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RRS James Clark Ross Cruises JR265 and JR254D, 27 Nov

1. comment This mstar file created from scs stream comment ea600 comment at 2009 11 14 11 31 25 comment Time converted from matlab day number to seconds after mstar time origin File last updated 2009 11 15 12 11 31 Type variable name or number of independent x variable 1 Type variable names or numbers of dependent y variables 3 Type the number of the variable you wish to edit from the list below 1 depth 57 which action s select data cycles list selected data w plot with selected data cycles removed o plot with original data zoom but make auto tick values Zoom to exact area chosen with cursor replot with first pdf go back to previous pdf edit selected data to NaN refresh q quit A window has appeared showing the change in depth with time Using the actions above s through to q we can clean up the data X Figure 2 File Edit View Insert Tools Desktop Window amp amp amp sim jr195 4316 vers 195 atsea 9 3000 2700 depth m 2400 mplxyed 2009 11 15 12 07 C 21000 1800 1500 1200 900 600 300 0 0 500 1000 1500 Start 20081112 daynum 316 000000 dc 1 time Stop 20081112 daynum 316 235957 dc 37303 minutes after start time in the matlab window at the action prompt type a You are taken to the depth vs tim
2. ILE ET 2 x 50 humidityt humidity2 barot 1000 baro2 102C 336 337 338 339 340 341 400 rel wind dir true wind dir rm c JEn S 200 Aside 7 A Wr D 0 336 339 340 341 _ 20F J E LIA j g 107 pow T li LA i eet CEN true wind speed ship sbeed ship speed 336 337 338 339 340 341 Julian Day Figure 8 2 b Same plots as in figure 8 2 a for days 336 340 8 4 Sensor performance Air temperature and humidity Two air temperature and humidity sensors were located on the bird table at the top of the foremast platform matlab ocl jr265 diff wil produce the differences between pairs of instruments The script produces jr265 01 diff nc and only selects night time air temperatures 265 01 air night nc Night time air temperatures are used to remove any heating effects of the ship from the comparison Night time is defined as TIR value 0 W m Figure 8 3 shows that the difference between humidity sensors The mean offset for humidity lt 70 is 0 15 with a st dev of 0 34 range 3 3 to 2 0 For higher humidities the 62 difference between the two sensors becomes much more variable with a total range of 11 to 11596 but the mean offset is still only 0 2 with a st dev of 1 14 15 humidity humidity2 95 50 60
3. for dir M eus a met surfmet met jr265 01 for jday day1 last_ day ocl ocl jr265 dJJJ nc ocl ocl jr265 01 nc dr 164 end mbest 01 nav seapos pos 1265 01 nav seapos pos 1265 26 nav seapos pos jr265 ave n 3 speed mbest 02 nav seapos pos jr265 spd nc course and distance run 30s vector mbest all mbest 03 nav gyros gyr jr265 01 nc nav gyros gyr jr265 ave nc averaged headings nav gyros gyr 265 01 2222 mbest 04 as nav bestnav bst 1265 01 nc heading onto average speed nav seapos pos 1265 01 jr265 01 calculide true met surfmet met jr265 01 n wand Speed apd direction 117 unix gt gt cd local users pstar jr265 data ocl unix gt gt setup v6 2 ferret unix gt gt ferret yes go make plot 126 1265 01 nc met 1265 316 318 ps make plots jr26 5 jnl met 1265 01 ferret jnl 5 jnl start stop yes quit e g go make plots jr26 5 jnl 316 318 would plot data between 316 and 318 Do not run daily Calculates the difference between meteorological variables Used 1265 01 diffinc to examine 1265 01 diff night nc offsets between different sensors Air temperature difference is selected for night time only diff 1265 1265 01 2 mplxyed editing of data The mstar routine mplxyed is used to plot data and interactively set d
4. 265 dJJJ nc once editing is complete 6 2 3 SEAPATH and GYRO The cleaned Seapath heading and gyro data are merged onto the Seapath position data and then the pos gyro heading difference is constructed to allow further data cleaning using gt gt mmerge pos gyr In this script medita 15 used to set head pos to a default value where the Seapath and gyro headings differed by more than 5 Only a very small number of points were removed in this process To reduce noise the data are averaged to 30s prior to generating the pos gyro difference The merged data are generated in file pos 1265 dJJJ nc overwriting previous file and a copy held in pos jr265 dJJJ mrg nc as a backup 55 6 2 4 ASHTECH Once converted to mstar format ash 1265 dJJJ raw nc files using mday_00 ash JJJ called from mday 00 get all JJJ the 1 Hz data were cleaned using mash 01 JJJ called from mday 00 clean all JJJ to give ash 1265 dJJJ nc files copied to ash jr265 dJJJ edit nc for manual cleaning with mp xyed Within the script the heading variable in the raw file was renamed as head ash backward and duplicate times were removed using mcalc and mdatpik and the following ranges were used to set out of range values to default values medita Ash O heading 360 Pitch 5 pitch 5 Roll 7 lt roll lt 7 Measurement RMS error 10 lt mrms lt 0 01 Baseline RMS error 10 lt brms lt 0 1 Consistent with the Seapath processing the Ashtech
5. 21 03 1 51 78852 57 82975 Balloon recovered to deck 27 11 2011 Shallow Test Wave 21 13 Buoy 1 51 78667 57 82185 Teather transfered to starboard side 27 11 2011 Shallow Test Wave 21 37 Buoy 1 51 76862 57 77539 Change heading to 270 degrees 28 11 2011 Shallow Test Wave 00 00 Buoy 1 51 76139 57 76414 Change heading to 230 degrees V L has moved 044 degrees x 0 6 NM since 0000 UTC 28 11 2011 Shallow Test Wave 01 15 Buoy 1 51 75732 57 75761 Commence recovery of buoy 28 11 2011 Shallow Test Wave 02 35 Buoy 1 51 75707 57 7573 Buoy recovered to deck V L moved 044 degrees x 0 4 NM since 0115 UTC 28 11 2011 03 06 Deep Test 53 46154 57 94652 V L stopped on station on DP for CTD 28 11 2011 12 23 Deep Test CTD 53 46157 57 94652 CTD deployed 28 11 2011 12 28 Deep Test CTD 53 46157 57 94651 CTD soaked veering to 2350 m 28 11 2011 12 34 Deep Test CTD 53 4616 57 94652 stopped 2350m 28 11 2011 13 13 Deep Test CTD 53 46155 57 94654 CTD recovered to deck 28 11 2011 14 59 1 CTD 1 54 78941 57 99588 Vessel on DP for CTD deployment water depth 265m 28 11 2011 21 48 1 CTD 1 54 7894 57 99588 CTD deployed 81 28 11 2011 57 99578 21 52 1 CTD 1 54 78942 CTD at 250m 28 11 2011 22 01 1 CTD 1 54 7897 57 99417 CTD secure on deck 28 11 2011 22 22 2 CTD 2 54 90
6. by comparing geostrophic velocities with those measured directly by the lowered ADCP to determine the size of ageostrophic motions and to attempt to estimate the barotropic components iv to examine the temperature and salinity structure of the water flowing through Drake Passage and thus identify the significant water masses v to calculate the total flux of water through Drake Passage by combining all available measurements 15 1 2 2 WAGES objectives for JR254D The overall aim of WAGES is to improve the parameterisations of the air sea fluxes and to understand their dependence on sea state wave breaking and whitecap fraction The aim of the IOPs is to deploy the buoy and aerial camera systems in a wide range of wind speeds and sea states and in both short fetch and open ocean conditions JR254D had 48 hours of dedicated ship time In addition to this the aim was to deploy the buoy and balloon systems during the deeper CTD stations whenever conditions allowed 1 3 Cruise Narrative 1 3 1 Mobilisation period 24 27 November The JR265 and JR254D science teams Figure 1 2 travelled south on the RAF flight from Brize Norton on the 20 November and arrived at the Falkland Islands on the evening of the 21 November The teams were met by BAS personnel and transferred to accommodation in Stanley The arrival of the JCR was delayed by bad weather and the science team did not get access to the ship in Mare Harbour until the 24
7. e g leaky 124 125 LADCP Logsheet JR265 For use with BAS setup single LADCP PC and BBTalk scripts CTD Cast JDAY a Lat Lon 1 Pre Deployment Checks Comms and Charge leads should be in place Is PC clock time synchronised Y N LADCP woken up with Break Time GMT Run PreDeployTest rds script Time in GMT Log file name Note any failed tests here Internal Moisture reading Are pitch and roll changing Y N Space Used Free Mb Tests completed time in GMT 2 Deployment Send Config file WHM265 txt Time GMT Disconnect cable attach blanking plug Y N Time in Water GMT 3 Recovery Connect cables attach blanking plug Y N Wake up with Break Time in GMT IT Latest Filename date and time Space Used Free Mb Change baud rate with cb811 Y N Recover Recorder data Filename Disable Window Output y n Change baud rate with cb411 time in GMT Power down with cz Time in GMT WinADCP Beam Intensity OK Correlation OK 4 Data File Copving Stage for Penny only Original Filename Copied to Legwork LADCP 000 Renamed filename Copied to Legwork LADCP log 126 JR265 TSG underway sampling log sheet CRATE IDENTIFIER colour code of bottles and or number NOTE JDAY or date if unsure and time the sample was taken Sampl
8. systems at 2 second intervals The oceanlogger also recorded the underway salinity and sea surface temperature These data will be discussed separately in Section 9 The meteorological instruments were mounted on the ship s foremast Figure 8 1 in order to obtain the best exposure The estimated heights of the instruments above the foremast platform were Sonic anemometer 0 65 m air temperature and humidity 0 25 m and the irradiance sensors 0 2 m The barometers were located in the ocean logger display cabinet in the UIC 58 Foremast platform Windmaster sonic 0 61m Bird table 0 61m 025m 0 20 5 7 m 14 04 m above water level Note not to scale Foremast Windmaster sonic 0 65 m table Foremast platform Figure 8 1 Schematic of the sensor positions on the foremast left plan view right side view Instrument Serial number Sensor position Parameter specified Last on cal sheet accuracy calibration Airtempl 0 3 16 3 2011 Rotronic HC2 S3 0060599556 foremast Humidity 1 1 0 16 3 2011 Airtemp2 0 3 16 3 2011 Rotronic HC2 S3 0060599558 foremast Humidity2 1 0 16 3 2011 Kipp and Zonen SP PAR Lite 400 110126 foremast port side Parl 5 1 2011 700nm Kipp and Zonen SP PAR Lite 400 110127 foremast port side Par2 5 1 2011 700nm kopp d d foremast starboard Lite2 335 to 004742 112
9. edit nc The edit files were interactively edited using see Appendix C 2 to remove outliers The clean edit files were then copied to use for further processing using matlab copyfile met jc031 dJJJ edit nc met jc031 dJJJ nc f These files were then appended together using mday_02 M_MET met JJJ called from mday 02 run all JJJ to generate a single cruise met file called met 265 01 NB Before further data processing the daily navigation file pos jr265 01 nc must exist and be up to date and the bestnav navigation file must be up to date and include all navigation data covering the time period of the met data see Section 6 See Appendix C 1 for the daily processing schedule Once the basic processing has been carried out running matlab mtruew 01 calculates the true wind speed and direction for 2 minutes averages over the cruise duration The wind direction is defined as the direction the wind is going to rather the meteorological convention of direction coming from Figure 8 2 gives the time series of the 2 minute average meteorological data Only the basic quality control criteria described above have been applied to these data Each page contains five plots showing different variables over a four or five day period 60 15 8 5 L 0 rS t _ 2 o SST zl 331 332 333 334 335 336 N 5 2000 T T T T J 1000
10. 175970 176005 8 8 Dec 16 2008 17 49 08 189407 189442 9 9 Dec 16 2008 17 58 40 203130 203165 10 10 Dec 16 2008 18 02 27 208577 208612 11 11 Dec 16 2008 18 05 01 212280 212315 12 12 Dec 16 2008 18 07 08 215319 215354 13 13 Dec 16 2008 18 09 12 218316 218351 14 14 Dec 16 2008 18 11 14 221245 221280 15 15 Dec 16 2008 18 12 56 223689 223724 16 16 Dec 16 2008 18 14 27 225878 225913 17 17 Dec 16 2008 18 15 59 228075 228110 18 18 Dec 16 2008 18 17 34 230366 230401 19 19 Dec 16 2008 18 18 24 231547 231582 B 3 Instrument calibration constants Numerical values for all of the constants can be found in Appendix B 4 which includes the configuration report for the cruise The final ASCII output file is of the form ctdnn ctm cnv This correction followed the algorithm Corrected Conductivity c where ctm 1 0 b previous ctm a dcdt dt dt temperature previous temperature dcdt 0 1 1 0 006 temperature 20 a 2 alpha sample interval beta 2 and 1 2 with alpha 0 03 and beta 7 0 All processed files were saved to the jrua pstar drive and the ctm cnv ros and bl files also copied to pstar data ctd ASCII FILES The pressure sensor was calibrated following 2 2 1 zx 1 D g J V where P is the pressure T is the pressure period uS U is the temperature in degrees Centigrade D is giv
11. 3500m 03 12 2011 01 20 26 CTD 16 57 73329 56 64278 CTD stopped 3459m 03 12 2011 02 18 26 CTD 16 57 73333 56 64281 03 12 2011 03 36 26 16 57 73332 56 64284 on deck 03 12 2011 05 44 27 CTD 17 58 05115 56 44594 Commence deployment CTD 03 12 2011 05 47 27 CTD 17 58 05109 56 44592 CTD veering to 3900m EA 600 depth 3985m 93 03 12 2011 56 44599 05 50 27 17 58 05092 stopped at 3933m 03 12 2011 07 01 27 CTD 17 58 05094 56 44604 CTD recovered on deck 03 12 2011 08 22 27 Apex 4 58 05095 56 44623 Apex buoy deployed 03 12 2011 10 28 28 CTD 18 58 36668 56 24868 CTD deployed 03 12 2011 10 34 28 CTD 18 58 36667 56 25026 CTD stopped 3876m 03 12 2011 11 45 28 CTD 18 58 36665 56 2502 CTD recovered to deck 03 12 2011 15 08 29 CTD 19 58 68376 56 05403 Commence deploying CTD 03 12 2011 15 11 29 CTD 19 58 68378 56 054 CTD deployed and soaking 03 12 2011 15 13 29 CTD 19 58 68378 56 05402 Veering CTD to near bottom EA 600 depth 3786m 03 12 2011 15 17 29 CTD 19 58 68378 56 0541 CTD stopped at 3730m 03 12 2011 17 19 29 CTD 19 58 68376 56 05401 Commence hauling CTD 03 12 2011 17 21 29 CTD 19 58 68374 56 0541 CTD at surface 03 12 2011 17 33 29 CTD 19 58 68374 56 0541 CTD recover
12. A I Morrison T Pollard and P Taylor 1993 SeaSoar data collected on RRS Discovery Cruise 198 Sterna across Drake Passage and in the Bellingshausen Sea Institute of Oceanographic Sciences Deacon Laboratory Internal Document No 320 59 pp Roether W R Schlitzer A Putzka P Beining K Bulsiewicz G Rohardt and F A Delahoyde 1993 Chlorofluoromethane and hydrographic section across Drake Passage deep waterventilation and meridional property transport J Geophys Res 98 C8 14423 14435 Sparrow M Hawker E J and et al 2005 RRS James Clark Ross Cruise 115 01 Dec 19 Dec 2004 Drake Passage repeat hydrography WOCE Southern Repeat Section 1b Burdwood Bank to Elephant Island Southampton UK Southampton Oceanography Centre 80pp Southampton Oceanography Centre Cruise Report 56 Stansfield K Meredith M and et al 2008 RRS James Clark Ross Cruise 139 05 Dec 12 Dec 2005 Drake Passage Repeat Hydrography WOCE Southern Repeat Section 1b Burdwood Bank to Elephant Island Southampton UK National Oceanography Centre Southampton 72pp National Oceanography Centre Southampton Cruise Report 24 Turner D R 1993 BOFS Sterna 92 Cruise Report Discovery 198 11 11 92 17 12 92 Plymouth Marine Laboratory Plymouth UK 85 pp Watson A JR276 cruise report n prep Williams A Hadfield R E and Quartly G D 2008 RRS James Clark Ross Cruise 163 07 Dec 15 Dec 2006 Drake
13. EA600 depth 364 05 12 2011 15 35 46 CTD 30 61 05012 54 58725 Wire out 345m Commence hauling 05 12 2011 15 45 46 CTD 30 61 05012 54 58725 CTD at the surface 05 12 2011 15 47 46 CTD 30 61 05012 54 58728 CTD recovered on deck 14 12 2011 23 59 47 Wave buoy 11 62 67009 59 8341 Stopped on station ready to deploy wave buoy 15 12 2011 00 07 47 Wave buoy 11 62 67002 59 8334 Wave buoy deployed off starboard quarter 15 12 2011 00 14 47 Wave buoy 11 62 67058 59 83441 Buoy tether fully deployed vessel stopped to drift with buoy 15 12 2011 01 00 47 Wave buoy 11 62 66801 59 82751 V L has moved 052 degrees x 0 25 NM since 2400 UTC Weather dry 3 8 cloud cover 15 12 2011 01 05 47 Wave buoy 11 62 66769 59 82653 Change heading to 275 degrees 15 12 2011 02 00 47 Wave buoy 11 62 66318 59 81618 has moved 048 degrees x 0 46 NM since 0100 UTC Weather dry 1 8 cloud cover 15 12 2011 02 14 47 Wave buoy 11 62 66279 59 81299 steaming 270 degrees at 0 5 knots towing the buoy at 1 0 knots through the water 101 15 12 2011 02 38 47 Wave buoy 11 62 66281 59 8198 stopped Change heading to 000 degrees 15 12 2011 03 00 47 Wave buoy 11 62 66199 59 81827 V L has moved 055 degrees x 0 19 NM since 0100 UTC Weather dry 1 8 cloud cover 15 12 2011 Commence recovering wave buoy vessel headin
14. LD111100000 LF0500 LN016 LP00001 LS1000 LV250 LWI LZ30 220 SMI 5 001 SW05000 CK CS 3 3 Pre Deployment The following steps were completed to test the LADCP and to set it pinging prior to deployment of the CTD at each station The instructions below include notes to record items in the LADCP log sheets Appendix D LADCP should be started just prior to CTD deployment Pre deployment checks and deployment activation only takes 2 minutes or so Make sure k9NT Debug is running on the LADCP PC and the time is set correctly synchronised to CTD PC time with NO daylight savings Open BBTalk connection if not already connected Send a Break End via B icon to establish comms should return BREAK Wakeup A WorkHorse Broadband ADCP Version Teledyne RD Instruments c YYYY YYYY All Rights Reserved gt Select test file File gt Send Script File gt PreDeployTest rds gt File can be found in C LADCP Scripts 1 35 Once file selected and accepted a dialog box for the LOG file appears Create log file associated with respective ADCP being tested 1 e C LADCP JR Logs V jr NNNS log Where 222 is the cruise number NNN is the station number and is either m master s slave or excluded if single LADCP On clicking OK the PredeployTest script will run and a series of tests will be performed Some tests Bandwidth s Transmit Receive may fail due to unit being in a
15. November leaving two full days to mobilise prior to sailing on the morning of the 27 day 331 BAS AME mobilised the hydrographic equipment in good time to train the hydrographic team prior to the ship sailing During the mobilisation period the WAGES team worked hard to ensure that as much as possible was ready before the ship sailed A major problem was found with one of the fundamental WAGES sensors on arrival at the ship the housing of the MotionPak sensor which measures the ship induced motion at the flux sensors on the foremast platform had leaked and the sensor had stopped working a few days previously Seth Thomas BAS AME worked flat out to build new interface circuit boards for this sensor in time for the ship departure from Mare Harbour Figure 1 2 The JR265 and JR254D science team aka the Valkyries arriving at Rothera Left to right Helen Vikki Robin Sarah Mairi Mags Penny 16 1 3 2 WAGES studies and Drake Passage section 27 November 5 December During the hydrographic team worked 12 hour watches 8 til 8 local time with Snaith and Fenton taking the night shift and Holliday and Frith taking the day shift This worked well since the deck crew and winch drivers worked the same watches The WAGES team and the NOC L team worked as appropriate to fit the other science work around the CTD section Below 15 a short day by day account of scientific operations and weather conditions times stated this cru
16. Passage repeat hydrography WOCE Southern Repeat Section 1b Burdwood Bank to Elephant Island Southampton UK Southampton Oceanography Centre 118 Southampton Oceanography Centre Cruise Report 38 Bacon S and et al 2003 RRS James Clark Ross Cruise 81 18 Dec 2002 02 Jan 2003 Drake Passage repeat hydrography WOCE Southern Repeat Section 1b Elephant Island to Burdwood Bank Southampton UK Southampton Oceanography Centre 86 Southampton Oceanography Centre Cruise Report 43 Cunningham S A 2001 RRS James Clark Ross Cruise JR55 21 Nov 14 Dec 2000 Drake Passage Repeat Hydrography WOCE Southern Repeat Section 1b Burdwood Bank to Elephant Island Southampton Oceanography Centre Cruise Report No 35 75 pp Gersonde R 1993 The Expedition Antarktis X 5 of RV Polarstern in 1992 Berichte zur Polarforschung 131 167 pp Hamersley D R C and D Quartly eds 20102 RRS James Clark Ross Cruise 193 29 Nov 8 Dec 2007 Drake Passage repeat hydrography WOCE Southern Repeat Section Ib Elephant Island to Burdwood Bank Southampton UK National Oceanography Centre 75 pp National Oceanography Centre Cruise Report 26 Hamersley D R C and G D Quartly eds 2010b RRS James Clark Ross Cruise 194 12 23 Dec 2008 Drake Passage repeat hydrography WOCE Southern Repeat Section 1b Elephant Island to Burdwood Bank Southampton UK National Oceanography Centre 46 pp National Oceanog
17. To circumvent this the ADCP pinging can be synchronised with the other acoustic instruments using the SSU This issue was investigated in detail on JR218 On JR265 there was a newly fitted 122 swath but this was not used during the transect except when it was turned on to do a brief survey for the deployment of the northernmost NOC L BPR In shallow water the ADCP was set in bottom track mode with varying depths and therefore ping rates The heading feed to the OS75 is the heading from the Seapath GPS unit 4 3 Configuration The OS75 was controlled using Version 1 42 of the RDI VmDas software The OS75 ran in various modes during JR265 narrowband with bottom tracking on and narrowband with bottom tracking off with different maximum depths Table 4 1 While bottom tracking the maximum water depth was set to 800m 50 bins each 16 metres SSU was not used Narrowband profiling was enabled with an 8 metre blanking distance The set modes configuration files as described in JR195 report were used during the cruise see Appendix E for cue cards File Start GMT End GMT Feature Command file 002 331 13 14 332 05 54 Short Fetch Study 250m BT 8m bins NotSSU 008 332 06 05 332 18 17 Deep water test station 800m WT 16m bins NotSSU 009 332 18 17 332 22 59 Burdwood Bank 500m BT 16m bins NotSSU 010 016 332 22 59 339 16 21 SR1b deep water 800m WT 16m bins NotSSU 019 339 16 25 339 20 42 Shallow water 80
18. Yelland 2012a The aim was to deploy the novel spar buoy developed at NOC S to measure wave breaking and whitecap fraction along with an aerial camera system to capture the whitecap coverage across a wider spatial area These deployments take place during cruises which are manned by members of the WAGES team As part of WAGES the JCR was instrumented in the summer of 2010 with the autonomous air sea interaction system AutoFlux Yelland et al 2009b to measure the air sea fluxes of CO2 sea spray aerosol momentum and sensible and latent heat a WAVEX directional wave radar system a webcam mounted on the bridge to capture whitecap fraction These systems measure continuously Previous IOPS and the continuous measurements are described Yelland 2012b WAGES activities during JR254D are summarised here and are described in detail in a separate cruise report Yelland 2012a 1 1 2 Hydrographic Section As described by Bacon and Cunningham 2005 the World Ocean Circulation Experiment established a repeat hydrographic section across Drake Passage and designated it SR1 This section was first occupied by the R V Meteor in 1990 Roether et al 1993 Subsequently the section was moved eastwards to lie on a satellite ground track with the northern end on the south side of Burdwood Bank south of the Falkland Islands and the southern end off Elephant Island at the tip of the Antarctic Peninsula This revised section location was designated SR
19. battery voltage cannot be checked directly due to reverse bias of diode RS232 IN 5232 OUT DATA RTN POWER POWER 5485 RS485B RS232 IN RS232 OUT DATA RTN POWER POWER RS485 B RS485A POWER POWER DATA RTN RS232 OUT RS232 IN POWER POWER DATA RTN RS232 OUT RS232 IN Figure 3 1 Star Cable Connections adi U N 2 2 N RS 232 IN CHARS 485A RS 422 OUT A RS 232 OUT CH A RS 485B RS 422 OUT B CH B RS 485A RS 422 INA CH B RS 485B RS 422 INB COMMUNICATION RETURN POWER POWER 4 1 t 8 Id E p 2 3 1 PA O C C WY af C 414059 VCO T 5 5 7 6 Figure 3 2 Comms Power cable connections The communications cable was passed through the cable duct from the bottle annex where the CTD is stored to the adjacent chemistry lab which housed the LADCP laptop and 34 power supply To test the LADCPs with the comms cable connected to the star cable we ran through the deployment and recovery routines in the BBTalk software see below The LADCP laptop was networked and had its time syncronised with the master clock The configuration command file for the downward looking LADCP used on JR265 contained the following commands 50 CF11101 EA00000 00000 ED00000 ES35 EX11111 EZ0011101 TE00 00 01 00 TP00 01 00 WMI15
20. for some stations carried out during heavy seas 10 11 and 12 the CTD started down from 10 or 12m and there are no surface data The surface data were accessed using the script matlab mctd 05 Which generates files called ctd 1265 surf nc in directory data ocl where NNN is the station number NB if you have a data from number of stations to read in ctd 05 can be run in a loop e g matlab gt gt for stn 1 30 ctd 05 end Now we need to create one file of data so we append them together using matlab gt gt 1265 surf 01 1265 surf f ctd surf files The output file is called ctd 1265 surf 01 and a list of input files in time order was generated using 18 ctd jr265 9 surf nc gt surf files Is 1 ctd 11265 0 surf nc gt gt ctd surf files Next we create a 2minute average file of the underway data using mavrge ocl jr265 01 ocl 1265 01 2minav time 28512001 29375998 120 Where the start and end times are taken from the times in the 1265 01 file Then merge the 2 minute averages onto the ctd 1265 surf 01 file using mmerge ocl jr265 001 merge ctd jr265 surf Ol time press temp temp2 psal psal2 time ocl_jr265_01_2minav time sstemp tstemp conductivity salinity k This gives file ocl jr265 001 merge nc containing all the coincident surface temperature conductivity and salinity data from the CTD and the TSG 9 3 Calibra
21. i e on jrlb 3 ed pstar jr265 data vmadcp jr265_o0s75 48 cshell script in local users pstar cruise data exec vmadcp_movescript redistributes raw data from rawdata to rawdataNNN rawdataNNN is created if necessary may need to edit movescript so that it parses the file names correctly 4 adcptree py jrCCCNNNnbenx datatype enx Note nb for narrowband ping and that the datatype has two dash characters 5 ed jrCCCNNNnbenx copy ina q py ent file Generally you only need to edit the dbname and datadir for each NNN An example q_py cnt file is q_py cnt is comments follow hash marks this is a comment line yearbase 2011 dbname jr265001nnx datadir local users pstar cruise data vmadcp jr265 0s75 rawdata001 datafile_ glob L TA datafile glob ENX instname 0875 instclass os datatype enx auto rotate angle 0 0 pingtype nb ducer depth 5 verbose end of q_py cnt end of q_py cnt At the start of the cruise check yearbase dbname 0875 or 08150 and datatype enx glob ENX Dbname should be of form jrCCCNNNPTT where P is n for narrowband b for broadband The instrument should be operated in narrow unless there is a good reason to choose broad TT is for ENX ns for ENS nr for ENR It for LTA st for STA Standard processing is to process ENX As far as I can tell dbname must not exceed 11 chars So if we use 9 for jr195NNNn there are onl
22. 01 29 40 CTD 27 60 83334 54 72148 CTD deployed 05 12 2011 01 39 40 CTD 27 60 83326 54 72158 CTD veering to approx 1600m 05 12 2011 01 44 40 CTD 27 60 83323 54 72166 CTD stopped at 1579m Finding bottom on echosounder 05 12 2011 02 11 40 CTD 27 60 83324 54 72166 CTD stopped 1729m 05 12 2011 02 33 40 CTD 27 60 83324 54 72169 CTD at the surface 05 12 2011 03 08 40 CTD 27 60 83325 54 7217 CTD recovered to deck 05 12 2011 03 12 41 CTD 28 60 85025 54 71174 Vessel on DP at CTD site 28 05 12 2011 03 32 41 CTD 28 60 85026 54 71174 Commence CTD deployment 05 12 2011 03 34 41 CTD 28 60 85034 54 71149 CTD deployed 05 12 2011 03 38 41 CTD 28 60 85042 54 71112 CTD veering EA600 depth 975m 05 12 2011 03 43 41 CTD 28 60 85043 54 71111 Wire out 978m Commence hauling 05 12 2011 41 CTD 28 60 85042 CTD at surface 98 04 00 54 71112 05 12 2011 04 24 41 CTD 28 60 85042 54 71111 CTD on deck 05 12 2011 04 47 42 Fetch 60 83318 54 72154 Commence Fetch deployment EA600 depth is 1640m vessel heading 306 degrees 05 12 2011 04 59 42 Fetch 60 83315 54 72166 Fetch released 05 12 2011 05 01 42 Fetch 60 83305 54 72195 Hydrophone deployed 05 12 2011 05 04 42 Fetch 60 83304 54 72195 Fetch at a depth of 900m 05 12 2011 05 13 42 Fetch 60 83306 54 7220
