Durban for 
installation during ship mobilisation. Once work had started it was soon 
realised that two of the cables were of insufficient length, and no spare 
connectors or cables were available on board. It was decided to source some 
locally, which was done, and at the last minute the two short cables were 
extended to complete the job.

Finally it was possible to perform a calibration of the ADU2. The results from 
this were fed back into the receiver. Once a fair amount of data had been 
gathered, it was clear that replacing the cables had improved the signal to 
noise ratio as well as the quality of data received overall.

Calibration Details

                           ____________________________

                                    X      Y       Z
                            ---  ------  -----  ------
                            1-2  -0.504  0.495   0.000
                            1-3   0.000  0.996   0.000
                            1-4   0.496  0.498  -0.011
                           ____________________________


General Navigation

GPS receivers: GPS 4000, GPS G12, and GPS Ashtec are logged to the level C as 
gps_4000, gps_g12, and gps_ash respectively. The GPS 4000 and G12 receive 
differential corrections from the Fugro SeaStar 3000L DGPS receiver, which is 
housed in the same case as the G12 receiver. The Churnikeef Log magnetic speed 
log is recorded as log_chf. The gyrocompass is recorded as gyronmea. Navigation 
processing includes automatic correction of navigation error due to receiver 
error or breakdown. The processed files relmov and bestnav are available as 10 
second interval datafiles.

Underway measurements

The SIG Surfmet instruments are logged through a PC known as the Surfmet PC. The 
data is displayed on the PC screen, and logged directly to the levelB computer. 
A processed wind data stream provides calculated absolute wind speed and 
direction using bestnav as the navigation input file.

The EA500 echo sounder is logged as ea500d1. Depth corrections were performed 
daily using the prodep command which produces Carter Area corrected depth 
measurements using the bestnav navigation data.

The hull mounted ADCP is logged directly to the LevelC. The CLAM winch 
monitoring system logs directly to the LevelB.

Dartcom

The Dartcom system consists of a satellite tracking antenna mounted in a large 
dome above the bridge, and a rack-mounted control system incorporating a 
processing PC running Windows. Most operations are performed on the PC, using 
the familiar Windows environment. The system tracks and downloads images from 
the passing NOAA and Feng Yun weather satellites. The resulting images are an 
aid to predicting the weather and avoiding storms.

Figure: Dartcom images of tropical cyclone Ikeda

LevelC and Networking

A Network hub was placed in the main lab. Seven computers were added to the 
network, 1 Sunblade, 3 Windows Pcs, and 3 Macs.  An HP1600CM colour printer was 
also connected, as well as several roaming laptop computers. There was a 
shortage of network cables, this could have been avoided if computers being 
brought on board came with their own network cables.

Various drives were cross-mounted between the Sunblade (sohydro6) and levelC 
system to enable files to be shared for processing by the pstar/pexec 
processors. The following drives were mounted on sohydro6

darwin3:/data31
darwin3:/data32
darwin3:/data33
darwin1:/rvs/raw_data
darwin1:/rvs/pro_data
darwin1:/rvs/def7
darwin2:/nerc/packages/rvs
darwin2:/nerc/packages/gmt

Backups were done on a daily basis to DLT tape from the darwin3 unix machine. 
Daily backups included: /data31 /data32 /data33 /rvs/raw_data /rvs/pro_data 
/rvs/def7/control and /users, and were performed on a two day rotation basis.

Printers

The following printers were available: HP Laserjet 4, HP 2000C, HP1200C/PS, HP 
Designjet 750C, and HP1600CM (not RVS/OED). After a few days the HP2000C printer 
broke down due to a failed printhead. A replacement printhead was not available 
on board, so this printer was rendered useless. The aged HP1200C was given a 
quick overhaul, involving repairing the slippery rollers and worked flawlessly 
throughout the rest of the cruise. The Laserjet started to develop a squeak 
towards the end of the cruise, perhaps this printer requires service.

Email

The Novell server that was previously in use on Charles Darwin, failed on a 
previous cruise, and although a replacement was sent out prior to this cruise, 
there was an error with the configuration which meant it could not be used as 
the main email server. The solution was to setup a POP3 email server on the 
levelC computer system. The program qpopper was installed on Darwin2 at the 
start of the cruise, which was hoped would enable conventional email programs 
such as Eudora, Outlook Express, and Netscape Mail to be used to receive mail. 
The email transfer machine, Darwin4 was used as the SMTP (outgoing mail) server 
and Darwin2 as the POP3 (incoming mail via Darwin4) server. Email users were 
given a unix account on Darwin2, and the option of using Netscape Mail on the 
unix system or to use their own email client of choice on their own computer. 
This arrangement worked satisfactorily throughout the cruise, apart from a few 
hiccups mostly to do with Darwin4.

Other PC problems

The main computer room PC (ibmpc2) running Windows98 experienced strange 
problems throughout the trip. It would unexpectedly freeze even when not being 
used, and CD writing was hopeless at best. The virus checker was removed because 
it seemed to blame for the PC not starting Windows properly. Later information 
was to leave a zip disk in the zip drive at all time. The USB Cdwriter was 
dismantled and the drive was installed inside the main computer case, and it 
worked first time without problems associated with buffer underruns and failure 
to recognise the drive.

The Master's PC was looked at on several occasions. This aged computer was 
struggling to run Windows 95/98, with a somewhat split personality. Eventually 
after a spectacular crash, Outlook Express stopped functioning, even after 
reinstalling it and the operating system. The Chief Engineer's PC running 
Windows95 had trouble sending attachments to email, this too was looked at, but 
a solution could not be found.
                                                                  Martin Bridger



NAVIGATION

Background

Data from three scientific navigational instruments on RRS Charles Darwin were 
processed. Position, heading and attitude were primarily obtained from the 
Trimble 4000 GPS receiver, Ashtech ADU-2 GPS receiver and the Arma Brown MK10 
Gyrocompass. Using a seaSTAR receiver, GPS correction data were passed to the 
Trimble 4000 to allow it to operate in differential mode (DGPS). On two 
occasions, no corrections were obtained due to crossing the boundary between 
different satellite coverage areas. All instruments were logged to the RVS Level 
A system before being transferred to RVS Level C system. Six Unix scripts were 
used to process the navigation data in 24 hour periods from 0000 to 2359. Each 
script, which required the JDAY as input, had to be altered slightly from the 
original version to deal with JDAY = 100.

