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User Manual for the Third-Generation, Advanced Piston Corer

1. 40 30 20 10 Steinhart Hart Coefficients A 9 27791854e 04 B 2 22345132e 04 C 1 2263852e 07 APC3 1858002C SIO calibration 8 06 Reference temperature with Steinhart Hart fit e Residual error factory zh Residual error SIO calibration Steinhart Hart Coefficients A 9 3166619E 04 B 2 2183365E 04 C 1 2375744E 07 APC3 1858004C SIO calibration 8 06 m Reference temperature with Steinhart Hart fit Residual error factory Residual error SIO calibration Steinhart Hart Coefficients A 9 2931769E 04 B 2 2203068E 04 C 1 2425852E 07 APC3 1858005C SIO calibration 8 06 Reference temperature with Steinhart Hart fit e Residual error factory Residual error SIO calibration 5 20000 40000 60000 80000 Resistance ohms 0 040 0 030 0 020 0 010 0 000 0 010 0 020 0 030 0 030 0 020 0 010 0 000 0 010 0 020 0 030 0 030 0 020 0 010 0 000 0 010 0 020
2. 0 030 0 040 100000 9 WSIW jenpisoy 9 WSIW jenpisoy 9 WSIW jenpisoy Figure A3 2
3. the morning of 16 August 2006 by inserting the three APCT 3 electronics sets in coring shoes and an upper sub and starting each of the tools with a logging interval of 10 seconds The shoes and subs were sealed with an end cap constructed for this purpose or a cross over sub and were bound together with straps and lowered to rest on a wooden frame on the bottom of the calibration tank The frame held the tools a few centimeters off bottom to allow tank water to circulate completely around the tools The tank was filled with water and ice and the chiller and heater were activated About two hours were required to find the right combination of system settings to hold APCT 3 User Manual Draft 2 July 2007 Page 34 the bath temperature constant near 0 C Reference data were logged from the digital probe readout by terminal emulation with a frequency of 5 seconds For calibration purposes each fixed bath temperature was held as steady as possible for 20 30 minutes allowing the tools to come to thermal equilibrium with the bath Rheostats on the bath temperature control panel were adjusted to strengthen or weaken the sensitivity of the heater and chiller switches in an effort to optimize stability If the sensitivity was set incorrectly the bath temperature would oscillate excessively or would drift away from the desired temperature When we wished to change the bath temperature always increasing from the previous stable temperature we turned
4. 10 minute penetration the smallest standard deviation may be 0 01 C or less This is the standard deviation of a particular fit of data to a function not an uncertainty in the equilibrium temperature To decide what may be an appropriate uncertainty look at the next plot This one shows the equilibrium temperature as a function of k and pc For high quality data there may be a range of 0 1 0 2 C or more in equilibrium temperatures based on selection of reasonable values of k and pc This is a more reasonable estimate of uncertainty in the final value assuming high quality data and a good fit of observations to the model The third plot shows how the best fitting time shift in penetration time varies with k and pc values and the fourth plot shows the difference between final temperatures calculated APCT 3 User Manual Draft 2 July 2007 Page 25 on the basis of the entire data window and those based on using only the final 1 3 of the data window On all contour windows the star shows the k and pc values that minimize the standard deviation of the misfit between model and observations and the white dot shows the currently selected value If you look back at the Results window you will see that it has been updated to show values of k and pc consistent with the position of the red star You can select different values of k and pc by moving the cursor over the top plot on the Contours window and eft clicking with the mouse The whi
5. 3 User Manual Draft 2 July 2007 Page 5 Fig II 1 If two electronics sets can be used simultaneously to determine correct in situ temperatures this will allow determination of a thermal gradient during a single coring run Creation of this capability required design of three new components cross over sub upper tool sub and a new core catcher sub Fig II 1 Prototypes of the first two of these components were created as part of the new tool development but as of Summer 2007 the last component will need to be constructed before the complete system can be run with two APCT 3 temperature loggers It is important to note that although the annular cavities of the upper tool sub and coring shoe are identical allowing the same electronics frames to be deployed in either location other geometries of these components are significantly different The coring shoe tapers near the cutting end Fig II 1 placing the APCT 3 thermistor probe within 1 2 mm of the outer surface of the shoe In addition the taper of the cutting shoe helps to assure that it makes good thermal contact with the surrounding formation In contrast the upper tool housing is cylindrical in cross section except for wrench flats that extend across the housing 90 from the hole containing the thermistor probe meaning that the wall between the thermistor probe and the formation is considerably thicker than in the coring shoe 8 9 mm Perhaps of greater concern the lack of a t
6. User Manual Draft 2 July 2007 Page 8 1d Before the electronics frame is installed in the APC coring shoe the thermistor probe should be coated with heat sink compound to assure a good contact with the shoe Tools were delivered to the US IO along with a small tub of AOS non silicone HTC heat sink compound part 52050 1J0 which has a thermal conductivity of 2 6 W m K considerably higher than conventional heat sink compounds Holding the frame in one hand with the handle on the insertion extraction tool use a small applicator wooden stick end of a zip tie etc with the other hand to apply a thin coating of heat sink perhaps 1 2 mm thick around the thermistor probe Be sure that you apply heat sink compound only to the thermistor probe and not to the empty prong the thermistor probe can be identified by the wires extending from the main circuit board into the probe Also try to keep the heat sink compound on the probe The heat sink compound will not damage the electronics but inevitably there is some spreading of the compound onto tool components and fingers and this can make the system more difficult to handle and could foul the electrical contacts le Align the probe with the APC coring shoe there should be a short vertical scratch or a paint mark extending from the lip of the coring shoe that indicates the location of the hole at the base of the annular cavity into which the thermistor probe will be placed Hold the insertio