23. 11 2011 15 Wave buoy 4 55 83827 V L has moved 085 degrees x 0 33 NM since 1200 UTC Weather occassional light drizzle very 86 12 49 57 81178 slight snow flurries 30 11 2011 13 00 15 Wave buoy 4 55 83948 57 79893 V L has moved 100 degrees x 0 46 NM since 1300 UTC Weather squally passing showers 30 11 2011 14 00 15 Wave buoy 4 55 84071 57 78472 V L has moved 099 degrees x 0 48 NM since 1400 UTC Weather squally passing showers 30 11 2011 15 00 15 Wave buoy 4 55 84074 57 77898 Heading Changed 240Deg 30 11 2011 15 23 15 Wave buoy 4 55 84034 57 77277 Heading changed to 230Deg 30 11 2011 15 48 15 Wave buoy 4 55 84035 57 76925 V L has moved 088 degrees x 0 51 NM since 1500 UTC 30 11 2011 16 00 15 Wave buoy 4 55 8405 57 75679 Hdg 230 091Deg x 0 43nm light snow showers Squally 30 11 2011 17 00 15 Wave buoy 4 55 84046 57 75288 Heading changed 240Deg 30 11 2011 17 16 15 Wave buoy 4 55 84045 57 74603 Changed Heading 235Deg 30 11 2011 17 45 15 Wave buoy 4 55 84039 57 74322 Vessel has moved 090Deg x 0 46nm since 1600UTC V L Hdg 235Deg 30 11 2011 18 00 15 Wave buoy 4 55 83975 57 72761 Vessel has moved 086Deg x 0 53nm since 1700UTC V L Hdg 235Deg 30 11 2011 19 00 15 Wave buoy 4 55 83963 57 7179 Change heading to 245 degrees 30 11 2011 19 32 15 Wave buoy 4 55 8392
24. 2009 updated 13 Oct 2009 updated for jr195 Nov 2009 gmon bim implementation during the 2011 Nov Dec cruise This table shows the sequence for ctd and bottle processing start processing CTD data on nosea2 NOT updated for JR265 see section 2 6 for cd jr195 cd data ctd step script example example comments requires infile s otfiles previous step 1 msam 01 none sam di344 016 nc create empty sam file eg list of vars is in sam 41344 varlist csv variable list file is kept in directory M TEMPLATES 2 mctd 01 ctd di344 016 ctm cnv ctd di344 016 raw nc read in ctd data may need to be edited for exact ctd file name 3 02 ctd di344 016 24hz nc ctd di344 016 24hz nc rename SBE variable names 2 4 metd 03 ctd di344 016 24hz nc ctd di344 016 lhz nc average to 1 hz and calculate psal potemp 3 ctd di344 016 psal nc 5 mdes 01 none des 41344 016 nc create empty dcs file this is used to store information about start bottom and end of good data in ctd file 6 mdes 02 des 41344 016 nc dcs di344 016 nc populate dcs file with data to identify bottom of cast 3 5 7 mdes 03 dcs di344 016 nc dcs 41344 016 nc populate dcs file with data to identify start and end of cast 3 6 ctd di344 016 surf nc 8 mdes 04 dcs di344 016 nc dcs 41344 016 pos nc merge positions onto ctd start bottom end times requires nav file 7 amp nav
25. 2011 17 11 22 Wave Buoy 6 57 0989 57 00719 Wave buoy fully recovered V L move 075Deg x 0 19nm since 1700UTC D P Hdg 268Deg 02 12 2011 17 21 21 CTD 14 57 09888 57 00722 CTD at surface 02 12 2011 17 48 21 14 57 09887 57 00717 CTD recovered to deck 02 12 2011 17 51 24 APEX 3 57 09887 57 00734 Apex Buoy deployed 02 12 2011 57 41549 Vessel on DP commence deployment of wave buoy 92 18 00 56 83109 02 12 2011 20 25 25 Wave Buoy 7 57 41582 56 83167 Wave buoy in the water 02 12 2011 20 29 25 Wave Buoy 7 57 41591 56 83375 Wave buoy deployed off port quarter 02 12 2011 20 35 25 CTD 15 57 41595 56 83301 CTD deployed 02 12 2011 20 43 25 Balloon 3 57 41614 56 82901 Balloon deployed 02 12 2011 21 20 25 CTD 15 57 41605 56 82626 CTD stopped at 3475m 02 12 2011 21 47 25 Balloon 3 57 41604 56 82618 Commence recovery of balloon 02 12 2011 21 48 25 Balloon 3 57 41608 56 82507 Balloon recovered to deck 02 12 2011 21 59 25 Wave Buoy 7 57 41647 56 82241 Commence wave buoy recovery 02 12 2011 22 26 25 Wave Buoy 7 57 41678 56 82094 Wave buoy recovered to deck 02 12 2011 22 36 25 CTD 15 57 41673 56 82094 CTD recovered on deck 03 12 2011 01 07 26 CTD 16 57 73303 56 64388 CTD deployed 03 12 2011 01 15 26 CTD 16 57 73305 56 64383 Veering to approx
26. 2011 21 36 55 52183 58 02038 Alter vessels heading from 265 degrees to 280 degrees 29 11 2011 22 43 13 CTD 9 55 52219 58 02053 CTD stopped at depth 4200m 29 11 2011 22 49 13 Wave buoy 3 55 52497 58 02151 Commence wave buoy recovery 29 11 2011 23 43 13 Wave buoy 3 55 52494 58 02154 Wave Buoy recovered to deck 29 11 2011 23 53 13 CTD 9 55 52495 58 02157 CTD recovered to deck 30 11 2011 00 29 55 8322 57 81839 V L on station on DP 30 11 2011 02 28 14 CTD 10 55 83283 57 81905 CTD deployed Wire jumped off sheave 30 11 2011 02 47 14 CTD 10 55 83383 57 81359 CTD recovered to deck Wire checked no damage 30 11 2011 02 57 14 CTD 10 55 83384 57 81359 Gantry and CTD secure Vessel W O W 30 11 2011 03 09 55 83389 57 81331 Vessel off W O W 30 11 2011 04 30 55 83009 57 82339 Vessel on D P assesing conditions 30 11 2011 06 35 55 83002 57 8209 Decision made that conditions are not workable vessel off DP heave too 30 11 2011 08 13 55 83797 57 82574 V L on DP in preparation for wavex deployment 30 11 2011 10 40 15 Wave buoy 4 55 83803 57 8254 Wave buoy deployed leading off port quarter 30 11 2011 11 22 15 Wave buoy 4 55 83868 57 82134 V L has moved 094 degrees x 0 19 NM since deployment Weather occassional light drizzle 30 11 2011 12 00 15 Wave buoy 4 55 83816 57 81355 Alter vessels heading from 240 degrees to 230 degrees 30
27. 21 1 50 21 59 20 00 55 39 07 3800 2 20 21 1 50 22 59 40 00 55 26 67 3600 2 10 21 1 50 23 60 00 00 55 14 28 3500 2 10 21 1 50 24 60 20 00 55 01 88 3400 2 00 21 1 50 25 60 40 00 54 49 49 3100 2 00 8 4 0 44 26 60 47 97 54 44 55 2500 1 30 2 1 0 11 27 60 49 99 54 43 30 1500 1 00 1 1 0 05 28 60 51 02 54 42 66 1000 0 50 8 2 0 43 29 60 58 86 54 37 80 600 0 30 4 3 0 22 30 61 03 00 54 35 23 400 0 30 4 6 0 24 Table 2 1 Nominal station positions for Drake Passage CTD section the right hand three columns show the estimates of distance and times as used by the bridge NOTE that stations 001 to 009 have been moved to lie along 58 W the positions for these stations are approximate and needed to be adjusted to get the correct depth see Table 2 2 Instructions given to the bridge stated that for the shelf edge stations i e 1 8 and 25 30 inclusive the station should be at a position where the depth is within 100 m of the nominal depth For stations 9 24 inclusive the position should be within 0 5 nm of the nominal position 20 Time CTD max True CTD Lat Lat Lon Lon Wire SB Date hh mm Jday og min W emit pressure wind GMT db m s 900 27 11 11 15 42 331 654 51 47 22 57 52 56 45 46 32 901 28 11 11 13 14 332 551 53 27 70 57 56 79 2350 2389 9 88 1 28 11 11 22 01 332 917 54 47 34 57 59 76 250 254 9 83 2 28 11 11 23 32 332 981 54 54 54 57 59 64 608 617 12 6 3 29 11 11 01 59 333 083 54 58 80 57 58 50 1075 1090 10 8 4
28. 70 80 30 100 Humidityl Figure 8 3 The difference between the humidity sensors Data for day 333 334 shown in red Night time temp 2 C Night time temp 1 Figure 8 4 Airtemp2 vs Airtempl night time temperatures only Data for days 333 amp 334 with slightly higher difference are highlighted in red 63 1111 T 7 Oo cheob d HER EH THIER e 005 denk coo e ee e HHHH HOHE IHH HREM oh He H WE Me Reg a oF HHMI RH dh ge 4 2 ape latalpa HA 3 ot 5 5 gt ae 49 01 2 4 B 8 10 12 14 18 18 20 True Wind Speed m s Figure 8 5 difference in night time air temperatures against true wind speed Data for days 333 amp 334 with slightly higher difference are highlighted in red Throughout the cruise airtemp2 measured consistently higher than airtempl with the mean night time temp difference being 0 05 C airtempl airtemp2 and a st dev of 0 03 C During jday 333 and 334 the offset decreased to 0 008 C with an increase in the st dev to 0 05 C Figure 8 4 shows the relationship of night time temperature from sensor 1 and sensor 2 with the jday 333 334
29. Dec 5 Dec 2011 Battle TSG Salinity after calib e3 Nov 3 Nov 01 0 2 O3Dec 04 Dec 05 Dec 2011 Figure 9 3 Bottle and TSG Salinity before and after conductivity calibration with salinity differences Note y axis on lower plot is 107 As an independent check on the calibration the TSG salinities were also compared to the surface CTD salinities as generated in Section 9 2 above After the TSG salinity data were re calculated from the calibrated conductivity values they were merged onto the surface CTD data and onto the sample bottle data and the residuals calculated The results are shown in Figure 9 4 The difference between the uncalibrated salinity values for the two sensors on the CTD is seen to be greater than the difference between the surface CTD values and the TSG values The rms of the residuals are 0 004 Salcrp Salrso 0007 Salcrp2 Salrsg and 0 006 Salgorrie Salrso 69 0 03 salinity difference pss 78 e 0 02 0 03 10 ARGO FLOAT DEPLOYMENT Helen Snaith and Penny Holliday 29 Nov 10 1 Introduction Six U K Met Office floats were deployed during JR265 Table 10 1 The floats were Full instructions a pre programmed and simply needed to be activated before deployment magnet and transmission detector were supplied in one crate 30 01 Dec 2011 Figure 94 The SBE45 salinity residuals after correcting the salinity data 02 0 03
30. WS 7 to 5 7 5 9 mod mod overcast 21 00 WSW 7 5 7 6 rough rough dry overcast 02 12 2011 00 00 WSW 7 6 5 5 9 rough high overcast 03 00 WSW 6 5 7 5 3 light rain overcast 06 00 260 3 4 2 7 dry overcast 12 00 W 4 3 3 1 4 slight mod dry overcast 15 00 W 4 3 2 1 3 slight mod dry 21 00 W 5 2 4 1 2 dry clear 03 12 2011 00 00 W 4 22 1 2 mod dry fog 06 00 W 5 2 3 14 slight mod fog 09 00 250 4 2 8 1 4 slight slight dry overcast 12 00 SW 2 0 14 slight low dry overcast 18 00 WNW 2 0 4 1 7 slight mod dry 21 00 WNW 2 0 6 1 3 slight slight dry fog 105 04 12 2011 00 00 NNW 3 0 7 11 slight slight broken cloud fog 06 00 NNW 4 1 1 1 slight slight fog 09 00 NW 4 to 5 1 1 1 2 slight slight dry fog 12 00 NNW 5 1 6 1 slight slight showers fog 15 00 NNW 4 ot 5 1 6 1 1 slight slight dry overcast 18 00 330 5 1 4 0 7 slight slight rain showers overcast 05 12 2011 00 00 NNW 4 0 9 1 slight low cloud with fog later 03 00 NNW 4 1 3 1 1 slight slight dry fog 06 00 NNW 2 4 3 0 9 slight low dry fog 12 00 NW 3 1 6 1 slight slight light rain fog 15 00 NNW 3 0 7 1 slight slight rain overcast 15 12 2011 00 00 W 5 2 6 1 1 slight low dry sun clear 03 00 NW 2 to3 3 9 1 slight dry 1 8th cloud 17 12 2011 12 00 W 8 1 2 0 mod dry 18 00 WNW 8 1 5 0 3 slight 21 00 WNW 7 to 8 1 8 0 2 mod slight dry cloud 18 12 2011 00 00 WSW 5 1 5 0 4 slight slight dry overcast 03
31. _ 50 _ 50 _ 50 8 8 8 _ 8 100 100 100 g 100 E 5 v A E 5 5 150 150 150 150 beam 3 weak 200 200 200 200 30 40 50 60 70 0 50 100 150 30 40 50 60 70 0 50 100 150 echo amplidute dB correlaion echo amplidute dB correlaion Figure 3 8 Beam Stats figures for station 008 faulty LADCP and station 009 replacement unit Station jr265008noctd Station jr265009noctd 4 U RED V GREEN blue dots down cast Stat 55 S121833 57 W596891 P U RED V GREEN blue dots down Stat 55 S 30 9378 58 W 1 0142 29 Nov 2011 16 33 43 29 Nov 2011 21 39 03 55 811 9078 57 W 59 2794 End 55 5 31 4960 58 W 1 2929 29 Nov 2011 18 55 03 30 Nov 2011 00 11 57 500 u mean 9 cm s v mean 1 cm s u mean 5 cm s v mean 7 cm s binsize do 10 m binsize up 0 m binsize do 10 m binsize up 0 m mag deviation 0 mag deviation 0 wdiff 0 08 pglim 0 elim 0 2 1000 wdift 0 08 pglim 0 elim 0 2 1000 smoo 0 01 baro 1 bot 0 shear 0 smoo 0 01 baro 1 bot shear 0 weightmin 0 05 weightpower 1 weightmin 0 05 weightpower 1 max depth 3544 m bottom 3588 m max depth 4181 m bottom 4208 m 1500 4 range of instuments m range ol instuments m 1500 Om 0 5 05 2000 J a H EI 3 3 5 15 2000 gs 2500 is c 5 8 25 25 8 2
32. a Meteorological data for days 331 to 336 eee 61 Figure 8 2 b Same plots as in figure 8 2 a for days 336 340 62 Figure 8 3 The difference between the humidity sensors eere 63 Figure 8 4 Airtemp2 vs Airtempl nighttime temperatures only 63 Figure 8 5 Difference night time air temperatures against true wind speed 64 Figure 9 1 TSG remote temperature vs CTD surface temperature measurements 66 Figure 9 2 Bottle and TSG Conductivity with conductivity differences 68 Figure 9 3 Bottle and TSG Salinity before and after conductivity calibration 69 Figure 9 4 The SBE45 salinity residuals after correcting the salinity data 70 ACKNOWLEDGEMENTS I am indebted to the science team for their professionalism and enthusiasm and to Graham Chapman JCR Master for a very successful and memorable cruise The staff of the JCR are a real pleasure to sail with and are always very efficient friendly and helpful Support from the BASE AME and IT staff on board was very much appreciated Special thanks to the three members of the science team who were at sea for the first time Mairi Fenton BAS Rothera volunteered to help the science team and saved my sanity by taking my place on the night watch Vikki Frith Reading University turned into a valuable hydrographer within hours of g
33. and any outliers were interactively selected and set to absent data values This is described in detail in Appendix C 2 NOTE only the depth in meters has been edited During periods when the NOC L team were deploying and recovering Bottom Pressure Recorders BPR the EA600 was put in passive mode This is to prevent the EA600 interfering with the release signal set to the BPR In passive mode the data logged by the SCS system uses the signal from the EM122 swath bathymetry when it is active and is obviously noisy and should be removed using mplxyed After plotting cleaning the sim_jr265_dJJJ_smooth nc files must be copied to sim jr265 dJJJ nc e g copyfile sim 1265 d334 smooth nc sims 1265 d334 nc f The daily position data from the Seapath system were merged on the bathymetry data and the corrected depths calculated from the carter tables using mmerge sim nav This step must be done after the Seapath file has been cleaned Refer to the daily processing table Appendix C 1 gt gt mmerge sim The daily merged files are then appended using mday_02 M_SIM sim JJJ run as part of mday 02 run all JJJ To reset all the files at a particular level to rerun processing from a specific point e g to usea new navigation file in mmerge sim nav from the unix command type unix gt gt foreach file sim 1265 d nc gt cp file r _smooth nc file gt end similarly for resetting to the raw values use c
34. data were merged with the cleaned daily ship s gyro data using mmerge ash gyr JJJ Within this script all data were set to default if the absolute calculated difference between the Ashtech and Gyro headings was more than 5 As the cruise progressed this accounted for large portions of the data and processing was not taken any further 6 3 Generating BestNav file Having generated a series of 1Hz daily cleaned and merged position files a single cruise long 1 Hz file was generated by appending all the daily pos 1265 dJJJ nc files using gt gt 02 POS pos JJJ creating or updating file pos 1265 01 Using the scripts mbest 01 mbest 02 mbest 03 and mbest 04 which can be run together using mbest all this file is processed to generate file bst 1265 01 nc in directory nav bestnav mbest 0 extracts the 30 second average positions from jr265 01 gt 1265 ave nc mbest 02 calculates the speed course and distance run from the 30s average positions gt pos 1265 spd nc mbest 03 generates a 30 s heading file from the gyro headings gt gyr jr265 ave nc mbest 04 merges the averages headings onto the speed course an distance run to generate the bestnav file gt 6 1065 01 nc 6 4 Summary No problems were encountered with the Seapath or gyro Navigation systems during the cruise The Ashtech data proved very unreliable particularly in terms of heading a
35. for completeness The Ashtech was very unreliable on this cruise and the heading information was regularly missing or very inconsistent compared with the ship gyro data and so no further processing was carried out The data from this system are held in data nav ash 6 1 5 Additional Data For completeness the emlog data were converted to matlab but no further processing was carried out 6 2 Routine processing 6 2 1 SEAPATH Data were transferred daily from the SCS system using mday 00 get all JJJ which includes calls to gt gt mday 00 gt gt mday_00 poshdg 7 54 where JJJ is the three figure jday This generated 2 files pos jr265 dJJJ raw nc and poshdg 1265 dJJJ raw nc containing the data for the 4 specified in data nav seapos NB the mday 00 get all script JJJ transfers the wind speed data ocean logger and bathymetry data as well as the navigation data streams All these data streams are processed in a similar manner A table showing the daily processing sequence is in Appendix 1 The raw pos daily file contain time seconds lat degrees long degrees inst time HHMM SS status Blank The raw poshdg daily files contain time seconds heading degrees The data are then cleaned using the script mday 00 clean all JJJ which calls gt gt mpos_O1 JJJ gt gt mhdg 01 JJJ The scripts remove duplicate or backward time steps using mcalc to generate a monotonic flag and mdatp
36. gt gt ctd in NNN 02 incorporates CTD data to LADCP profiles using CTD to calculate exact sound speed etc gt gt exit 13 cd proc Fitd matlab gt gt plist NNN 02 gt gt fd 41 check vertical velocities from ctd and adcp agree gt gt exit 14 final steps proc perl S add ctd prl NNN 02 perl 5 domerge prl cl NNN 02 matlab gt gt plist NNN 02 gt gt do abs gt gt exit cd casts jNNN 02 merge lpr Php4550 duNNN02h ps To simplify the process a script was written on JR195 which will run through steps 3 9 in the initial UH processing pstar jr265 data ladcp uh script3 9 A further script will run through the remaining processing steps once the CTD data has been processed to the appropriate stage pstar jr265 data ladcp uh script uh withctd These short cuts were not used on JR265 because this user preferred to examine the information written to screen at every stage jr1112 j005 02 55 04 S 58 00 W h 1112 006 02 55 09 5 58 00 W h T T T b 006 a 005 500r 1000 1500F Depth m Depth 2000 2500 60 500 F _ 1000F 1500 2000F 2500 L L 60 40 20 0 20 40 V cm s dn up mn 1 1 Depth m 2500 i 1 60 40 20 0 0 40 60 V cm s up mn jr1112 j007 02 55 16 S 58 00 W h p1112 j012 02 56 47 5 57 42 W h T
37. heading 285 degrees V L COG 112 degrees x 0 2nm Buoy Brg 070 degrees 17 12 2011 20 56 51 Wave buoy 12 60 69118 45 53028 Commence recovery of wavex buoy 17 12 2011 21 10 51 Wave buoy 12 60 69116 45 52769 Wavex buoy recovered to deck Table A 1 Scientific events obtained from the bridge log A 2 Bridge weather log date time GMT wind dir force air temp sea temp sea state swell state precip cloud 27 11 2011 15 00 4 11 4 8 5 slight slight overcast 21 00 NNW 6 11 2 8 6 dry clouds forming 28 11 2011 00 00 slight low dry clear 03 00 4 6 8 77 12 00 overcast cloud developing 21 00 5 7 4 6 5 showers 104 29 11 2011 00 00 SW 6 3 6 6 3 mod dry overcast 06 00 SSW 6 3 8 6 2 mod slight rain at times 09 00 SW 6 4 1 5 9 mod dry overcast 15 00 SSW 6 4 1 5 9 mod mod dry overcast 18 00 SSW 4 3 7 5 7 mod mod sleet overcast 30 11 2011 00 00 NW 6 5 3 5 9 mod mod dry overcast 03 00 NW 6 5 1 5 9 mod to high mod to high light rain 09 00 296 8 to 6 6 2 rough mod wet overcast 12 00 232 6 5 5 6 2 mod high overcast 18 00 231 8 4 1 6 1 rough rough overcast 01 12 2011 00 00 SW 8 4 5 6 1 rough high snow overcast 03 00 SW 7 3 7 6 mod to high heavy snow showers overcast 06 00 250 7 4 9 6 mod to rough mod to rough showers overcast 12 00 266 7 4 3 5 9 rough high rain showers overcast 18 00
38. li AN p jl M M 0 pari um l Sm tir W m tir2 331 332 334 335 336 80 paren oC IP ees 60 RH db S 20F _ T humidity humidity2 parot t000 baro2 102C 331 332 333 334 335 336 400 rel wind dir ship hdg true wind dir c S ooo trend Mb cra 5 0 332 332 5 333 333 5 334 334 5 335 335 5 336 TN MA h yt i g 10 Y AU a uu UNUA NT N cmi true ide speed ship speed ship speed 332 332 5 333 333 5 334 334 5 335 335 5 336 Julian Day Figure 8 2 a Meteorological data for days 331 to 336 Top panel air temperatures and sea surface temperature Upper middle panel downwelling radiation from the two shortwave TIR and PAR sensors Central middle panel Atmospheric humidity and atmospheric pressure pressure offset Lower middle panel relative wind direction reldd 180 degrees for a wind onto the bow and true wind direction Note the wind direction is degrees to not the usual convention of degrees from The ship s heading is also shown Bottom panel relative and true wind speeds in m s from the anemometer The ship s speed over the ground is also shown in m s 61 8 T T T T 6r 7 aar 4 Po Xe _ 2r 4 336 341 t E 9 E
39. logging as they are open for writing If there are errors in the data scs raw files not corrected by the sed scripts SCS logging has to be stopped the file edited to remove offending lines and the logging restarted In order to make loading subsets of files acceptably fast in Matlab the scs sed ACO files are converted to Matlab The results are located in local users pstar jr265 data scs mat mat These files be updated at any time in Matlab Ensure m setup has been run then run matlab gt gt update_allmat which will update all the mat files It is not necessary to run this script before doing daily processing as the scripts that access SCS files automatically run the Matlab update first The Underway processing covered 4 main areas 1 Navigation see Section 6 held in local users pstar jr265 data nav seapos data nav seapos local users pstar jr265 data nav gyros data nav gyros local users pstar jr265 data nav ash data nav ash local users pstar jr265 data nav bestnav data nav bestnav local users pstar jr265 data nav tss data nav tss 2 Bathymetry see Section 7 local users pstar jr265 data sim data sim 3 Underway Meteorological Sampling see Section 8 local users pstar jr265 data met surfmet data met surfnmet 4 Underway Temperature Salinity transmittance and Fluorensence see Section 9 local users pstar jr265 data ocl data ocl The processing strategy was the same for all the und
40. off starboard quarter Paying out line 02 12 2011 15 03 22 Wave Buoy 6 57 10178 57 03934 Wave Buoy fully deployed tethered line approx 200m 02 12 2011 15 07 21 CTD 14 57 10184 57 03935 Commence CTD deployment 9 02 12 2011 57 03885 15 13 21 CTD 14 57 10182 deployed and Soaking 02 12 2011 15 17 21 CTD 14 57 10177 57 03791 CTD veering to near bottom EA 600 depth 4237m 02 12 2011 15 20 22 Wave Buoy 6 57 10149 57 03248 Teather transfered to Port quarter 02 12 2011 15 38 23 Balloon 2 57 10144 57 03106 Balloon deployed 02 12 2011 15 43 23 Balloon 2 57 1014 57 03038 Camera attached 02 12 2011 15 46 23 Balloon 2 57 10141 57 03017 Balloon fully deployed 0 31nm x 087Deg since 1500UTC 02 12 2011 15 47 22 Wave Buoy 6 57 10127 57 02757 V L on D P Hdg 268Deg 02 12 2011 16 00 21 CTD 14 57 10067 57 02086 Wire out 3870m Commence hauling EA600 depth 3913m 02 12 2011 16 28 23 Balloon 2 57 10062 57 02039 Commence balloon recovery 02 12 2011 16 30 23 Balloon 2 57 10031 57 01796 Camera detached 02 12 2011 16 40 23 Balloon 2 57 10027 57 01769 Balloon fully recovered 02 12 2011 16 41 22 Wave Buoy 6 57 09964 57 0128 Vessel moved 078 T x 0 50nm Hdg 268deg since 1600UTC 02 12 2011 17 00 22 Wave Buoy 6 57 09946 57 00938 Commence wave buoy recovery 02 12
41. since 1300 UTC 89 01 12 2011 57 31495 13 58 15 Wave buoy 4 55 74566 Wave Buoy broken in two during recovery bottom section recovered to deck 01 12 2011 14 15 15 Wave buoy 4 55 74568 57 31492 V L off DP Proceeding to CTD 10 to assess conditions 01 12 2011 14 31 16 CTD 10 55 83452 57 83101 Vessel on D P assessing conditions 01 12 2011 18 06 16 CTD 10 55 8347 57 82929 Vessel on D P assessing conditions 01 12 2011 18 11 16 CTD 10 55 8348 57 8296 Commence deployment of CTD 01 12 2011 18 36 16 CTD 10 55 83472 57 82911 CTD deployed and soaking 01 12 2011 18 41 16 CTD 10 55 83413 57 82494 CTD veering to 4700m EA600 depth 4739m 01 12 2011 18 44 16 CTD 10 55 83206 57 81231 CTD stopped at 4720m 01 12 2011 20 09 16 CTD 10 55 82886 57 79325 CTD recovered to deck 01 12 2011 22 02 56 14969 57 62291 V L on DP 02 12 2011 00 51 17 CTD 11 56 14998 57 62388 CTD deployed 02 12 2011 01 05 17 CTD 11 56 14972 57 6224 Veering to approx 3400m 02 12 2011 01 09 17 CTD 11 56 14505 57 59586 CTD stopped 3489m 02 12 2011 02 10 17 CTD 11 56 13989 57 56989 CTD at surface 02 12 2011 gt 03 18 17 CTD 11 56 13966 57 56874 CTD recovered to deck 02 12 2011 03 20 18 APEX 2 56 13938 57 56729 Commence deployment Apex Bouy 02 12 2011 03 27 18 APEX 2 56 19564 57 50141 Apex
42. station 030 in the south These are data prior to final quality control and calibrations Preliminary calculations suggest that the geostrophic transport across the section was 133 0 Sv 29 PntTemp ag d 500 MR des Figure 2 1 Potential temperature across JR265 Drake Passage section 5060 e 1000 I 1500 Depth dbar ha gt gt c na 3000 HP 3500 c 40060 Salinity PSU 400 500 70D Distance km 500 1000 1500 gt o Depth dbar 3000 3500 4000 4500 Figure 2 2 Salinity PSU across JR265 Drake Passage section 30 Density kom 1027 75 500 1000 1027 5 1500 2000 Depth dbar 3000 3500 1027 4000 4500 Distance km Figure 2 3 Density across JR265 Drake Passage section Oxygen micromol kag 300 500 1000 1500 250 n3 c o n3 c o Depth dbar 3000 d s 5500 4000 150 4500 100 200 300 400 500 00 700 Distance km Figure 2 4 Nominally calibrated dissolved oxygen concentration umol kg across JR265 Drake Passage section 31 3 Fluorescence mg m 0 20 30 40 a c 50 E 60 Q au 100 Distance km Figure 2 5 Nominally calibrated chlorophyll fluorescence mg m in top 100m across JR265 Drake Passage section The distribution shows much patchines
43. the non toxic supply e Salinometer operations completed by the person operating the Autosal salinometer e Underway log sheet completed by the person performing watchkeeping checks 122 CTD Sampling Deck Log for JR265 Drake Passage 2011 Station Date Julian Day Operator Water depth 600 Deck Pressure db Start End Start Lat S Start Lon W Time in water Time start down Time at bottom Wire Out m Pressure db Altimeter m Time start up Time inboard End Lat S End Lon W Rosette Niskin Actual Pressure Temp Salinity Expected Actual Comments Num Bottle 1 db C Niskin to Niskin expected wire out Num m samlpe sampled pre cast 1 1 2 2 3 3 4 4 5 5 6 6 7 7 8 8 9 9 10 10 11 11 12 12 13 13 14 14 15 15 16 16 17 17 18 18 19 19 20 20 21 21 22 22 23 23 24 24 Salts sample crate number Sea Ice obs colour 123 JR265 NISKIN sampling log sheet CRATE IDENTIFIER colour code of bottles and or number CTD operator to fill in columns 2 and 3 SAMPLER to fill in columns 1 and 4 Once crate is full move to BIO LAB and NOTE DATE AND TIME SAMPLE NUMBER STATION NISKIN BOTTLE COMMENT label on bottle NUMBER NUMBER Niskin etc
44. this step is done twice the cal is applied twice when you have done the edits and applied the time varying heading adjustment After inspecting the cal out files and deciding what the amplitude and phase of the calibration should be quick adcp py cntfile q_pyrot cnt note two dashes before cntfile where q_pyrot cnt contains q_pyrot cnt is comments follow hash marks this is a comment line yearbase 2011 rotate_angle 1 0564 rotate_amp 1 0116 steps2rerun rotate navsteps calib auto end of q_pyrot cnt Final calibration values used were those given by the JR265 Bottom Track data 13 In each directory re create Matlab files gt gt cd local users pstar cruise data vmadcp jr265_0s75 jr265NNNnbenx gt gt mcod_01 gt gt mcod_02 Then remove and recreate the appended matlab file gt gt cd local users pstar cruise data vmadcp jr265 0875 gt gt bin rm 0875 jr265nnx 01 nc gt gt mcod_mapend 51 555 a 56 E 4 85 7 N 574 58 L 4 Lat es 58 5 x M 9f 595 Y N X 82 4 ft 4 lt 1 1 1 L 1 1 J 301 5 302 3025 303 3035 304 3045 305 3055 Lon boo 300 5 301 301 5 r7 302 5 303 Lon Figure 4 1 Calibrated surface currents from a Drake Passage section b short fetch study Falklands Is and c Livingston Is Note that the length of the sticks is not consistent from one plot to another S
45. to Signy again arriving around 16 30 local time the same day The ship had to stay at Signy while technical staff worked on the new V SAT system so on the 19 the science teams had the chance of a walk to Gourlay Point to see Adelie and Chinstrap colonies Ship sailed evening of the 19 and headed towards Bird Island via the Lewthwaite Strait Arrived Bird Island around 1300 local on the 215 No run ashore because of danger from fur seals and the need to make the visit a short one so ship departed about 15 30 local and headed for Stanley One short stop was made on the morning of the 2214 for another test of the NOC L Sonar bell and a short CTD dip so that the BAS AME staff could test the software changes made at the end of the cruise that were necessary to implement the updated Seasave and SBE Data Processing software version 7 JCR arrived in Stanley on the afternoon of the 24 2 CTD Vikki Frith 2 1 Introduction A Conductivity Temperature Depth CTD unit was used to record vertical profiles of the temperature and salinity of the water column Two test stations one shallow 900 and one deep 901 were carried out before starting the Drake Passage transect They allowed us to test the equipment and sensors configuration Thirty stations were occupied across the Drake Passage SR1b transect The locations of the nominal stations across Drake Passage are listed in Table 2 1 The actual locations of the stations occupied during JR265 alongsi