Trimble 4000

The Unix script gpsexec0 was used to process the GPS data. Initially datapup 
transfers data from the RVS datastream gps_nmea, converting it into binary pstar 
format. The raw data flag is reset and new dataname and header details are 
created using pcopya and pheadr respectively. Data are edited using pdop 
(position dilution of precision based on the number of satellites to fix 
position). At the start of the cruise, the script was set to remove any data 
outside pdop < 4. However, as we headed eastward away from South Africa the 
number of data fixes reduced causing datpik to eliminate too much reasonable 
data. A greater amount of interpolation was required later to fill in the gaps, 
which caused problems when merging GPS with ADCP data. To eliminate problems we 
narrowed the editing to data outlying pdop < 7. This change took place on 17 
March (JDAY 76) and the new criterion remained until the end of the cruise. 
Daily files 139gps[JDAY] were appended to a master file 139gps01.

Ashtech ADU-2

Ashtech GPS data is used to correct heading errors in the ships gyrocompass 
before the gyrocompass is used in the ADCP processing. This correction is 
necessary because of the inherent error in the gyrocompass which causes it to 
oscillate for several minutes after a manoeuvre.

Processing the ashtec data was broken down into four execs.

Ashexec0: The initial exec retrieves the raw data from the RVS datastream 
          gps_ash. The raw data flag is reset and header information set using 
          pcopya and pheadr respectively. The output file created is 
          139ash[JDAY].raw.

Ashexec1: This exec merges the raw ashtech data with the master gyro file using 
          pmerg2. The difference between the ashtech and gyro headings are 
          calculated and set in the range between -180 and 180. The output file 
          created is 139ash[JDAY].mrg.

Ashexec2: This exec edits the merged file 139ash[JDAY].mrg using a series of 
          pexec programs: datpik removes data outside the limits for the 
          following variables: 

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

pmdian    removes shortlived spikes in 'a-ghdg' greater than 1 degree with a 
          five point mean.
pavrge    creates a two minute averaged file 139ash[JDAY].ave
phisto    is run on the averaged file to determine the mean pitch and its 
          limits.
datpik    then removes further spikes from the  average file, namely those 
          outside the pitch limits calculated by phisto and where mrms is 
          outside 0 and 0.004.
pavrge    puts the file back into two minute average.
pmerge    remerges the gyro heading from the master file onto 139ash[JDAY].ave.
pcopya    then reorders the variables in the average file.
Output    files are 139ash[JDAY].edit and 139ash[JDAY].ave.

Ashedit.exec: The final stage in the ash processing is running ashedit.exec. 
          This allows final interactive editing of 'a-ghdg' with plxyed to 
          remove any outlying data points. The resulting file is then 
          interpolated to fill in missing data values to allow the easy merge of 
          adcp data later on in the processing. The daily output files are 
          139ash[JDAY].dspk, which were appended to the master file 139ash01.

No ashtech data was recorded on one occasion (JDAY 090 00:40 - 01:10). The 
reason for this is unknown.

Gyrocompass

The most continuous information available on ship's heading can be obtained from 
the gyrocompass. It is used in Acoustic Doppler Current Profiler (ADCP) and 
meteorological processing. The gyrocompass was processed with the script 
gyroexec0. Raw data is read in from the RVS data stream gyronmea using the pexec 
program datapup. The raw data flag and header information is set using pcopya 
and pheadr. Data is forced to lie between 0 and 360 degrees before being sorted 
on time. The output file 139gyr[JDAY].raw is created daily and appended to the 
master file 139gyr01.

The processing stages for gps, gyro and ash (first three execs) were combined 
into one UNIX script (called dailynav1) for daily processing.

Investigating the EM-log

On JDAY 073 an investigation was carried out to compare the ships speed as 
determined from the VMADCP and emlog. It was observed that the emlog was 
apparently reading ship speeds higher than expected. This was affecting our 
progress overground, and we wanted to speed things up a little!

Initially, the first row from the master adcp file adpall was copied out from 
the beginning of jday 060 to the end of jday 070. The first row from the VMADCP 
provides the closest data to the surface with which we can compare emlog data. 
Heading data was merged on from the master gyrocompass file, 139gyr01 (ver AQ), 
and the calibrated ADCP velocities were converted to speed and direction of the 
ship over water. By subtracting the gyrocompass heading from the VMADCP 
direction we determined the direction of the ship over the water relative to the 
ships heading, 'dirn_rel'. The VMADCP speed and dirn_rel were reconverted to 
give the speed of the ship from the adcp in the fore-aft and port-starboard 
directions. The output file created was emlog_05.

Data from the emlog was retrieved from the RVS datastream, log_chf, using 
datapup. After averaging into two minute intervals (to match the adcp time) the 
emlog fore-aft and port-starboard speeds were merged on time to the adcp 
emlog_05 file. A comparison was made of the VMADCP and emlog fore-aft and port-
starboard speeds.

Results from our investigation are summarised in the table below. Plots of ADCP 
ship speed versus emlog ship speed indicated the emlog was reading higher, by 
approximately 5% in the slope and 5% in the offset, than expected. For example, 
at a speed of 10 knots the emlog was reading speeds 10% higher. Therefore, 
during station 55 (JDAY 73) new coefficients were entered as shown in the table. 
A repeat investigation made after station 55 on JDAY 76 showed the difference 
was minimal.


Table v1: Change in calibration of EM Log
          ________________________________________________________________

           EMLOG speed   Initial calibration    After jday 75 calibration 
             (knots)           (knots)                  (knots)  
                        (what speed should be)   (what speed should be)
           -----------  ----------------------  -------------------------
              2.81               3.77                     2.99
              3.87               5.03                     4.19
              7.77               9.69                     8.62
              9.88              12.06                    10.88
          ________________________________________________________________

                                                    Louise Duncan and Brian King



VESSEL-MOUNTED ACOUSTIC DOPPLER CURRENT PROFILER (VMADCP)

Instrument Configuration

The Acoustic Doppler Current Profiler (ADCP) on the RRS Charles Darwin is an RD 
Instruments 153.6 kHz unit. Situated within a recess of the hull, the ADCP is 
orientated such that the transducer head is offset by 45° to the fore-aft 
direction. This offset is corrected for in daily processing using 139adpexec0a.