7. and cross over they should still be connected upside down with the cutting edge facing up on the catwalk and hose off the inside and outside of the assembly You may need to run a brush or some rags through the inside of the shoe to get all the mud off Do this outside where there is plenty of water and it will not matter if APCT 3 User Manual Draft 2 July 2007 Page 14 you make a mess If you let the mud dry it will be tougher to clean off later When the shoe is clean carry it to the lab and set it on the counter again with the cutting edge facing up Wipe off the shoe and sub with a dry rag If the sub has water on it when you open the tool cavity the water could drip down inside the cavity in the shoe and onto the electronics When the shoe and sub are clean and dry unscrew the coring shoe You will need to either have someone hold the sub or put it in the vise to hold it until you get it unscrewed past the o rings 4c When the coring shoe is free turn it over and place it on the stand on the counter If you look down inside the shoe the top ring should be visible at the top of the annular cavity Wipe off grease and mud from around the ring using Kimwipes Q tips and rags Use the frame insertion extraction tool to remove the ring then gently wipe any water drops off the top of the frame before attaching the electrical connector to recover the data NB do not remove the APCT 3 electronics from the coring shoe unless it require
8. change one or both values rerun Pick you can just choose APCT 3 User Manual Draft 2 July 2007 Page 24 Done immediately without changing the pick but you must enter the Pick window and choose Show Fit TP Fit will update the results window and plots with your new values 7 If you are satisfied with the processing at this stage and would like to save your work use the Save Session button to put the workspace into a Matlab mat file that can be reloaded later You can also send results of the fit analysis to a text file for plotting with different software by pressing Make Report 8 Two additional buttons are used to process APCT data using a variety of k and pc values Press Compute Contours and the program will cycle through all available models using a range of k and pc values and calculate best fitting equilibrium temperatures for each model As of summer 2007 models are available for 0 5 lt k lt 2 5 W m k and 2 3 x 10 lt pe lt 4 3 x 10 J m K in increments of 0 1 This range of values should accommodate the needs of most APCT 3 tool users When the calculations are complete press the Explore button to see the results of the analysis You are presented with four contour plots in a new plot window labeled Contours The top plot shows the smallest standard deviations achieved by least squares best fitting of each combination of k and pc values For high quality data rapid tool penetration no motion during 8
9. colored green the latter indicates the segment of data to be processed Zoom in on the window of data that starts before penetration and ends after penetration including several minutes of data prior to tool penetration Press the Pick button adjacent to the 70 box then move the cursor to the point you would like to select to represent the time of tool penetration and eft click with the mouse Because 7P Fit will shift the time between penetration and the data window as part of processing selection of exactly the right penetration time is not essential 7P Fit assumes a data window to process of 9 minutes from 60 seconds after penetration to 600 seconds after penetration You can adjust one or both of these times by choosing the appropriate APCT 3 User Manual Draft 2 July 2007 Page 23 Pick button and using the cursor and mouse to select preferred times When you have selected all three times press Done 5 Press Show Fit on the vertical button window You are presented with a plot window labeled Results containing four windows The top window shows the penetration record with the data points used for processing colored green and red Points not used in processing are colored blue Points colored red comprise the final third of the selected data window Also shown in the top Results window are two estimates of the equilibrium formation temperature labeled with green and red dashed lines The green line is based on the full data win
10. contributions of time and advice and to the US IO to IODP for the loan of equipment needed to develop and test the new tools The last generation of tools developed for measurement of temperatures while APC coring was introduced to the scientific drilling community in 1991 Much has changed in the last 16 years including increasing demand for capabilities to quantify subseafloor thermal conditions and remarkable improvements in computational speed and electronics stability accuracy and resolution We do not imagine that this will be the last APC tool development or that this document will comprise the final word on use of the third generation tools We encourage users to make modifications to this User Manual as needed If changes are made to this document please be sure that they are carefully noted that all copies of the User Manual are updated and that electronic materials are archived APCT 3 User Manual Draft 2 July 2007 Pagei Table of Contents Acknowledgements and Preface Table of Contents List of Figures List of Tables L Introduction A Goals and Organization B Brief history of APCT measurements and tools II APCT 3 Components and Operation A APCT 3 Components 1 Coring hardware 2 Electronic components B Collecting APCT 3 Data 1 Physically preparing the APCT 3 tool 2 Programming for data collection 3 Running the station 4 Recovering the tool and data C APCT 3 Operation Quickstart HI APCT 3 Data P
11. described earlier this temperature may not be consistent with that of bottom water unless the tool is held stationary just above mud line for 10 15 minutes with the pumps off The tool is lowered to the bit pressure is accumulated in the drillstring and the core barrel is fired into the mud There is an abrupt temperature rise associated with frictional heating of the coring shoe and for most stations the tool temperature begins to decay towards the true in situ temperature Fig III 1A For stations in unusually warm sediments the tool temperature may continue to rise after penetration Fig 1 1 It is not possible to leave the tool in the seafloor long enough to achieve complete equilibration This would require 40 60 minutes or more risking loss of the tool and the APC core barrel with settling of sediment around the core barrel Instead partial equilibration is achieved and the core barrel is recovered by wireline Processing of APCT 3 data to infer the in situ formation temperature requires extrapolation of a short record of thermal equilibration The programs used for this purpose with the first and second generation APCT tools were based on the assumption that tool response was consistent with a one dimensional radial geometry Horai 1985 Fitting data to a model based on this geometry is based on the assumption proven to be APCT 3 User Manual Draft 2 July 2007 Page 19 largely appropriate that radial heat transfer away