46. unit had a high percentage of 3 beam solutions Table 3 1 with higher values on deeper stations Similarly in the pre deployment checks the PT200 test showed beam 3 to have significantly larger values for the High Gain RSSI Good quality VM ADCP data exists for these stations and those data should be used in preference to the LADCP data Cast No 3 bm solution High Gain RSSI value from pre deployment PT200 test beam 1 beam2 beam3 beam4 901 36 73 76 100 76 001 0 74 77 101 77 002 31 75 79 101 78 003 32 75 7 99 78 004 32 74 78 101 79 005 34 76 77 102 79 006 35 75 72 101 79 007 37 76 76 100 78 008 40 75 76 99 78 009 0 new unit 36 40 42 38 Table 3 1 Indication of a failing beam percent of 3 beam solutions and High Gain RSSI values 4 VESSEL MOUNTED ACOUSTIC DOPPLER CURRENT PROFILER Penny Holliday 4 1 Introduction A 75 kHz RD Instruments Ocean Surveyor OS75 model 71A 1029 00 SN 2088 ADCP was used during this cruise This has also been used on JR139 in Dec 2005 Chief Scientist Stansfield JR161 Oct Dec 2006 Shreeve JR165 Feb 2007 Shoosmith JR193 Dec 2007 Quartly JR177 Jan 2008 Tarling JR218 Oct 2008 Woodward and JR200 Mar 2009 Korb JR195 Dec 2011 Yelland The 0575 is capable of profiling to deeper levels in the water column than the previous 150 kHz ADCP and can also be configured to run in either narrowband or broadband modes 4
47. variables e ctd jr265 NNN 2db nc a 2 db file of the downcast with all variables sam jr265 NNN nc a bottle sam file containing upcast data at bottle firing time and bottle salinity data jr265 cordep txt containing corrected water depth data extracted from the LADCP processed files for each cast 2 7 Calibrations 2 7 1 Pressure Pressures on deck were logged at each start and end of cast No correction was required 2 7 2 Temperature Initial comparison was made between the primary and secondary sensors The agreement between the two sensors was excellent the mean difference and one standard deviation were T1 T2 0 000007 0 000288 2 7 3 Salinity Initial comparisons were made between the conductivities and derived salinities from the primary and secondary conductivity sensors the agreement was good Mean differences and one standard deviation between the primary and secondary sensors were as follows 2 0 0071 0 0022 mS cm 51 62 0 0088 0 0008 PSU At the end of the cruise when the salinity bottle samples had all been merged into the sample files and residuals calculated see Phase 4 in section 2 6 above the final salinity calibration was made S1 and S2 First visually examine the differences between the bottle and CTD salinity plotting the residuals against pressure and time to look for any trends and outliers This is most easily done by appending all the residual files into one mstar file map
48. 0 CTD 1 TSG CTD 2 TSG Bottle TSG 04 0 05 Dec All 6 floats were deployed successfully and their deployment reported to Brian King NOC and Jon Turton Met Office Argo Float Date Jday Time Time CTD Lat S Lon W Number Serial Activated deployed Station Number GMT GMT Number ARGOI 4900 29 11 11 333 14 20 15 54 CTD 007 55 09 45 058 00 00 ARGO2 4901 02 12 11 336 02 33 03 35 CTDO011 56 08 40 057 34 25 ARGO03 4902 02 12 11 336 16 26 17 56 CTD 014 57 05 93 057 00 43 ARG04 4903 03 12 11 337 07 13 08 35 CTD 017 58 03 10 056 26 80 ARGO05 4999 03 12 11 337 21 09 22 24 CTD 020 59 00 00 055 51 80 ARG06 4998 04 12 11 338 10 51 11 55 CTD 023 59 59 96 055 14 33 Table 10 1 JR265 ARGO Float Deployment details 10 2 Deployment procedure A Prepare Float Get float crate on deck and opened a few hours before deployment Leave float in crate until deployed if possible 70 Remove plastic the sensor and 3 labeled plugs Keep grease oil away from the sensors B Activate Float Record the float serial number on the checklist Place transmission detector between sensor and aerial you can hang it over the aerial Hold the supplied magnet against the RESET location on the case for approx 5s e After approx 10s you should hear 6 beeps each of 3s 8s apart Ifyou don t hear
49. 0 depth 3623m 29 11 2011 Tether switched to STBD side D P current 221deg x 1 8Kts Wind 230deg x 19Kts Ships HDG 16 43 11 Wave Buoy 2 55 20217 57 99412 235deg 29 11 2011 16 53 12 CTD 8 55 19975 57 99031 CTD all stopped wire out 3550m 29 11 2011 17 44 12 CTD 8 55 19963 57 99001 Commence hauling CTD 29 11 2011 17 47 11 Wave Bouy 2 55 19873 57 98874 Sleet Wind 239deg x 15Kts D P current 223deg x 1 8Kts 29 11 2011 18 17 11 Wave Buoy 2 55 19876 57 98856 Sleet passed now dry 29 11 2011 18 20 11 Wave Buoy 2 55 1985 57 98803 Commence W Buoy recovery 29 11 2011 18 26 11 Wave Buoy 2 55 19845 57 98798 Wave buoy fully recovered Vessel moved 040 T x 0 37nm whilst wave buoy deployed 29 11 2011 18 31 12 CTD 8 55 19845 57 9879 CTD at surface 29 11 2011 18 58 12 CTD 8 55 19848 57 98794 CTD on deck 29 11 2011 19 08 13 Wave buoy 3 55 51486 58 01071 Commence deployment of Wave Buoy 29 11 2011 21 09 55 51529 58 01651 Vessel on DP 29 11 2011 21 18 13 Wave buoy 3 55 5151 58 01403 Wave buoy deployed leading off starboard quarter 29 11 2011 21 19 13 Wave buoy 3 55 51519 58 01569 Transfered wave buoy to port quarter 29 11 2011 21 22 13 CTD 9 55 51527 58 01652 Commence deployment of CTD 85 29 11 2011 58 01671 21 30 13 9 55 51537 deployed 29 11
50. 00 SW 5 06 1 0 1 slight slight dry Table A 2 Bridge weather observations for the Drake Passage section and subsequent WAGES deployments 106 APPENDIX B JR265 CTD INSTRUCTIONS B 1 CTD deck unit setup processing and data transfer Pre sail checks CTD unit configuration Make a list of the sensors with serial numbers deployed on the CTD frame Cross check with list provided by BAS technician Highlight any discrepancies CON file checks 1 Once the configuration of the CTD package is known the SeaBird configuration master file needs to be checked or written from new For JR265 the CTD configuration had been used previously so the default CON file was used Open SeaSave and under the Configure menu go to New Instrument Configuration Click Create new or Modify depending on whether or not you already have a CON file to edit If creating from existing config save the new configuration under a new name using Save as In addition to the list of sensors deployed on the frame and their serial numbers you will need the sensors calibration sheets and the mapping between voltage ports V0 V1 V2 V7 and the ancillary sensors or for conductivity and temperature whether the sensor is used as primary or secondary sensor Remove any unused sensor setup and ensure that all sensors on the CTD frame are represented in the CON file Enter the new serial numbers calibration date and calibration
51. 001 I 5 83630963e 004 J 5 65767279 005 3 2500e 006 CPcor 9 57000000e 008 Slope 1 00000000 Offset 0 00000 6 A D voltage 0 PAR Irradiance Biospherical Licor Serial number 7235 Calibrated on 12 07 2010 M 1 00000000 B 0 00000000 Calibration constant 38610038610 04000100 Multiplier 1 00000000 Offset 0 03666484 7 A D voltage 1 Free 8 A D voltage 2 Fluorometer Chelsea Aqua 3 Serial number 088 249 Calibrated on 13 11 2007 VB 0 181700 Vi 2 097600 Vacetone 0 202800 Scale factor 1 000000 Slope 1 000000 Offset 0 000000 9 A D voltage 3 Free 10 A D voltage 4 Transmissometer WET Labs C Star Serial number CST 1279DR Calibrated on 26 08 2009 M 22 4505 B 1 4144 Pathlength 0 250 11 A D voltage 5 Free 12 A D voltage 6 Oxygen SBE 43 Serial number 0242 Calibrated on 21 01 09 Equation Sea Bird Soc 4 16500e 001 Offset 4 97900e 001 A 9 13570e 004 B 1 62030e 004 C 2 34710e 006 E 3 60000e 002 112 Tau20 DI D2 HI H2 H3 1 20000e 000 1 92634e 004 4 64803 002 3 30000e 002 5 00000 003 1 45000e 003 13 A D voltage 7 Altimeter Serial number 2130 27001 Calibrated on 10 11 2006 Scale factor 15 000 Offset 0 000 113 B 5 Details of MSTAR processing NB The file MUST contain the scan number and pressure temperature as one of the output variables 3 Feb
52. 0m BT 16m bins NotSSU Elephant Island 020 348 01 08 348 20 38 Shallow water 500m BT 16m bins NotSSU Livingston Island 021 351 13 31 352 11 14 Shallow water Signy 500m BT 16m bins NotSSU Table 4 1 ADCP set up modes during JR265 Reducing the maximum water depth to less than twice the actual water depth as measured by the EA600 has two significant advantages see JR218 report for full details Firstly it speeds up the ping rate as the instrument spends less time waiting for echoes The second advantage is that the instrument stops listening before it can hear double bottom echoes sounds that goes transducer bottom surface bottom transducer This leads to cleaner plots of the water column velocities Note however that if you choose a variety of maximum water depths the files produced by the CODAS processing need a bit of tweaking before they can be appended see step 11 Salinity at the transducer was set to zero and Beam 3 misalignment was set to 60 08 degrees Data logging was stopped and restarted once a day to keep files to a manageable size for processing 46 4 4 Outputs The ADCP writes files to a network drive that is samba mounted from the Unix system The raw data ENR and N1R are also written to the local PC hard drive For use in the matlab scripts the raw data saved to the PC would have to be run through the VMDas software again to create the ENX files When the Unix system 15 accessed via samba fro
53. 1 14 03 49 APEX Recovery 60 62591 51 98377 V L off DP Proceeding to last received PSN 16 12 2011 49 APEX Recovery 60 63678 V L on DP Searching for buoy 102 14 29 51 96164 16 12 2011 14 56 49 APEX Recovery 60 63322 51 95017 Buoy sighted 7 points off stbd bow Approx 80m off 16 12 2011 15 02 49 APEX Recovery 60 63144 51 94695 Buoy alongside Commence recovery attempting to catch with net 16 12 2011 15 40 49 APEX Recovery 60 62393 51 92452 APEX buoy hooked and recovered onboard V L stopped on D P 16 12 2011 15 54 50 Sonar Bell 60 62348 51 92344 Commence deploying Sonar Bell 16 12 2011 15 57 50 Sonar Bell 60 62347 51 92353 Sonar Bell deployed veering to 1000m 16 12 2011 16 23 50 Sonar Bell 60 62304 51 923 stopped at 1000m EA600 depth 3665m 16 12 2011 16 31 50 Sonar Bell 60 6228 51 92277 Cable veering further 500m to total of 1500m 16 12 2011 16 40 50 Sonar Bell 60 62254 51 92244 stopped at 1500m 16 12 2011 16 43 50 Sonar Bell 60 62251 51 92242 commence hauling sonar bell 16 12 2011 17 01 50 Sonar Bell 60 6221 51 92184 Cable stopped at 500m 16 12 2011 17 03 50 Sonar Bell 60 62206 51 92176 Re commence hauling to 250m 16 12 2011 17 07 50 Sonar Bell 60 62198 51 92163 Stopped hauling at 250m 16 12 2011 17 13 50 Sonar Bell 60 62184 51 92
54. 1 Fetch on seabed and hydrophone recovered 05 12 2011 05 29 60 83304 54 72198 Vessel off DP 05 12 2011 06 04 43 BPR 1 60 82514 54 72183 Vessel on D P for BPRI deployment 05 12 2011 06 20 43 BPR 1 60 82493 54 722 Commence deploying 1 05 12 2011 06 32 43 BPR 1 60 82493 54 7221 BPR released EA600 depth 920m ish 05 12 2011 06 34 43 BPR 1 60 82491 54 72207 BPR at depth 520m 05 12 2011 06 44 43 BPR 1 60 82492 54 72209 BPR on seabed 05 12 2011 07 10 43 BPR 1 60 82491 54 72209 V L off D P commencing boxing in of BPR 05 12 2011 07 14 43 BPR 1 60 82333 54 72268 Finished boxing in of BPR 05 12 2011 07 40 43 BPR 1 60 82821 54 72317 V L on D P talking to BPR 05 12 2011 07 50 43 BPR 1 60 82847 54 72464 BPR released 05 12 2011 08 01 43 BPR 1 60 82851 54 72496 FETCH sighted at surface 99 05 12 2011 54 72633 08 51 43 BPR 1 60 82798 FETCH grapeled 05 12 2011 09 05 43 BPR 1 60 82774 54 72665 FETCH buoy on deck 05 12 2011 09 06 43 BPR 1 60 82039 54 73124 BPR sighted 05 12 2011 09 18 43 BPR 1 60 81878 54 72873 BPR grapeled 05 12 2011 09 28 43 BPR 1 60 81724 54 72817 BPR recovered to deck 05 12 2011 09 37 44 BPR 2 60 85241 54 70429 V L stopped on D P at BPR 2 site 05 12 2011 10 03 44 BPR 2 60 85288 54 70502 BPR released E T A to sur
55. 1 13 15a mwin 01 techsas files win di344 016 nc times extracted from start and end of ctd 1hz file plus 10 minutes at 4 either end 15 mwin 03 fir di344 016 time fir di344 016 winch nc merge winch wireout onto fir file only relevant 1f winch data 12 amp 15a win di344 016 nc available 16 mwin 04 fir di344 016 winch nc sam di344 016 paste win fir data into sam file 1 15 17 msal 01 none sal di344 016 read in the bottle salinities 18 msal 02 sal 41344 016 nc sam di344 016 nc paste sal data into sam file 1 17 19 msam 02 sam di344 016 nc sam di344 016 resid nc calculate residuals in sam file 14 18 115 APPENDIX C UNDERWAY DATA PROCESSING Helen Snaith C 1 Daily underway data processing schedule Note that these steps need to be done in the order listed here Run m setup first script calls input file s output file s Comments d oll ACO nav seapos pos 265 dJJJ raw pos scs sed seapos g pestis scs sed seapos hdt ACO nav seapos poshdg jr265 dJJJ r updates nda n eta aw nc scs mat mat ia m des sed gysrA C nav gyros gyr jr265 dJJJ raw n files for all streams dida OO instr ash scs sed ashtech ACO nav ash ash jr265 dJJJ raw nc converted given m chf scs sed emlog vhw ACO chf chf 265 dJJJ raw nc stre
56. 139 Re commence hauling 16 12 2011 17 18 50 Sonar Bell 60 62177 51 9212 Sonar bell at surface 16 12 2011 17 20 50 Sonar Bell 60 62172 51 92116 Sonar bell recovered to deck 17 12 2011 13 18 60 69543 45 55697 V L on DP for deploying wave buoy 17 12 2011 13 50 51 Wave buoy 12 60 69535 45 56706 Buoy deployed over STBD quarter 103 17 12 2011 45 56885 13 58 51 Wave buoy 12 60 69535 Tether fully deployed Weather dry 7 8 cloud cover 17 12 2011 15 00 51 Wave buoy 12 60 69424 45 56282 V L has moved 067 degrees x 0 18 NM since 1358 UTC Weather dry 7 8 could cover 17 12 2011 16 00 51 Wave buoy 12 60 6924 45 55673 Vessel moved 059 T x 0 20nm Dry Hdg 270 T since 1500UTC Buoy brg 070 T 17 12 2011 16 23 51 Wave buoy 12 60 69149 45 55494 Changed Heading 295 T 17 12 2011 17 00 51 Wave buoy 12 60 69017 45 5516 Vessel has moved 050 x 0 20nm since 1600UTC V L Hdg 295 T Dry Buoy brg 076 T 17 12 2011 18 00 51 Wave buoy 12 60 68865 45 54737 Vessel has moved 051 x 0 15nm since 1700UTC V L Hdg 295 T Dry Buoy brg 080 T 17 12 2011 18 17 51 Wave buoy 12 60 68827 45 54599 Change heading 285 T 17 12 2011 19 00 51 Wave buoy 12 60 68932 45 54302 Vessel has moved 109 T x 0 14nm since 1800UTC V L Hdg 285 T Dry Buoy brg 090 T 17 12 2011 20 00 51 Wave buoy 12 60 69066 45 53652 Vessel
57. 1b and was first occupied by the R V Polarstern in 1992 Gersonde 1993 The first UK occupation of SRIb took place on RRS Discovery later the same year using SeaSoar a profiler which undulates between the surface and 400 m Turner 1993 Read et al 1993 only i e no CTD profiles Between that time and the present there have been 16 UK NOCS BAS complete occupations of SR1b at nearly one section per year all with full depth CTDs and since 1996 with full depth LADCP also See Table 1 1 for a list of cruises dates and references The scheduling of the cruises usually makes use of the BAS logistical requirement to re supply the base at Rothera at the start of the austral summer hence all bar two have taken place on the RRS James Clark Ross JCR 13 start date end date designator LADCP cruise report 1992 11 11 1992 17 12 1992 D198 SeaSoar only N Turner 1993 1993 20 11 1993 18 12 1993 JROa or JROO 1 N Bacon and Cunningham 2005 1994 13 11 1994 12 12 1994 JROb or JROO 2 N Bacon and Cunningham 2005 1996 13 11 1996 07 12 1996 JR16 Y Bacon and Cunningham 2005 1997 17 12 1997 08 01 1998 JR27 Y Bacon and Cunningham 2005 1999 12 02 2000 16 02 2000 JR47 N Bacon and Cunningham 2005 2000 21 11 2000 14 12 2000 JR55 Y Cunningham 2001 2001 19 11 2001 17 12 2001 JR67 Y Bacon et al 2002 2002 18 12 2002 02 01 2003 JR81 Y Bacon et al 2003 2003 27 11 2003 17 12 200
58. 2 showers 01 12 2011 06 00 15 Wave buoy 4 55 80338 57 52224 Changed Heading 255Deg 01 12 2011 06 12 15 Wave buoy 4 55 79785 57 50518 moved 062Deg x 0 77nm HDG 255Deg Light rain 01 12 2011 07 00 15 Wave buoy 4 55 79549 57 49798 Change heading to 250degrees 01 12 2011 07 17 15 Wave buoy 4 55 79097 57 48082 Vessel moved 063 degrees x 0 94nm in last hour 01 12 2011 08 00 15 Wave buoy 4 55 7889 57 47153 Teather transfered to starboard quarter 01 12 2011 08 22 15 Wave buoy 4 55 78588 57 45375 Vessel moved 073 degrees x 0 97 nm in last hour 01 12 2011 09 00 15 Wave buoy 4 55 78549 57 45187 Change heading to 260degrees 01 12 2011 09 04 15 Wave buoy 4 55 78236 57 43709 Change heading to 250 degrees 01 12 2011 09 38 15 Wave buoy 4 55 77974 57 42343 Change heading 260 degrees 01 12 2011 10 11 15 Wave buoy 4 55 77844 57 41952 Change heading 255 degrees 01 12 2011 10 21 15 Wave buoy 4 55 77507 57 40342 Vessel moved 068 degrees x 0 85 nm 01 12 2011 11 00 15 Wave buoy 4 55 76753 57 37509 V L has moved 063 degrees x 1 06 NM since 1100 UTC Weather showers seen not at station 01 12 2011 12 00 15 Wave buoy 4 55 75748 57 34463 has moved 060 degrees x 1 17 NM since 1200 UTC Weather passing moderate showers 01 12 2011 13 00 15 Wave buoy 4 55 7464 57 31573 Commence recovery of wave buoy V L has moved 055 degrees x 1 24 NM
59. 2 57 71562 Change heading to 240 degrees 30 11 2011 19 39 15 Wave buoy 4 55 83904 57 70975 Vessel moved 086 degrees x 0 63nm in last hour 30 11 2011 20 00 15 Wave buoy 4 55 83774 57 68916 Vessel moved 085 degrees x 0 67 nm in last hour 30 11 2011 21 00 15 Wave buoy 4 55 83712 57 67924 Change heading to 230degrees 30 11 2011 21 31 15 Wave buoy 4 55 83674 57 67351 Change heading 240 degrees 30 11 2011 21 48 15 Wave buoy 4 55 83648 57 66989 Vessel moved 083 degrees x 0 67 nm in last hour 87 30 11 2011 22 00 15 Wave buoy 4 55 83514 57 65213 Vessel moved 083 degrees x 0 60 nm in last hour 30 11 2011 23 00 15 Wave buoy 4 55 83512 57 65117 Change heading 250 degrees 30 11 2011 23 03 15 Wave buoy 4 55 83407 57 64469 Change heading 245 degrees 30 11 2011 23 15 15 Wave buoy 4 55 83427 57 64713 Change heading 240 degrees 30 11 2011 23 18 15 Wave buoy 4 55 83284 57 63221 V L has moved 078 degrees x 0 66 NM since 2300 UTC Weather squally wintry showers 01 12 2011 00 00 15 Wave buoy 4 55 83179 57 62645 Change heading to 230 degrees 01 12 2011 00 15 15 Wave buoy 4 55 82913 57 61454 Change heading 240 degrees 01 12 2011 00 46 15 Wave buoy 4 55 82777 57 60914 V L has moved 069 degrees x 0 88 NM since 2400 UTC Weather squally wintry showers 01 12 2011 01 00 15 Wa
60. 2 6 T S plot for Drake Passage section 2 1 4 0 eene en setenta ann 32 Figure 2 7 Geostrophic velocity on Drake 33 11 Figure 3 1 Star Cabl Connections sessessoesoossessoesoossoesoesoossoesoesooesoesoesooesoesoesooesoesseseossoe 34 Figure 3 2 Comms Power cable connections eese eese eene nennen tenen seta 34 Figure 3 3 Deck Test with weak Beam 3 Intensity offset with high counts 38 Figure 3 4 Data close to bottom showing Intensity offset and poor correlation 38 Figure 3 5 Correctly functioning unit with 1 2212 4 4 0 eene 39 Figure 3 6 Close to bottom Profiles eese esee eee eene eene en seen netta tnn astu asino 39 Figure 3 7 Velocity profiles generated by the UH processing 42 Figure 3 8 Beam Stats figures for station 008 and station 009 44 Figure 3 9 Velocity profiles for station 008 and station 009 44 Figure 4 1 Calibrated surface currents eese eee 32 Figure 7 1 Depth profile vs latitude icone S8 Figure 8 1 Schematic of the sensor positions on the foremast S9 Figure 8 2
61. 2 Instrumentation The OS75 unit is sited in the transducer well in the hull of the JCR This is flooded with a mixture of 90 de ionised water and 10 monopropylene glycol With the previous 150 kHz unit the use of a mixture of water antifreeze in the transducer chest required a post processing correction to derived ADCP velocities However the new OS75 unit uses a phased array transducer that produces all four beams from a single aperture at specific angles A consequence of the way the beams are formed is that horizontal velocities derived using this instrument are independent of the speed of sound vertical velocities on the other hand are not hence this correction is no longer required 45 The 75 transducer on the JCR is aligned at approximately 60 degrees relative to the centre line This differs from the recommended 45 degrees Shortly after sailing for JR139 the hull depth was measured by Robert Patterson Chief Officer and found to be 6 47m Combined with a value for the distance of the transducer behind the seachest window of 100 200mm and a window thickness of 50mm this implies a transducer depth of 6 3m This is the value assumed for JR200 but note that the ship was very heavily laden during cruise JR139 and for other cruises it may be shallower During the trials cruise JR139 it was noted that the OS75 causes interference with most of the other acoustic instruments on JCR including the 120 swath bathymetry system
62. 25 the pumps took around 5 minutes After a 3 minute soak the package was raised to just below the surface and then continuously lowered at a speed of about 60 m min to a nominal 10 m above the seabed Due to large swell on station 010 the CTD was taken straight down after the pumps activated Three bottles were fired 30 seconds after reaching the bottom of the downcast with a 10 second wait between each bottle firing to allow for power recharge of the firing mechanism and the 8 second reading from the SBE 35 temperature probe Subsequent Niskin bottles were fired during the upcast with identical waiting times The detailed procedure for CTD casts used during this cruise is given in Section 2 4 below Bottles were fired at 3 to 6 depths with 2 bottles fired at each depth Water was only sampled for salinity analysis to calibrate the conductivity sensors so sampling depths were therefore selected according to the shape of the salinity profile avoiding strong gradients Data logging was stopped when the CTD was back on deck but the deck unit left on for the first stage of processing Log sheets for CTD deployments and salt sampling operations are given in Appendix D 2 4 Data acquisition The CTD data were logged via the deck unit to a 1 4 GHz P4 PC running Seasave Win32 version 5 30b Sea Bird Electronics Inc for data acquisition The software allows numerical data to be listed to the screen in real time together with several graphs of var
63. 29 11 11 03 59 333 166 54 59 94 57 59 82 1490 1514 13 9 5 29 11 11 05 48 333 242 55 02 34 57 59 88 2025 2061 18 5 6 29 11 11 11 50 333 493 55 05 70 57 59 94 2450 2495 12 2 7 29 11 11 14 43 333 613 55 09 42 58 00 06 3000 3060 14 5 8 29 11 11 17 45 333 740 55 12 00 57 59 40 3550 3622 16 2 9 29 11 11 22 49 333 951 55 31 32 58 01 26 4200 4295 16 2 10 01 12 11 20 11 335 841 55 49 92 57 48 72 4720 4829 13 1 11 02 12 11 02 10 336 090 56 08 70 57 35 76 3489 3556 8 5 12 02 12 11 06 52 336 286 56 27 90 57 25 14 3663 3739 13 2 13 02 12 11 11 43 336 488 56 47 04 57 13 14 3267 3325 8 4 14 02 12 11 16 28 336 686 57 06 06 57 01 26 3870 3951 3 3 15 02 12 11 21 47 336 908 57 24 96 56 49 56 3475 3546 3 1 16 03 12 11 02 18 337 096 57 43 98 56 38 58 3459 3532 5 3 17 03 12 11 07 02 337 293 58 03 06 56 26 76 3933 4022 8 1 18 03 12 11 11 44 337 489 58 22 02 56 15 00 3876 3963 1 9 19 03 12 11 16 21 337 681 58 41 04 56 03 24 3730 3811 9 5 20 03 12 11 21 01 337 876 59 00 00 55 51 48 3752 3833 8 8 21 04 12 11 01 41 338 070 59 19 98 55 39 06 3736 3813 6 5 22 04 12 11 06 10 338 257 59 40 02 55 26 64 3654 3733 6 7 23 04 12 11 10 37 338 442 60 00 00 55 14 28 3478 3552 5 0 24 04 12 11 15 25 338 642 60 19 98 55 01 92 3420 3491 6 4 25 04 12 11 19 48 338 825 60 39 84 54 48 30 3060 3115 4 1 26 04 12 11 22 44 338 947 60 47 94 54 44 58 2530 2577 8 5 27 05 12 11 02 34 339 107 60 49 98 54 43 32 1729 1758 14 9 28 05 12 11 04 01 33
64. 3 JR94 Y Hawker et al 2005 2004 01 12 2004 19 12 2004 JR115 Y Sparrow et al 2005 2005 5 12 2005 12 12 2005 JR139 Y Stansfield et al 2008 2006 7 12 2006 15 12 2006 JR163 Y Williams et al 2008 2007 29 11 2007 8 12 2007 JR193 Y Hamersley and Quartly 2010a 2008 Dec 2009 Dec 2009 JR194 Y Hamersley and Quartly 2010b 2009 3 2 2009 3 3 2009 JC031 Y McDonagh et al 2009 2009 18 11 2009 29 11 2009 JR195 Y Yelland et al 2009a 2010 6 11 2010 10 12 1020 JR240 Y Maksym CTD 030 023 007 2010 9 4 2011 25 4 2011 JR276 Y Watson CTD 020 007 2011 27 11 2011 25 12 2011 JR265 Y This report Yelland 2011 Table 1 1 List of UK occupations of Drake Passage section WOCE designation SRIb adapted from Bacon and Cunningham 2005 Notes Year is the year of the start of the relevant southern season shows which cruises carried that instrument JR115 experienced some technical difficulties with the LADCP All occupations aimed to occupy the station positions see Section 2 shown in Figure 1 1 DI98 was occupied with an undulating profiling instrument SeaSoar with no full depth CTDs indicates the two partial occupations which took place in late 2010 and early 2011 to replace the cancelled 2010 JR242 cruise sew 60 879 545W 5134 Figure 1 1 The CTD section across Drake Passage Red dots indicate the position of the CTD stations for clarity only some stations are numbered 14 In 2010 the planned hydrog
65. 4 SCS On jday 327 2153 GMT continuous acquisition was started Acquisition still running at the time of writing this report Anticipate closing this leg down and starting a new leg on the 24 at the latest All back end processes scs to levc raw2compress and web displays presented no problems Nav streams were provided to POL for their above deck equipment 13 5 Em122 SWATH system Kongsberg EM122 installed July 2011 using the original transducer array installed 2007 running from Elephant Island North No problems with it SVP currently running at approx 1449 m s 13 6 Vsat On 16 Dec 0300 GMT it was reported that vsat was still out despite heading being ok As the ship was doing a figure of eight for POL myrtle recovery I noticed that satellite tracking would attempt to track for a few seconds before reporting syncro gyro failure and return to its home position Woke the RO who found the problem in a blown fuse in the syncro gyro repeater box Once the fuse was replaced the vsat gear returned to normal function 14 SUMMARY AND RECOMMENDATIONS The JR265 and JR254D cruises both went very well Combining the hydrographic work with the WAGES air sea interaction study worked to the benefit of all For example when conditions were too rough to deploy the CTD the time was used to deploy the WAGES wavebreaking buoy instead This meant that a the WAGES study obtained the high wind data required and b there was no down time when the ship wa
66. 41344 01 be left until calibration stage 9 mdes 05 dcs di344 016 pos nc dcs di344 016 pos nc apply positions to set of files Any of this list have positions set if the 8 ctd di344 016 raw nc file exists ctd di344 016 24hz nc ctd 41344 016 lhz nc The list should be extended to include any other chemistry files and 114 ctd di344 016 psal nc ctd di344 016 surf nc ctd di344 016 2db nc fir di344 016 bl nc fir di344 016 time nc fir di344 016 winch nc fir di344 016 ctd nc sal di344 016 nc sam di344 016 nc sam di344 016 resid nc dcs di344 016 nc the winch file if it exists It can be used at any time once step 8 is complete Can be left until calibration stage see 8 10 mctd 04 ctd di344 016 psal nc ctd di344 016 2db nc extract downcast data from psal file using index information in dcs 4 8 file sort interpolate gaps and average to 2db Plot t s curves using 2bd file 11 mfir 01 ctd di344 016 bl fir 41344 016 bl nc read in bl file and create fir file 12 mfir 02 fir di344 016 bl nc fir di344 016 time nc merge time from ctd onto fir file using scan number 4 11 ctd 41344 016 lhz nc 13 mfir 03 fir di344 016 time nc fir di344 016 ctd nc merge ctd upcast data onto fir file 4 12 ctd 41344 016 psal nc 14 mfir 04 fir di344 016 ctd nc sam di344 016 nc paste ctd fir data into sam file
67. 430 33 7281 0 0063 TSG 336 5576389 4 2 24 1 93585 33 7412 0 967925 33 7474 0 0062 TSG 336 76875 Table 9 1 example TSG salinity calculation excel file The output csv file was then converted to MSTAR format and the dates and times were converted into seconds since midnight on 1 January 2011 using mtsg 01 jr265 To give files called botsal 1265 cNN nc where NN is a sequential file number These files are the appended using mapend to give a single botsal 1265 Ol nc file containing all the TSG sample values 67 9 4 3 Calibration of Underway salinity with bottle samples The calibration of the TSG salinity is carried out via the conductivity The difference between the underway bottles and the TSG values are calculated using mtsg 02 jr265 which merges the 2min average files calculated in Section 9 2 ocl 1265 01 2minav nc with the botsal tsg jr265 Ol nc file The scripts then calculates the bottle conductivity at the temperature of the TSG sample and calculates the difference between the TSG and bottle conductivities only retaining values where the conductivity difference 15 less than 02 S m NB only one point was rejected by this test from the region of the strongest salinity gradient matlab gt gt mtsg 03 jr265 can then be used to calculate the calibration required for the TSG conductivity This was determined as Cond Cond 0 008189 2 896e 10 x time The conductivity calibration was then appl