Data from the VMADCP was set to record in 64x8m bins, in ensembles of two-minute 
duration. The 'blank beyond transmit' was set to 4m and the approximate 
transducer depth was set to 5m. This gives a centre depth for the first bin as 
17 metres.

The system uses 17.10 firmware and version 2.48 of RDI Data Acquisition 
Software, run on an IBM-type 300 MHz PC. With the PC interfaced to GPS, the 
Userexit program four (UE4) is able to correct the PC time using the GPS time. 
This eliminates the need for clock correction later in the data processing. Two-
minute ensembles of data are passed directly to the Level C.

At the beginning of the cruise, working just off the South African coast, the 
system was set to record in bottom track mode. However, as we entered deeper 
water after station 16 (JDAY 63) we switched to water track mode. No bottom 
track data was collected again until after station 143 (JDAY=104), just off the 
Australian coast. The instrument was set to make one bottom track ping for every 
four water track pings using command FH00004.

Data Processing

Data were processed in 24-hour periods, from 00:00 to 23:59, using six Unix 
scripts. Each script was altered slightly from the original to deal with JDAY 
inputs after JDAY = 99.

Reading in Raw Data (139adpexec0): Data were read in from the RVS level C system 
and separated into non-gridded data, such as heading, temperature, depth and 
bottom track velocities; and gridded data, such as water velocities and 
bindepth. Velocities are converted into millimetres per second. The two output 
files created were 139adp[JDAY] and 139bot[JDAY].

Rotating transducer heading (139adpexec0a): The heading of the VMADCP transducer 
was rotated by -45° in the bottom track non-gridded file.

Clock correction (139adpexec1): In previous cruises, the VMADCP data stream has 
been time-stamped with a clock other than the ship's master clock. This often 
resulted in time drifts in the raw data files. However, no clock correction was 
required on CD139 as the ship's master clock was used to time-stamp the VMADCP 
data stream. The exec was run nevertheless to keep file names and procedures the 
same as in previous cruises. The time difference of zero was applied to the 
data. The output files from the exec are 139adp[JDAY].corr, 139adp[JDAY] and 
clock[JDAY].

Ashtech corrections (139adpexec2): The VMADCP determines water velocities 
relative to the ship. To calculate absolute velocities the ships heading is 
required. The gyrocompass is used in ADCP processing as it can provide 
continuous measurements of heading. However, after manoeuvres the gyrocompass 
can oscillate for several minutes, which can be corrected using the Ashtech GPS. 
Since the Ashtech system does not provide continuous data, corrections are made 
on an ensemble-by-ensemble basis (See navigation section). The ashtech-minus-
gyro heading correction ('a-ghdg') from the master ashtech file 139ash01 is 
merged with the VMADCP water track file, 139adp[JDAY].corr, and bottom track 
file, 139bot[JDAY].corr, on time; and the velocities are then corrected for this 
heading error. Output files are 139adp[JDAY].true and 139bot[JDAY].true.

Calibration (139adpexec3):  Two further corrections required for the VMADCP are
  i) A an inherent scaling factor associated with VMADCP velocities
 ii) φ the misalignment angle between the ashtech antenna and the
     VMADCP transducers heading 
     Initial values for A and φ were set as A = 1 and φ = 6.35.

Data from the first four days of the cruise were used to determine the ADCP 
calibration. In this period two long steams occurred: a) from Durban to the 
first test station, travelling perpendicular to the coastline; and b) between 
stations 13 and 14 travelling parallel to the South African coastline.

The two-minute ensembles of bottom-track data were initially merged with the 
master GPS file, 139gps01, on time to retrieve navigation. Following a 30-minute 
average, the ship velocities and bottom velocities were converted into speed and 
direction. On station data were removed from the calibration by discarding 
bottom track speeds outside the range 100-750 cm/s.

   A and φ were calculated using
      A = UˇGPS/UˇVMADCP
      φ = φˇGPS-φˇVMADCP

where UˇGPS, φˇGPS, UˇVMADCP and φˇVMADCP are the 30-minute average speed and 
direction from both the GPS and VMADCP respectively. The direction of φ was 
reversed to put it in the correct orientation and then put in the range -180° < 
φ < 180°. Excluding major outliers, we derived 

                             A = 1.0035 and φ = 6.00.

Data were reprocessed with the new calibration values for A and φ to produce 
correct water velocities relative to the ship. The new output files are 
139adp[JDAY].cal and 139bot[JDAY].cal.

At the end of the cruise, we made another bottom-track calibration run, to 
verify the first calibration. After station 147, we steamed back along the 
cruise track to station 143 before heading back towards the shore on a heading 
of 130 degrees (the same track heading off South Africa). The same steps 
described above were made to find the new calibration. Excluding major outliers, 
we derived a new calibration 

                            A = 1.0038 and  φ = 5.80

This new calibration was not applied at the end of the cruise.

Calculate absolute velocities (139adpexec4): The master GPS file was merged with 
bottom track data on time to calculate the ship's velocity over two minute 
periods. The ship's velocities were then merged onto the water track file 
139adp[JDAY].cal and absolute velocities calculated. Absolute velocities were 
output to the files 139adp[JDAY].abs and 139bot[JDAY].abs. The final daily ADCP 
files 139adp[JDAY].abs and 139bot[JDAY].abs were appended onto master files 
adpall and botall respectively.

All the ADCP processing stages were put into two UNIX scripts called dailynav2 
and dailynav3.

Separating Processed VMADCP Data into On-Station and Off-Station Data

For analysis, the master adpall file was separated into on-station, cast and 
steaming data for each cast. A single bin file, at a depth of 51 m, was used to 
work out when the ship was in these three different states. Using changes in the 
ship's speed and heading to determine when the ship was on station and steaming, 
and the ctd/ladcp cast times to determine time in water, we listed appropriate 
datacycle numbers from bin5. These datacycles corrected for the complete gridded 
data were then used to extract the appropriate part of file adpall. Output files 
were called 139[NUM]S, 139[NUM]C and 139[NUM]A, where NUM is station number, for 
on-station, cast and between-station data respectively.

Results

Various analyses on the ADCP data were performed. During the cruise, daily 
figures of ten-minute averaged ADCP data were made from 51 metres depth. One of 
the first analyses followed the completion of the Agulhas section, where 
transport estimates were made. These results are shown in Table A1. 