12. duration indicated and will complete logging somewhat sooner than the time listed in the Calculated End Time display WinTemp presents a Verification window that shows selected parameters giving the operator a chance to revise the logging plan The time until logging will begin is shown If WinTemp finds no problem the OK button will be colored green If the OK button is grayed out there must be a problem with the selected program Press Cancel and return to Setup if needed to revise the sampling plan 3 Running the station APCT 3 User Manual Draft 2 July 2007 Page 11 3a After the tool is programmed to run remove the electrical connectors from the top of the tool Place the top ring with clean dressed o rings above the electronics frame NB if you insert the top ring by hand rather than using the insertion tool be sure that you leave the threaded holes facing up If you do not do this it will be difficult to get the top ring out later 3b The core tech should provide a core catcher sub Clean and dress the o rings then insert the core catcher sub into the top of the coring shoe and make it up by hand so that only a few threads remain exposed to limit opportunities for water dirt or grease to foul the electronics Hand the untightened assembly to the core tech or another member of the rig crew The rig crew will tighten the core catcher prior to deployment using the special wrench made for the APCT shoe You will ge
13. have enough experience yet to know how long a single set of APCT 3 User Manual Draft 2 July 2007 Page 10 batteries will last during normal operations collection of this data will be helpful in evaluating tool performance over the long term 2d Choose Logger gt Clear data to prepare the tool to collect new data Confirm your choice WinTemp will tell you if data are already cleared 2e Choose Logger gt Setup to prepare for a new deployment There is a check box listed in the Logger Time part of the Setup window that will synchronize the tool clock to the computer clock Make sure that the computer clock is properly set before proceeding having the tool clock set at a time different from the correct time could lead to problems later with data interpretation Also be sure you know if you are working in local time or GMT UTC and mark the data sheet accordingly NB Use of GMT UTM is standard in marine science observations Choose the intended date and time at which you would like the tool to start logging Make sure that this time is at least several minutes ahead of the present time Choose the duration of logging and the logging interval Check the Calculated End Time display to make sure that the tool will run for the time intended When the tool is configured to your satisfaction press Activate As an alternative you can press Start Now and the logger will begin logging immediately In this case the tool will run for the
14. may be inferred This issue illustrates one of the great challenges in processing APCT data in general a high quality statistical fit does not assure that the extrapolated formation temperature is correct Experience has shown that in many cases extrapolated temperatures from what appear to be excellent records are inconsistent with in situ temperatures determined at higher and lower depths i e an extrapolated value falls of an otherwise consistent thermal gradient Sometimes the conundrum can be resolved by reexamining the questionable data record but in other cases the reason for the inconsistent extrapolated temperature remains enigmatic APCT 3 User Manual Draft 2 July 2007 Page 21 B TP Fit TP Fit is a Matlab program created for processing of APCT 3 data Because the geometry of the new tool is essentially identical to that of the second generation tool 7P Fit will also work with older data provided they are properly formatted Installation and general Matlab and program operation are discussed in Appendix A4 In this section it is assumed that Matlab and 7P Fit are properly installed on the computer to be used and that the user has access to one or more APCT 3 data sets Example data sets are provided with the 7P Fit software As with the earlier discussion of WinTemp instructions for TP Fit follow some general conventions Typed commands are listed in bold In almost all cases after entering something at the keyboard you ne
15. off the chiller and turned on the heater and watched as the bath temperature rose then reset the controllers to maintain temperature when a change of about 5 C had been achieved We made no attempt to obtain specific temperatures in the tank e g exactly 15 000 C 20 000 C etc instead we chose temperature increments of about 5 C across a working range of 0 to 45 C Tables A3 1 to A3 3 After the first calibration point it generally took 30 60 minutes to change to a new temperature and we held each temperature for 20 30 minutes In fact the bath could not maintain a completely stable temperature but tended to oscillate about the target temperature with an amplitude of 0 005 0 010 C and a period of 2 3 minutes Temperatures recorded with the ACPT 3 tools also oscillated but with a slightly reduced amplitude Collection of 20 30 minutes of data for each calibration point allowed the tank and tool oscillations to be averaged out Fig A3 1 Calibration over a range of 0 30 C was completed during the first day and additional calibration points at 35 45 C were completed on the second day The tools were recovered and data downloaded and reviewed briefly before draining the bath and ending the calibration session to make sure that the instrumentation worked as expected Data were processed to determine calibration coefficients First the reference temperature records were reviewed to determine the timing of stable temperature
16. out as events occur to help with data interpretation after the station is complete 2 Programming for data collection 2a Connect the serial cable to the computer and to the deck box then connect the deck box to the tool cable which ends with the curved connector NB Shipboard technical staff should have configured the computer to be used for operating the APCT 3 electronics Ask if you are not sure where to find the operating software where to store data files etc 2b Run WinTemp Insert the mini banana plugs on the curved connector into the contacts on the top of the tool electronics In the following WinTemp instructions typed commands are listed in bold In almost all cases after entering something at the keyboard you need to press the lt enter gt or lt return gt key or select the Enter button or the OK button in a pop up window Occasionally you may need to press a special key or button VII identify these by placing the key name inside lt triangular brackets gt Finally you may need to select a menu or window item listed in this manual in italics 2c Verify that electronics are working and you have communication by choosing Logger gt Online from the main menu You will see a real time listing of digital counts resistance and temperature updated once second Choose Offline to return to the main screen Choose Logger gt Battery and record the Voltage and Total Sample Count on the Data Sheet We don t