68. 5 0316 Teather transfered to Port quarter Change heading to 320 T 04 12 2011 s 15 15 35 CTD 24 60 3331 55 03162 Wire out 3420m Commence hauling 04 12 2011 15 24 34 Wave buoy 9 60 33309 55 03159 Commence recovering wave buoy vessel heading 320 T buoy brg 180 T Dry 04 12 2011 16 00 35 CTD 24 60 33307 55 0316 CTD at the surface 04 12 2011 16 32 35 CTD 24 60 33307 55 0316 CTD recovered on deck 04 12 2011 1 16 40 60 66841 54 82049 Vessel D P at CTD site 25 04 12 2011 18 32 36 Wave buoy 10 60 66727 54 82156 Commence deploying wave buoy on the port quarter 04 12 2011 18 34 36 Wave buoy 10 60 66684 54 82095 Wave buoy deployed leading off port quarter paying out line 04 12 2011 36 Wave buoy 10 60 66623 Wave buoy fully deployed 96 18 37 54 82133 04 12 2011 18 42 37 CTD 25 60 66624 54 82134 Commence deploying CTD 04 12 2011 E 18 46 37 CTD 25 60 66623 54 82134 CTD deployed and soaking 04 12 2011 18 50 36 Wave buoy 10 60 66619 54 82071 Teather transfered to starboard quarter 04 12 2011 18 54 37 CTD 25 60 6661 54 81975 Veering CTD to near bottom EA 600 depth 3130m 04 12 2011 18 57 36 Wave buoy 10 60 66595 54 81862 Vessel heading 280 T Wave buoy 080 T Dry 04 12 2011 19 00 36 Wave buoy 10 60 66575 54 81708 Alter heading to 300 degrees 04 12 2011 19 04 38
69. 500l zd 35 40 6080 0 100 0 01 40 6080 0 100 0 005 01 target strength dB vel error mis target strength dB vel error m s 3000 3500 _ 4000 3500 E 400 i i LL a 250 8 250 500 t 200 met g 200 200 5 150 150 1000 8 2 100 1000 500 0 500 100 200 0 200 400 600 800 2 H CTD position blue and ship green east west m 50 CTD position blue and ship green east west m 50 0 o 20 0 20 40 20 10 0 10 20 velocity m s velocity cm s LDEO LADCP software Version 7b Dec 2002 LDEO LADCP software Version 7b Dec 2002 Figure 3 9 Velocity profiles for station 008 faulty LADCP and station 009 replacement unit Examples of the velocity profiles generated are shown in Figure 3 9 also from stations 008 and 009 Note the poor quality data at station 008 left hand panel with large difference 44 between up and down cast large difference between water track and bottom track velocities and high velocity error 3 8 LADCP problems on JR265 The significant problem with the LADCP on JR265 was the faulty beam 3 on the first LADCP installed The result of the faulty beam is that casts 001 to 008 of the section have poor quality LADCP velocity data Once the problem had been identified the LADCP was replaced and the data from the new unit was examined after each cast it performed satisfactorily for the remainder of the cruise The early stations with the faulty
70. 5360 5380 5400 5420 5440 5460 5480 5500 5520 5540 5560 5 5 5 5 5 5 Ensemble 5575 S i 11 11 29 22 56 24 07 Date Time 11 11 29 23 01 03 87 5 g 8 0007 0 0000 Lat Lon 0 0000 0 0000 1 1 2 2 Bm3 Bm3 Bm4 Bm4 Ensemble Date 11 11 29 ime 22 58 45 64 Technical B Figure 3 6 Close to bottom Profiles showing maintained close intensities and good correlations 3 7 Data processing Data from the LADCP instruments was processed when possible between each station to allow early detection of any problems with the ADCP workhorse Two sets of software were 39 utilized University of Hawaii uh Lamont Doherty Earth Observatory at Columbia University Ideo programs Both were run to allow a full picture of the LADCP performance to be obtained Instructions are given below for initial shipboard LADCP processing during JR265 3 7 1 UHDAS processing Bold text denotes commands to enter at the X window terminal prompt gt gt preceding bold text indicates commands to be entered in the Matlab window Notes are in italics 1 Log on as pstar password pstar Note You must be logged on to the jruh station to get access to the matlab licence this should be set up when NOSEA2 is connected to the ship s network and not required at each subsequent log in 2 Move raw LADCP files to appropriate place on the Unix system copy files in j265 NN
71. 7 55 0946 57 9992 Vessel stopped ready for CTD deployment 29 11 2011 10 57 8 CTD 6 55 09457 57 99917 CTD deployed veering to 2450m depth 29 11 2011 11 05 8 CTD 6 55 09459 57 9992 stopped 2450m 29 11 2011 11 46 8 CTD 6 55 0946 57 99915 CTD recovered to deck 29 11 2011 12 51 55 15751 58 0009 V L on station for CTD 7 29 11 2011 13 36 9 CTD 7 55 15748 58 00092 CTD deployed for soak 29 11 2011 13 45 9 CTD 7 55 15754 58 00097 CTD veering to 3000m 29 11 2011 13 50 9 CTD 7 55 15749 58 00093 CTD stopped 3000m 29 11 2011 14 41 9 CTD 7 55 15752 58 0009 CTD at surface 29 11 2011 15 44 9 CTD 7 55 15753 58 00093 CTD on deck 29 11 2011 15 51 10 Apex 1 55 15757 58 00099 Commence deployment Apex Buoy 29 11 2011 15 56 11 Wave Buoy 2 55 20233 57 99407 V L on D P 29 11 2011 16 21 11 Wave Buoy 2 55 20292 57 99464 Commence deployment of Wave Buoy 29 11 2011 16 24 11 Wave Buoy 2 55 20218 57 99385 Buoy released Paying out line 29 11 2011 11 Wave Buoy 2 55 20305 Wave Buoy fully deployed tethered line approx 200m 84 16 26 57 99483 29 11 2011 16 31 12 CTD 8 55 20295 57 99468 Commence CTD deployment 29 11 2011 16 38 12 CTD 8 55 20277 57 99454 CTD in the water and soaking 29 11 2011 16 41 12 CTD 8 55 20268 57 9944 CTD Veering EA60
72. 9 167 60 51 00 54 42 66 978 993 15 6 29 05 12 11 14 23 339 599 60 58 86 54 37 80 570 578 8 9 30 05 12 11 15 35 339 649 61 03 00 54 35 22 345 350 5 9 Table 2 2 Actual CTD stations carried out during JR265 The time GMT and positions given for each station correspond to the time and position of the ship when the CTD was at the bottom of each cast CTD carried NOC L microcats for calibration prior to deployment with BPR Calibration required three 15 minute stops at 1500 1000 and 500 m wire out during the ascent WAGES buoy deployed during CTD Altimeter noisy CTD may have touched bottom Altimeter swapped out after station 013 2 1 1 Problems and significant events during operations On stations 901 and 026 the CTD was stopped for three 15 minute periods at 1500 m 1000 m and 500 m to allow the NOC L microcat calibrations WAGES buoy deployments were carried out at several stations shown in Table 2 2 At these stations the buoy was deployed before the CTD and brought in before the CTD finished coming up Bad weather stopped CTD deployments from 21 35 on 29 11 to 18 41 on 01 12 The first few deployments after were not brought back to the surface before descending The altimeter was changed after station 013 due to noisy readings On station 012 the CTD may have touched the bottom 2 2 2 Configuration A 24 bottle BAS CTD frame was used throughout the cruise The CTD frame was equipped with a SBE 32 Carousel Water
73. 944 57 99372 V L stopped on station for CTD 2 28 11 2011 23 13 2 CTD 2 54 90944 57 9937 CTD deployed for soak 28 11 2011 23 16 2 CTD 2 54 90943 57 99372 CTD veering to 600m 28 11 2011 23 21 2 CTD 2 54 90944 57 99373 CTD stopped 608m 28 11 2011 23 32 2 CTD 2 54 90939 57 9937 CTD recovered to deck 28 11 2011 23 49 2 CTD 2 54 90939 57 99367 V L off DP proceeding to CTD 3 28 11 2011 23 55 54 97387 57 99483 Commence swath survey 29 11 2011 00 23 55 00285 57 94578 Complete swath survey 29 11 2011 01 07 3 CTD 3 54 97974 57 97507 V L on station for CTD 3 29 11 2011 01 29 3 CTD 3 54 9799 57 97525 CTD deployed for soak 29 11 2011 01 35 3 CTD 3 54 97989 57 97526 CTD veering to 1100m 29 11 2011 01 40 3 CTD 3 54 98007 57 97509 CTD stopped 1075m 29 11 2011 01 59 3 CTD 3 54 98003 57 97511 CTD recovered to deck 29 11 2011 02 27 4 BPR 1 54 98003 57 9751 BPR released 29 11 2011 02 41 4 BPR 1 54 98015 57 97513 BPR on the seabed Vessel off D P 29 11 2011 5 CTD 4 54 99908 Vessel all stoped on D P 82 03 05 57 99723 29 11 2011 03 24 5 CTD 4 54 99908 57 9972 Commence deploying CTD 29 11 2011 03 25 5 CTD 4 54 99908 57 9972 CTD in the water and soaking 29 11 2011 03 29 5 CTD 4 54 99908 57 9972 Veering CTD to near bottom EA 600 depth 1517
74. 992 Tirl 0 14u V W m 26 1 2011 side 2200nm Zonen ep foremast starboard 2 Lite 335 to 004742 112993 Tir2 0 14u V W m 26 1 2011 side 2200nm Vaisala PTB210 145002 UIC 5 logger 20 01 10 4 2000 Vaisala PTB210 visos V mocan ance 0 01 Hpa 10 4 2000 cabinet Windmaste sonic BA aun No information Foremast 7 Direction 2 to 4 N A Table 8 1 Meteorological instrument properties 59 8 3 Routine processing The data were routinely processed according to the underway method outlined in Section 5 please refer to Appendix C 1 for the daily processing guide The data were transferred from SCS to mstar files using matlab mday 00 met JJJ called by mday 00 get all JJJ The raw calibrated wind speed data files were located on NOSEA2 under surfmet met 1265 dJJJ raw nc where JJJ represents the day number The raw data were cleaned to remove backward and repeated timesteps mcalc and mdatpik using 01 JJJ called from mday clean all The script also set all data outside the following ranges to absent using medita Air temperature 50 to 50 C Humidity 0 1 to 110 TIR 50 to 1500 PAR 0 0001 to 50 These values are set in the mmet 01 m script found in local users pstar cruise data mexec processing scripts which can be edited using matlab gt gt edit mmet 01 m The daily data files met jr265 dJJJ nc were also copied to met 1265
75. APPENDIX B JR265 CTD 8 2 107 CTD DECK UNIT SETUP PROCESSING AND DATA 5 000 22202 2 60100 0 000000000000 107 B 2 BOTTLEFIEEFORMATS o denen eene 108 INSTRUMENT CALIBRATION CONSTANTS ennemi nennen inneren nre enin nen ener enne 109 B 4 SEABIRD CTD CONFIGURATION FILE AS USED THROUGHOUT 8265 000 110 5 DETAILS OF MS TAR PROCESSING RR e EN e ETE SEES pee 114 APPENDIX UNDERWAY DATA PROCESSING eerte ee 116 DAILY UNDERWAY DATA PROCESSING 5 116 MPEXYED EDITING OF DATA cx 118 APPENDIX D LOG SHEETS sscssssvsosvessensssososecsesonsosnssonsesunessoasescyeosseveesenndsonossosadessebonsocesseseesosnssenses 122 APPENDIX E VM ADCP 130 SCIENTIFIC TECHNICAL PERSONNEL JR265 Margaret Yelland PSO Mairi Fenton Vikki Frith Naomi Penny Holliday Helen Snaith JR254D Margaret Yelland PSO Sarah Norris Robin Pascal JR264 Miguel A M Maqueda PSO Geoff Hargreaves Stephen Mack BAS technical support Julian Klepacki Seth Thomas Johnnie Edmonston SHIP S PERSONNEL Graham P Chapman Joanna L Cox Simon D Evans Ben P Thompson Charles A Waddicor Heather L Williams Harry Taylor John Roberts Dav
76. BTalk or anything before disconnecting ADCPs at CTD otherwise a character may be sent stopping ADCP acquisition Check LADCP s is pinging Due to location not easy to hear Master Single ADCP pinging with much ambient noise wind rattling doors gossiping etc Often simply cannot be heard pinging prior to deployment Sometimes the slave ADCP if used can be heard pinging easier location but not always If cannot hear pinging and passed tests have faith deploy and all should be good Disconnect comms cable s from star cable at CTD Re connect dummy plug s new grease sparingly if necessary CHECK BATTERY VENT PLUG IF CHARGING CARRIED OUT Re install if not fitted Making sure its clean and using some new grease sparingly Lock in place pinching collar cap screw ADCP s now ready to deploy 3 5 Recovery Send a Break B in BBTalk to wake up ADCP Type command cb811 to change baud rate to 115200 to minimise download time 36 Choose data file File gt Recover Recorder Select File s OK Only either ALL or single file can be selected Save in LADCP JR Data V where 222 is cruise number speed up data recovery check the Disable Window Output box Download times at 115200 baud are approximately 3 minutes per Mb with disabled output window e Once data recovery complete and successful Go to data and change file names to jr NNN 000 where 222 is the cruise number NNN is the station number
77. Balloon 4 60 66493 54 81363 Ballon deployed from port quarter 04 12 2011 19 19 36 Wave buoy 10 60 66417 54 81116 Alter heading to 290 degrees 04 12 2011 19 27 37 CTD 25 60 66369 54 8054 depth 3060m 04 12 2011 19 47 36 Wave buoy 10 60 66353 54 80179 Vessel heading 290 degrees moved in last hour 074 degrees x 0 55nm buoy on bearing 080 degrees 04 12 2011 20 00 38 Balloon 4 60 66347 54 80122 Commence recovery of balloon 04 12 2011 20 02 38 Balloon 4 60 66318 54 79828 Balloon recovered to deck 04 12 2011 20 14 36 Wave buoy 10 60 6631 54 79761 Commence recovery of wavex buoy 04 12 2011 20 17 36 Wave buoy 10 60 66309 54 79518 Wavex buoy recovered to deck 04 12 2011 20 29 37 CTD 25 60 66352 54 79267 CTD recovered to deck 04 12 2011 20 57 39 CTD 26 60 79939 54 7445 V L on DP for CTD 26 04 12 2011 21 50 39 CTD 26 60 79946 54 74379 CTD deployed 97 04 12 2011 54 74334 21 59 39 CTD 26 60 79947 CTD 2530 metres 04 12 2011 22 43 39 CTD 26 60 79947 54 74335 CTD recovered to deck 05 12 2011 00 21 60 79947 54 74334 V L off DP 05 12 2011 00 23 60 83334 54 71703 V L on DP 05 12 2011 00 49 40 POL APEX 1 60 83484 54 72019 POL APEX deployed 05 12 2011 01 18 40 POL APEX 1 60 83432 54 72068 Communications with buoy tested OK 05 12 2011
78. Buoy deployed 02 12 2011 19 CTD 12 56 46745 Commence CTD deployment 90 05 40 57 43384 02 12 2011 05 45 19 CTD 12 56 46731 57 4333 CTD Soaking 02 12 2011 05 48 19 CTD 12 56 46711 57 43189 Veering CTD to near bottom EA 600 depth 3770m 02 12 2011 05 52 19 CTD 12 56 46534 57 41873 Wire out 3663m Commence hauling 02 12 2011 06 54 19 CTD 12 56 46362 57 40447 CTD recovered to deck 02 12 2011 08 06 19 CTD 12 56 46362 57 40447 CTD secure on deck 02 12 2011 10 13 20 wave buoy 5 56 78289 57 2293 Commence deployment of wavex buoy from stbd quarter 02 12 2011 10 18 20 wave buoy 5 56 78306 57 2303 Wave buoy in the water leading off starboard quarter 02 12 2011 10 22 20 wave buoy 5 56 78324 57 23188 Wave buoy fully deployed and secure 02 12 2011 10 27 20 CTD 13 56 78341 57 23025 CTD deployed 02 12 2011 10 38 20 CTD 13 56 7843 57 21849 CTD stopped 3267m 02 12 2011 11 44 20 wave buoy 5 56 78456 57 21185 Commence recovery of wave buoy 02 12 2011 12 25 20 wave buoy 5 56 78407 57 20858 Wave buoy recovered to deck 02 12 2011 13 01 21 CTD 14 57 10119 57 03603 V L on D P site 14 02 12 2011 14 57 22 Wave Buoy 6 57 10168 57 03793 Commence deployment of Wave Buoy 02 12 2011 15 01 22 Wave Buoy 6 57 1017 57 03839 Wave buoy deployed leading
79. EP IS ONLY DONE ONCE If you need to do it again for example if you discover an error in step 5 then must delete the database files first i e proc casts j NNN_02 scdb blk 40 8 perl S domerge prl 0 NNN 02 merge single pings into long shear profiles 9 Grabs navigation for the LADCP profile cd Rnav matlab gt gt m setup gt gt make sm gt gt exit proc 10 first look at profile matlab gt gt plist NNN 02 this is a decimal number in matlab gt gt do abs Check figure 1 for X character in profiles indicative of ADCP failure Check Figure 5 for good heading i e CTD not rotating gt gt exit Next print the useful figures examine them and put into First Look folder The Ipr command for printing did not work on JR265 so you can ftp the figures to your laptop and print from there Open a new Terminal window or tab At the prompt type sftp pstar nosea2 pwd pstar cd local users pstar cruise data ladcp uh pro jr1112 ladcp proc casts jNNN 02 merge mget duNNN02h ps File printout in the JR265 LADCP first look folder Stop UH processing here if CTD has not been processed as far as 1Hz and perform the LDEO processing in Section 3 7 2 11 If when the CTD has been processed as far as a 1hz file cd proc cd Retd matlab gt gt m setup gt gt mk ctdfile NNN makes ascii version of CTD Ihz file in preparation for ladcp use gt gt exit 12 ed proc Pctd matlab
80. ETEOROLOGICAL SAMPLING SYSTEM ee eee 58 STINTRODUCTION 505 58 82 INSTRUMENTATION Aeon le bre eO 58 S SJROUTINE PROCESSING RR RU bu ERE tens M RE ni ERR 60 8 4 00 62 9 UNDERWAY TEMPERATURE AND SALINITY 64 OL INTRODUCTION zeit e EE DEREN E REN UE QUERN EE REA RUE 64 9 3 CALIBRATION OF UNDERWAY SEA SURFACE TEMPERATURE 65 9 4 CALIBRATION OF UNDERWAY SALINITY 66 9 4 Introduction 66 9 4 2 Calculating sample salinity eese esent ener entente enter entere 67 9 4 3 Calibration of Underway salinity with bottle samples see 68 9 S RESIDUAES oett m RE PEOR QE ee EO E QE tb RO EE ums 68 10 ARGO FLOAT DEPLOYMENT 75 2 eoo eee eee oae Cu eaae eoe PP a ao or PE ao neas oe sone uon paa o 70 10 1 INTRODUCTION p es 70 10 2 DEPLOYMENT PROCEDURE sereoo sireci ena e EE EE o dee eere tiep 70 TD SALTINOMETER deo 71 IT b INTRODUCTION e eene ie at alat aue dan atte b atu
81. Figure 3 8 The left panel shows that the LADCP had a faulty beam 3 on station 008 but the new unit used for station 009 onwards was fully functional For station 008 the high echo amplitude and low correlation of Beam 3 matches with the information observed in the raw data in WinADCP see section 3 6 43 W station jr265008noctd W station jr265009noctd W as function of bindepth and time W as function of bindepth and time E 50 E 50 100 100 B E uo ME 500 1000 1500 2000 2500 2000 3500 4000 4500 5000 1000 2000 3000 4000 5000 6000 7000 8000 ensemble ensemble 0 500 1000 1500 2000 2500 3000 3500 4000 4500 5000 0 1000 2000 3000 4000 5000 6000 7000 8000 30 T M9 M Mr r 1 1 30 T T T T T T T T go 1 g 20 10 1 10 0 0 0 500 1000 1500 2000 2500 3000 3500 4000 4500 5000 0 1000 2000 3000 4000 5000 6000 7000 8000 a T T 360 270 2 P 180 3 3 5 0 0 500 1000 1500 2000 2500 3000 3500 4000 4500 5000 0 1000 2000 3000 4000 5000 6000 7000 8000 260 T T T T T T T T T T 240 T T T T T T T T 3 8 240 4 E 220 220 1 1 1 4 1 1 1 1 1 1 200 n n 1 1 1 n 2 0 500 1000 1500 2000 2500 3000 3500 4000 4500 5000 0 1000 2000 3000 4000 5000 6000 7000 8000 ensemble ensemble test all beams test all beams test all beams test beams 0 0 0 0 _ 50
82. NSITY Avg Avg 73 1 71 72 74 Correlation min 1 2 3 4 Intensity 2 E 2 5 20 100 120 140 160 10 20 20 240 3 E 5 5 3 1 Ensemble 256 z 5 z E 8 11 11 29 21 18 5386 Dale Time 11 11 29 21 23 28 92 z 8 8 0 0000 0 0000 0 0000 0 0000 1 2 2 Bm3 Bm3 Bm4 Bm 0 0 9 945 9 9 050500005 0002052 505250202020202000000000000 00 0 0 000 0 0 00 0 4 4 1 Date 11 11 29 ime 21 23 28 92 Dj Edt Options Animate Export Utiles Window Monitor Help DCP Informatio n ole Set Deployme atio 4 10 12 265 13 265 009 000 ECHO INTENSITY Avg Sel 1 to 9916 File Size 5 562 976 bytes 94 425 Sub 5320 to 5575 B WH Ensemble Length 561 bytes 0 3 hj System Frequency 307 2 kHz Ast Bin 15 25 m Bin Size 10 00 m o Bins 16 Pings Ens l Time Ping 00 00 01 First Ensenble 00000001 11 11 29 21 Last Ensemble 00009916 11 11 30 00 20 werage Ensemble Interval 00 00 01 10 Range m 1 soo asmo soog s5 Ensemble 9907 11 1 29 Date 11 11 30 21 18 53 86 00 20 47 96 4 00 0 0 Profile ECHO INTENSITY Avg Avg 83 15 Intensity Correlation D min z m 2 100 3 10 12 150 H gt 5 18 t 5340
83. National Oceanography Centre NATURAL ENVIRONMENT RESEARCH COUNCIL National Oceanography Centre Cruise Report No 10 RRS James Clark Ross Cruises JR265 and JR254D 27 NOV 24 DEC 2011 Part The Drake Passage hydrographic repeat section SR Ib Principal Scientist MJ Yelland 2011 National Oceanography Centre Southampton University of Southampton Waterfront Campus European Way Southampton Hants 5014 3ZH UK Tel 44 0 23 8059 6406 Email m yelland noc ac uk O National Oceanography Centre 2011 DOCUMENT DATA SHEET AUTHOR PUBLICATION Yelland M J et al DATE 2011 TITLE RRS James Clark Ross Cruises JR265 and JR254D 27 Nov 24 Dec 2011 Part 1 The Drake Passage hydrographic repeat section SR1b REFERENCE Southampton UK National Oceanography Centre Southampton 135pp National Oceanography Centre Cruise Report No 10 ABSTRACT This report describes the 17 complete occupation of the Drake Passage CTD section established during the World Ocean Circulation Experiment as repeat section It was first occupied by National Oceanography Centre previously IOSDL and then SOC in collaboration with the British Antarctic Survey in 1993 and has been re occupied most years since then Thirty two full depth stations were performed during JR265 two test stations and all 30 of the nominal stations for the SR1b Drake Passage section An initial result is that the estimated total transport
84. Nm 000 format from jr b legwork mounted on nosea2 as mnt current work jr265 LA DCP to pstar cruise data ladcp uh raw r1112 ladcp 3 setup matlab paths at the prompt enter ladep cd uh source LADall 4 change location to processing directory proc this is not a typo although the ladcp directory does not contain a subdirectory proc the path to proc is set in the LADall file cd Rlad linkscript Check the raw ladcp data there should be a raw file called jr265 NNNm 000 Linkscript will make a symbolic link from jNNN 02 000 to the real raw file We use 02 for compatibility with other cruises when there is more than one LADCP The convention adopted on CD139 was that 02 is a down looking workhorse WH and 03 is an upward looking WH Hence until the instruments are changed use 03 in the following XXs For JR265 there is only the downward looking WH so NN 02 5 scan data file proc perl S scan prl NNN 02 This will output to screen check that times and depth are sensible i e Zmax is approximately the same as the expected depth and Zmin and Zend should be 50m for shallow casts and 200m for deep ones 6 Update cruise navigation files matlab amp gt gt m setup gt gt putpos NNN 02 check syntax gt gt magvarsm NNN 02 check syntax ignore decimal year warning gt gt exit 7 perl S load prl NNN 02 loads into database correcting for magvar tab IT IS VERY IMPORTANT THAT THIS ST
85. Passage repeat hydrography WOCE Southern Repeat Section Ib Burdwood Bank to Elephant Island Southampton UK Southampton Oceanography Centre 80pp National Oceanography Centre Cruise Report 25 Yelland M J 20092 RRS James Clark Ross Cruise 195 18 Nov 29 Nov 2009 Drake Passage repeat hydrography of WOCE section SR1b a beginner s guide Southampton UK National Oceanography Centre 123 pp National Oceanography Centre Cruise Report 45 Yelland M J R W Pascal P K Taylor and B I Moat B I 2009b AutoFlux an autonomous system for the direct measurement of the air sea fluxes of CO2 heat and momentum Journal of Operational Oceanography 2 1 15 23 Yelland M J 2012a JR254D cruise report n prep Yelland M J 20125 WAGES 2010 11 season JCR and JR254A B C cruise report In prep 79 APPENDIX A BRIDGE LOGS A 1 Bridge log of scientific operations GMT Event Lat Lon Comment 27 11 2011 Shallow Test Wave 15 06 Buoy 1 51 78724 57 87571 Commence deploying W Buoy 27 11 2011 Shallow Test Wave 15 10 Buoy 1 51 78711 57 87575 Tethered buoy in the water 27 11 2011 Shallow Test Wave 15 14 Buoy 1 51 78653 57 87579 Tethered buoy fully deployed Approx 200m of line Vessel HDG 355deg DP current 048deg X 0 5kts 27 11 2011 15 21 Shallow Test CTD 51 78655 57 8758 Commence deployment CTD 27 11 2011 15 29
86. R Once located CTD 004 done prior to the BPR deployment and SWATH was turned off 0245 GMT since it was thought that it may interfere with the VM ADCP 1 Argo float 4900 deployed after CTD 007 WAGES buoy deployment 2 was done during CTD 008 After CTD 008 the LADCP beam 3 was found to be weak The LADCP model WHM300 i ug306 S N 14443 was swapped for WHM300 i ug301 S N 15060 in time for dip 009 WAGES buoy deployment 3 took place during CTD 009 The IRIDIUM unit on the buoy was not sealed properly so became flooded and never recovered 30 November jday 334 Pudsey went on strike for the day The ship was in position for CTD 010 in the early hours but the wire came off the roller at the very start of the deployment and the CTD was brought back on deck A strong current combined with large seas and a strong wind led to the decision to wait for conditions to improve station 010 is the deepest of the section and was thought to be at or near the Sub Antarctic Front and was therefore thought important to complete The conditions did not improve overnight and the forecast was bad so WAGES buoy deployment 4 was begun at about 1100 GMT 1 December jday 335 The WAGES buoy was recovered at around 1300 GMT The large waves encountered while the buoy was being hauled in caused the 4 rods at the base to bend and the buoy to lie horizontally in the water The top half of the buoy tore away and the IRIDIUM unit flashing light and camera mounted on the u
87. SCS UNDERWAY DATA AQUISITION Helen Snaith 5 1 Underway data acquisition using the SCS system The underway data are logged in ascii SCS files located under jr1b jcr nerc bas ac uk san datavol data cruise jcr current scs Compress which is a mounted on NOSEA2 as mnt 20111123 and linked as local users pstar jr265 data scs raw The original SCS files in data scs raw have file extension ACO and these files are not easily parsed as they are mixed characters with comma separation The SCS files are cleaned up using sed scripts that run on nosea2 At the beginning of the cruise or if the sed scripts hang type unix sedexec stopall unix sedexec startall This will restart all the sed scripts and create the data scs sed ACO files from scratch from the beginning of the cruise It will take a while to catch up if parsing a whole cruise of data but sed is very quick The files in data scs sed are versions of the ACO files with commas colons characters etc removed so they are plain numerical files that can be loaded into Matlab To check that sed is running use 54 unix top and watch for sed entries appearing every 10 seconds or so If no sed 15 present then stop and restart the sed scripts using the commands above Occasionally the sed scripts will not completely clean the data and leave behind odd characters The data scs sed and data scs raw ACO filles cannot be edited manually without stopping and restarting the SCS
88. Sampler configured with 24 12 litre Ocean Test Equipment Niskin bottles connected to an SBE 9 plus CTD controlled and powered by an SBE 11 plus deck unit The Niskin bottles 98 5 cm high were mounted vertically 15 to 20 cm above the sensors The distance measured between the pressure sensor and the top bottom of the bottles was 114 cm 15 5 cm An SBE 35 high precision temperature sensor was attached vertically on one side bar of the frame approximately level with the water bottles This provided independent 8 second average temperature measurements each time a bottle was fired The underwater SBE 9 plus unit was equipped with the following sensors dual temperature and conductivity sensors a pressure sensor encased in the SBE underwater unit a SBE 43 oxygen probe an Aquatracka MKIII fluorometer a transmissometer an upward looking downwelling PAR sensor and an altimeter The altimeter was changed after station 013 due to increasingly noisy readings Table 2 3 gives details of sensors serial number and calibration date The mapping between sensors and voltage or frequency channels remained the same throughout A report of the CON file settings used for JR265 is listed in Appendix B 1 For all stations a self logging downward looking LADCP was attached to the main CTD frame see section 3 of this report for detail of LADCP operations The frame was equipped with a fin to reduce rotation of the package underwater Sensor Manufacturer Mo
89. Shallow Test CTD 51 78656 57 87579 CTD the water and soaking EA 600 depth 54m 27 11 2011 15 31 Shallow Test CTD 51 78666 57 87581 CTD veering 27 11 2011 15 35 Shallow Test CTD 51 78678 57 87585 All stopped wire out 45m 27 11 2011 15 37 Shallow Test 51 78763 57 8763 CTD at surface 27 11 2011 15 47 Shallow Test CTD 51 78773 57 87636 CTD commence hauling 27 11 2011 15 49 Shallow Test 51 78783 57 87644 CTD recovered on deck 27 11 2011 15 51 Shallow Test 51 78827 57 87671 Gantry block and CTD secure 27 11 2011 Shallow Test Wave 15 59 Buoy 1 51 79412 57 87169 Wind 345Deg 27Kts DP Current 211Deg 0 8Kts V L HDG 355Deg 27 11 2011 Shallow Test Wave 18 00 Buoy 1 51 79309 57 85044 Commence altering heading to 180 degrees Since deployment vessel moved 291 degrees x 1 03nm 27 11 2011 Shallow Test Wave 51 79477 Altered heading to 260 degrees now altering back to 000 degrees 80 19 54 1 57 84116 27 11 2011 Shallow Test Wave 20 23 Buoy 1 51 79015 57 83607 Heading stead on 325 degrees 27 11 2011 Shallow Test Balloon 20 49 1 51 79004 57 83605 Commence balloon deployment 27 11 2011 Shallow Test Balloon 20 50 1 51 78958 57 83483 Balloon deployed 27 11 2011 Shallow Test Balloon 20 57 1 51 78943 57 83293 Commence recovery of balloon 27 11 2011 Shallow Test Balloon
90. T T T T T T 500 1000F 1500f 2000 2000F 2500F Depth m Depth m T e 3000 60 40 20 0 500 U ems dn 1000 1500 1000F 2000F T 2500F Depth m T e is 40 20 0 20 40 60 V dn up mn Depth m 8 8 8 B8 0 40 20 0 20 40 60 7 V cms dn mn Figure 3 7 Velocity profiles generated by the UH processing a to c profiles from the faulty LADCP stations 005 006 and 007 and d a good profile from the second LADCP station 012 42 One check of the LADCP performance was to compare the velocity profiles from the down and upcasts at each station This is the duNNNO2 ps figure Figure 3 7 which is printed to go in the processing file Preferably the up and down cast velocities do NOT form an X which indicates poor quality data and a possible fault This is a tricky diagnostic test for a non expert however because adjacent stations can have profiles with varying degrees of the X characteristic This is illustrated in Figure 3 7 where profiles from stations 005 006 and 007 show X profiles that range from subtle to obvious all from the faulty LADCP and the profile from station 012 with the new and fully functional unit 3 7 2 LDEO processing This is a easy check of LADCP beam strength but it usefulness depends on timely processing which can be hard to achieve du