Table A1: Estimates of the Agulhas Current Transport from Vessel Mounted ADCP
          ______________________________________________________________

                      Transport above  Transport above  Transport above 
                         60 m (Sv)        200 m (Sv)       280 m (Sv)
           ---------  ---------------  ---------------  ---------------
           Stn 14-32       -3.8              -14.5            -19.4
           Stn 14-31       -4.0              -14.8            -19.8
           Stn 14-27       -3.7              -13.5            -18.1
          _____________________________________________________________


Accumulated transport between stations 14 (the start of the final Agulhas 
section) and station 145 were calculated for the ADCP data. The station data was 
combined using papend and station pair averages calculated using adcponsta2.m, 
creating the output file trans14-145.1. The transport across the section, 
between the depths 60 and 200 metres, was calculated by accumulating the 
difference in distance between the stations multiplied by the depth multiplied 
by the velocity average for the stations. The final output file is trans14-
145.10. Figure A1 shows the alongtrack and cross-track accumulated transports.


Figure A1: The accumulated transport perpendicular to (darker curve) and along 
           (lighter curve) the cruise track from stations 14 to 145, between the 
           depths of 60 and 200 m.
                                                   Louise Duncan and Matt Palmer



UNDERWAY METEOROLOGICAL MEASUREMENTS

Instrumentation

The RVS Surfmet system was used throughout the cruise to record near-surface 
meteorology and sea surface temperature and salinity. The instruments used with 
their serial numbers and manufacturer are shown in Table U1.


Table U1: Instruments used in Surfmet system on board RVS Charles Darwin.
          _____________________________________________________________

           Instrument                      Manufacturer  Serial Number
           ------------------------------  ------------  -------------
           OTM (Temperature)               Housing FSI      1334
           OTM (Temperature)               Remote FSI       1401
           Barometric Pressure (PTB 100A)  Vaisala          S3440012
           OCM (Conductivity)              FSI              1353
           Anemometer                      Vaisala          S45517
           Wind Vane                       Vaisala          R05426
          _____________________________________________________________


Unfortunately, the vane direction 0°/360° was set to be fore-ship, so that on-
station when the wind was blowing towards the bow the vane registered values 
alternately in the ranges 0° to 10° and 350° to 360°. When one-minute 
averages were made of these one-second vane readings, a meaningless average vane 
direction was arrived at. Because one-minute averages are archived and 
subsequently processed, wind-direction values for on-station periods are not 
generally useful.

Processing

From JDay 95 (6 March) a number of c shell scripts were used to process the 
underway data on a daily basis. Data up until JDay 94 were processed as a single 
batch.

Surexec0: This script transferred the data form the surfmet system to PSTAR 
          format producing files 139sur*** and a master file 139sur01, where 
          *** are consecutive numbers.

Surexec1: This merged the ship's position, speed and heading from the navigation 
          system to the surfmet data and calculated thermosalinograph (TSG) 
          salinity using housing temperature, conductivity and a zero pressure 
          value. It also removed absent data values and performed a de-spiking 
          function.  The temperature variables were corrected with values taken 
          from the most recent calibration sheet according to the equations 
          below where T is the measured temperature. 

OTM (Temperature) Housing=-6.96*10^-2+1.00(T)-4.50*10^-5(T)^2+1.1*10^-6(T)^3
OTM (Temperature) Remote =-1.66*10^-4+1.00(T)-8.66*10^-5(T)^2+1.9*10^-6(T)^3

The data were then further edited using PLXYED to manually remove obvious spikes 
remaining in the data.  This created file 139sur02.

Salinity Calibration of Underway Data

Samples were drawn every four hours from the uncontaminated seawater supply for 
salinometer analysis. The resulting bottle salinities were then used to 
calibrate the underway salinity values as follows.

Sur.exec: This script reads data from excel files containing salinity data for 
          the uncontaminated seawater samples into PSTAR format. The files 
          created are called surio***.

Surexec2: This script converts the time from days, hours and minutes to total 
          seconds to enable comparisons with the underway data. This master file 
          was called 139tsg.samples.

The underway salinity data were added to the 139tsg.samples file and a new 
variable was formed of bottle salinity-TSG salinity(s-corr). This was then made 
into a continuous function and smoothed with a three point moving average. This 
smoothed function was then subtracted from the continuous salinity values to 
produce calibrated salinity data, (sal+corr).
                                                                    Melanie Witt



ATMOSPHERIC SAMPLING

Background

Atmospheric input, primarily via precipitation, is now recognised as a major 
source of metals to the oceans. There has been much interest in the atmospheric 
transport of metals such as Cd, Pb, Hg, Cu, and Zn as these have been observed 
in atmospheric deposition in concentrations high enough to be harmful to aquatic 
organisms (Galloway et al, 1982). Aerosol samples collected at remote marine 
regions give important information regarding background concentrations and the 
extent of transport of continental material to the oceans. Material released as 
a result of biomass burning and dust transported from desert regions may be 
delivered to remote marine environments via the atmosphere.

Aerosol Collection

During this cruise aerosol samples were collected using high volume aerosol 
samplers positioned on the port side of the crane deck (Table M1). Samples were 
only collected when there was a headwind to avoid contamination from ship's 
emissions. There were a number of periods during the crossing when sampling was 
not possible due to tailwinds.

Initially sampling was only undertaken during passage and the samplers were 
switched off with the filters still in place 15-20 minutes prior to arriving at 
stations and only switched back on 15-20 minutes after leaving the station. 
Several rust coloured spots were noticed on the filter papers when they were 
retrieved after sampling which indicated they had been contaminated by the ship. 
To avoid this when the samples were not being collected the filter paper was 
covered with metal plates. When tailwinds were following the ship's course 
samples were collected while on station as this involved turning the ship to 
head into the wind.

Trace Metal Analysis

Aerosol samples collected during this passage are to be analysed for a number of 
trace metals. The concentrations of metals such as lead, copper, zinc, nickel, 
cobalt and cadmium will be investigated with graphite furnace atomic absorbance 
spectrometry(GFAAS), a technique with the low detection limits that are required 
to measure the low concentrations expected.

The aerosols for trace metal analysis were collected on acid cleaned filter 
papers and the material will be extracted with a number of solutions. A 
determination of the total metal content involving total digestion of a part of 
the filter with HF, a weak acid digest and extraction with artificial rain and 
seawater are planned for other parts of the papers. This will investigate the 
solubility of the metals to help to establish the availability of metals 
delivered via the atmosphere.