17. recovered without removing the electronics frame from the APC coring shoe A frame insertion extraction tool is used when placing the APCT 3 electronics frame in the coring shoe or removing it for servicing Ideally a tool might be placed in a coring shoe near the start of an expedition and not removed until the end of the expedition minimizing opportunities for damaging the electronics A top ring machined steel with inner and outer o rings fits above the APCT 3 electronics frame when it is inserted in the coring shoe protecting the tool and particularly the electrical contacts which are otherwise exposed on the top surface of the tool frame from water grease and mud APCT 3 User Manual Draft 2 July 2007 Page 7 B Collecting APCT 3 Data 1 Physically preparing the APCT 3 tool la If you are not familiar with operation of the APCT 3 tool take time in port or during transit to review these instructions and run bench tests Find an APC coring shoe with the annular cavity and place it on the lab bench on a stand that will prevent the shoe from falling over The tools are kept in plastic cylinders that help to keep them clean and prevent the electronics or prongs from being damaged Please keep the APCT 3 electronics either inside the plastic cylinder or in an APC coring shoe the electronics should not be left exposed on the counter Unserew the top of the plastic cylinder and remove the tool If you just want to inspect or clean the el
18. to model Every third observation is plotted for clarity Note how much equilibrium temperatures deviate from final in situ temperatures indicating why modeling of tool response is required to estimate equilibrium tempertures APCT 3 User Manual Draft 2 July 2007 Page 41 Figure A3 1 Example calibration data from 2006 experiments with APCT 3 tools A Temperatures determined with NIST traceable reference probe All measured values are shown with thin line Filled squares indicate time period during which data were averaged to yield the mean standard deviation shown The reference probe and logging system were shut down for the night after 18 20 00 although the tank was left running to allow work to continue the following day with minimal disruption B Resistances recorded simultaneously by the three APCT 3 tools All data recorded during the period shown are indicated with thin lines Symbols indicate data used to derive mean resistances for this reference temperature as shown See discussion in text concerning selection of data windows Figure A3 2 Calibration temperatures and residual errors plotted against tool resistance In all plots the left axis shows temperature measured with the reference probe indicated with open squares and a thin line The right axis shows residual errors between mean temperatures determined with the reference probe and those determined using factory calibrations provided by the thermistor manufacture
19. working directories It may be that future releases of WinTemp provide more flexibility in file locations 4e Complete the Data Sheet recording any anomalous events or tool behaviors If you plan to deploy the APCT 3 tool again soon you can leave the APC shoe tool out on the counter in the stand 4f this is the last station for several days or the end of the cruise it would be a good idea to clean up and put the tool components away for safe keeping Use the insertion extraction tool to remove the electronics frame from the coring shoe Make sure that the central piston and shaft in the extraction tool is backed out about 3 cm by turning the large wing nut counter clockwise Lower the insertion extraction tool onto the top of the electronics frame and turn the thumb knobs to engage the threaded holes in the top of the frame Make up the screws snug but not too tight so that you don t strip the threads in the frame If the insertion extraction tool will not fit completely down on top of the frame it is likely that you need to back out the central piston and shaft by turning the wing nut When the extraction tool is fully secured to the frame turn the wing nut clockwise This moves the central piston downward and pushes against the inner wall of the coring shoe Continuing to turn the wing nut will jack the electronics frame up and out of the cavity Keep turning the wing nut until the frame becomes loose then raise the handle
20. 2 8 D 5 s E U D 89 K ali 3 5 O 6 7G wnugijinba pejeunsg D o El uljpnui Je 0121 wnugijinba payewnsy LO 66 eg ee pe Pre a SL gt o o PNW olul 100 Bumu 1s q SUOREAH SQO 0012 0092 0092 0 0002 0002 0001 S OWIL 9 Temperature C Resistance ohms 30 020 APC3 Calibration IO Hydraulics L Soie 5 7 aulics Lab 30 005 0 004 C 30 010 k ii H H 4 5 i m p p i 30 005 P 1 i l F T Ala u y l H 30 000 Ni iy 4 29 995 29 990 17 50 00 18 00 00 18 10 00 18 20 00 18 30 00 Time 16 August 2006 24250 WL TT APC3 Calibration Roc 7 94211 Q SIO Hydraulics Lab 24245 Point 7 r 1 T 24240 R 94104 Q 002C 24235 V m 7 241 w dln dn Fi um e 2 Hk jh duh hr B el 5 1 n r e d A H A ik da d d 24230 N I H ji idi m A H D Hi Dol diri gt S d U A y 1 74 j W li R 93978 0 7 005 24225 17 50 00 18 00 00 18 10 00 18 20 00 18 30 00 Time 16 August 2006 Figure A3 1 Reference temperature C Reference temperature C Reference temperature C 50 40 30 20 10 40 30 20 10
21. H Villinger R D Macdonald R D Meldrum and J Grigel A robust rapid response probe for measuring bottom hole temperatures in deep ocean boreholes Mar Geophys Res 19 267 281 1997 Erikson A J R P Von Herzen J G Sclater R W Girdler B V Marshall and R Hyndman Geothermal measurements in deep sea drill holes J Geophys Res 80 2515 2528 1975 Fisher A T and K Becker A guide for ODP tools for downhole measurements pp 148 Ocean Drilling Program College Station TX 1993 Hartmann A and H Villinger Inversion of marine heat flow measurements by expansion of the temperature decay function Geophys J Int 148 3 628 636 2002 Heesemann M H Villinger A T Fisher A M Trehu and S Witte Testing and deployment of the new APC3 tool to determine insitu temperature while piston coring in Proc IODP edited by T S Collett M Riedel and M J Malone pp in press Integrated Ocean Drilling Program College Station TX 2007 Horai K A theory of processing down hole temperature data taken by the Hydraulic Piston Corer HPC of DSDP Lamont Doherty Geological Observatory Palisades NY 1985 Horai K and R P Von Herzen Measurement of heat flow on Leg 86 of the Deep Sea Drilling Project in Init Repts DSDP edited by G R Heath and L H Burckle pp 759 777 U S Govt Printing Office Washington D C 1985 Hyndman R D M G Langseth and R P Von Herzen Deep Sea Drilling Project geotherm