91. The left hand plot shows beam intensity and beam correlation for the period of the data file that is indicated by a red box on the top coloured contour panel echo intensity You can change the period by sliding the bar below the plot left or right for example you can see how parameters change from in air to in water and over the duration of the cast e Check Beam Intensity i in air if one beam has much higher counts than the other three 75 then it may be faulty This is not a secure test though even our good instrument showed one beam slightly higher than the other 3 in air 2 5 counts in water if one beam has consistently higher counts than the others then it is faulty JR265 Bm 3 was 10 20 counts higher sometimes more especially on lower part of these plots e Check Beam Correlation 1 In air this is not a useful test because in our faulty unit the correlations all matched in air ii In water if correlations from one beam are consistently lower than the other 3 then it is faulty In our faulty unit the beam 3 correlations were 60 70 counts lower than the other 3 The beam correlations do vary though the duration of the cast but 1f all four are consistently grouped together then there is not a problem Figure 3 3 shows a screen capture below of a failing unit Beam 3 on the Intensity profile bottom left can be seen to have a considerable offset whilst out of water sitting on the deck 37 Scrolling the time line also
92. W ee V ae borse eee TA Id OU P oL Sete 13 1 1 INTRODUCTION AND BACKGROUND 2 13 LT WAGES ssi GUERRE MI MU IN REDI 13 T 1 2 Hydragraphic Secti n ide e Pu i OC AE RU E 13 1 2 SCIENTIFIC OBIEGIIVESS s stes pi temi ERE et utm re e edd 15 1 2 1 JR205 Hydrographie section v eee meet ie ete iet opt en e et ei 15 1 2 2 WAGES objectives for JR254D eese 16 S CRUISENARRATIVE tret teet e e tvi eee mme e bte e ie gie et edes ep eese que 16 1 3 1 Mobilisation period 24 NG VOI DEN sad ahi cet Arnett A ure e EE ER ain an 16 1 3 2 WAGES studies and Drake Passage section 27 November 5 17 1 3 3 Antarctic Peninsular 6 13 December 0 18 1 3 4 Antarctic Peninsular to Stanley 14 24 December 19 PM M 19 2 1 INTRODUGTION 2 ee meat RRR 19 2 1 1 Problems and significant events during operations esseere 21 2 2 CONFIGURATION I E pes 22 2 S DEPLOYMENT iere ipei e iei e Vi a ER reus 23 ZA DATA ACQUISITION teretes te te e T te reete 23 2 4 Prescast procedue us e pe ect Ree det a e e e ere I Ee REO 23 2 4 2 Procedure for the Casta iiio eO D eat AQ TR 24 2 4 3 Immediate post cast operations essen e
93. ams to for instr tss scs sed tsshrp ACO nav tss tss jr265 dJJJ raw nc MSTAR format sim scs sed ea600 ACO sim sim jr265 dJJJ raw nc as long as output met surfmet met jr265 dJJJ raw directory exists met scs sed anemometer ACO ae ocl scs sed oceanlogger ACO ocl ocl jr265 dJJJ raw nc rA nav seapos pos 265 dJJJ nc bel En nna ata cycles wi mhdg 01 nav seapos poshdg jr265 d nav seapos poshdg 1265 dJJJ n repeat or JJ JJJ raw nc c backwards time Ea nav gyros 2 vigyrosgyt 1265 dme Pe soda Pe nav ash ash T MENS er set _all JJJ mchf 01 msim 01 D chf chf 1265 dJJJ raw nc chf chf 11265 dJJJ nc generates 30s di Miro sim sim j1265 dJJJ raw nc sim sim _jr265_dJJJ nc mmet 01 met surfmet met 265 dJJJ s copied as JID awie met surfmet met jr265 dJJJ nc lt file gt edit nc ready for editin sd ocl ocl 1265 raw nc ocl ocl 1265 dJJJ nc step 5 4222 nav seapos pos jr265 dJJJ nc nav gyros gyr jr265 dJJJ e 20 290000 dituc nav gyros gyr jr265 dJJJ nc files edited in 2 place then spa nav ash ash jr265 dJJJ nc copied to replace msm i 265 alm ih original files sim BE do 5moo sim sim 265 dJJJ nc Can be used to restart NM uu 4 met surfmet met jr265 dJJJ nc processing ocl ocl ocl 1265 dJJJ edit nc ocl ocl 1265 dJJJ nc nav seapos pos jr265 edit nc 511 511 E 5 plots met surfmet met
94. and is either m master s slave or left out if single ADCP Record default names and changes e AtBBTalk command prompt type cb411 to reset baud rate to 9600 e to power down ADCP e the raw files and the log files to jr b legwork mounted on PC as E jr265 LADCP 3 6 Initial Data Quality Check Standard pre deployment test PA checks the major WorkHorse modules and signal paths Additional tests are performed to be comprehensive prior to deployment In some instances these are not effective because some tests fail in air even though the instrument performs fine in water A new user may be primed to expect failures Transmit Receive and Bandwidth but interpreting the other tests to spot a fault requires knowledge of subtleties within the results Previously we had relied on diagnostic plots generated at the end of the data processing stages described below However with the usual busy period at the start of the cruise it took several casts before we recognised there was a fault in the first LADCP unit In order to avoid this making this mistake again we recommend that the user examines the data in WinADCP on the LADCP computer after every cast Open WinADCP File Menu gt Open gt c LADCP jr265 Data jr265NNN 000 This opens a graphical display of the data see Fig 3 Choose Option Menu Chart Options Profile In dialogue box tick boxes to select Beam Intensity and Correlation for all 4 beams e
95. arried out in two phases Immediately after the cast the data were processed using SeaBird Data Processing routines on the CTD logging PC SeaTerm was used to save the bottle files The data were then copied to the ship s network drive and on to the 25 NOCS Linux Sun workstation NOSEA2 for further processing using the MSTAR processing routines On the CTD logging computer SBE Data Processing software version 7 21d was used for initial processing as soon as the cast was finished by running the following 1 Data Conversion to convert the raw frequency and voltage data to engineering units as appropriate by applying the manufacturer s calibrations stored in the CON file and save both downcast and upcast to an ASCII format file Input File ctd 1265 NNN dat Output File ctd 11265 2 Align CTD to align the oxygen sensor in time relative to pressure To find the optimum setting for the oxygen measurement the deep test station 901 was used see Appendix B 1 Input File ctd 1265 NNN cnv Output File 1265 3 Cell Thermal Mass to correct the pressure and conductivity The SeaBird recommended settings of alpha 0 03 and l beta 7 0 were used on both primary and secondary conductivities Input File ctd 1265 Output File 1265 actm cnv SeaTerm version 1 59 was used to communicate with the SBE35 and save the bottle files The deck unit must be switched on Connec
96. ata cycles to absent A description of how to use mplxyed is described here using the bathymetry data A matlab session should be started and m setup need to be entered at the matlab prompt gt gt pwd ans local users pstar jr265 data sim gt gt mplxyed mplxyed Enter name of input disc file Type name of mstar file e g sim jr265 d335 smooth Data Name sim 1265 4316 version 11 site jr265 atsea Platform ship RRS James Clark Ross Cruise 195 Instrument dpthi 999 00 dpthw 999 00 Position lat lon 999 00000 999 00000 Position lat lon 999 00 000 999 00 000 Data time origin 2009 01 01 00 00 00 Fields 5 Dimension sets set nrows ncols 121 37903 37903 name units dims min max nabs absval 1 time seconds 1 27216000 000 27302397 000 0 99999 000 2 depth feet feet 1 00 7170 660 0 99999 000 3 depth m 2150 2185 620 21619 99999 000 4 depth fathoms Fathoms NaN NaN 37903 99999 000 118 5 deltat seconds 1 1 000 796 000 0 99999 000
97. ate can be increased to speed up fill flush but the advantage is very marginal 11 4 Potential problems If difficulty is encountered obtaining a stable reading the external pump can be turned off to prevent the sample running out 74 When running the SSW the salinometer display should be within 20 in the last digits compared to 2 15 If it is more than this the salinometer may need the RS trim knob adjusting but this should be avoided if at all possible it is best to keep the same RS trim value throughout a cruise If large offsets 0 1 PSU or more are seen in the salinometer CTD comparison this may be due to the second decimal place in the salinometer readout not being noted correctly The 1 decimal is usually constant but the second sometimes changes un noticed by the operator Air in cell The Autosal can be used without an external pump but in this case the internal pumps require an airtight seal to be made around the neck of the sample bottle at the sample intake tube The external pump removes this requirement and also allows quicker filling of the conductivity cell However a potential drawback is that the external pump requires a longer sample intake tube and this can harbour bubbles which may significantly affect the conductivity reading In the absence of an external pump air can be prevented from entering the cell uptake tube by turning the internal pump to low when the tube was not submerged The pump was turned to
98. averaged data Don t touch this LTA 600 for 10 minute averaged data 132 User Exits tab h Simulated Inputs tab SL MOF Amira Ds Somma Vow Fa Toten rs erry EJ 1 EET 2 Coma tee bas com MEL DSL ees j Cera an he n oem Page i Don t enable or use any of this Collect real ADCP data from a serial port Collect real NMEA data from a serial port 7 To start the ADCP pinging and collecting data click on blue arrow in top left corner under File menu looks like a play button or click on go in the Control menu If it is working the log screen should run through a number of commands and eventually say something like ADCP pinging and then disappear and data should appear and change regularly 8 To stop the ADCP pinging either click on stop in the Control menu or click on the blue square in the top left hand comer 133 9 To change the data display use the Chart menu and or f 21272 _ the toggle buttons gt M To find out more see the VmDas User s Guide which is on the ship in both printed and electronic format Note on command files Command files have been created for different scenarios personnel on cruise depth need to calibrate instrument These be found in C ADCP Comma
99. ay with salt sampling log sheet Appendix D to sample salt Do sampling without gloves Before sampling put just enough clean plastic inserts into a little cup or clean plastic bag Use a clean piece of blue roll and between use leave it on a clean dry surface eg the logsheet not on a salty aluminium box or chair 1 Empty sample bottle giving it a good shake as you do so 2 Open tap by pressing with fingers not the sample bottle you can chip or break the bottle on the metal pin 3 Rinse the bottle 3 times each time half fill with water give it a shake and empty completely Use the last rinse to pour over the NISKIN tap to rinse it of surface water or drips from the frame Fill the bottle by holding in the water stream not against the tap Fill to halfway up the shoulder of the bottle Rinse the black cap in the water stream Dry the outside of the bottle neck NOT the inside Put clean plastic insert in neck Do NOT rinse the insert Make sure it is pressed all the way in if it wont go in use another one OO GON son aS 9 Dry the inside of the black lid do it up and place the bottle the right way up in the crate unused bottles should be upside down 10 Write salinity bottle numbers in log sheet against CTD Niskin bottle numbers 11 When the crate is full place it in the Bio Lab next to salinometer and make a note of the date and time on the logsheet 2 5 SBE Data processing SBE data processing was c
100. bilisation the salinometer was set up by adjusting the RS trim knob until the reading agreed with 2 value of the SSW The Bio Lab is not a constant temperature lab but is surrounded by other labs and is as far from external doors as possible The salinometer bath temperature was set to 24 degrees and the lab temperature was kept at about 22 degrees Unlike previous cruises no problems were encountered in keeping the lab at roughly the correct temperature but see Yelland 20092 for problems on JR195 and their solutions Standard seawater SSW batch P151 was used throughout the cruise P151 has a Kis of 0 99997 i e 2 5 1 99994 Table 11 1 contains the SSW readings obtained at the start and end of each crate of samples plus the standby and zero values at the start and end These latter values are an indication of electronic drift The salinometer was very stable apart from a small shift that occurred in the measurements of the SSW and in the standby and zero values that occurred between the analysis run 71 before after day 338 339 shown in bold in the Table The reason for this small shift is not known The following sections describe how to set up the salinometer at the start of a cruise and how to re standardise if the bath temperature is changed the procedure for obtaining bottle samples and how they should be stored obtaining a stable lab temperature routine operation of the salinometer once it is set up and potential probl
101. bottle should be used each time We are aiming for 0 001 PSU accuracy i e conductivity display good to 5 in the last digit Experience of an open SSW bottles showed that after being open for just 1 hour the salinity had increased by 0 01 PSU i e an order of magnitude greater than the accuracy we need Make sure that the second digit is noted properly there were at least two occasions when this digit was wrong and the salinity value was way out 73 1 Note bottle details time date and lab temperature Get zero and standby value Work out twice the conductivity k ratio shown on the SSW vial label and note on the log sheet Appendix D 2 Gently agitate the bottle to mix out any salinity gradients which can develop in the standards and samples Don t shake it this introduces small bubbles 3 Check function knob is on STANDBY whenever flushing filling If cell is empty at any time when knob is on READ turn to STANDBY fill and leave for 1 hr to recover 4 Turn the flow rate on the salinometer to full and leave it there Switch on the external pump to its first setting and leave it there 5 Open the SSW vial and insert the sample intake tube using a tissue to hold the tube The tube should be wiped before and after each sample 6 Fill and flush the cell 3 times 7 Allow the chamber to refill make sure there are no bubbles in the cell and switch the function knob to READ 8 If the display is flashing adjust the suppress
102. calibration results for previous cruises e eee 48 Table 8 1 Meteorological instrument properties esee eere eerte ee eren eerte nete nte 59 Table 9 1 Underway SST and salinity instrument details eee 65 Table 9 1 example TSG salinity calculation excel file eere 67 Table 10 1 JR265 ARGO Float Deployment details 70 Table 11 1 Standardisation history of the salinometer used on JR265 72 Table A 1 Scientific events obtained from the bridge 1 222 104 Table A 2 Bridge weather observations eee sees eee eee ee enne tense etant tense tease tona 106 LIST OF FIGURES Figure 1 1 CTD section across Drake 14 Figure 1 2 The JR265 and JR254D science team arriving at Rothera 16 Figure 2 1 Potential temperature across JR265 Drake Passage section 30 Figure 2 2 Salinity PSU across JR265 Drake Passage 30 Figure 2 3 Density across JR265 Drake Passage 0 0 00 00 31 Figure 2 4 Nominally calibrated dissolved oxygen concentration 31 Figure 2 5 Nominally calibrated chlorophyll fluorescence 1 4 32 Figure
103. code expects the XXX number to increment so the data collection should be stopped and immediately restarted cach day if the data is being processed during the cruise The file number should be changed in OS75_JCR_JRNNN and the program run Data can then be checked for problems or used 135
104. coefficients for each sensor Save as you go along 2 Print the CON file report and cross check against calibration sheets again to catch any typing mistakes 3 Save the final CON file under the JR265 cruise directory ready for use on the first station SBE Data processing set up Data Conversion settings Process scans to end of file selected Scans to skip over 0 Output format ASCII Convert data from Upcast and downcast Create file types both data and bottle files Source of scan range data Scans marked with bottle confirm bit Scan range offset 0 Scan range duration 2 Merge separate header file selected Selected Output Variables Pressure in db Primary and secondary conductivity in mS cm 107 Primary and secondary temperature ITS 90 in deg Scan count Pressure temperature in deg C Altimeter in m Time elapsed in seconds Oxygen SBE43 in umol kg PAR irradiance Beam transmission and beam attenuation note that we used a calibration based on transmission relative to water Fluorescence Oxygen Voltage SBE43 Voltage V4 transmissometer voltage AlignCTD settings To find the optimum setting for the oxygen measurement the deep test station 901 was used The shallow test station 900 could not be used to determine the settings as oxygen gradients were not significant enough Align CTD was run multiple times with the oxygen data advanced by 0 2 4 6 8 and 10
105. creasing tell winch driver 90 m to go Check altimeter height and wire out reading Wire out altimeter reading depth to go Underwater Unit error may be indicated by alarm on Deck Unit ok if occasional but 1f persistent then problem with the termination call the technician e When altimeter starts reading call out distance from the bottom and stop at 10 m though higher depending on sea state and or bottom slope At bottom wait for 10 15 s for things to settle Go to View gt Fire gt Bottle Control to bring up the bottle firing window 24 Close the first bottle Red light will come on briefly Wait for a further 10 s for SBE35 to capture if set to 8 sec and bottle firing power to recharge fire other 2 bottles as required and using the same waiting routine Fill in the Cast log sheet Appendix D with appropriate pressure temp and sal values Up to next depth fire 3 bottles allows for 2 missing bottles following the waiting times as above 10 15 s after arriving at firing depth and 24 s after closing each bottle Continue up to surface firing bottles at chosen depths and filling in Cast Logsheet Fire all remaining bottles at the surface Complete Cast Logsheet DO NOT SWITCH THE DECK UNIT OFF until the SBE35 data are downloaded see next section Click RealtimeData gt Stop Acquisition 2 4 3 Immediate post cast operations Niskin bottle sampling protocol Go down to CTD b
106. dard deviation of the residuals to the Primary CTD salinity is only 0 0021 9 4 2 Calculating sample salinity The conductivity ratio of each sample was measured by the Autosal salinometer Section 11 The conductivity ratios were recorded and salinity was calculated using a Microsoft Excel 95 spreadsheet along with the date and time of collection The measured salinities of the samples were transferred to text files using matlab script convert tsg ascii2 NB this script will not work with excel 98 format files and looks for file names including TSG The script expects the excel file to have 9 header lines for SSW measurements and offsets etc followed by up to 24 rows corresponding to bottles with salinity in column 4 the first column being non numeric bottle number eg1 1 and the jday in column 9 see table 9 1 for an example file If the sample column is entered as numeric values eg 1 2 3 the script will need to be edited Any unused bottles should have a blank value entered for Salinity 15 label 0 99997 Label Std 0 0005 0 0056 0 0066 0 0375 0 0636 0 0144 K15 2 1 99994 Label 2 0 0162 SSW Measured meas 1 99994 Std stndby stndby Scorr 0 00000 Correction start 6091 end 6090 Rs 5 7 zero start 0 0001 zero end 0 00015 lab tmp lab temp start 23 end 22 Sample Data Crate 1 Bath CTD Samp Temp G Ratio Salinity Rt Sal 1 Sal 2 stn jday 4 1 24 1 93486 33 7218 0 967
107. data directory under mnt on nosea2 set where pwd find current directory set d date y m d_ H M used to set tar and log file names if 0 t backup then echo Backing up nosea2 cruise directory rsync aSv e ssh delete pstar nosea2 cruise Volumes vol cruise nosea2_ cruise gt Volumes vol Scruise nosea2 rsync d cd Volumes vol Scruise nosea2 S cruise tar cf Volumes vol cruise nosea2_ d tar cruise cd where else if 0 t backup 16 then echo Backing up Ibdata folder for cruise from nosea2 mnt Slbdata rsync a v e ssh delete pstar nosea2 mnt lbdata Volumes vol cruise Ibdata_ cruise gt Volumes vol cruise Ibdata_rsync d cd Volumes vol cruise Ibdata_ cruise tar cf Volumes vol cruise Ibdata_ d tar lbdata cd where endif 13 ICT CRUISE REPORT Johnnie Edmonston 13 1 Netware system No problems were encountered with the netware systems 13 2 Unix Systems All unix systems on board presented no problems during the cruise Nosea2 on board for the purpose of the cruise and administered by Brian King had the cruise data area mounted for MSTAR processing 13 3 Linux Systems Linux Systems including AMS3 jrla jrlb presented no problems during the cruise AMS was syncing on schedule but from time to time individual users would wait several hours at a time as the system presumably struggled with large quantities of mail and or large attachments 76 13
108. data highlighted in red These data were collected during a period of higher wind speeds as shown in Figure 8 5 Wind speed and direction The windmaster sonic anemometer was located on the bird table Only data from one anemometer was logged by the ship system so no comparisons with other anemometers were made There were no obvious instrument problems during the cruise A comparison with the AutoFlux anemometer mounted on the foremast platform will be made in the WAGES JR254D cruise report Yelland 20122 and PAR sensors The ship carried two total irradiance sensors and TIR2 on the bird table These measure downwelling radiation in the wavelength ranges given in Table 8 1 The mean difference between the two sensors was 6 5 W m TIR2 higher than with a st dev of almost 10 W m During darkness both the TIR sensors had a very small 0 5 W m offset In addition to the TIR sensors the ship carried two PAR sensors which measured downwelling radiation The mean difference between the two PAR sensors was 2 5 W m PARI higher than PAR2 std dev 7 5 9 UNDERWAY TEMPERATURE AND SALINITY Helen Snaith 9 1 Introduction Near surface oceanographic parameters were measured by sensors located on the non toxic supply These included a Fluorometer which measures fluorescence and a SBE45 thermosalinograph TSG measuring conductivity and water temperature at the point it reaches the instrument The TSG S N 0016 was re
109. de the water depth and other information are listed in Table 2 2 Bad weather led to a 45 hour break in science between stations 009 and 010 19 Additional details are given in Appendix B 1 gives details on pre sailing setup mobilisation B 2 the bottle file formats B 3 SeaBird instrument calibration B 4 calibration details contained in the SeaBird Configuration file B 5 a detailed explanation of the MSTAR processing that is summarised in Section 2 6 est time distance est time Station Lat S Lat min Lon W Lon min Depth to next to next m station station station hh mm nm hh mm 900 50 0 30 10 1 00 901 53 30 0 58 04 36 2300 2 30 70 2 6 06 1 54 40 00 58 00 0 250 0 30 15 4 1 20 2 54 55 34 58 00 0 600 0 30 3 3 0 17 3 54 58 6 58 00 0 1000 0 50 1 6 0 10 4 55 0 39 58 00 0 1500 1 10 12 1 00 5 55 04 20 58 00 0 2000 1 30 3 1 0 15 6 55 07 26 58 00 0 2500 1 40 2 9 0 15 7 55 10 16 58 00 0 3000 2 00 2 7 0 14 8 55 12 86 58 00 0 3700 2 30 18 2 1 34 9 55 31 00 58 00 0 4200 2 50 20 2 1 45 10 55 50 00 57 49 23 4800 3 00 20 2 1 45 11 56 09 00 57 37 45 3400 2 20 20 1 1 45 12 56 28 00 57 25 67 3800 2 30 20 1 1 45 13 56 47 00 57 13 90 3200 2 00 20 1 1 45 14 57 06 00 57 02 12 3700 2 30 20 1 1 45 15 57 25 00 56 50 35 3700 2 30 20 1 1 45 16 57 44 00 56 38 57 3400 2 00 20 1 1 45 17 58 03 00 56 26 79 3900 2 30 20 1 44 18 58 22 00 56 15 02 3800 2 30 20 1 44 19 58 41 00 56 03 24 3800 2 20 20 1 44 20 59 00 00 55 51 47 3800 2 20
110. del Serial Number Calibration date Pressure SBE SBE 9 0771 20 07 2010 CODES SBE SBE 04 1912 25 06 2010 primary Conductivity SBE SBE 04C 041912 25 06 2010 secondary Temperature SBE SBE 03 4874 25 06 2010 primary a SBE SBE 03 2191 23 06 2010 secondary Oxygen SBE SBE 43 0242 21 01 2009 Chelsea Fluorometer Technologies Aquatracka MkIII 0088 3598C 09 11 2009 Group Ltd Transmissometer WETLabs a eli CST 846DR 16 02 2011 PAR sensor QCD 905L4S 7274 23 03 2011 Instruments Inc Altimeter Station System 900 013 Technologies PA200 20 6K8 7742 163162 30 05 2007 Altimeter Stations System 014 030 Technologies 200 20 6 8 2130 26993 03 12 2008 High Precision SBE SBE 03Plus 03P2191 23 06 10 Temperature Table 2 3 Details of the sensors model serial numbers and calibration status The mapping between sensors and voltage channels was found to be as follows VO PAR V1 empty V2 fluorometer empty V4 transmissometer V5 empty oxygen V7 altimeter 22 2 3 Deployment The CTD was deployed from the mid ship s gantry The deck unit was turned on before the CTD was moved The deployment procedure was to start data logging on deck with the pressure noted on the log sheet The CTD was deployed and lowered to 10 m of cable out The pumps were automatically water activated and should come on 60 seconds after the CTD is in the water on station 0
111. duals calculated and examined Again no trends were found in the residuals just a simple offset for each cell The calculation of bottle sample conductivity and residuals was carried out in a matlab script stuff m Prior to calibration the statistics were mean botc ucond1 SD 0 00234 0 00096 150 of 153 samples C2 mean botc ucond2 SD 0 00500 0 00133 146 of 153 samples therefore an offset of 0 0023 was applied to 1 and 0 0050 applied to cond2 in the 24 Hz files after saving the original as a back up and new PSALI and PSAL 2 calculated do morestuff m Next re run the following grouped into ctd all part4 mdes 05 mctd 03 mctd 04 mfir 03 mfir 04 02 oO o o msam 02 re creates the residual files for each station so they can be appended into a new summary file and the statistics for the calibrated salinities calculated If you have done the calibration correctly the new means should be zero and the standard deviations similar to the pre cal values For JR265 after conductivities were calibrated and salinity recalculated the statistics were calibrated S1 mean botpsal upsall SD 0 0000 0 001 150 of 153 samples calibrated S2 mean botpsal upsal2 SD 0 0002 0 001 147 of 153 samples 2 8 Initial results The following figures show the data across the Drake Passage transect as a function of distance from CTD station 001 in the north to
112. e window Using the cross hares click a box around the early part of the time series were the data is noisy 119 X Figure 1 File Edit Yiew Insert Tools Desktop Window Help a Deug i aan Enl na NUI 2200 gt 2100 a 155 2 o 3 2000 1900 1800 1700 1600 1500 1400 1300 1200 30 0 30 60 90 120 150 180 210 240 270 Start 20031112 daynum 315 000000 dc 1 time Stop 20031112 daynum 316 235857 dc 37303 minutes after start time we can now select the obvious outliers as absent At the action point in the matlab window press s You are taken to the depth vs time window Use the cross hares select the data you wish to set to absent see cyan box below X Figure 1 File Edit View Insert Tools Desktop Window Help Deug i aay 2200 2100 depth m 2000 mplxyed 2008 11 15 12 1900 1800 1700 1600 1500 1400 1300 1200 30 0 30 60 90 120 150 180 210 240 270 Start 20031112 daynum 315 000000 dc 1 time Stop 20081112 daynum 316 235957 dc 37903 minutes after start time At the action point in the matlab window press w This shows you the data without the data cycles you have select If you are happy press e which will edit selected data to absent NaN in matlab After repeating this a few times the window has lots of cyan boxes around so lets refresh it using r Repeat this process and the data will look something like 120 X Fi
113. ean angle notes JR276 April 2011 water 1 0179 1 1023 CODAS processing JR276 April 2011 bottom 1 0116 1 0564 CODAS processing JR195 Nov 2009 water 1 0155 0 2060 CODAS processing JR195 Nov 2009 bottom 1 0381 10 6080 CODAS processing JR200 Mar Apr 2009 water 1 0150 0 0876 JR177 Jan 2008 water 1 0124 0 0559 JR165 Mar Apr 2007 1 0127 0 0078 JR158 Feb 2007 water 1 0161 0 1245 JR161 Oct Dec 2006 bottom 1 0127 0 0481 Table 4 3 Mean calibration results for previous cruises Note that this software sometimes outputs a decimal day calculated from time in seconds since the start of the year Decimal day is 0 5 for noon on the 1 January this contrasts with a jday of 1 5 for noon on 1 January Below is a summary of the processing steps UH HTML documentation in local users pstar cruise sw uh adcp programs adcp doc index html 1 Created once at start of cruise data vmadcp jr265_os75 data vmadcp jr265_os75 rawdata 2 For dataset NNN eg NNN 002 copy raw data files ENX NIR etc from mnt data cruise jcr current adcp into local users pstar jr265 data vmadcp jrCCC_os75 rawdata file names like OS75 JR265NNN 000000 ENX NNN increments each time the ADCP logging is re started Data logging was stopped and started once every day The 000000 increments each time a new file is started when the previous one reaches 10 Mb raw files are automatically transferred to mnt data cruise jcr current adcp