Table M1: Sampling locations and dates during the Indian Ocean Cruise 
_____________________________________________________________________________

 Sample No.           Longitude of  Sample    Sampling     Volume of air 
                       sample (°E)   Time       Dates     sampled in trace
                       at ~32°S.    (Hours)    (2003)     metal sample (m^3)
 -------------------  ------------  -------  -----------  ------------------
 Durban 30.4°E
  1 (Size segregated)  31.9-32.6      5.7      2-3 March        353
  2 (Size segregated)  31.6-30.3      3.2        4 March        217
  3                    32.8-36       19.2      8-9 March        797
  4                    36.8-43       31.7    10-13 March       1559
  5                    43.3-46.2     25.7    13-14 March       1719
  6                    47.4-58.1     20.4    15-19 March       1152
  7                    59.4-68       23.7    20-23 March       1337
  8                    73.8-77.7     22.6    25-28 March       1376
  9                    78.5-78.5      3         29 March        190
 10                    85.5-88.5     24        1-2 April       1865
 11                    88.5-93.7     13.5      2-4 April       1042
 12                    96.5-103.5    23        5-8 April       1274
 13                    105-107        9.5     9-10 April        628
 14                    107-114       23.7    10-13 April       1352
 Perth 115.4°E
_____________________________________________________________________________
  

Major Ion Analysis

A second aerosol sampler has been used with filter papers not exposed to acid. 
These filters are to be analysed with ion chromatography for major ions such as 
sulphate and chloride. This should help to correct for seasalt collected on both 
samples. Phosphate analysis through the formation of molybdo-phosphoric acid and 
spectrophotometry will be used to establish the importance of the atmosphere in 
providing nutrient phosphate to oceans.

Lead Isotope Signatures

Lead has four naturally occurring long lived isotopes (^204Pb, ^206Pb, ^207Pb 
and ^208Pb). The amount of each isotope present in an iron ore is unique and is 
determined when it is formed. Each ore thus has its own isotopic lead signature. 
During environmental and industrial processes this isotopic ratio remains 
unchanged as there is no further fractionation (Doe, 1970). As different regions 
of the world use lead from different ores, analysis of the isotopic ratio of 
lead in the atmosphere may be used as a tracer of the source of anthropogenic 
lead.

Lead isotope measurements are planned on the aerosol samples collected on this 
cruise with a multi-collector inductively coupled plasma mass spectrometer (MC-
ICP-MS). The ratios of the stable lead isotopes present in the aerosols along 
with back trajectories of air masses and weather maps of the region should help 
to identify the source of the aerosols sampled and the extent of transport of 
pollutant lead to the Indian ocean.

Rain Collection

A number of rain samples have been collected from the monkey island above the 
bridge. Samples were taken in acid cleaned bottles and funnels for trace metal 
analysis; for major ion work the bottles and funnels were cleaned without the 
use of acid. The samples are stored frozen and a similar suite of analysis to 
the aerosol samples is planned for the rain samples on return to the laboratory 
at University of East Anglia. This should enable both the wet and dry flux of 
metals to the Indian Ocean to be investigated. Along with total metal 
concentration determinations electrochemical measurements of the organic 
complexation of copper in rainwater is also planned.

There have been several large rain events during passage across the ocean and 
this has enabled samples to be collected both close to the South African coast 
and in remote marine regions. A summary of the rain samples gathered during the 
cruise is shown in Table M2.


Table M2: Rain Samples Collected
     ___________________________________________________________________

        Date sampled     Position   Volume sampled  Volume sampled  pH
            2002                      (Major Ion     (Trace Metal 
                                        Sample)         Sample)  
      ----------------  ----------  --------------  --------------  --- 
      7th March         31°S, 31°E       100 ml          150 ml      4.5
      23rd-25th March   34°S, 70°E       150 ml          500 ml      4.5
      25th-26th March   33°S, 72°E       200 ml          300 ml      4.5
      26th March        32°S, 75°E        50 ml           50 ml      
      31 March-1 April  31°S, 84°E       500 ml           50 ml      5.0
      4th April         32°S, 92°E       400 ml          250 ml      5.0
      6th April         34°S, 96°E       500 ml          500 ml      4.0
     ___________________________________________________________________


Organic Copper Complexation

Copper is an essential nutrient at low concentrations but becomes toxic at 
elevated levels. Copper also plays an important role in atmospheric chemistry 
for reactions such as oxidation of SOˇ2 and production of OH radicals (Losno, 
1999). Its bioavailability and catalytic capabilities are strongly influenced by 
chemical speciation with the free metal ion being the most readily available 
biologically and chemically (Sunda and Guillard, 1976).

Strong organic complexation of copper has already been observed in rain samples 
collected at UEA. Measurement of the free copper, and organic ligand 
concentrations along with total copper analysis in rain samples collected on 
this cruise will establish how widespread this complexation is.


REFERENCES

Doe, R.B. 1970 Lead Isotopes. Springer-Verlag, Berlin.

Galloway J.N., Thornton J.D., Norton S.A., Volchok H.L. & McLean R.A.N. 1982 
    Trace metals in atmospheric deposition, a review and assessment. Atmospheric 
    Environment, 16, 1677-1700.

Losno R. 1999 Trace metals acting as catalysts in a marine cloud: a box model 
    study. Physical Chemistry of the Earth (B), 24(3), 281-286.

Sunda W. & Guillard R.R.L. 1976 The relationship between cupric ion activity and 
    the toxicity to phytoplankton. Journal of Marine Research, 34(4), 511-529.

                                                                    Melanie Witt



ARGO FLOATS

Setup

25 APEX floats from Webb Research were deployed, as a contribution to the Argo 
programme. The floats were purchased through the UK Met Office. Funding was from 
Met Office Argo funds and JRD. Initial enquiry was made about the possibility of 
sea freighting the floats directly to Durban, but the Webb agent in Europe 
believed this to be too great a challenge. The floats were therefore delivered 
to SOC and travelled to the ship in the JRD container. The floats were packed in 
13 crates, 12 with 2 floats plus one single. Before leaving Durban, all float 
crates were opened, the numbers checked, and the crate lids secured with just 
two screws. This made the task of accessing the floats later in the cruise much 
easier. Floats were stored in the JRD container and brought into the main lab 
one at a time when needed.