22. User Manual Draft 2 July 2007 Page 22 3 Choose Edit Meta Data and enter appropriate values Initial values are already entered on the basis of the data file and the last values that were saved when the program was used In addition values for k and pc may have been set by default Part of data processing is evaluating the uncertainty in final temperatures caused by uncertainty in k and pc values but it is best to enter something that you think to be reasonable In the last generation of APCT processing software the user was asked to enter only a value for k and thermal diffusivity K k pc was calculated from the empirical relation of Von Herzen and Maxwell 1959 3 657 x k 0 70 K 107 where k is in W m k and x is in m s Other studies have explored relations between k and K and the user is advised to choose a favored relation initially but to explore the significance of this relation as part of APCT processing as described below Choose OK to close the Edit Meta Data window 4 Choose Pick to select the data segment to process and a plot window will open showing the complete data record Three values must be selected tool penetration time labeled 70 the initial data point to fit to the model Data Start and the final data point to fit to the model Data Stop Because the data are shown in a standard Matlab plotting window you can zoom in and out adjust axes etc Most of the data are colored blue but a subset is
23. User Manual for the Third Generation Advanced Piston Corer Temperature tool APCT 3 Fisher A T Villinger Heesemann M Earth and Planetary Sciences Department and Institute for Geophysics and Planetary Physics University of California Santa Cruz CA 95064 USA 5 Department of Geosciences Universitat Bremen Klagenfurter Strade 28359 Bremen Germany in preparation for delivery to the US IO for IODP draft XX July 2007 Acknowledgements and Preface This doeument describes tools and programs that were developed in support of international scientific drilling Primary funds in support of this work were provided by German Science Foundation DFG grants Vi 133 9 1 and Vi 133 9 2 to H Villinger University of Bremen Bremen Germany and by grants JSC 2 04 from the U S Science Support Program to ODP and OCE 0326699 from the U S National Science Foundation to A Fisher University of California Santa Cruz CA Many individuals contributed to this development effort including members of the engineering and operations groups at the U S Implementing Organization to IODP formally ODP particularly Kevin Grigar who designed the new APCT 3 coring components and prepared machine drawings the tool development group at Antares Sturh Germany staff from the Scripps Institution of Oceanography Hydraulics Lababoratory and scientists and technicians of IODP Expedition 311 We are grateful to these individuals for their generous
24. al measurements a review Rev Geophys 25 1563 1582 1987 Koehler R and R P Von Herzen A miniature deep sea temperature data recorder design construction and use Woods Hole Oceanographic Institution Woods Hole MA 1986 Langseth M G Techniques of measuring heat flow through the ocean floor in Terrestrial Heat Flow edited by W H K Lee pp 58 77 Am Geophys Union Washington DC 1965 Pribnow D F C M Kinoshita and C A Stein Thermal data collection and heat flow recalculations for ODP Legs 101 180 pp lt http www odp tamu edu publications heatflow gt Institute for Joint Geoscientific Research GGA Hanover Germany 2000 Shipboard Scientific Party Explanatory Notes in Proc ODP Init Repts edited by E E Davis M J Mottl and A Fisher pp 55 97 Ocean Drilling Program College Station TX 1992a Shipboard Scientific Party Site 858 in Proc ODP Init Repts edited by E E Davis M J Mottl and A Fisher pp 431 572 Ocean Drilling Program College Station TX 1992b APCT 3 User Manual Draft 2 July 2007 Page 28 Uyeda S and K Horai Heat flow measurements on Deep Sea Drilling Project Leg 60 in Init Repts DSDP edited by D Hussong and S Uyeda pp 789 800 U S Govt Printing Office Washington D C 1980 Villinger H and E E Davis A new reduction algorithm for marine heat flow measurements J Geophys Res 92 12 846 12 856 1987 Von Herzen R P and A E Maxwell T
25. alled 1858002C wtc When data are retrieved from an APCT 3 tool WinTemp looks in the current working directory for the appropriate file for the tool being used and requests that the user identify the file if it can not be found When data are retrieved from a tool they are stored in a binary wtf file This file contains a set of temperatures used to create the calibration coefficients applied by WinTemp to convert from resistance to temperature Thus calibration data are embedded within each wtf file When a user wishes to export ASCII data the header of the dat file contains a list of calibration coefficients used to generate the file but not the original calibration data that are embedded within the wtf file In order to change calibration coefficients one must open a wtf file as this allows access to a set of calibration data Once a wtf file is open choose Calibration gt Temperature from the main menu You are shown a set of three resistance temperature APCT 3 User Manual Draft 2 July 2007 Page 37 R T pairs and are allowed to change these values Apparently WinTemp always uses three temperatures to determine the values of the three calibration coefficients 4 B and C Follow these steps to get WinTemp to use coefficients determined with a greater number of R T pairs Determine coefficients based on calibration using more than three R T pairs with a least squares approach with Excel Kaleidagraph Matlab or a simi
26. ally important residual errors following fit of new coefficients are distributed randomly about zero with no systematic bias Curiously for all three tools the temperature at which there is the greatest residual error in the new calibration is 35 C This suggests that the reference reading may be in error or may have been averaged incorrectly but the data were checked carefully and there seems to be little difference between the reference record for this temperature and those at other temperatures The residual errors at this temperature while larger than those at other temperatures are still 0 002 well within the acceptable range We had originally intended to explore calibration options for use with the new ACPT 3 tools including converting directly from digital counts to temperature or cross plotting apparent and true temperatures but the basic calibration attempted initially worked out so well that there was no need for additional analyses The new calibration coefficients determined during 2006 tests have been entered into updated calibration files wtc for the three new tools Copies of these files are provided to the US IO with this manual along with back up copies of the original factory calibrations A note on updating calibration coefficients using WinTemp WinTemp uses unique calibration coefficients associated with each tool stored in wtc files For example the coefficients for tool 1858002C are stored in a file c