114. ed to deck 03 12 2011 19 33 30 wave buoy 8 59 0004 55 85178 Commence deployment of wavex buoy from stbd quarter 03 12 2011 19 35 30 wave buoy 8 59 0005 55 85255 Buoy in water 03 12 2011 19 38 30 wave buoy 8 59 00082 55 85488 Wave buoy fully deployed and secure 03 12 2011 19 44 30 CTD 20 59 00087 55 85527 CTD deployed 03 12 2011 30 wave buoy 8 59 00081 Ship moving 302 degrees at 0 1 knots Ship heading 267 degrees Buoy leading 060 degrees 94 19 55 55 85548 03 12 2011 20 00 30 wave buoy 8 59 00004 55 85781 Ship stationary Vessel heading 267 degrees Wave buoy bearing 055 degrees 03 12 2011 21 00 30 CTD 20 59 00005 55 85779 depth 3752m 03 12 2011 21 01 30 wave buoy 8 59 00004 55 85965 Commence recovery of wavex buoy 03 12 2011 21 47 30 wave buoy 8 58 99995 55 86049 Wavex buoy recovered to deck 03 12 2011 21 58 30 CTD 20 58 99997 55 86048 CTD recovered to deck 03 12 2011 22 18 30 APEX 5 59 55 86207 Apex float deployed 04 12 2011 00 27 31 CTD 21 59 33347 55 65163 CTD deployed 04 12 2011 00 33 31 CTD 21 59 33343 55 65165 CTD veering to approx 3700m 04 12 2011 00 38 31 CTD 21 59 33335 55 65112 CTD stopped 3736m 04 12 2011 01 41 31 CTD 21 59 33332 55 65114 CTD recovered to deck 04 12 2011 04 57 32 CTD 22 59 66698 55 44535 C
115. ems which can be encountered during routine operation end SSW SSW stndby stndby Zero Zero jday crate start start end start end start end 334 standardisation 1 99995 n a 6094 n a 0 0001 n a WAGES TSG 334 orangel2 0 00003 1 99995 1 99998 6094 6094 0 0001 0 0001 334 orange23 1 0 00001 1 99998 1 99997 6094 6094 0 0001 0 0001 334 orange38 0 00001 1 99997 1 99998 6094 6094 0 0001 0 0001 337 bluegreen10 0 00000 1 99997 1 99997 6093 6093 0 0 BEEyellowblack 337 TSG 0 00000 1 99997 1 99997 6093 6093 0 0 337 orange30 0 00001 1 99997 1 99998 6093 6094 0 0 340 orange26 0 00001 1 99992 1 99993 6090 6091 0 0002 0 0001 340 redyellowA 0 00000 1 99993 1 99993 6091 6091 0 0001 0 0001 341 orange23 2 0 00001 1 99993 1 99994 6090 6091 0 0001 0 0001 341 blackyellowB 0 00000 1 99994 1 99994 6091 6091 0 0001 0 0001 341 green4 TSG 0 00000 1 99994 1 99994 6091 6090 0 0001 0 0001 Table 11 1 Standardisation history of the salinometer used on JR265 Note that the 2 value of P151 was 1 99994 Throughout the analysis SSW batch P151 was used RS trim was 5 7 and bath temperature was 24 throughout Bold indicates a small shift in standardisation values which was accompanied by a small shift in standby and zero values 11 2 Running the Salinometer Autosal 11 2 1 Initial setup of the Salinometer The salinometer should be s
116. en by D D D U C is given by C C CGU GU Tois given by T TU T U 7 07 The conductivity sensor was calibrated following cong rhs tif I 10 i 0t 6 where is pressure t is temperature and 6 CTcorr and Cpcorr The temperature sensor was calibrated following 109 Temp TS 90 xi 273 15 h n f P an f P yl where fis the frequency output by the sensor The oxygen sensor was calibrated following where V is voltage output from SBE43 T temperature S Salinity Oxsat T S is oxygen saturation and P pressure while Soc Tcor Pcor are the constants from calibration sheet characteristic to instrument PAR Irradiance sensor was calibrated following where calibration constants M and B are dependent on sensor type V is output voltage while multiplier cal const and offset are the constants from calibration sheet characteristic to instrument Fluorometer was calibrated following where V is output voltage measured by CTD and VB V1 Vacetone SF offset are the constants from calibration sheet characteristic to instrument B 4 Seabird CTD configuration file as used throughout JR265 Date 12 15 2011 Instrument configuration file C Documents and Settings ctd Desktop JR265 jr265config xmlcon Configuration report for SBE 911plus 917plus CTD Frequency channels suppressed 0 Voltage words suppressed 0 Comput
117. end Outliers are samples with large differences that can be caused by mistakes in files or samples 28 from high salinity gradient regions where the bottle may not be sampling the same water as the CTD but are often due to contaminated samples A large difference might be greater than 1 standard deviation from the mean You might typically find 2 to 4 outliers per 100 samples and those can be excluded from the analysis It is also common for there to be higher variability in the residuals in water shallower than 1000m where the salinity gradients tend to be higher If the scatter is significant above 1000m it can be useful to use only the deeper samples to obtain a calibration but it is better to pick shallow sampling depths where gradients are lowest in order to make use of the full range of salinities measured On JR265 a total of 153 samples were taken of which up to 7 were considered outliers Plots showed that there were no trends with pressure or time just a simple offset for each conductivity cell Prior to calibration the statistics were S1 mean botpsal upsall SD 0 0027 0 0008 150 of 153 samples 52 mean botpsal upsal2 SD 0 0060 0 0012 146 of 153 samples Salinity calibrations are best carried out by actually calibrating conductivity which has the added benefit of taking care of any pressure effects To do this the conductivity of the bottle samples need to be derived and the conductivity resi
118. er interface RS 232C Deck unit Firmware Version gt 5 0 Scans to average 1 NMEA position data adde No NMEA depth data added No NMEA time added No Surface PAR voltage added No Scan time added No 1 Frequency 0 Temperature Serial number 4874 Calibrated on 25 06 2010 G 4 30432453 003 6 35938529 004 2 05234495e 005 110 1 72243973e 006 F0 1000 000 Slope 1 00000000 Offset 0 0000 2 Frequency 1 Conductivity Serial number 3248 Calibrated on 25 06 2010 G 1 01194759e 001 H 1 52674111e 000 I 4 22561427 004 J 4 58098975e 005 CTcor 3 2500e 006 CPcor 9 57000000e 008 Slope 1 00000000 Offset 0 00000 3 Frequency 2 Pressure Digiquartz with TC Serial number 0771 Calibrated on 25 06 2010 CI 4 785925e 004 C2 3 416160e 001 C3 1 442400e 002 DI 3 781000e 002 D2 0 000000e 000 1 3 011158 001 2 3 924450e 004 T3 4 201770e 006 T4 2 250320e 009 T5 0 000000e 000 Slope 0 99992000 Offset 0 89300 AD590M 1 284610e 002 AD590B 8 492760 000 4 Frequency 3 Temperature 2 Serial number 2191 Calibrated on 23 06 2010 G 4 31985118 003 6 39204988 004 2 30432597 005 1 2 23447131e 006 0 1000 000 Slope 1 00000000 Offset 0 0000 5 Frequency 4 Conductivity 2 Serial number 1912 Calibrated on 25 06 2010 G 4 16170047e 000 111 5 36176393
119. ere nennen entere ener enne 25 2 5 SBE DATA PROCESSING ite piece res be e e uei ir er ee 25 2 6 MSTAR DATA PROCESSING etenim bee eee drei eir esee 27 2 ERI 28 2 TO PFOSSMFO EUR ERE M atu eui 28 2 7 2 e ec eto oe e een i t tet e oes 28 De PS Saliniiy taxe oo MM LIAS SA Deos o DAs Att Ae al Ss Medeiros tp Me der doeet ee Lets e 28 2 6 INITIAL RESULTS eret Re Y ERN Ere ep ert Ok RENS MENSES SERIE IERI OTRO OTHER 29 LOWERED ACOUSTIC DOPPLER CURRENT PROFILER 0 2 2 33 3 J INTRODUCTION cO cet E stented des cdurtuaephetseveus a 33 BD WADCP SET UP Pm amo I US 34 3 2 PRE DEPEOYMENGT reete are REV E ee m a tr NB des 35 3 4 DEPEOYMENT s eere iet e ent 36 RECOVERY e L 36 3 6 INITIAL DATA QUALITY CHECK 5 ee get te ceste tegit tero eve 37 J T DATA PROCESSING E deo rede 39 ZI UHDAS processing io e EC e EORR ERE 40 S AZ EDEO processings sis aan MEHR 43 3 8 LL ADGCP PROBEEMS ON JR205 t E e o FEET 45 VESSEL MOUNTED ACOUSTIC DOPPLER CURRENT PROFILER e eere etes 45 119 ME 45 4 2 INSTRUMENTATION cra eet ono o
120. erway data streams 1 Convert SCS data stream to daily mstar format files using mday_00 instr jday 2 Perform basic cleaning of the raw daily files removing duplicate or backward timesteps and data outside acceptable ranges using m 01 jday scripts At the end of this step optional manual data file editing could be carried out using mp xyed to remove further spikes see Appendix C 2 for more details 3 Merge edited daily files with other data streams as necessary eg merging navigation streams or adding navigation using mmerge scripts 4 Appending merged daily files to generate single best file for the entire cruise using mday_02 dir instr jday 5 Carrying out final processing of cruise files This scheme meant that the different streams could be easily scripted either to run processing daily or to re run an entire stream Eg mday 00 get all jday will run mday 00 for all instruments active on the ship and generate the daily raw files for day jday Appendix C 1 details the daily processing schedule 53 6 NAVIGATION Helen Snaith 6 1 Instrumentation 6 1 1 Seapath system The primary accurate navigation system onboard the JCR is the Seapath 200 logged via the seatex SCS data streams at 1Hz In addition to position seatex gll ACO files the Seapath system outputs heading in the seatex htg file and heave and roll via the seatex psxn ACO files Unfortunately there is no ind
121. es to be taken at least every 4 hours Once crate is full move to BIO LAB and NOTE DATE AND TIME SAMPLE NUMBER label on bottle JDAY or date TIME GMT i e ship t 3 hours COMMENT 127 SALINOMETER OPERATION LOG SHEET Ship Cruise JR265 2011 Day date Analyst Lab Temp Start End Cell temp SSW Batch K15 2 15 Crate No Colour Standby Start Zero start Rs set Stanby End Zero End File name Sample number Guildline Ratio measured Comments final value 128 JR2 65 Watch keeping sheet complete every 4hours Ea600 ADCP TSG JDAY Time Depth m SCS Wind spd NAV feed Ensemble Flow AirT C Varying Time of Salinomet GMT logging number l min T S Chl sample er Lab T RR 129 APPENDIX E VM ADCP SETUP 4 Run VmDas icon on ICR ADCP Turn ADCP on at the wall switch above monitor labelled ADCP Power needs to be switched to ON and should light up red Check there is sufficient space on the hard drive at least 3GB Make sure the Navigation Repeater is running find this in the Start menu JR165 is now the default no need to crea
122. es were filled to half way up the shoulder and the necks were wiped dry to prevent salt crystallisation at the bottle opening The bottles were closed using airtight single use plastic inserts and secured with the original bottle caps just as done for CTD salinity samples The samples were stored in open crates and left beside the salinometer in the bio lab for a minimum of 24 hours before analysis This allowed their temperature to adjust to the ambient temperature of the laboratory A total of 38 TSG samples were taken over the duration of the cruise Using the surface salinity values from the near surface CTD casts see Section 9 2 we were able to carry out a secondary check on the TSG salinity values In total 29 out of the 32 stations were used in the analysis The uncorrected surface salinities from the CTD were used in this analysis This is believed to be acceptable as the usual correction to be applied to the measured surface 66 CTD salinities will be of the order 0 01 whereas the correction for the 45 will be of the order 0 1 The merged underway salinity and the CTD values are contained in the file created in Section 9 2 ocl jr265 001 merge nc Prior to calibration with the sample data the TSG salinity already has a small difference with the uncalibrated CTD salinity For the two CTD conductivity cells the regressions give Salsa Saler 0 005153 7 557e 09 x time Salsa Sal 0 001938 1 097e 08 x time And the stan
123. et up on the bench in the bio lab at least 24 hours before use to allow time for the water bath to equilibrate to room temperature and to perform checks Connect the deionised water supply Millipore to the tank fill drain nozzle and run a tube from the tank overflow to the drain sink all pipes are push fit Make sure the tank fill drain valve is open and fill the chamber until water runs out of the overflow tank is about 18 litres Turn the cell drain knob on bottom left Turn off the water supply Close the tank drain fill knob and remove the tubing from the nozzle Making sure the standby read zero switch is set to standby turn on the unit at the mains Set the bath temperature to 2 3 C above the lab temperature bath was set to 24 C in the bio lab on JR265 Both heating lamps in the water bath should come on until the water has come to the right temperature Once up to temperature one lamp stays on and the other flashes intermittently to maintain the bath temperature a few degrees above ambient The check check heater lamp also flashes intermittently but if it is ALWAYS on then there is a lamp problem A short length of tubing should be connected to the cell drain valve Ideally this should drain into an isolated bucket that it does not touch The cell drain must not provide an electrical path to ground nor must it be long enough to cause a siphoning effect out of the conductivity cell meaning the cell does not fill fully after
124. etting on board Seth Thomas BAS AME saved the WAGES scientific bacon by working all hours during mobilisation to build replacement circuit boards for the MotionPak interface 12 1 OVERVIEW Margaret Yelland 1 1 Introduction and background The research cruises JR265 and JR254D began from Mare Harbour Falkland Islands on the morning of the 27 November 2011 and finished at Stanley Falkland Islands on the 24 December 2011 The objective of JR265 was to perform a CTD section across Drake Passage Figure 1 1 repeating the measurements made during previous research cruises for the purpose of long term monitoring The aim of JR254D was to deploy a wavebreaking buoy Pascal et al 2011 and an aerial whitecap camera system in a range of wind speed and sea state conditions WAGES activities are summarised in this cruise report but are described in detail in a separate report Yelland 2012a A third cruise JR264 was run by staff from NOC Liverpool with the aim of recovering and deploying various Bottom Pressure Recorders which have been deployed across Drake Passage and elsewhere on the Antarctic Peninsular for more than 20 years NOC L also serviced various tide gauges in the Falkland Islands and along the Antarctic Peninsular JR264 is described in detail in a separate cruise report Morales Maqueda in prep 1 1 1 WAGES JR254D was one of a series of Intensive Observation Periods IOPs for the Waves Aerosol and Gas Exchange Study
125. face 20mins 05 12 2011 10 21 44 BPR 2 60 84833 54 71593 BPR sighted at surface 05 12 2011 10 49 44 BPR 2 60 84682 54 71528 BPR recovered to deck 05 12 2011 11 00 44 BPR 2 60 85239 54 71058 Signal to BPR sent 05 12 2011 11 11 44 BPR 2 60 85341 54 7095 BPR sighted at surface 05 12 2011 11 32 44 BPR 2 60 84777 54 71171 Buoy hooked 05 12 2011 11 45 44 BPR 2 60 84767 54 71151 BPR on deck 05 12 2011 11 48 44 BPR 3 60 84933 54 7112 BPR released 05 12 2011 12 17 44 BPR 2 60 84932 54 71125 Buoy on seabed 05 12 2011 12 37 44 BPR 3 60 84933 54 71125 Vessel off DP Boxing in on BPR 05 12 2011 12 40 44 BPR 3 60 85094 54 71148 Buoy boxed in proceeding to CTD site 29 05 12 2011 45 CTD 29 61 05111 CTD deployed 100 13 58 54 58701 05 12 2011 14 07 45 29 60 98145 54 62983 CTD veering to approx depth 560m 05 12 2011 14 11 45 CTD 29 60 98118 54 63001 CTD stopped at 520m 05 12 2011 14 21 45 CTD 29 60 98113 54 63006 CTD recovered to deck 05 12 2011 15 19 46 CTD 30 61 05022 54 58776 Vessel on D P at CTD site 30 05 12 2011 15 23 46 CTD 30 61 05011 54 58723 Commence deploying CTD 05 12 2011 15 26 46 CTD 30 61 05012 54 58726 CTD deployed and soaking 05 12 2011 15 28 46 CTD 30 61 05012 54 58725 CTD veering to near bottom
126. flushing 72 When not in use the conductivity cell should be filled with deionised water Flush the cell by placing a finger over the flush hole until completely drained and no significant flow 1s coming out of the cell drain tube Refill Repeat at least twice When filled with deionised water switch the function knob to read and turn the suppression knob fully anticlockwise The readout should be no higher than 0 020050 When finished with the reading switch back to standby Then switch off the pumps leaving the chamber full Note that the function knob should never be switched to read unless the cell is full Doing otherwise can damage the cell and lead to unstable readings 11 2 2 Initial standardisation Use RS trim knob to set salinometer so that it reads the same as a standard sea water with 2 or 3 places in the last digit Suppression knob will need turning clockwise a long way until the display stops flashing and shows a positive reading This should only be done once at the start of the cruise unless serious problems are encountered Note that if the display on the salinometer is in ratio this is twice the value of the standard seawater marked k on the standards Note SSW should be stored on bench near salinometer so the sample is at lab temp 11 2 3 Taking bottle samples Procedure for sampling Niskin Bottles old sample bottles are upside down in the crate newly filled ones right way up Protect from contamina
127. g 000 T wave buoy leading 090 T since 0300 GMT 04 00 47 Wave buoy 11 62 66093 59 80348 vessel has moved 080 T x 0 42nm 15 12 2011 04 07 47 Wave buoy 11 62 66092 59 80085 Wave buoy clear of the water 15 12 2011 04 09 47 Wave buoy 11 62 66094 59 80081 Wave Buoy recovered on deck 16 12 2011 03 37 48 Myrtle recovery 60 61865 53 84551 V L stopped on D P 16 12 2011 03 42 48 Myrtle recovery 60 61862 53 84551 V L off D P carrying out figure of eight for Myrtle location 16 12 2011 05 06 48 Myrtle recovery 60 61878 53 85119 Completed fix for Myrtle Myrtle position 60 37 197 S 053 50 3459 W 16 12 2011 05 21 48 Myrtle recovery 60 61928 53 83866 V L on D P 16 12 2011 05 27 48 Myrtle recovery 60 62039 53 83987 stopped on D P For sending release command 16 12 2011 05 33 48 Myrtle recovery 60 62037 53 83985 Release command sent no confirmation 16 12 2011 08 40 48 Myrtle recovery 60 62035 53 83987 Release failed Decision taken to move off station 16 12 2011 08 46 48 Myrtle recovery 60 62042 53 83976 Vessel off DP heading East for swath survey 16 12 2011 09 31 48 Myrtle recovery 60 61818 53 84381 End of swath survey proceeding to recovery position for APEX whilst on passage to Signy 16 12 2011 13 58 49 APEX Recovery 60 62684 51 98521 V L on DP 16 12 2011 13 59 49 APEX Recovery 60 62636 51 98484 PSN received by email 16 12 201
128. gure 2 File Edit View Insert Tools Desktop Window Help Densa kaaya DEB File name sim jr195 d316 nc sim jr195 0316 vers jr195 atsea 7 3000 gt 2700 o Q o 2400 2100 1800 1500 1200 900 600 300 0 0 500 1000 1500 Start 20031112 daynum 316 000000 dc 1 time Stop 20081112 daynum 316 235857 dc 37903 minutes after start time When you are happy use the action q to quit out of mplxyed Now the IMPORTANT bit Copy the sim j1265 d316 smooth nc sim jr265 d316 nc We can do this in matlab by using gt gt copyfile sim_jr265_ d316 smooth nc sim jr265 d316 nc If the sim jr265 d316 nc file is not present the sim jr265 d316 raw nc file will be appended instead Retain edit copy of the file so you can use it if you need to reprocess data for this point on at a later date eg change the nav file and want to re merge the data 121 APPENDIX D LOG SHEETS Margaret Yelland The following log sheets are appended below e CTD deck sampling log used by the operator of the CTD deck unit CTD salt sampling log sheet partly filled in by the operator of the CTD deck unit then passed to the people taking the salt samples from the Niskin bottles e LADCP log sheet completed by the person setting up the LADCP before and after each CTD cast e TSG sampling log sheet completed by the person performing the watchkeeping check when sampling
129. he cruise or left until the end While the ship is steaming the main signal that the ADCP instrument records is the ship speed 12 knots 6 m s is 1 2 orders of magnitude greater than the water velocity This velocity is removed using GPS derived ship velocities but there is clearly the potential for a significant error associated with this process as the output data is the small difference between two large numbers To address this the velocity of the bottom can be measured and compared directly to the GPS velocity of the ship This should give the amplitude error for the ADCP and the misalignment with the ship heading This only works in water where the bottom track ping can reach the sea bed 800m or shallower In deeper water the processing uses changes in the ship velocity to assess what proportion of the ship velocity is contaminating the calculated water velocity This calculation necessarily invokes assumptions that the true water velocity is relatively constant in space if slowing down or time if turning round and is therefore considered less precise than bottom tracking Similarly to JR177 and JR200 a large number of water track data were collected during JR265 from slowing down and speeding up from stations Table 4 2 lists the calibrations obtained from bottom tracking or water tracking They are similar to calibrations found during previous cruises Table 4 3 Each daily file was approximately 24 hours long note that ensemble coun
130. he distance and a lone chinstrap penguin close to the ship 6 ARGO float 4998 deployed after CTD 023 JCR spent about 30 minutes doing engine checks WAGES buoy deployment 9 done during CTD 024 with Pudsey as passenger At the start of CTD 025 the pumps were very slow switching on They were tested after the cast and were OK pump was tested after the cast and seemed to be ok so left on WAGES buoy deployment 10 and balloon deployment 4 with Pudsey were done during CTD 025 CTD 026 had three 15 minutes stops at 1500 m 1000 m and 500 m to allow calibration of the other NOC L microcat 5 December jday 339 CTDs 027 030 NOC L team deployed APEX float before start of CTD 027 With 1580 m of wire out and an EO600 depth of 1630 m the altimeter had still not kicked in which it should at about 100 m off the bottom The cast was stopped while Johnnie switched the EM122 on briefly to check the depth This gave a reading of 1778 m so the cast was continued the altimeter detected the bottom when there was about 1640 m wire out and the cast stopped at a depth of 1729 m Given the under read on the EA600 on the previous cast the EMI22 was switched on briefly to check the depth before the start of CTD 028 depths agreed within 20 m so the EMI22 was switched off and the cast was carried out as normal NOC L then deployed and recovered BPRs from the deep 2000 m and shallow 1000 m sites they also deployed a FETCH mooring but this surfaced again
131. ication of which channels are which in the psxn files Instead the main system for measuring pitch and roll is the tsshrp system see Section 6 1 3 The data from the Seapath system are contained in directory data nav seapos Separate feeds from the Seapath system are used for the LADCP and VMADCP processing chains 6 1 2 Ship s Gyro The ships gyro on the bridge was logged via the SCS data stream as gyro ACO at 1Hz The gyro data were used to remove any large outliers in the Seapath system The data from this system are contained in data nav gyros 6 1 3 TSS Roll and Pitch The ship has a TSS pitch and roll sensor located in the grav room together with the Seapath pitch and roll sensors The data from this system are contained in data nav tss Early in the cruise it was found that the copy of the tsshrp ACO file in the data scs sed directory had approximately 30 corrupted lines at the top of the file These lines prevented the file being converted to matlab format successfully It was decided that these data were not essential during the cruise and that the disturbance to the other underway data outweighed the benefits of stopping the logging editing the data scs raw tsshrp ACO file and restarting the logging and sed script 6 1 4 Ashtech The Ashtech used to be the primary system for obtaining the most accurate measurement of the ship s heading and has been replaced by the Seapath and tsshrp systems Data from the Ashtech were collected
132. id J Cutting Glynn Collard James C Ditchfield Steven J Eadie Simon A Wright Nicholas J Dunbar Hamish James Gibson James Rudd George M Stewart Derek G Jenkins Clifford Mullaney John J McGowan Colin J Leggett John P O Duffy Anthony J Estibeiro Mark A Robinshaw NOC S BAS Rothera University of Reading NOC S NOC S BODC NOC S University of Leeds NOC S NOC L NOC L NOC L BAS AME BAS AME BAS ITC Master Chief Officer 2 Officer 3 Officer ETO Comms Cadet Cadet Cadet Chief Engineer 2 Engineer 3 Engineer 4 Engineer Deck Engineer ETO Eng Purser Doctor Bosun Bosun s Mate SGI SGI SGI SGI SGI MGI Matthew B Ashworth Keith A Walker Padraig G Molloy Kenneth Weston James Newall Derek W Lee Thomas Patterson 10 MGI Cook 2nd Cook Steward Steward Steward Steward LIST OF TABLES Table 1 1 List of UK occupations of Drake Passage section 2 14 Table 2 1 Nominal station positions for Drake Passage CTD section 20 Table 2 2 Actual CTD stations carried out during 265 6 21 Table 3 1 Indication of a failing 2 esee rennen eene eerte enero netten netta seen naso 45 Table 4 1 ADCP set up modes during JR265 eere eee 0 46 Table 4 2 Calibrations derived from the CODAS processing eere 48 Table 4 3 Mean
133. ied to the cruise TSG data file ocl jr265 01 using matlab mtsg 04 To give final calibrated values in ocl jr265 01 cal nc and 10 minute averaged values in 1265 01 cal av nc 9 5 Residuals The initial bottle TSG conductivity residuals had a std dev of 0 00018 S m reducing to 0 00017 after calibration Figure 9 2 shows that the SBE45 conductivity and sample bottle conductivity and conductivity residuals before and after calibration e cond potcond corrected cond cond 3 Nov 3 Nov 01 Dec O2 Dec 03 Dec 04 0 05 0 2011 btc cond S m and linear fit e3 Nov 30 Nov 01 Dec 02 03 Dec 05 Dec 2011 igure 9 2 Bottle and TSG Conductivity with conductivity differences Note y axis on lower plot is 107 68 In terms of salinity the initial difference between the bottle and TSG salinity had a regression of Sal Sala T 0 1211 4 266e 09 X time with an rms difference of 0 0022 After calibration of the conductivity and recalculation of the salinity the rms dropped marginally to 0 0019 but the regression of TSG salinity against bottle data is improved significantly to give Saltsa Sal 4 0 005197 1 817e 10 x time Figure 9 3 shows the effect of the conductivity calibration on the salinity differences when compared to bottle salinity values _ botpsal TSG sal calib 2 3 Nov 30 Mov 01 Dec 02 0 03 0 O04
134. ik to remove data where flag 0 5 or 71 5 and only retain data within valid ranges 90 lt lat lt 90 180 lt long lt 180 or 07 lt lt 360 setting data out of range to default values with medita The Seapath heading variable in the raw file is renamed head pos Files called pos 265 dJJJ nc and poshdg 1265 dJJJ nc are created holding the cleaned data These files are copied to versions with the suffix edit which can be used by mplxyed to manually remove any remaining spikes or dubious data after inspection see Appendix C 2 This was not deemed necessary for any of the 1265 files If changed during editing the pos jr265 dJJJ edit nc and poshdg 1265 d265 edit nc files must be copied to pos jr265 dJJJ nc and pos 1265 dJJJ nc e g gt gt 1265 d334 edit nc pos 1265 d334 nc f The edit files can be retained as backups to resume later processing from 6 2 2 GYRO Data are imported from the SCS using 00 gyr JJJ called from within mday 00 get all JJJ to produce files called gyr jr265 dJJJ raw nc in data nav gyros These data are then cleaned using an identical process to that used for the Seapath heading data using 01 JJJ called by mday 00 clean all JJJ with the gyro heading variable renamed head gyr As for the Seapath data edit version of the files is saved for manual editing using if necessary to be copied to
135. im ne ev n e ERU 45 4 3 CONFIGURATION c dte erm Re ER EE Reo tat S 46 A AS OUTPUTS eire turbare ente taeda e EAE ERR 47 4 5 CODAS HAWAILBROCGESSING c eei EO Ep Rb PE E EO EE pA Eee 47 SCS UNDERWAY DATA AQUISITION 20 52 5 1 UNDERWAY DATA ACQUISITION USING THE SCS SYSTEM sese e een n eren 52 s NAVIGATION ec 54 O LINSTRUMENTATION c torte iei epe er edo vro nes roe een eeu gelu tees Pe edis 54 O21 TS eapath SVEM sitat eet etas ete o ed 54 6 1 2 ISI S GYTYO ee ett etant 54 6 1 3 TSS Rolland dads DR Dm E 54 6 RTE edem 54 6 1 2 4ddititonabDaia o Mes ete 54 6 2 ROUTINE PROCESSING i de Pei v E a PEE SNE er OP Eee 54 6 2 SEAPATH eter est he certi erede te pee e te oer PR eU es 54 6 2 IER suu EE I I cue qu MM 55 6 2 3 SEAPATH and 55 ASEPIEC EI nt eer ma 56 6 3 GENERATING BESTNAV FICE 56 6 4 SUMMARY deese etes 56 7 ECHO SOUNDER BATHYMETRY eese eee eee ee enne etta eso seen ses tasse etae se ena seen 56 8 SURFACE M