A depth table of 55 depths had been defined based on examination of data from 
the 1987 cruise (Table F1). Compared with the table of 70 depths used for the 
UK's North Atlantic floats, there are fewer depths near the surface, but some 
extra entries deeper. Thus 12 different Argos messages make up the complete 
profile. All floats were set to drift at 2000 m, and profile once per 10 days.

In view of the fact that the depth table was shorter than is sometimes the case, 
and because the float activation times could be chosen to be optimal relative to 
the passes of the Argos satellites, it was decided that a time on the surface of 
6 hours would be sufficient. Satellite pass predictions were based on satellite 
orbit data from January 2002. The satellite pass times in January 2002 had been 
compared with data from 6 months earlier and had not changed significantly. 
Argos data are relayed using the multi-satellite service. The satellites 
returning data in March 2002 were NOAA 11(H), 12(D), 14(J), 15(K), 16(L). At 
optimum times of day, and with a 45 second repetition rate, a 6 hour surface 
period is expected to return about 150 messages. Even allowing for change of 
satellites or orbits during the lifetime of the floats, this should be 
sufficient to ensure all data are recovered.

The floats had a nominal Argos repetition rate of 45 seconds. In practice this 
meant 44 or 46 seconds. The time of activation of floats was monitored. Where 
two floats were expected to be on the surface at the same time (i.e., activated 
10 or 20 days apart) they were chosen where possible to have different 
repetition rates. This avoids the possibility that their entire transmissions 
will be exactly synchronised, which can result in data loss. The satellites 
cannot receive two transmissions simultaneously. An instance had been noted in 
the N Atlantic where two floats surfaced and were transmitting simultaneously, 
with the same repetition rate. Very few data were acquired from one of the 
floats until the second float ceased transmission and dived.

Floats were tested and reprogrammed using the laptop also used for the BroadBand 
LADCP. The terminal programme was used with settings 1200/8/N/1 and Xon/Xoff. 
The test sessions were saved to ASCII files by cutting and pasting into Notepad. 


Table F1: Argo profile sample depths.
            ______________________________________________________

             Sample  Pressure  Sample  Pressure  Sample  Pressure
             point             point             point 
             ------  --------  ------  --------  ------  --------
               1       2000      20      750       39      160
               2       1900      21      700       40      150
               3       1800      22      650       41      140
               4       1700      23      600       42      130
               5       1600      24      550       43      120
               6       1500      25      500       44      110
               7       1400      26      450       45      100
               8       1350      27      400       46       90
               9       1300      28      360       47       80
              10       1250      29      330       48       70
              11       1200      30      300       49       60
              12       1150      31      280       50       50
              13       1100      32      260       51       40
              14       1050      33      240       52       30
              15       1000      34      220       53       20
              16        950      35      200       54       10
              17        900      36      190       55    4 or surf
              18        850      37      180           
              19        800      38      170                      
            ______________________________________________________


Deployment

Early in the cruise, two floats were deployed in 'dive mode', that is to say the 
initial period of 6 hours had elapsed, so the floats dived immediately. This was 

due to a mismatch between the optimum reset time and the CTD station timing. For 
the early deployments it was considered preferable to deploy the float when 
steaming away from the station. Later on, with greater familiarity all round, 
floats were deployed either when approaching or when leaving stations. Float 
number 1 (Argos 09410) was deployed three hours after dive time. Previous 
consultation with Webb Research had suggested that while this is not ideal, a 
delay of a few hours should not be a problem. In Jan 2001, the first batch of 
Irminger floats (17127 et al.) had been reset several days before deployment. 
Some floats had taken a few cycles to settle down to the correct park depth. If 
the float attempts to dive but finds pressure not increasing, it will tend to 
adjust the dive piston position to an incorrect value. Float number 2 was 
deployed 90 minutes after the dive time. All other floats were deployed before 
the dive time.

Floats were deployed by lowering off the starboard quarter, at speeds between 
0.5 and 2 knots. Difficulty was experienced with only one float, number 21, 
Argos 09390. When the loose end of the rope was paying through the hole in the 
damper plate, the last metre or so managed to get snagged between the annode and 
the sensor head assembly, such that it would not run through and release the 
float. It was decided that the float would need to be hauled back on board and 
redeployed. As the float was lifted out of the water and more weight came on the 
rope, it freed itself and the float dropped back into the water from a height of 
no more than 2 metres. No sign of damage to the sensor head was observed.

Three extra floats were deployed after leaving station 117. This was for the 
purpose of setting up a dispersion experiment. A float was deployed at 117 as 
normal, with further floats at a range of 5, 15 and 35 miles along track, so the 
6 pairs of initial separations are 5, 10, 15, 20, 30, 35 miles. The floats were 
reset as near to simultaneously as possible, subject to satisfactory Argos 
tests.

All floats transmitted to Argos after reset. We have only a short amount of 
Argos data from Float 1. Due to a misunderstanding, it was carried from the lab 
to on deck only shortly before the end of transmissions. Floats 1 and 6 have not 
surfaced. Other floats appear to be functioning normally, and are returning good 
data. Table F2 contains float deployment details. All floats were set with UP = 
12, DOWN = 228, P9 = 8. The expected rise time is about 6 hours, giving 6 hours 
on the surface. The details for four other floats operating in the area, 
deployed from Charles Darwin in 2001, are included for reference, although of 
these, 10309 has not reported since 23 Nov 2001. 
                                                                      Brian King



Table F2: Deployment details for CD139 floats. For reference, some details of 
          four other floats in the region are given. Dive times represent the 
          nominal dive times on a day number near the start of CD 139. Positions 
          of these floats are latest positions relayed to the ship during the 
          cruise. Float 10309 has not reported since 23 Nov 2001.

