GP6-03-RB NOAA Ship Ronald H. Brown Panama City - Panama City, Panama October 24 - November 22, 2003 Chief Scientist: Mr. Ben Moore Survey Department: CST Jonathan Shannahoff CTD Personnel: CST Shannahoff Final Processing: K. McTaggart ACQUISITION: Sixty-two CTD profiles were collected during this cruise. Thirty-nine profiles were collected from 12N to 8S along 95W. Twenty-three profiles were collected from 8S to 8N along 110W. Six casts were deep (>3000 m), twelve were shallow (200 m), and the rest were to 1000 m. PMEL's Sea-Bird 9plus CTD s/n 93450-0209 measuring pressure (s/n 53586), temperature sensors (s/n 1455, 1370), conductivity sensors (s/n 1177, 1180), and SBE 43 oxygen sensor (s/n 312) were used for all casts. Also mounted were a load cell (s/n 1108) and two optical sensors installed by the NASA group. The CTD was mounted in a yellow 24-bottle frame with PMEL Sea-Bird rosette sampler s/n 63. The CTD data stream was passed through Sea-Bird 11plus deck unit s/n 367 (ship's) with factory settings. An analog signal was recorded onto the audio portion of VCR tape as a backup. Digitized data were sent to the ship's Gateway G6-200 personal computer equipped with Sea-Bird's SEASAVE for Windows acquisition software (Win32 v5.28) where calibrated data were displayed in graphical form in real-time, as well as stored in raw form onto hard disk. Backups of the raw data were made on Zip disks and CD-ROM and returned to PMEL for post-cruise calibration and processing. SALINITIES: Twelve samples were taken each cast for the majority of casts. Two samples were taken for each shallow casts. Only 6 samples were taken for nine casts in order to catch up on batches. Salinity analysis was performed using Guildline Autosal 8400B salinometer s/n 61.668 (aka Dallas) and OSI computer interface, ACI2000. IAPSO standard seawater batch P141 (June, 2002) was used for all casts. Analysis was performed by CST Jonathan Shannahoff. Laboratory operating temperature is assumed to have been 24 degrees Celsius. OXYGENS: Oxygen samples were collected and analysed at sea by Jan Kaiser of Princeton. The results were provided to PMEL in an Excel spreadsheet email attachment. Station, niskin number, and dissolved oxygens in umol/kg were extracted from the spreadsheet and used to calibrate the SBE 43 oxygen sensor, s/n 312. Where duplicate samples were taken, the concentrations were averaged. Samples noted to have bubbles in them were thrown out. POST-CRUISE CONDUCTIVITY CALIBRATIONS: Primary sensor data (te 1455, co 1177, ox 312) were calibrated and processed. Final pressure and temperature calibrations were pre-cruise. A viscous heating correction of -0.0006 C was applied to temperature sensor s/n 1455 (no drift was applied since the sensor was calibrated right before this cruise). Conductivity fit coefficients were determined using Matlab program CALCOS1 for conductivity s/n 1177 stations 1-52. number of points used 469 total number of points 570 % of points used in fit 82.28 fit standard deviation 0.002944 fit bias -0.017162315 min fit slope 1.0006714 max fit slope 1.0007877 Slope and bias correction values were applied to CTD data and converted directly into netCDF format using CNV_EPS1_OX; and to bottle file data using CALMSTR and CLB_EPS_OX. An additional salinity offset of -0.006 was applied to all the data to bring the deep profiles into the historical envelope (baseline CGC94 along 110W). POST-CRUISE OXYGEN CALIBRATIONS: After looking at the oxygen profiles on the acquisition plots of the deep stations, it was decided that there was significant enough hysteresis between the down and the up profiles to warrant using the downcast oxygens for calibration. The process was the same as A16N. Primary sensor data were extracted from the .BTL files using SBECAL1K.f. 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_312K.m. Greg's program 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=0.32, bias=-0.58, lag=8.6s, tcor=0.0008, pcor=0.0001, and weight=0). About 89% of the data were used in the fit with a standard deviation of 0.5523 (surprisingly good!). After examining calibrated up/down profiles with bottles overplotted, it was evident that the 8.6s lag was over- shooting on both sides of the steep thermocline. The lag was forced to be 4.0s when the calibrations were applied and this resulted in more acceptable minimums. There were just too few bottles to contrain the fitting routine. FINAL 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, as well as primary and secondary temps and conds. Oxygen was carried along as volts. Optical data were not processed. Markscan was used to determine the start of each profile just beneath the surface. ROSSUM averages the bottle data specified in the DATCNV output and derives salinity, theta, and oxygen (umol/kg). Bottle data are used to calibrate the CTD post-cruise. Data were averaged over 8 seconds. ALIGNCTD advances secondary conductity by 0.073 seconds. The deck unit does this automatically for primary conductivity. 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 both primary and secondary salinity. TRANS converts the data file from binary to ASCII format. Program CALCTD_K.m applied a viscous correction to temperature, calcos1 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 were compared with historical profiles, especially along 110W, and it was determined that an additional offset of -0.006 was needed to bring the GP603 salinity profiles into the historical envelope. This was also done in CALCTD_K.m. On Nansen, program CNV_EPS1.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 (.CLB) and Nansen program CLB_EPSO.f converted the data into NetCDF format. Final CTD and bottle files were moved to /plover/insitu2/DATA/hayes/gp603 and included in the MySQL data management tables on February 24, 2004.