GP2-05-KA NOAA Ship KA'IMIMOANA San Diego, CA - Galapagos, Ecuador - Manzanillo, Mexico April 5 - May 11, 2005 Chief Scientist: Dave Zimmerman Survey Department: ST Shawn Gendron CTD Personnel: ST Shawn Gendron, Patrick Rafter Final Processing: K. McTaggart ACQUISITION: Fifty-three CTD profiles were collected at 49 stations during this cruise. Twenty-seven profiles were collected from 12N to 8S along the northern trackline and 110W. Twenty-six profiles were collected from 8S to 13N along 125W and northern trackline. The majority of casts were to 1000m. Seven casts were deep (>3000m) and 4 were shallow (400m). There was one test cast (500m) at the start of the cruise to test the termination but these data were neither archived or processed. PMC's Sea-Bird 9plus CTD s/n 09P13807-0439 (pressure s/n 59788) was used for all casts during this cruise, along with primary temp sensor s/n 1710 and primary cond sensors s/n 1467 (casts 0011-0121), and s/n 524 (casts 0131-0491). An SBE 43 oxygen sensor (s/n 313) was installed in line with the primary TC pair. Secondary temp sensor s/n 4211 and secondary cond sensor s/n 1537 were used for all casts. The CTD was mounted in the TAO spare custom 24-bottle frame with TAO SBE carousel pylon s/n 407. The CTD data stream was passed through TAO 11plus deck unit s/n 376 with factory settings. Digitized data were sent to a new Dell personal computer using Windows XP OS equipped with SBE's SEASOFT Windows acquisition software. Calibrated data were displayed in fixed listing and graphical form in real-time, as well as stored in raw form onto hard disk. Backups of the raw data were made on a Sony thumb drive and DVD. DVDs were returned to PMEL for post-cruise processing. Apparently the air-bleed hole in the y-piece of the primary plumbing was clogged during casts 0011-0141. Then the air-bleed hole in the y-piece of the secondary plumbing was clogged intermittently throughout the rest of the cruise. Air in the plumbing results in low surface salinities and bad oxygen data as deep as 60 dbar. It was noted that the pumps even shut off after soaking at 10 m. Also, during cast 0481, the tubing at the top of the primary conductivity cell wasn’t secured and the data for this cast were bad. SALINITY SAMPLES: No duplicate samples were taken this cruise. Salinity analysis was performed using Guildline Autosal 8400B salinometer s/n 61.667, Ocean Scientific ACI2000, and IAPSO standard seawater batch #P143 dated February 2003. The bath temperature was set to 24 degrees Celsius. Only 8 samples are collected per cast instead of 12, and no samples are collected from the half-degree stations between 3N-3S. Raw data were archived along with CTD data on CD. At PMEL, ACI2000 .dat files were ammended in Excel such that only 1 header line, 1 standard correction line, and 3 salinity lines per sample were included in the file. Corrected salinity values were fixed to 4 decimal places and the file overwritten in the NT folder as a space delimited file. OXYGEN SAMPLES: Oxygen samples were collected and analysed at sea by Eric Gehrie of University of Chicago. Final results were emailed to KEM by Eric on June 7, 2005. CONDUCTIVITY CALIBRATION: GP205S.CAL of secondary sensor data (te 4211, co 1537) was created at PMEL and used to calibrate stations 1-14 and 48. Primary sensor data (te 1710, co 524) was used to calibrate stations 15-47 and 49. Final pressure and temperature calibrations were pre-cruise. A viscous heating correction of -0.0006 C was applied to each temperature sensor but both drift corrections were near zero. The best fit was determined using CALCOP0 for secondary sensor casts 1-49: number of points used 247 total number of points 287 % of points used in fit 86.06 fit standard deviation 0.00194 fit bias -0.01315362 fit co pressure fudge 6.1756615e-007 min fit slope 1.0005676 max fit slope 1.0005676 CALCOP1 was the best fit for the primary sensor, casts 13-49: number of points used 169 total number of points 206 % of points used in fit 82.04 fit standard deviation 0.001753 fit bias -0.0044737858 fit co pressure fudge 3.8782887e-007 min fit slope 0.99997246 max fit slope 1.0000748 Slope and bias correction values were applied to CTD burst data and converted directly into netCDF format using CALMSTR and CLB_EPS on PC Pacific. Final calibrations, including oxygen, were applied using CALCTD_K and CALCLO_K. Calibrated data files were converted to netCDF format using CNV_EPSO.f and CLB_EPSO.f. OXYGEN CALIBRATION: Following the same procedures as GP504-KA, primary sensor data were extracted from the .BTL files using SBECAL1K.f. Because oxygens were drawn from some Niskins where salinities were not drawn, ALLSALT.TXT in the /oxy folder was padded in those cases with sample salinities of -9.9999. Then sample salinities were matched to CTD records by station/sample number using ADDSALK.f. Sample oxygen data were matched to CTD records by station/sample number using ADDOXYK.f. -9's were used for missing sample salinities and oxygens. Upcast bottle data were matched to downcast profile data by sigma-2 using MATCH_SG2_313K.m. RUN_OXYGEN_CAL_1.m was used to determine an overall group fit with a station dependent slope. Final coefficients were stored in FINAL.mat (roughly, slope=0.48, bias=-0.55, lag=4.6s, tcor=-0.0054, pcor=0.0001, and weight=0). 