_____________________________________________________________________________________________

CD  WRC   Argos  Argos WMO   Test     Reset     Deploy     Dive   Argos CTD  Deploy   Deploy
139 Apex decimal  hex  no    time     time       time      time   rep   stn   lat      lon
no  no                                                            rate  no
--- ---- ------- ----- --- --------  --------  --------  -------- ----- ---  -------  -------
 1  485   09410  930AC     066/1034  066/1201  066/2108  066/1801  44   031  -32°08'  031°52'
 2  466   09315  918C6     068/1129  068/1200  068/1930  068/1800  44   039  -33°01'  036°21'
 3  465   09309  91763     070/1123  070/2225  070/2319  071/0425  44   046  -33°01'  040°00'
 4  427   09108  8E527     071/2215  071/2224  072/0350  072/0424  44   050  -33°00'  042°50'
 5  435   09208  8FE11     074/1010  074/1200  074/1421  074/1800  44   059  -33°33'  048°16'
 6  451   09213  8FF5D     075/2112  075/2200  076/0049  076/0400  44   063  -34°01'  052°10'
 7  458   09214  8FFA8     077/0901  077/1200  077/1735  077/1800  46   070  -34°00'  056°15'
 8  469   09348  9210F     079/2025  079/2058  079/2319  080/0258  46   078  -34°00'  060°32'
 9  470   09349  9215C     081/0930  081/1000  081/1103  081/1600  46   083  -34°00'  064°59'
10  462   09218  90082     082/2005  082/2100  082/2317  083/0300  46   087  -33°59'  069°00'
11  461   09217  90077     084/0746  084/0907  084/1220  084/1507  46   091  -33°35'  072°49'
12  460   09216  90024     087/0740  087/0800  087/0930  087/1400  44   097  -31°07'  077°44'
13  459   09215  8FFFB     089/0734  089/0800  089/0918  089/1400  44   100  -31°11'  080°10'
14  467   09322  91AAB     090/1002  090/1008  090/1416  090/1608  44   103  -31°13'  083°12'
15  468   09347  920E5     092/0649  092/0803  092/1232  092/1403  44   109  -31°47'  088°29'
16  481   09385  92A70     093/0730  093/0759  093/1314  093/1359  46   113  -32°08'  090°52'
17  464   09255  909C3     094/2040  094/2058  094/2359  095/0258  46   117  -33°31'  094°37'
18  471   09350  921A9     094/2018  094/2059  094/2359  095/0259  44   117  -33°32'  094°42'
19  463   09219  900D1     094/2034  094/2100  095/0056  095/0300  46   117  -33°36'  094°52'
20  478   09351  921FA     094/2026  094/2101  095/0249  095/0301  44   117  -33°44'  095°14'
21  482   09390  92B9A     096/0635  096/0804  096/0853  096/1404  46   121  -34°31'  098°20'
22  484   09397  92D7E     097/1742  097/1754  097/2139  097/2354  44   125  -34°30'  102°29'
23  483   09391  92BC9     099/1752  099/1755  099/2050  099/2355  44   130  -32°30'  106°29'
24  480   09382  929A4     101/0803  101/0808  101/1326  101/1408  44   134  -31°30'  109°52'
25  479   09352  9222E     103/0303  103/0555  103/0621  103/1155  44   138  -31°31'  113°10'
          10313                                          071/0800  44        -32°26'  046°30'
          10310                                          072/0400  44        -30°24'  049°39'
          10309                                          072/2000  44        -28°22'  042°25'
          10308                                          073/1630  44        -31°13'  033°48'
_____________________________________________________________________________________________

 
 
 
CCHDO DATA PROCESSING NOTES

DATE      CONTACT   DATA TYPE      DATA STATUS SUMMARY  
--------  --------  -------------  ---------------------------------------------
12/13/04  Bryden    CTD/BTL        No Data Submitted; DQE Begun
          We did go across 32°S in the Indian Ocean in 2002 on Charles  
          Darwin.  I was Principal Scientist.  We sent the CTD data to BODC 
          but I think we have not yet finished our own quality control on 
          the nutrient, CFC, pH and alkalinity bottle data.  I prefer to 
          submit data only once so there is a single data set.  Do you want 
          to ask BODC for the CTD data?  When we finish the bottle data we 
          could send it both to you and BODC at the same time.
          
01/28/05  Kozyr     Cruise ID      Provided basic cruise info.  
          No Data Available  You can find the information for Indian Ocean in 
          2002 on Charles Darwin cruise at: 
          http://cdiac.ornl.gov/oceans/RepeatSections/clivar_i05.html
          
          and 26∞N in the Atlantic
          http://cdiac.ornl.gov/oceans/RepeatSections/clivar_a05.html
          
          However we do not have any data submitted by PIs from these 
          cruises.
          
11/16/05  Diggs     Cruise ID      Website Updated, Line # & expocode assigned   
          The only change is that the subject line now has the related WOCE line 
          number and expocode so that we can more easily reference this message 
          and insert it into the relevant data histories.

11/16/05  Bryden    CTD/BTL        DQE Complete; Available @ BDOC  
          We corresponded last December (messages included below) 
          about our Charles Darwin transect of the 32S section across the 
          Indian Ocean in 2002.  We have just finished our quality control 
          of the bottle data (includes CFC's, carbon components, some 
          helium/tritium as well as standard salinity, oxygen and nutrients) 
          and we have just sent the bottle data set to BODC.  As I said last 
          December, the CTD data was finalised earlier and sent to BODC as 
          well.
          
          We would be happy to have comments from CCHDO on the 32S data sets 
          and to have them included among CliVar resources easily available 
          to interested scientists.  Can you get the CTD and bottle data 
          sets easily from BODC?  I generally prefer to submit a data set 
          only once to avoid any possible confusion about origin; but we 
          would be happy to help you access the data sets if you have 
          difficulty with BODC formats.
          

DATE      CONTACT   DATA TYPE      DATA STATUS SUMMARY  
--------  --------  -------------  ---------------------------------------------
12/22/05  King      CTD/BTL/SUM    Data Request  sent to Toshimasa
          Thank you for your emails about the Indian Ocean I5 data 
          from 2002.
          
          Here in Southampton we have been working on the bottle data this 
          year, re-combining chemistry tracer data (carbon,  helium/tritium 
          and so on) with the physical data.
          
          The most recent bottle datset was submitted to our national data 
          centre (BODC) in late October this year, and they acknowledged 
          receipt of it on 1 November 2005. The CTD data were submitted to 
          BODC a long while ago (at least one year, maybe 2 years ?).
          
          Our expectation was that the data should move rapidly to CCHDO, so 
          that they could be made available in standard format, for the 
          convenience of all users. But it is obvious from the CCHDO website 
          that they do not yet have our data in their database.
          
          By copy of this email, I will ask BODC and CCHDO to find out where 
          the data are, to set a high priority on passing them through the 
          system, and to provide the recipients of this email with an 
          estimate of how soon the CTD and bottle data will be available on 
          the CCHDO web site.
          