136. ion knob until it stops flashing and shows a positive reading usually a suppression of 1 9 for seawater 9 Wait for the reading to stabilise and note the entire display 10 Switch to STANDBY and flush and fill the chamber once before the next reading 11 Repeat until 3 consecutive near identical readings are obtained 2 or 3 in last digit 12 Run a crate of samples Make sure to prevent contamination by wiping the sample tube and try not to touch it with bare fingers Turn external pump off when swapping samples 13 Again agitate turn over the samples and follow steps 6 to 11 in the procedure above 14 Note any and all problems For example stopper may be missing neck of bottle crusty with salt fluff shrimps floating in the sample do not use anything else 15 After analysing a sample put bottle upside down in the crate 16 Once the crate is done run another SSW vial to standardise again 17 Fill and flush chamber 3 times with MilliQ de ionised water 18 Allow chamber to refill with MilliQ and switch pumps off 19 Note zero and standby again this is a sign of electrical drift and should not change by more than 5 in the last digit between standardisations Note lab temp advice re pump flow rates varies a great deal see notes below However having the internal pump on full and the external pump on low has always worked reliably and simplifies the procedure If very pushed for time the external pump r
137. ious parameters The file naming convention was adapted to match the filename structure expected by the MSTAR processing routines Four files were created by the software module for each station ctd jr265 NNN dat a binary data file jr265 NNN CON an ASCII configuration file containing calibration information ctd jr265 NNN HDR an ASCII header file containing the sensor information ctd jr265 NNN BL a file containing the data cycles at which a bottle was closed on the rosette where NNN refers to the CTD cast number These files were saved directly to the PC s hard disk under D Mata yr265 2 4 1 Pre cast procedure n CTD annexe o Set up CTD ensuring bottles are ready for firing all taps are closed pulled out all air valves closed o Make sure salt crate and plastic bottle stoppers are ready n CTD operation winch control room o Fill in a CTD Cast log sheet Appendix D with lat long time etc o Prepare the CTD salt sampling log sheet Appendix D 23 Setup of Seasave for data acquisition Start seasave exe Check water sampler configuration under Configure gt Water Sampler Configuration Check instrument configuration under Configure gt New Style Instrument Configuration gt Select instrument configuration select the correct con file under data jr265 config jr265 CON Check depth of water from the main echosounder EA600 on JR265 Setup the display window by right click over plo
138. ir this is normal Should see initial hardware tests pass and Pitch and Roll changing when displayed during tests Pay attention to Internal Moisture at the beginning of P7200 test section values beginning 92th or 8 h are good Lower lt 7 or decreasing values indicate increasing moisture and units are ingressing water and will eventually fail This is most likely with numerous cold deep casts due to failing transducer potting Also under the P7200 test section is a list of RSSI high gain values for each beam NOTE that if one beam has a value significantly higher than the others e g a few 10s greater then this may indicate a failing beam Last command of pre deployment script sets the ADCP clock to that of the PC time synchronised to the NTP server Finally note ADCP recorder space shown as the following line RS nnn NNN REC SPACE USED MB FREE MB On completion of PreDeployTest script hit return to exit script Command prompt gt will now be available Erase recorder if data storage space insufficient with re ErAsE command Otherwise leave as data backup MAKE SURE ALL DATA BACKED UP BEFORE ERASE On JR265 there was sufficient space for all data to be left on the hard disk 3 4 Deployment On BBTalk select configuration file File Send Script File WHMJR265 txt Or press F2 to select a configuration script file Scripts found in LADCP Scripts Do not close down B
139. ise report are GMT unless specified otherwise Notes on wind speed sea state and ice conditions are courtesy of the bridge scientific log see Appendix A 1 and the bridge weather observations Appendix A 2 Section 2 gives details of the nominal and actual positions and depths of the CTD stations 27 November jday 331 JCR departed Mare Harbour 0900 local 1200 GMT and headed eastwards to perform a 12 hour short fetch study for WAGES Once on station did a shallow 50 m test CTD at station 900 with Pudsey the mascot on the frame then a 12 hour WAGES buoy deployment 1 at short fetch from 1200 to 2400 local including balloon deployment 1 during which the altimeter was lost The VM ADCP was set to bottom tracking mode during the fetch study SWATH was turned on prior to the start of the CTD section proper 28 November jday 332 Deep test CTD to about 2300 m at CTD station 901 During this second text dip the CTD frame carried one of the NOC L microcats for calibration prior to deployment with the NOC L BPR Three 15 min stops at 1500 1000 and 500 m depths were made for this purpose CTDs 001 and 002 were done some time was spent locating the correct depths since the northern part of the CTD section was moved east to longitude 58 W 29 November jday 333 CTDs 003 to 009 again involved some hunting for the correct depths A short SWATH survey was done to find a good location for the 1100 m depth deployment of the northern NOC L BP
140. jr265 dJJJ png files edit nc ocl ocl jr265 dJJJ edit nc 116 nav seapos pos jr265 dJJJ ne nav seapos pos 265 dJJJ nc ue Dus mmerge pos g nav seapos poshdg 1265 d 2265 di mod 237 amp poshdg yr JJJ JJJ nc THEN merged but not nav gyros gyr jr265 dJJJ n ui vector averaged mgd file has mmerge ash g 222 m nav ash pos jr265 dJJJ nc gyro merged but yr JJJ nav ash pos 1265 mgd nc not vector E averaged mmerge sim n av JJJ sim sim 1265 dJJJ nc nav seapos pos jr265 dJJJ nc Carter corrected depths merged sim sim 265 dJJJ nc lat amp sim sim jr265 dJJJ merged nc lon sim sim jr265 dJJJ merged co merged cor rnc file is copy of sim jr265 dJJJ nc mmerge ocl na ocl ocl jr265 dJJJ nc nav seapos pos 265 dJJJ ocl ocl 1265 dJJJ nc merged files 18 v JJJ ue ocl ocl 1265 dJJJ merged nc a copy M POS p nav seapos pos 1265 dJJJ naviseabosgos 41265 UL ie Just appends os nc current day to ier g nav gyros 2 j1265 dJJJ n os CE mday 02 run a M ASH a If reprocess E nav ash ash 1265 dJJJ nc nav ash ash jr265 01 nc previous files runs M SIM si Pong od start again rm mday_02 dir v sim sim jr265 dJJJ nc sim sim jr265 01 1265 0l nc instr JJJ 4
141. l stages of the UH processing and LDEO processing routines in order to diagnose any problems promptly As with other NOCS cruises the LADCPs were configured to have standard 10x16m bins with one water track and one bottom track ping in a two second ensemble Full description of the deployment and recovery procedures are provided below Several casts into the section we realised that the first LADCP unit a brand new instrument from RDI Teledyne was faulty with a failed Beam 3 WHM300 I UG306 S N 14443 The unit was replaced in the CTD frame after cast 008 new unit WHM300 I UG301 S N 15060 33 3 2 LADCP set up Once ADCP s installed and battery charged use AME laptop to perform installation test s and confirm operation of unit s The built in tests require the immersion of the transducer faces in water If not some of the tests may fail Running the tests in air will not harm the ADCP Read ADCP testing BBTalk documentation Monitor Sentinel RDITools Users Guide for insight and better understanding of what follows Any problems refer to the WorkHorse Technical Manual Section 5 Troubleshooting Figure 1 shows the cabling connections for LADCP star cable Figure 2 shows wiring pin outs for the comms power cable The ADCP charger plugs into the power connector at the PC end of the comms lead Battery voltage can be checked by turning on the charger and measuring the voltage via the two DVM leads Due to a diode in the Star Cable Patch Lead
142. low rather than off completely to prevent water running back down the tube and contaminating the new sample During JR265 the external pump was left at the low setting at all times Occasionally small bubbles could be seen entering the cell from the left and entering the first of the 4 arms of the cell In this case the cell was flushed and re filled before a reading was taken Even if bubbles are not noticed an indication of their presence can be seen in an unusually low and or wandering reading 11 5 Calculation of salinity in EXCEL spreadsheets NOTE that the results for each crate need to be entered into an excel spreadsheet that calculates the salinities from the conductivities and bath temperature For the MSTAR scripts to work the spreadsheet must a be in excel 1995 version c have a file name that includes the word crate or TSG as appropriate c the bottle number column must be text format for the TSG and number format for the CTD bottle files Note that the MSTAR scripts convert sal ascii for the CTD files and convert tsg ascii for the TSG that convert the spreadsheet to an ascii file can change in their demands from one version to another If the format etc is not correct then the resulting ascii files cause problems with the subsequent calibration processing 12 DATA ARCHIVE OF NOSEA2 AND LABDATA At the start of the cruise a tar file of the initial sate of nosea2 was made on an external usb disk To maintain an offli
143. lowing msam 01 creates an empty sam file sam 1265 NNN nc make sure that the list of variable contains the expected channels e mctd 01 reads in 24Hz CTD data into 1265 raw nc e mctd 02 renames SeaBird variable names and creates 1265 24hz e mctd 03 averages data to output to 1265 lhz nc and calculates derived variables output to 11265 psal nc e 01 creates empty dcs file which will store information about start bottom and end of good data in CTD file e 02 populates dcs file with data to identify bottom of cast The second phase consisted of running mdes 03 and manually input the scan number corresponding to the start of good downcast data and the end of good upcast data therefore excluding any measurements taken in air A list of scan number pressure and salinity was produced allowing the scan number aligning with the start of downcast and end of upcast to be found Phase 3 routines grouped under ctd all part2 ran the following mctd 04 extract downcast data from psal file using index information from dcs file sort interpolate gaps and average to 2db output to ctd 265 2db nc e mdes 04 merge positions of start bottom and end cast from navigation file into dcs file mfir 01 read in information from SeaBird bl file and create netCDF fir file mfir 02 merge time from ctd file onto fir file using scan number outp
144. m 29 11 2011 03 34 5 CTD 4 54 99909 57 99723 Wire out 1490m commence hauling 29 11 2011 04 00 5 CTD 4 54 99909 57 99723 CTD at surface 29 11 2011 04 33 5 CTD 4 54 9991 57 99723 CTD recovered to deck 29 11 2011 05 00 6 CTD 5 55 03924 57 99832 Commence deployment CTD 29 11 2011 05 05 6 CTD 5 55 03922 57 99833 CTD in the water and soaking 29 11 2011 05 07 6 CTD 5 55 03924 57 99834 CTD Veering EA600 depth 2051m 29 11 2011 05 11 6 CTD 5 55 03923 57 99837 Wire out 2025m Commence hauling 29 11 2011 05 47 6 CTD 5 55 03928 57 9983 CTD at surface 29 11 2011 06 31 6 CTD 5 55 03929 57 99832 CTD on deck 29 11 2011 06 41 7 BPR recovery 54 94314 58 3397 on DP 1000m due east of BPR for recovery 29 11 2011 08 02 7 BPR recovery 54 94315 58 33959 Move to 500m due east 29 11 2011 08 10 7 BPR recovery 54 94266 58 34903 All stopped 460m due east sending release signal 29 11 2011 08 18 7 BPR recovery 54 94274 58 34962 Release signal sent 29 11 2011 08 26 7 BPR recovery 54 94271 58 34954 Buoy released 83 29 11 2011 58 34749 08 31 7 54 94263 Buoy on surface 29 11 2011 08 48 7 BPR recovery 54 9412 58 34807 Buoy grapnelled 29 11 2011 08 59 7 BPR recovery 54 94064 58 34781 Buoy recovered to deck 29 11 2011 10 4
145. m a separate networked PC this enables post processing of the data without the need to move files Output files are of the form JRNNN XXX YYYYYY ZZZ where XXX increments each time the logging is stopped and restarted and Y Y Y Y YY increments each time the present filesize exceeds 10 Mb ZZZ are the filename extensions and are of the form NIR NMEA telegram ADCP timestamp ASCII ENR Beam co ordinate single ping data binary These two are the raw data saved to both disks VmDas configuration ASCII NMS Navigation and attitude binary ENS Beam co ordinate single ping data NMEA data binary LOG Log of ADCP communication and VmDas error ASCII ENX Earth co ordinate single ping data binary This is read by matlab processing STA Earth co ordinate short term averaged data binary LTA Earth co ordinate long term averaged data binary N1R and ENR files are saved to the secondary file path and can be reprocessed by the software to create the above files 4 5 CODAS Hawaii processing The data were processed using the CODAS software The processing route can be summarised as copying the raw files converting them into a working format merging navigation data deriving velocities quality control and conversion of data to matlab and netcdf files Calibration information can be obtained after several water and bottom track data files have been processed calibration can be performed at any time during t
146. measured across the section was 133 Sv which compares well to an average transport measured from the 16 previous UK cruises of 135 Sv standard deviation of 7 Sv In conjunction with the hydrographic cruise a Waves Aerosol and Gas Exchange Study WAGES intensive observation cruise JR245D was also carried WAGES involves continuous measurement of the air sea turbulent fluxes of CO2 sea spray aerosol momentum and sensible and latent heat fluxes plus directional sea state and whitecap parameters using systems installed on the ship in May 2010 In addition to the continuous measurements a number of intensive observation periods IOPs have been carried out by WAGES staff on board the ship These involve deployments of a spar buoy to measure wave breaking and an aerial camera system to measure whitecap fraction The activities of JR254D are summarised here but are described in detail in a separate cruise report Cruise JR264 was carried out by NOC L staff at the same time as JR265 and JR254D JR264 is also the subject of a separate cruise report The CTD was an underwater SBE 9 plus unit equipped with the following sensors dual temperature and conductivity sensors a pressure sensor encased in the SBE underwater unit a SBE 43 oxygen probe an Aquatracka MKIII fluorometer a transmissometer an upward looking downwelling PAR sensor and an altimeter A downward looking LADCP RDI Workhorse Monitor 300 kHz was deployed on all stations Various
147. nd Files SetModes JCR BT250 txt 250m Bottom Track 8mBins Through SSU JCR_BTS00 txt 500m Bottom Track 8mBins Through SSU JCR BT opp txt 500m Bottom Track amp mBins Not Through SSU JCR WC opp txt 800m Water Track 8 mBins Not Through SSU JCR_WC800 txt 800m Water Track 8mBins Through SSU Note Bottom tracking data on is very important for calibration purposes but reduces the temporal resolution and does not work when ADCP is synchronised with other acoustic devices on the ship Note These all use Narrowband mode which is recommended unless there is a specific requirement for broadband at which point you will know what you re doing anyway To switch mode for different depths stop data collection options edit data options ADCP setup change command file appropriate depth bottom track on off not through SSU Should be 16 m bins rather than 8 m Under C ADCP Command Files there are files from JR 193 2007 Drake Passage OS75NB BT om 1000m 16mBon Potential Problems The ADCP can run into problems mostly if it does not receive a trigger from the SSU to ping causing it to timeout This causes a white window to appear and start scrolling Sometimes the ADCP recovers and continues pinging though the ensemble number may reset to though the actual data file recorded is fine despite this Other times the instrument stops recording and it should be stopped and restarted immediately 1f this fails then check the SSU i
148. nd were not processed beyond simple generation of raw and cleaned daily files 7 ECHO SOUNDER BATHYMETRY Helen Snaith Bathymetry data are measured every 2 seconds by a Kongsberg EA600 single beam echo sounder and are processed daily using the basic procedure outline in Section 5 1 56 Specifically the data are transferred from the SCS system to MSTAR format using the MSTAR routine mday OO0 sim JJJ run as part of the from mday 00 get all JJJ where JJJ is the three figure jday as part of the daily processing see Appendix C 1 A file sim 1265 dJJJ raw nc containing the data for the jday specified was created in sim The raw daily file contains time seconds depth feet depth m and depth fathoms These raw files are cleaned using gt gt msim_01 JJJ called from mday clean all JJJ which performs basic cleaning of the data The script removes any data with duplicate times or backward timesteps using mcalc to generate a monotonic flag and datpik to select valid flagged data The script then sets depths outside the range of 5m to 100km to absent data using medita A version of the de spiked 2s values was saved as sim 1265 dJJJ despike nc As the data were often very noisy the cleaning script then reduced the data to 30s median values and output file sim jr265 dJJJ was copied to sim 1265 dJJJ smooth nc for possible further editing using gt gt mplxyed Using mplxyed the daily smooth data file was plotted
149. ne archive of the jr265 data on nosea2 and also the data held on the jr265 areas of jrlb jcr nerc bas ac uk a copy was taken daily using rsync onto an external usb disk mounted on one of the Apple macs After each rsync the usb disk contained complete copies of nosea2 users pstar jr265 nosea2 mnt 20111123 NB 20111123 was the mount point for jr265 but will change depending on the start date of the cruise Within the pstar home directory all links current scs_rawship scs_raw point to the mnt current directory which will change to point to the actual mount point on a cruise by cruise basis List the mnt directory using 15 l to see what the current link points at After the rsync was complete a tar file of each of the rsynced directories was generated to give a complete tar file at each backup time whilst only needing to transfer changed or new files to the usb disk 75 The transfer was simplified by a script held on the external usb drive called backup nosea and also linked as backup Ibdata in the same directory When called using backup nosea the files in nosea2 users pstar jr265 are backed up and a dated tar file generated When invoked using backup lbdata the nosea2 mnt 20111123 data are backup up and tarred The script file reads bin tcsh set vol 1265 2 name of external usb disk on mac set cruise jr265 of cruise directory on nesea2 and external disk set Ibdata 20111123 name of leg
150. ommence deploying CTD 04 12 2011 05 00 32 CTD 22 59 66693 55 44517 CTD deployed and soaking 04 12 2011 05 04 32 CTD 22 59 66688 55 44502 CTD veering to near bottom EA600 depth 3714 m 04 12 2011 E 05 07 32 CTD 22 59 6667 55 44438 Wire out 3654m Commence hauling 04 12 2011 06 09 32 CTD 22 59 66669 55 44435 CTD recovered to deck 04 12 2011 07 33 33 CTD23 59 99902 55 23601 V L on DP at site CTD 23 04 12 2011 09 27 33 CTD23 59 99899 55 23642 CTD deployed 95 04 12 2011 55 23833 09 33 33 CTD23 59 9996 all stopped 3478m 04 12 2011 10 36 33 CTD23 59 9996 55 23834 CTD recovered to deck 04 12 2011 11 54 33 APEX 6 59 99959 55 23835 Float released drifting clear V L remaining on station for stern tube inspection 04 12 2011 11 55 33 APEX 6 59 99944 55 23871 Float upright 04 12 2011 14 05 34 Wave buoy 9 60 33505 55 0306 Wave buoy deployed off stbd quarter Leading 140 degrees true 04 12 2011 14 09 34 Wave buoy 9 60 3334 55 03134 Buoy fully deployed Ships heading 330 degrees 04 12 2011 14 16 35 CTD 24 60 3331 55 03158 CTD deployed 04 12 2011 14 24 35 CTD 24 60 33311 55 03158 CTD veering to approx 3440m 04 12 2011 14 27 34 Wave buoy 9 60 3331 55 03159 HDG 330 T Weather dry Buoy leading 150 T 04 12 2011 15 00 34 Wave buoy 9 60 33307 5
151. p file r _ raw nc file The depth vs latitude with station locations is shown in Figure 7 1 The EA600 was very noisy and did not provide accurate depth readings for much of the cruise The data were particularly noisy when underway presumably as detection of the single beam is sensitive to ship movement For much of the cruise the EA600 was over reading by up to 50 m when compared to the altimeter readings during CTD cast especially during the deeper casts 57 However on at least one occasion station 027 the EA600 was under reading by more than 100m 0 LL T T 500 UN 1000F 2 1500 1 2000 F U 2500 o E a 3000F 3500 4000r 4500F 52 53 54 55 56 57 58 59 60 61 Latitude N Figure 7 1 Depth profile vs latitude Actual CTD station locations are marked 8 SURFACE METEOROLOGICAL SAMPLING SYSTEM Helen Snaith 8 1 Introduction The surface meteorological conditions were measured throughout the cruise A brief discussion of the performance of the meteorological sensors is given in this section All times refer to GMT 8 2 Instrumentation The RRS James Clark Ross was instrumented with a variety of meteorological sensors to measure air temperature and humidity atmospheric pressure short wave radiation TIR photosyntheticly active radiation PAR and wind speed and direction These are logged as part the oceanlogger at 5 second intervals and met
152. placed before the beginning of the cruise and the new unit S N 0130 had a replacement conductivity cell at its last calibration 23 July 2010 The salinity was calculated in real time using the SBE45 housing temperature and conductivity measurements The sea surface temperature SST was measured by a PRT100 temperature sensor located close to the non toxic supply intake on the hull at a depth of 6 m See Table 9 1 for serial numbers etc The SST and salinity are recorded in the oceanlogger file see Appendix C 1 for routine processing This section describes the calibration of the underway temperature 64 Section 9 3 and salinity Section 9 4 measurements using underway bottle measurements of salinity and SST and salinity measurements from the near surface CTD data Section 9 2 Instrument Serial number Woe PERO Parameter Calibration position Remote temperature PRT100 SST RS 455 4056 Pre 2008 Near intake Sea surface temperature 10 AU No serial number Fluoromet t visible pre 2000 prep lab Fluorescence SBE45 Micro TSG 4538936 0130 23 July 2010 prep lab temperature Wet entr 088249 27 08 2009 prep lab transmissivity Transmissometer Flow Meter OSSPFA4O 05 8119 13 6 2011 prep lab flow rate Table 9 1 Underway SST salinity and other flow instrument details 9 2 Selecting surface CTD data SST and salinity measurements were selected at 5 and 7 dbar from each of the 2db average CTD file NB
153. pper part were lost but the bottom half of the buoy along with the data logger and current meter were recovered successfully Once the buoy was recovered the 17 JCR steamed back on station CTD 010 was performed Since the swell was still large the CTD was sent straight down from 13 m rather than brining it back to the surface before performing the cast 2 December jday 336 CTDs 011 to 15 The 27 ARGO float S N 4901 was deployed after CTD 011 During CTD 012 the altimeter became noisy and intermittent and a big transmissometer spike implied that the CTD may have touched the bottom although on recovery it was found to be completely undamaged and only a smudge of mud was found on the base of the frame WAGES buoy deployment 5 took place during CTD 013 and the altimeter was swapped out after that station was completed WAGES buoy deployment 6 and balloon deployment 2 were performed during CTD 014 and the 37 ARGO float 4902 was deployed immediately afterwards The JCR did about 30 minutes of circuits and bumps for engine testing on the way to CTD 015 during which WAGES buoy deployment 7 and balloon deployment 3 took place 3 December jday 337 CTDs 016 020 The 4 ARGO float 4903 was deployed after CTD 017 WAGES buoy deployment 8 was done during CTD 020 The 5 ARGO float 4999 was deployed after CTD 020 4 December jday 338 CTDs 021 026 CTD 021 was accompanied by several whales possibly humpbacks in t
154. r strong winds from the west or north so the deployment was done about 2 nm off the coastline that runs from SW to NE In the event the winds proved to be rather light and variable Collected two passengers from Jubany base King George Island The arrived at the NOC L MYRTLE site in the early hours of the 16 MYRTLE responded to pings but did not release so triangulation and SWATH surveys were done to get an accurate position for any future recovery attempt On the way from the MYRTLE site towards Signy the CR stopped to recover the NOC L APEX float that was deployed free drifting earlier on the 5 December Once this was on board the NOC L SONAR bell a gel sphere designed to be a target was deployed to 1500 m but failed to show up on the EA600 The JCR then continued towards Signy The wind was from astern i e a bad direction for flux measurements so the pump for the new Licor 7200 was turned off to get null shrouded data On arrival at Signy on the morning of the 18 it was too windy to transfer people ashore in the small boats so WAGES buoy deployment 12 was done for about 7 hours 1100 to 1800 local time with the LICOR pump turned back on until the wind dropped enough to get people ashore CR headed to Cape Geddes overnight and arrived on the morning of the 18 While people were transferred ashore the old LICOR 7500 was shrouded and the pump for the new LICOR turned off again and the inlet taped over The ship then headed back
155. raphic section JR242 was cancelled at short notice due to problems with the Dash 7 aircraft The plan had been to fly the science team in to Rothera and perform the section northbound scientists on the preceding cruise JR240 Maksym in prep were due to fly out from Rothera on the same aircraft but had to stay on board the JCR back to Stanley they performed the southernmost 9 CTD sections on their way north stations 030 to 023 inclusive from Table 2 1 below plus station 007 from the standard section list see Yelland 2009a A subsequent cruise JR276 in April 2011 performed 14 CTD casts in the northern end of the section from station 020 to about 007 see Table 2 1 omitting the 6 most northerly stations due to lack of time Watson in prep It should be noted that the northernmost 9 CTD stations carried out during JR265 followed a line directly north south along 58 West similar in position to those used by McDonagh 2009 and Watson in prep rather than the standard CTD location used in most of the previous occupations of the section e g Yelland 20092 This report will describe each major hydrographic data stream in turn Each data stream was the primary responsibility of one science team member CTD Vikki Frith LADCP and VMADCP Penny Holliday underway data meteorology navigation echosounder etc Helen Snaith salinometer operations Margaret Yelland A practical aim during this cruise was to update the detailed g
156. raphy Centre Cruise Report 54 Hargreaves G W M A M Maqueda and S Mack 2010 RRS James Clark Ross Leg 1 October 27 2009 November 12 2009 Leg 2 Cruise JR198 November 17 2009 November 28 2009 Sea Level Measurements in the Drake Passage and Southern Ocean Proudman Oceanographic Laboratory Cruise Report No xx 15 pp Hawker E J King B A Sparrow M and et al 2005 RRS James Clark Ross Cruise 94 01 Dec 15 Dec 2003 Drake Passage repeat hydrography WOCE Southern Repeat Section Ib Burdwood Bank to Elephant Island Southampton UK Southampton Oceanography Centre 56pp Southampton Oceanography Centre Cruise Report 55 Maksysm E JR240 cruise report n prep McDonagh E L and et al Hamersley D R C and McDonagh E L eds 2009 RRS James Cook Cruise JC031 03 Feb 03 Mar 2009 Hydrographic sections of Drake Passage Southampton UK National Oceanography Centre Southampton 170pp National Oceanography Centre Southampton Cruise Report 39 In Press Morales Maqueda M JR264 cruise report n prep Pascal R W M J Yelland M A Srokosz B I Moat E Waugh D Comben A Cansdale M Hartman D Coles P C Huseh and T G Leighton 2011 A spar buoy for high frequency wave measurements and detection of wave breaking in the open ocean Journal of Atmospheric Ocean Technology 28 590 605 dox 10 1175 2010JTECHO764 1 78 Read 1 J T Allen P Machin W J Miller