27. aper near the thermistor probe in the upper tool sub means that the development of a damaged zone or skin outside the upper tool sub could limit the thermal contact between the tool and the formation The numerical models developed for use with the coring shoe as discussed in Chapter III will have to be revised for interpretation of tool from the upper tool sub which is expected to have a somewhat slower equilibration response Finally deployment of the complete APCT 3 system including the cross over sub and upper tool sub will place the butyrate core liner back about 40 cm 16 in relative to the front of the coring shoe compared to conventional APC operations making the core pass through a longer section of metal before entering the liner It is not known if friction between the core and metal components will cause greater core disturbance or limit recovery Testing will be required to resolve this question and determine if the complete APCT 3 system can be run routinely without compromising recovered core APCT 3 User Manual Draft 2 July 2007 Page 6 3 Electronic components The primary APCT 3 electronics are built into an aluminum cylindrical frame Fig H 2 Four flat surfaces are machined onto the frame two of which are currently used to hold electronic boards and two of which remain empty for potential future use One of the boards holds the measurement circuit for the thermistor probe processor analog digital converter an
28. at depths 300 m or more using a drill over technique The APC drill bit was advanced the length of recovery following incomplete stroke and another APC barrel was launched This approach requires more time since the depth increment of each core might be only a few meters but it allows collection of high quality APC samples and APCT 3 data to much greater depths than have been attained previously Discuss this option early in the expedition or during pre expedition planning if deep APC and APCT 3 penetration is important to scientific goals for your expedition 4 Recovering the tool and data 4a When the tool comes back on deck the rig crew will break the shoe and core catcher sub connections Be sure that they use the special APCT wrench to break the connection and that they unscrew the cross over by one thread only The core techs are well aware of the need to use the APCT wrench but sometimes one of the less experienced crew members will use a regular pipe wrench and this could deform the shoe or damage the electronic components inside the shoe After the shoe and sub have been removed from the core barrel the IODP core techs may need to hammer the sediment out of the shoe If the sub is loosened too much more than one thread they could drive mud and grease into the cavity above the retaining ring and damage the electronics 4b After the core catcher portion of the core has been removed from the coring shoe place the shoe
29. ctronics vendor Appendix A3 comprises a discussion of APCT 3 calibration and compilation and interpretation of calibration data collected for the first three production tool sets in Summer 2006 This information is helpful for evaluating tool accuracy and calibration limitationsm Appendix A4 contains installation and other information on 7P Fit the new APCT 3 processing program that runs through Matlab B Brief history of APCT measurements and tools Measurements of in situ temperature have been made in oceanic sediments during scientific drilling since before the Deep Sea Drilling Project DSDP began Von Herzen and Maxwell 1964 New tools were developed and modified during DSDP Horai 1985 Uyeda and Horai 1980 and during the Ocean Drilling Program ODP Davis et al 1997 Fisher and Becker 1993 Shipboard Scientific Party 1992a the successor to DSDP In some cases temperature tools were run during drilling programs to resolve specific geothermal hydrogeologic or paleoceanographic questions but in other cases data were collected during routine operations even though they were not central to primary expedition goals see summaries of DSDP and ODP thermal studies Erikson et al 1975 Hyndman et al 1987 Pribnow et al 20001 Temperature measurement tools in scientific ocean drilling comprise a subset of third party tool developments designed built and tested independent of the primary scientific operator or its subcontract
30. d memory The second board holds two 1 5 V batteries in series providing the 3 V power supply to the tool On the top of the cylindrical frame are threaded holes for use with the tool insertion extraction tool and female mini banana plug contacts for communication with the deck box and computer There are two o rings on the cylindrical frame one near the top one near the base On the bottom of the cylindrical frame are two prongs one of which is empty and the other containing the thermistor probe nominal 30 kOhms at 25 C A second thermistor or other sensor could be placed in the empty prong as part of a later tool modification Fig H 2 The electronics are programmed using a desktop or notebook computer running Windows XP no tests have been run using Vista limited testing has been performed using Windows 98 but vendor specifications do not include support for this operating system Communications is accomplished using serial communication either through a DB 9 serial port on the computer or a USB port and a serial adapter The communications cable attaches to a deck box from which a second cable connects to the APCT 3 electronics There is a special connector at the end of this cable with male mini banana plugs attached to a curved form shaped to fit into the top of the annular cavity in the APC coring shoe when the electronics frame is installed Fig 11 2 This allows the APCT 3 electronics to be programmed and deployed and data to be