          Hopefully it should be trivial for BODC to forward our files to 
          CCHDO if they have not alrady done so. Since Jim Swift reported at 
          the repeat hydrography workshop that CCHDO presently has spare 
          capacity for taking in and reformatting data, I am hopeful that 
          the data can appear at CCHDO very quickly.
          
          I would be grateful if BODC and CCHDO could email me directly if 
          they foresee or encounter any difficulty, so that I can help 
          resolve it. 
          
01/06/06  Rickards  CTD/BTL        Answer to B. King's 12/22/05 email  
          The data are not yet at CCHDO, but, as this is important to Argo, we 
          have allocated some of Stephanie's time to the task of submitting 
          CTD/bottle data to CCHDO. She, Alex and I will sort out the priorities 
          for this early next week - CD139 will be top of the list, but there 
          are other data to send as well. I have a list of 20 or so post-WOCE 
          cruises from NOC and other labs that need to be sent. We do not hold 
          all of the data yet, but Stephanie will begin chasing up data in the 
          next few weeks. So I hope that we will be in touch with CCHDO in the 
          next week. We will try to set up a fairly routine transfer of data 
          over the next few months as we had during WOCE. 
          

DATE      CONTACT   DATA TYPE      DATA STATUS SUMMARY  
--------  --------  -------------  ---------------------------------------------
01/13/06  Gardiner  BTL            Submitted T/S/O/NUTS/CO2/HE/NE
          Here is the bottle data for CD139 (I05-Bryden/SOC). It is in 
          zipped, CSV format with the parameter information in a flat ascii 
          text file called cd139_bot.hdr.  Please let me know if you have 
          any questions relating to the submitted data.
          
01/26/06  Gardiner  Cruise Report  Submitted; pdf only
          Please find attached the cruise report for CD139.
          
02/02/06  Gardiner  CTD            Submitted; CTDSAL/TMP/OXY  
          I've obtained some more data which goes with the CD139 (I05-
          Bryden/SOC) bottle data I sent to you a while back. The data are 
          salinity, temperature and oxygen extracted from the CTD sensors at 
          bottle firing depths.
          
03/26/07  Kappa     Cruise Report  pdf & text files online

03/27/07  Muus      BTL            Produced WOCE/Exchange formatted data files
          Bottle data taken from matlab file received from Elaine McDonagh 
          (elm@noc.soton.ac.uk) on March 5, 2007.
          Justin Fields made text files from the matlab file.
          No cast, sample or bottle numbers in matlab file. Used cast #1 for all 
          casts per Elaine McDonagh.
          Used BODC bottle # for sample and bottle #s
          No units in matlab file. Used standard WOCE(per kilogram) units per 
          Elaine McDonagh.

          BODC# 159713, Station 50 10.8db has only one water sample value: 
          salinity 34.7746 qf=2 which is 0.9 low.
          BODC# 159712, Station 50 10.6db has complete set of water samples with 
          salinity 35.6755.
          Deleted sample 159713.

          Over 150 samples in matlab file have CTD trip data only, no water 
          samples. These were not in the BODC file so have no BODC #s. Most were 
          duplicate levels. These samples were not included in the CCHDO files.

          TCARBN, ALKALI and PH had no quality flags. Used "2"s for all values.

04 17/07  Muus      BTL/SUM        dates corrected
          Station dates have been corrected in the I05_2002 sumfile and bottle 
          exchange file on the CCHDO website.

04/19/07  Gardiner  BTL            More parameters Submitted
          Here is the new bottle data for CD139 (I05-Bryden/SOC). It is in CSV 
          format. Please let malh@bodc.ac.uk know if you have any questions 
          relating to the submitted data. 
          

DATE      CONTACT   DATA TYPE      DATA STATUS SUMMARY  
--------  --------  -------------  ---------------------------------------------
06/22/07  Key       pH/ALKALI      Submitted M. Alvarez corrections report
          Additional information mentioned in web submission "note". Alvarez 
          2007 mentions corrections to data other than pH and alk, however, 
          corrections were NOT applied to anything else, i.e. they were only to 
          to produce phcorr and alkcorr.
          In the data file the measured and corrected values are flagged 
          separately.

07/28/08  Muus      CTD            woce & exchange format files online
          1. Original data taken from cd139_ctd.zip from            
                     newcchdo:/admin_home/sdiggs/BODC_DATA
             cd139_ctd.zip dated Jan 24, 2006.
             Individual files are dated Jan 12, 2006.
          2. Station data from i05_74AB20020301su.txt dated 20070417CCHDOSIODM.
          3. CTD Oxygen units in original data given as umol/l. Same problem as 
             bottle file oxygens. Cruise report says CTD units are umol/kg.
             Brian King msg says bottle oxygens are umol/kg. 
             Assume when units stripped for MATLAB files the wrong units were 
             added later.
             Used umol/kg
          4. CTD "CPHLPR01" (chlorophyll?) units in original data file are           
             mg/m^3. Fluorimeter units given in Cruise Report are ug/l. WOCE 
             fluorimeter units are MG/CUM. Assume all are identical.
          5. CTDTMP and CTDSAL each have two values in original data file. All 
             are 3 decimal places and were averaged and reported to 4 decimal 
             places to show the trailing 0 or 5.
          6. The original data file had flags "M" on some values which appear to 
             be questionable. Used WOCE flag "3" for the "M"s. If both 
             temperature or salinity values had "M"s they were averaged and 
             flagged "3". If only one of the two values was flagged "M" it was 
             deleted and the unflagged value was reported to 3 decimal places 
             and flagged "2". 

11/19/08  Willey    CFCs           Units don't match
          I have a question about the I05 2002 cruise, specifically 
          i05_74AB20020301.csv and i05_74AB20020301hy.txt. The column headers 
          for cfcs in the WOCE file (txt) have pmol/kg units, but the cfc column 
          headings in the Exchange (csv) file have pmol/l units. Can you tell me 
          if/which column headings are correct (at a glance, the values are not 
          identical in both files)? My problem is that I need a csv file with 
          pmol/kg units to read in ODV. 

11/20/08  Muus      CFCs           Units corrected
          I unfortunately posted a 20070417WHPOSIOdm version of the Exchange
          file made from a March 5 version of the WOCE format file. The correct 
          version, 20070418WHPOSIOdm made from the March 9 WOCE format file, is 
          now on line.

01/09/09  Kappa    Cruise Report  Website updated; report expanded
          • Added Marta Álvarez's Database Corrections report
          • Updated these Data Processing Notes