157. ring the early stages of the section It was done after the first running the UH processing which generates the required navigation files but you don t need to have done the CTD processing first In a terminal window enter pstar data ladcp ldeo jr1112 matlab gt gt sp input NNN when prompted when asked for run letter enter noctd or withctd as appropriate gt gt warning off gt gt Ip gt gt print_Ideo fig 2 13 Save useful figures not automatically saved by ldeo processing gt gt warning on Turn warnings off because often calls FINITE which still works although Mathworks has re placed will soon replace with ISFINITE Beam strength and correlation figures should show good agreement between the four five for the Bangor unit beams gt gt exit If processed without CTD data the following figures were printed for the JCR LADCP FIRST LOOK file jr265NNNnoctd beam stats ps jr265NNNnoctd ps jr265NNNnoctd ensembles ps Open a new Terminal window or tab At the prompt type sftp pstar nosea2 pwd pstar cd local users pstar jr265 data ladcp Ideo jr1112 jr265NNN mget ps As with the UH processing there are c shell scripts developed on JR195 to run the LDEO processing all the through processing with CTD pstar jr265 data ladcp uh script ldeo script Ideo withctd though they were not typically used Examples of the useful beam stats figures are shown in
158. s No chlorophyll sample was taken during the cruise to calibrate the fluorometer against extracted chlorophyll T 5 Diagram Temperature C 33 7 233 8 33 4 a4 534 1 24 2 34 4 34 4 34 5 34 6 34 7 Salinitu Figure 2 6 T S plot for Drake Passage section of JR265 using data from the 2db binned CTD profiles 32 Geostrophic Velocitu Depth dbar 3500 4000 4500 Distance km Figure 2 7 Geostrophic velocity on Drake Passage referenced to zero at seafloor Geostrophic transport across the section was 133 0 Sv 3 LOWERED ACOUSTIC DOPPLER CURRENT PROFILER LADCP Penny Holliday and Julian Klepacki 3 1 Introduction The LADCP setup installed by Julian Klepacki BAS AME was a single RDI Workhorse Monitor 300 kHz instrument battery pack and logging PC Julian was responsible for charging and venting the battery pack A single LADCP was deployed in downward looking mode instead of a 2 LADCP upward downward slave master configuration The LADCP was connected to the controlling laptop located in the Chemistry Lab just forward of the water bottle annex while the CTD was on board Pre deployment the LADCP was woken up and the appropriate configuration command file was sent to start the instrument pinging before disconnecting the comms cable and blanking off the free ends Post recovery the comms cable was reconnected to download the data The data was examined in WinADCP on the PC then run through the initia
159. s 71 11 2 RUNNING THE SALINOMETER AUTOSAL essere 72 11 2 1 Initial setup of the Salinometer sse eee 72 1122 Initial standardis tion e e e ere epe ete iue epe ee e 73 11 2 3 Taking bottle samples iio eo tua Tat E ea 73 11 3 ANALYSING A CRATE OF SAMPLES ONCE THE SALINOMETER IS SET eee 73 112 POTENTIAL PROB EMS 6 eee etre ert E E re RR ERR RARE RERO TNR 74 11 5 CALCULATION OF SALINITY IN EXCEL SPREADSHEETS eene eene nennen nne 75 7 12 DATA ARCHIVE OF NOSEA2 AND LABDATA eese enitn 141 01 0 80 75 CRUISE p 76 I3 L NETWARE SYSTEM eve p aree 76 13 2 WNDGSY STEMS cave A RN QE pt e E re 76 13 3 LINUX SYSTEMS iiie hem irit DRE 76 TRA SCS 77 13 5EM122 SWATH SYSTEM 2 ud ke o neueste detecte etes 77 13 6 VSAT zn eed te re dite ta OE Ed 74 14 SUMMARY AND RECOMMENDATIONS 00 ss sense esse toss 77 15 REFERENCES 2 78 APPENDIX A BRIDGE LOGS oct eaae Vas ux eek soanesososunsoded xe esee Nene EXPE se 80 BRIDGE LOG OF SCIENTIFIC 2 80 A2 BRIDGE WEATHER LOG iden nEn OEE tre rH COUR en EORR 104
160. s unable to do science In addition it was possible to deploy the WAGES buoy and sometimes the balloon too during the longer CTD stations thus maximising the amount of data obtained for the WAGES study at no extra cost in terms of ship time The success of both cruises was due to the very helpful and professional approach of the staff of the JCR Many of the recommendations from the previous Drake Passage hydrographic cruise JR195 Yelland 2009a have already been addressed thanks to Julian Klepacki and his colleagues at BAS AME e g replacement of the ship s meteorological sensors upgrading the Seasave and SBE data processing software and the addition of air pressure to the Oceanlogger display Minor recommendations from this cruise A fan in the Bio Lab would prevent large gradients in air temperature and would make monitoring and regulation of the lab temp easier when using the AutoSal salinometer A winch repeater in the CTD hanger bottle annex would be useful to people working on that deck 77 15 REFERENCES Bacon S and Cunningham S A eds 2005 Drake Passage summary report Cruises on RRS James Clark Ross 1993 2000 Drake Passage repeat hydrography WOCE Southern Repeat Section 1b Elephant Island to Burdwood Bank Southampton UK Southampton Oceanography Centre 151pp Southampton Oceanography Centre Cruise Report 44 Bacon S and et al 2002 RRS James Clark Ross Cruise 67 19 Nov 17 Dec 2001 Drake
161. seconds The profiles of oxygen concentration on both downcast and upcast were plotted The downcast and upcast matched best using an advance of 8 seconds The test was repeated using advances of 7 7 5 8 8 5 and 9 seconds again finding 8 seconds gave the best results An advance of 8 seconds was applied to all stations CellTM settings The SeaBird recommended settings of alpha 0 03 and l beta 7 0 were used on both primary and secondary conductivities O O O O OOOO Data path directory setup Check that there are at least 5 Gbytes free on hard drive Create new directory for cruise data path under D data e g D data jr265 Create sub directory config under D data cruise to store the master config file and SeaSave windows setup B 2 Bottle file formats BL files This file is output by the SeaBird data acquisition software SeaSave and should be located under local users pstar jr195 data ctd BOTTLE FILES file name format is 1265 001 bl Pylon number firing number date time firing start scan number firing end scan number e g Data yjrl94Mataygr194 02011194 020 BL RESET Dec 16 2008 15 37 33 1 1 Dec 16 2008 16 49 16 103197 103233 2 2 Dec 16 2008 16 55 17 111862 111897 3 3 Dec 16 2008 17 01 03 120159 120194 108 4 4 Dec 16 2008 17 11 09 134704 134739 5 5 Dec 16 2008 17 20 47 148582 148617 6 6 Dec 16 2008 17 30 20 162331 162366 7 7 Dec 16 2008 17 39 48
162. shows this intensity offset especially as depth increases Also a poor correlation is maintained between beams These offsets high counts and poor correlations are all indicative of a failing beam requiring manufacturer attention Read the WinADCP user manual for better insight but really only a rudimentary knowledge is required to see if things are working properly It is worth checking data as often as possible in this simple quick manner to monitor unit performance and performance degradation 15 often experienced Edi Options Animate Export Utiles Window Monitor Help E E X lt Whole Set Deployment Duration 02 38 13 05 ECHO INTENSITY Avg 1 Time Ping 00 01 00 00000001 11 11 29 16 27 22 08 00006150 11 11 29 19 Tageuble Interval 00 00 01 55 Peele 11 1 28 Date 16 27 22 08 4 lt gt Sub Set Deployment Duration 00 06 35 23 EEX ECHO INTENSITY Avg Avg 63 43 Intensity Correlation D min 100 120 140 160 180 200 220 240 Ensemble 256 11 11 29 16 27 22 08 Date Time 11 11 29 16 33 57 31 0 0000 0 0000 Lat Lon 2 0000 0 0000 128 count 192 count 128 count Ensemble 256 Date 11 11 29 ime 16 33 57 31 WinADCP F JR265Wata jr265_008m 000 Edit Options Animate Export Utilties Window Monitor Help 0 265 265_008 000 EHO INTENSITY Sel 1 to 6150 File Size 3 450 150 bytes Sub 2591 to 2846 IB WH Ensemble Length 561 bytes Sys
163. step through the file Del bad times sets bad flags for a section of time or for a whole profile rzap allows single bins to be flagged Note that list to disk must be clicked each time for the flags to be saved Applying edits identified in gautoedit The gautoedit process in Matlab sets flags but doesn t change the data To apply the flags and recalculate a calibration quick adcp py cntfile q_pyedit cnt note two dashes before cntfile where q pyedit cnt contains q_pyedit cnt is comments follow hash marks this is a comment line yearbase 2009 steps2rerun apply_edit navsteps calib matfiles instname 0575 auto end of q_pyrot cnt 10 To get data into MSTAR gt gt local users pstar cruise data vmadcp jr265_0s75 jr265NNNnbenx gt gt mcod 01 produces output file 0875 jr265NNNnnx nc which has a collection of vars of dimensions Nx1 1xM NxM gt gt mcod 02 will calculate water speed and ship speed and get all the vars onto an NxM grid This step makes data available for comparison with LADCP data 11 Append individual 48 hour files using 50 gt gt mcod_mapend This script will append individual files to create a single cruise file It does seem to depend on the files having the same bin number and bin depths which was not the case on JR265 12 local users pstar cruise data vmadcp jr265_0s75 jr265NNNnbenx In directory apply the final cal ONLY ONCE adjustments are cumulative so if
164. t setup modify display params Set up full depth plots of primary temp conductivity salinity and oxygen and 300 sec of primary temp minus secondary temp primary conductivity minus secondary conductivity and altimeter Set depth range on plots Ensure other ranges temp cond etc are suitable for location Check the PC clock adjust to GMT if required Switch on the SBE911plus Deck Unit red button Click RealtimeData gt Start Acquisition Select correct CON file for the cruise and enter output data filename e g ctd 11265 Start Acquisition with the still deck Check deck pressures in the real time display window f station depth gt 100 m check that altimeter reading is about 100 m at surface Altimeter readings start 100 m from bottom 2 4 2 Procedure for the cast The winch should be zeroed by the winch operator when the CTD is just in the water Lower CTD to 10 m for 3 minutes 60 s after immersion check pumps are on 0010 changes to 0011 on Deck Unit The pump comes on approximately 1 minute after the enters the water If conductivity frequency drops below 3500Hz the pump will stop and delay will start again Bring CTD back to near surface Lower CTD at reasonably constant speed e g 60 m min to 10 m above seabed e Monitor SeaSave display for unusual features with close attention to the ALTIMETER When altimeter height start de
165. t allowed the CTD data from the deck unit to be accessed Capture allowed the data to be saved Output File 1265 NNN cap Three command were used dc to record calibration coefficients ds to record the time date and status dd to record the data Click capture to stop saving data Before disconnecting from the SBE35 samplenum 0 was used to clear the data Check time on the SBE35 clock Accurate time makes merging the data with CTD bottle data easier To check reset time do ds check clock is accurate compared to GPS time if not reset by ddmmyy 311109 hhmmss 123000 for example NOTE both date and time must be set together It is not possible to execute the time command only After disconnecting the deck unit was switched off BAS SVP was used to copy the processed files from D Mata yr265 to U data jr265 the ship s network drive inputting the cruise name and station number as prompted 26 2 6 MSTAR Data Processing The CTD stations were processed using NOCS MatLab based MSTAR processing routines see Appendix B 5 for more details do 265copyctdfiles local users pstar cruise data ctd was used to copy the data from the ship s network drive to the NOCS Sun workstation NOSEA2 The station number in this file was altered for each station MatLab was opened and m setup used to setup the environment for mexec processing The MSTAR processing was split into several phases ctd all part1 included the fol
166. t in out cal files does not make sense neither does the jday range so the time and ncols information in the nc files is recorded below The weighted average of the median value of the bottom track calibrations was considered most useful and was close to the weighted mean of the water track calibrations Calibrated surface currents during the cruise are shown in Figs 4 1 and 4 2 Water track mode average amplitude 1 0163 phase 0 1674 Bottom track mode amplitude 1 0100 phase 0 0218 AT File BT WT Amplitude Phase ncols Start Date End Date NNN Median 002 BT 1 0079 0 0438 0 0012 331 13 14 332 05 54 002 WT 1 0080 0 2930 0 0000 331 13 14 332 05 54 008 WT 1 0035 0 5595 0 9694 332 06 05 332 18 17 009 WT 1 0115 332 18 17 332 22 59 009 BT 1 0106 0 0159 0 0925 332 18 17 332 22 59 010 WT 1 0060 0 1570 0 2635 332 22 59 333 13 06 011 WT 1 0160 0 1247 0 4003 333 13 06 334 18 04 013 WT 1 0200 0 1633 0 4262 335 11 29 336 13 54 014 WT 1 0225 0 3187 0 6132 336 13 54 338 12 28 015 WT 1 0205 33812 28 339 11 59 016 WT 1 0255 339 11 59 339 16 21 019 Br 1 0174 1 0173 0 0013 0 0124 0 0272 0 0765 51 339 16 25 339 20 42 Table 4 2 Calibrations derived from the CODAS processing BT indicates bottom tracking mode and WT indicates water tracking cruise date bottom water mean amplitude m
167. t may have crashed 134 Outputs The ADCP writes a series of files to the unix drive the primary path and the raw data to the secondary path sufficient to recover the data but needs to go through VmDas again to be processed in matlab The file types and numbering 18 JRNNN XXX YYYYYY EEE Where XXX is a number that increments when the data collection 1 stopped and restarted The matlab processing expects this to change so data collection has to be stopped and restarted before matlab processing as things stand with the code This is usually done once per day YYYYYY is a number that increments once the file size has reached 10Mb the matlab code scrolls through these for each XXX Different file types see below have different rates of data collection so YY Y Y YY may be different between them This is finc EEE is the file extension NIR NMEA telegram ADCP timestamp ASCII ENR Beam co ordinate single ping data binary These two are the raw data saved to both disks VMO VmDas configuration ASCII NMS Navigation and attitude binary ENS Beam co ordinate single ping data NMEA data binary LOG Log of ADCP communication and VmDas error ASCII ENX Earth co ordinate single ping data binary This is read by matlab processing STA Earth co ordinate short term averaged data binary LTA Earth co ordinate long term averaged data binary This is used for google earth real time plotting The matlab
168. te for each cruise desktop and in start menu If you get the following Autostart screen click Yes a me tee te mmn Le le teet een m This window should then J 9 appear 130 5 Inthe File menu click on Collect Data this actually starts the setting up to collect data 6 Inthe Options menu select Edit Data Options Communications tab Caesa ers Fed aret Das homme m ms mtn o o 2 we om ie r r tomatoe ans OS poe er i 2 8 Y ou shouldn t have to touch any of this it should Enable ADCP Setup from File be set up as above Set to Ping as fast as possible not as shown Click on Browse to pick command file ene saima See note at mot OUS a tee oe o 131 c Recording tab di Transform tab Name JRNNN where NNN cruise number Heading Source NMEA PRDID eg JRIGS Tilt Source Fixed Tilts 0 for both Number 1 or 2 make sure this increments Heading Correction Enable 0 EV 60 08 EA since last time or you will over write data Correction don t enable Max Size 10 Primary Path U data Backup Path C ADCP_ Data Secondary JRNNN c Averaging tab f Data Screening tab STA 120 for 2 minute
169. tem Frequency 307 2 kHz st Bin 15 25 m Bin Size 10 00 m jo Bins 16 Pings Ens 1 Time Ping 00 01 00 irst Ensemble 00000001 11 11 29 16 27 22 08 Last Ensemble 00006150 11 11 29 19 06 12 33 werage Ensemble Interval 00 00 01 55 n 16 27 22 08 19 06 35 13 4 gt Deployment Duration 00 0 Profile ECHO INTENSITY Avg Avg 96 315 Intensity Correlation 0 4 min 1 H sO 252 2000 2700 272 2740 270 200 280 8 8 8 8 Dato Time nma X 52 z 0 0000 0 0000 Lat Lon 0 0000 Bm1 1 2 2 Bm3 Bm3 Bm4 Br ZZ lll Date 11 11 29 ime 17 402517 Figure 3 4 Data close to bottom showing Intensity offset and poor correlation 38 WinADCP F UR265lDataVjr265 009m 000 File Edt Options Animate Export Utilities Window Monitor Help mpm plo Duration 03 0 0 F JRZ65 Data 3 265 009 000 Seaton NNI Sel 1 to 9916 File Size 5 562 876 bytes 20 94 168 Sub 1 to 256 B N Ensemble Lengeh 561 byes System Frequency 307 2 kHz lst Bin 15 25 m Bin Size 10 00 n o Bins 16 Pings Ens 1 Time Ping 00 00 01 First Ensemble 00000001 11 11 29 21 18 53 86 Last Ensemble 00009916 11 11 30 00 20 57 61 werage Ensemble Interval 00 00 01 10 600 soog eongo 7000 740 soon sson 950 Ensemble 9907 1 1128 Date 1 1180 21185388 E 00 20 47 96 4 Profile ECHO INTE
170. the beeps try the magnet again for a bit longer Sometimes a stronger magnet is required e g Bilge magnet supplied by Simon Wright e Listen for hum and feel for vibration as the air bladder inflates can take up to 10 mins If in doubt you can take out the bung in the bottom of the float and feel the bladder inflating but make sure you put the bung back easier before fully inflated Alternatively the bottom of the float will bulge slightly when bladder is fully inflated Once bladder is inflated float sends messages every 90 seconds and transmission detector will pick them up as beeps If you don t hear the 90s beeps DO NOT DEPLOY THE FLOAT e Once 90s beeps are heard place float in the sea within 1 hour see step D IFIN DOUBT AS TO ACTIVATION DO NOT DEPLOY C Deploy Float Do not drop place in the water Make sure no plastic bags ropes etc are still attached before releasing Record time lat amp long of deployment in comments section of checklist and make other obs for checklist If not deployed within 2 hours of activation put the float back in its crate until ready to deploy and start again from step B hold the magnet against the RESET location for at least 10 minutes 11 SALINOMETER Margaret Yelland 11 1 Introduction An Autosal salinometer S N 68533 last serviced and aligned in February 2011 was set up in the Bio Lab by Julian and Seth AME during the pre cruise mobilisation During mo
171. tion by rain salt e g only put a few stoppers out ready for use each time use a new small plastic bag each time to prevent the stoppers becoming salty through exposure Rinse bottles 3 times Fill to just below neck of bottle need room to mix the water but want to minimise evaporation into air space Once a crate is full move it in to the Bio Lab where the salinometer lives Put the log sheet Appendix D in with the crate and note on it the date and time it was put in the lab Samples need to be in the lab at least 24 hrs before analysis so they come to lab temp Getting the lab temp stable is a balance between the thermostat inside the lab and an external thermostat in the bottle annex CTD hanger The external thermostat regulates temps in the chem lab but the hot air duct runs through the bio lab and can cause the temp to rise in there uncontrollably If turning the external thermostat down does not work ask the engineers to adjust the A C in that part of the accommodation fan in the Bio Lab would help mix the air since large temperature gradients seem to exist Putting one of the three PRT temperature probes in or near the crates to be sampled will give a better indication of when they are up to temperature 11 3 Analysing a crate of samples once the salinometer is set up A standard seawater SSW sample is run at the start and end of each crate If possible run 2 crates back to back using a total of 3 SSW NOTE that a new SSW
172. tion of underway sea surface temperature The SST measurements were compared to the surface temperature measurements from the primary temp and secondary temp1 sensors on the CTD frame Figure 9 1 shows that the remote TSG temperature underestimates the CTD measurements by around 0 15 C The offset was represented by the following linear regression offset 0 144 3 455e 08 x time The calibration has not been applied to the data 65 ctd tsq degC and linear fit TSG temp 23 Nov 30 Nov D1 Dec D2 Dec 03 Dec 04 Dec 05 0 2011 Corrected temp with CTD in red corr temp deg C 23 30 Nov 01 Dec D2 Dec 03 04 05 0 2011 Figure 9 1 TSG remote temperature surface temperature measurements 9 4 Calibration of underway salinity data 9 4 1 Introduction There are two sources of independent salinity data to calibrate the underway salinity data measured by the SBE45 1 salinity samples collected from the non toxic water supply outflow and 2 the surface salinities measured from near surface CTD We have used salinity samples to provide the primary calibration method for the TSG salinity and the CTD comparison has been used to check the resultant corrected salinity values Water samples were collected approximately every 4 hours during the section Water was taken from the clear white non toxic supply pipe that feeds the underway sensors in the prep lab The sample bottl
173. uides written during JR195 Yelland 20092 for each data stream including how to set the systems up operations while on station or underway initial examination of data to ensure that the systems are working correctly through to data analysis to the level required for a cruise report Much of the data analysis was performed using MSTAR a suite of Matlab programs developed at NOCS by Brian King used on the JCR for the first time during JR195 Some of these detailed guides are included in the main body of the report whereas others are included as appendices Unless stated otherwise times are given in GMT Jday of 1 5 represents 1200 GMT on 1 January the same date and time is given by a decimal day of 0 5 Jday is used in this report but some data outputs include a decimal day time stamp 1 2 Scientific Objectives 1 2 1 JR265 Hydrographic section Drake Passage is the narrowest passage through which the Antarctic Circumpolar Current ACC flows and thus is a convenient location for making measurements across the entire ACC The objective of this section is to look at changes on interannual to decadal scales The key objectives for the JR265 CTD section across Drake Passage are i to determine the interannual variability of the position structure and transport of the Antarctic Circumpolar Current ACC in Drake Passage ii to examine the fronts associated with the ACC and to determine their positions and strengths
174. underway measurements were obtained including navigation VM ADCP sea surface temperature and salinity water depth and various meteorological parameters A practical aim during this cruise was to update the detailed guides for each of the hydrographic data streams which were first written during JR195 in 2009 The hydrographic data analysis was performed using MSTAR a suite of Matlab programs developed at NOCS by Brian King and used on the JCR for the first time during JR195 KEYWORDS Acoustic Doppler Current Profiler ADCP air sea flux Antarctic Circumpolar Current cruise 265 2011 CTD observations Drake Passage gas exchange James Clark Ross JR265 LADCP lowered ADCP sea spray aerosol SOLAS Southern Ocean 5 Valkyrie vessel mounted ADCP WAGES wave breaking waves whitecap WOCE World Ocean Circulation Experiment ISSUING ORGANISATION National Oceanography Centre University of Southampton Waterfront Campus European Way Southampton SO14 3ZH UK Tel 44 0 23 80596116 Email nol noc soton ac uk A pdf of this report is available for download at http eprints soton ac uk Page intentionally left blank CONTENTS SCIENTIFIC TECHNICAL 00 9 SHIP S PERSONNELEL iir eei eerte ege tie eee A tie tees estre e eU 9 LIST OF TABLES TE cette 11 IST OB FIGURE cec 11 AGEKNOWLEDGEMENT ctc Cc 12 I OVERVIE
175. unexpectedly and was recovered The last two CTD stations were then done and all completed by about 1230 local time 1 3 3 Antarctic Peninsular 6 13 December At the end of the CTD section it was decided to postpone both the attempted recovery of the NOCL L MYRTLE system and the NOC L visit to Vernadsky to maintain the tide gauges there until the JCR was on passage northbound This decision was made in order to arrive on time in Rothera on the 8 December so that three of the JR265 and JR254D science teams could catch their scheduled flight northwards on the DASH 7 Unfortunately on the 6 December it was decided that the DASH had to leave on the 7 a day early due to unforeseen circumstance The JCR continued down the west side of the peninsular and arrived at Rothera at 0700 local time on the 8 Rothera relief was completed on time and the ship sailed on the 11 Sea ice prevented the ship landing any people at Vernadsky but on the evening of the 13 the NOC L 18 tide gauge equipment and instructions in Russian were landed on the shore with the aid of some skilful ship parking by the Master a fishing rod wielded by Mark Robinshaw and two of the staff of Vernadsky hauling on a rope 1 3 4 Antarctic Peninsular to Stanley 1 48 24 December On the way north from Vernadsky to King George Island WAGES buoy deployment 11 was done off the coast of Livingston Island in the early hours of the 15 December jday 349 The forecast was fo
176. ut to fir jr265 NNN time nc mfir 03 merge CTD upcast data onto fir file mfir 04 paste CTD fir data into sam file and output to sam 1265 NNN nc mwin 01 creates win file which will hold winch data and extracts times from start and end of 1Hz ctd file mwin 03 merge winch wire out data onto fir file mwin 04 paste winch fir data into sam file mdes 05 apply position from dcs pos file to set of files 27 If ctd all part2 m was run before the processed navigation file was available then mdcs 04 mdcs 05 and mctd 04 were run again using one script all part3 m This populates the position fields and recalculate depth from pressure Phase 4 consisted of adding the bottle salinity data first the bottle salts files were copied into the folder ctd BOTTLE SALTS Then the following were run convert sal ascii on all crates to produce sal 265 NNN csv files msal 01 jr195 to read bottle salinities msal 02 original to paste salinities into sam file msam 02 jr195 to calculate residuals botpsal upsall and botpsal upsal2 The latter three scripts were used because more recent versions of msal 01 msal 02 and msam 02 were not compatible with the bottle salinity file format The final files from the initial processing carried out on board were for each station e ctd jr265 NNN 24hz nc a 24Hz time series for the full cast all variables ctd jr265 NNN psal nc a 1 Hz time series for the full cast all
177. ve buoy 4 55 82574 57 60119 Change heading 245 degrees 01 12 2011 01 20 15 Wave buoy 4 55 82403 57 59255 Change heading 250 degrees 01 12 2011 01 38 15 Wave buoy 4 55 82338 57 58933 Change heading 245 degrees 01 12 2011 01 45 15 Wave buoy 4 55 8225 57 58518 Change heading 240 degrees 01 12 2011 2 01 54 15 Wave buoy 4 55 82195 57 58247 V L has moved 069 degrees x 0 98 NM since 0100 UTC Weather squally wintry showers 01 12 2011 02 00 15 Wave buoy 4 55 81963 57 57356 Change heading 245 degrees 01 12 2011 02 22 15 Wave buoy 4 55 81658 57 56248 V L has moved 064 degrees x 0 73 NM since 0200 UTC Weather squally wintry showers 01 12 2011 03 00 15 Wave buoy 4 55 81414 57 55313 Change heading 240 degrees 01 12 2011 Vessel has moved 068 T x 0 54nm since 0300UTC V L Hdg 240Deg Weather squally wintry 03 33 15 Wave buoy 4 55 81318 57 54782 showers 01 12 2011 15 Wave buoy 4 55 81062 Change heading 250 degrees 88 04 00 57 54154 01 12 2011 04 43 15 Wave buoy 4 55 81017 57 54044 Change heading 245 degrees 01 12 2011 Vessel has moved 054 T x 0 40nm since 0400UTC V L Hdg 245Deg Weather squally wintry 04 50 15 Wave buoy 4 55 80923 57 53813 showers 01 12 2011 Vessel has moved 054 T x 0 53nm since 0500UTC V L Hdg 245Deg Weather squally wintry 05 00 15 Wave buoy 4 55 80394 57 5253
178. y two left to identify ENX ENS LTA STA 6 still in directory data vmadcp jr265_0s75 jr26500 1nbenx quick adcp py cntfile q_py cnt killed matlab engine is the normal message received This takes a minute or two per 24 hours of ENX data Note cntfile has two dash characters 7 To see the BT bottom track or WT water track calibration look at the ascii output of jr265001nbenx cal out note that a calibration is not always achieved for example if the ship has made no manoeuvres while the ADCP is in water tracking mode so there may be no out Note also that additional calibration information maybe saved after flags applied after gautoedit process 49 8 To access data in Matlab matlab amp gt gt m setup gt gt codaspaths 9 Can manually clean up data by applying flags to suspected bad data cycles this can be done post cruise ie omitted go straight to step 10 This step can also be a useful first look at the data Note that the uncalibrated files may show a slight bias in u and or v which will appear as stripes that coincide with periods of on station and steaming This effect will disappear when you correct for the amplitude and phase error step 12 gt gt cd data vmadcp jr265 0s75 jr265001nbenx edit gt gt gautoedit ow Clean up data Select day and step typically 0 1 or 0 2 days to view then show now show now may have to be done twice to get the surface velocity plot show next to

RRS James Clark Ross Cruises JR265 and JR254D, 27 Nov

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