31. dow whereas the red line is based on the final third of the data window This plot also shows a thick gray line that falls behind the data points This line shows the model curve to which the observational data are compared The second Results window shows deviation from the model by the observations The deviations are plotted on a log scale as absolute values with overestimates and underestimates shown with open and filled symbols respectively The bottom two plots show how the equilibrium formation temperature was estimated The left bottom plot shows a cross plot of measured and modeled temperatures Early data appear on the upper right corner of this plot and later data appear towards the lower left corner Extrapolation of the hopefully linear trend shown in this plot back to the x 0 value indicates the interpreted formation temperature at equilibrium what the tool would have recorded eventually if it were left in place for a sufficiently long time Once again two values are indicated one in green using the full data window and one in red using the last third of the data window The right bottom plot shows the standard deviation of the misfit between the model and observations the green straight line shown in the left bottom plot as a function of the time shift added to or subtracted from the penetration time 6 If you would like to adjust specific k or pc values the fastest way to do this is to return to Edit Meta data
32. e penetrates 9 5 m ahead of the bit actual depth will be calculated on the basis of recovery However if normal pressure bleed off does not occur this generally indicates an incomplete stroke of the APC and the driller will release the pressure manually Once again APC shoe penetration can be calculated on the basis of recovery A note about APC pull out and partial penetration Normally the crew will switch over to XCB coring after an APC pull out of 60 100 klbs this decision is left to the rig crew Operations Superintendent Tool Pusher and Operations Manager You may wish to discuss this decision in advance so that you can determine when to run the APCT 3 system Leaving the APC barrel in the mud for the extra minutes required by APCT operation allows the formation to settle in around the tool and may increase the pull needed to remove the tool from the mud During some APCT runs when the sediment firmed up at shallow depths researchers agreed to pull APCT 3 User Manual Draft 2 July 2007 Page 13 out after just 6 8 minutes If the tool is left in for any time period less than this it may be difficult to get enough of an equilibration curve to extrapolate a meaningful temperature but much depends on drilling conditions water depth sea state lithology and other factors You can experiment with the length of measurement with the 7P Fit software During later ODP and early IODP operations drilling crews continued to APC to gre
33. e tool held stationary in the sediment How much the temperature of the tool electronics varies and how uniform this drift is across the electronics cannot be determined Also there may be significant differences in electronics temperature from run to run Electronic components are much more stable now than they were in the past Functionality that used to require multi layer circuit board or even two boards is now found within a single IC chip Certainly this has helped to improve electronic stability in the presence of changing temperatures But there may still be some thermal drift with modern electronics and there are other largely unknown factors that may contribute to variations in electronic performance The point is not to bring into question the entire basis for APCT 3 measurements but rather to note that the conditions of tool calibration are inevitably somewhat different from those of standard tool operation This is another reason why it is probably not worthwhile to attempt to calibrate the APCT 3 tools to an absolute accuracy better than 0 002 0 004 C although the resolution of the instrument should make higher accuracy possible Even absolute accuracy of 0 01 0 02 C should be acceptable for the vast majority of applications given the much larger uncertainties associated with data processing APCT 3 User Manual Draft 2 July 2007 Page 33 2 Summer 2006 calibration The first three sets of production APCT 3 electronic
34. e values However applications involving assessment of changes in seafloor temperature do require acquisition of absolutely accurate data In addition use of multiple tools requires that data from these tools be directly comparable although comparison of bottom water readings provides a loose intercalibration between tools differences in operational procedures can make direct comparison of apparent bottom water temperatures difficult As described earlier in this manual there will always be uncertainty in estimated in situ temperatures determined with the APCT tool because many processes and properties are not determined Even when very high quality data is collected ambiguities in processing generally result in uncertainties in equilibrium temperatures on the order of 0 1 0 2 C Thus the goal of calibration should be to determine the temperature recorded with the tool at any time with an absolute accuracy at least as good as 0 01 0 02 C and perhaps as good as 0 002 0 004 C There are limited benefits to be gained from achieving greater accuracy in calibration with this tool system Absoluate calibration of APCT 3 tools requires two additional instrument systems a stable calibration bath capable of achieving the desired temperature range and a precision temperature reference that has itself been calibrated to the desired accuracy e g with a NIST traceable certificate of accuracy Most calibration baths operate with simultaneous wat
35. ectronics you can extract the frame from the plastic case by pushing your hand inside the frame then lifting up However if you are planning to insert the frame into the APC shoe use the insertion extraction tool 1b The insertion extraction tool has two screws topped with thumb knobs that are used to secure the tool to the electronics frame Place the insertion extraction tool on top of the electronics frame and turn the thumb knobs to make up the insertion extraction tool tight to the frame There are two sets of threaded holes in the top of the frame that are compatible with the insertion tool As of summer 2007 one set of threaded holes is blocked protected with set screws and the other set includes holes that will align the insertion extraction tool with the electrical contacts on the top of the tool frame When installed properly a small vertical groove near the top of the insertion tool will align with the thermistor probe making is easier to insert the frame in the coring shoe Before lifting the frame using the insertion extraction tool back out the large wing nut in the center of the insertion extraction tool so that 3 cm of threads are exposed This will raise a central piston inside the insertion extraction tool allowing the electronics frame to be landed in the base of the annular cavity 1c Clean the o ring grooves and clean and grease the o rings on the electronics frame Use Dow 4 or similar o ring grease APCT 3