98.9% of the 67 data points were used in the fit with a standard deviation of 1.74 umol/kg. Calibrated up/down profiles with bottles overplotted were examined to verify the fit using PLOT_OX.m. Although there were up to 20 dbar up/down differences, the lag seemed appropriate with few instances of over/undershooting in oxygen, even in high gradient regions. For casts 0011-0141, oxygens in the top 60 dbar were replaced with upcast oxygens using FIX_OX.m. PROCESSING: The following are the standard SEASOFT processing modules used to reduce Sea-Bird CTD data: DATCNV converts raw data to engineering units and creates a bottle file if a Sea-Bird rosette sampler was used. Both down and up casts are processed. ROSSUM averages the bottle data specified in the DATCNV output and derives salinity, theta, and sigma-theta. Bottle data are used to calibrate the CTD and O2 sensor post-cruise. WILDEDIT makes two passes through the data in 100 scan bins. The first pass flags points greater than 2 standard deviations; the seond pass removes points greater than 20 standard deviations from the mean with the flagged points excluded. Data were kept within 100 of the mean (i.e. all data). FILTER applies a low pass filter to pressure with a time constant of 0.15 seconds. In order to produce zero phase (no time shift) the filter is first run forward through the file and then run backwards through the file. CELLTM uses a recursive filter to remove conductivity cell thermal mass effects from the measured conductivity. In areas with steep temperature gradients the thermal mass correction is on the order of 0.005 psu. In other areas the correction is negligible. The value used for the thermal anomaly amplitude (alpha) is 0.03. The value used for the thermal anomaly time constant (1/beta) is 7.0. LOOPEDIT removes scans associated with pressure slowdowns and reversals. If the CTD velocity is less than 0.25 m/s or the pressure is not greater than the previous maximum scan, the scan is omitted. BINAVG averages the data into 1 db bins. Each bin is centered around a whole pressure value, e.g. the 1 db bin averages scans where pressure is between 0.5 db and 1.5 db. There is no surface bin. DERIVE uses 1 db averaged pressure, temperature, and conductivity to compute salinity, theta, sigma-theta, and dynamic height. TRANS converts the data file from binary to ASCII format. Program CALCTD_K.m applied a viscous correction to temperature, calibration coefficients to conductivity, and final oxygen coefficients to compute oxygen (umol/kg). Pressure calibrations were pre-cruise. CALCTD_K.m also computed a calibrated salinity profile. Deep TS profiles compared well with historical profiles for the most part, although casts 0052 and 0081 were salty by 0.003-0.005 PSU. Calibrating them more closely with the bottles in a grouping of casts 0011-0141 would only make them saltier so they were left they are. Program CNV_EPSO.f converted the calibrated ASCII data files into NetCDF format, filling in the surface to 1 dbar, and computing theta, sigma-t, sigma-theta, and dynamic height. Likewise for burst data, program CALCLO_K.m applied post-cruise calibrations to the bottle file (gp205o.fin) and program CLB_EPSO.f converted it into NetCDF format. There were 4 bad sample salinities: station 0241 sample 11, 0261 13, 0411 11, and 0451 12. There were 3 bad sample oxygens: station 0051 sample 11, and 0251 samples 108 and 109. Bad points were not included in the final bottle data files. Final CTD and bottle files were moved to /home/plover/insitu2/DATA/hayes /gp205/ctd/ and /bot and included in the MySQL data management tables on June 30, 2005. JULY 21, 2005 Calibrated profile data for this cruise include conductivities from secondary sensor s/n 1537 for casts 0011-0141 and 0481; and conductivities from primary sensor s/n 524 for casts 0151-0471 and 0491. This is because of intermitently clogged y-bleed valves in the primary and secondary plumbing, except for cast 0481 where the tubing was detached from the primary conductivity sensor at the snap fitting. No changes were made to these data on July 21, 2005. However, calibrated burst data for this cruise include only primary conductivities from sensor s/n 1467 for casts 0011-0121, and from sensor s/n 524 for casts 0131-0491. This is because the oxygen sensor s/n 313 was plumbed with the primary TC and calibrated with the primary TC. Upcast data were not affected by the y-bleed problems mentioned above, and there is no bottle data for cast 0481. Only one sample oxygen is associated with a bad CTD oxygen (cast 0051 sample 15) from matching upcast values with downcast values for calibration purposes where the CTD oxygen trace was affected by the clogged y-bleed valve. \oxy\calclo_k.m was modified to apply only primary conductivity cals and rerun to produce gp205o_eps.fin containing all values (n=352). The 4 bad sample salts and 3 bad sample oxygens were changed to -9.9s before rerunning clb_epso.f for revised PMEL bottle files in NetCDF format. PMEL bottle files don't include CTD salinity or CTD oxygen, just bottle data. gp205o_eps.fin was sent to Eric Gehrie at his request with mention of the 8 bad values in an email.