36. ed to press the lt enter gt or lt return gt key or select the Enter button or the OK button in a pop up window Occasionally you may need to press a special key or button UU identify these by placing the key name inside lt triangular brackets gt Finally you may need to select a menu or window item listed in this manual in italics NB most TP Fit functions can be run without the graphical user interface from the Matlab command line but all instructions herein assume that the user is running TP Fit using the Graphical User Interface See Appendix A4 for more information 1 Start Matlab then ed to the working directory This directory should contain the main TPFit m script and folders subdirectories called RefModels and TP Fit In general it will be best to have a single working directory for an expedition and to bring data files into this directory for processing then move results files out of the directory when work is complete Be sure to follow Matlab conventions with regard to naming directories and files avoid spaces unusual characters etc 2 Run 7PFit from the Matlab command line You are presented with a vertical button window showing the typical work flow for processing APCT 3 data In general buttons will be used from top to bottom Select Load Data to load a data file and begin processing When you have successfully opened an APCT data file the Load Data and Edit Meta Data buttons will turn green APCT 3
37. eloped by Adara Systems in collaboration with ODP staff first deployed during ODP Leg 139 Shipboard Scientific Party 1992al Figure II 1 Machine drawing of complete APCT 3 measurement system including optional configuration with two electronics sets The primary APCT 3 coring components comprise these pieces coring shoe with annular cavity drawing OP4375 cross over sub drawing OM0701 upper tool housing drawing OM0702 and a core catcher sub drawing OM0703 Other components include o rings and core catcher components and test plugs for sealing the coring shoe and upper tool housing during lab testing and calibration Conventional use of the APCT 3 involves deployment of only a single electronics set in the coring shoe See text for discussion of parts and deployment options and Appendix A2 for detailed drawings of tool components Figure II 2 Photo of APCT 3 electronics and related components Figure 1 1 Examples of second generation APC tool data from ODP Leg 139 in Middle Valley Shipboard Scientific Party 1992b A Complete deployment in relatively cool sediments B Expanded view of record from in sediment including fit of observations to model Every third observation is plotted for clarity Early time data are not used in fit because these data tend to not follow the theoretical decay curve C Complete deployment in relatively warm sediments D Expanded view of record from in sediment including fit of observations
38. er chillers and heaters that work against each other to hold the temperature within a narrow operating range The APCT 3 tool system is physically large APCT 3 User Manual Draft 2 July 2007 Page 32 and thermally massive so it is best to use a large stirred calibration bath like those used for calibration of CTD systems In principle it might be possible to calibrate an APCT 3 tool in a smaller bath with the coring shoe oriented vertically and the top of the shoe extending above the water level but in practice it will be difficult to maintain constant bath temperature with this configuration It is not possible to calibrate APCT 3 tools under conditions identical to those of standard operation When the tool is deployed at sea it begins at room temperature then cools towards bottom water temperature as the tool is pumped down the drill pipe the tool may reach bottom water temperature if it is held steady at in bottom water with the pumps off for a sufficient time When the tool is lowered to the bit and fired into the formation the electronics changes temperature as a result of frictional heating of the coring shoe but at a rate that is probably much lower than that of the temperature probe itself because the tool electronics are not in good thermal contact with the wall of the coring shoe It is during this time when the tool electronics are drifting in temperature that the most important data are collected for 8 10 minutes with th
39. from the tool is much more important than vertical heat transport along the tool and that the temperature probe is sufficiently far from the end of the coring shoe that there is little influence associated with the contrast in properties between the shoe and deeper sediment As part of the development of the APCT 3 system new cooling curves were calculated numerically on the basis of the geometry of the coring shoe and core barrel In addition earlier programs were based on a fixed analytical relationship between sediment thermal conductivity k and heat capacity pc New cooling curves have been calculated using a wide range of k and pc values allowing the user to select values that seem most appropriate and to explore the influence of parameter selection interactively The general procedure is to select formation properties select an interval of data to be processed and shift the tool penetration time so as to minimize the statistical misfit between the measurements and the model Once an appropriate fit is achieved temperatures are extrapolated to infinite time using the model to infer the in situ formation temperature Users typically neglect the first 30 60 seconds of data following penetration as these measurements often deviate from theory for several reasons including the non instantaneous and variable rate of tool penetration and the non uniform distribution of frictional heat The data interval selected for processing is usually n
40. g Tref T005C orig T005C new Tref Toosc new CC ohms CC CC CC CC 0 1992 93978 0 215 0 0158 0 1997 0 0005 4 9558 74535 4 975 0 0192 4 9561 0 0003 10 0300 58607 10 052 0 0220 10 0294 0 0006 14 9440 46733 14 969 0 0250 14 9433 0 0007 19 9130 37401 19 939 0 0260 19 9128 0 0002 24 9210 30063 24 946 0 0250 24 9210 0 0000 30 0050 24230 30 029 0 0240 30 0051 0 0001 35 0350 19685 35 058 0 0230 35 0367 0 0017 40 1180 16049 40 136 0 0180 40 1179 0 0001 45 1260 13193 45 139 0 0130 45 1252 0 0008 APCT 3 User Manual Draft 2 July 2007 Page 39 Table A3 4 Calibration coefficients for APCT 3 tools based on fit to Steinhart Hart equation 7 A B lnR C InR Tool ID A B C 1858002C 92779185 x 107 2 2234513 x 107 1 2263852 x 107 1858004C 9 3166619 x 107 2 2183365 x 107 1 2375744 x 107 1858005C 9 2931769 x 107 2 2203068 x 107 1 2425852 x 107 Notes T is calculated in Kelvin win ohms Also read section on entering coefficients for use by WinTemp actual coefficients used are slightly different than those listed above for reasons explained at the end of Appendix A3 APCT 3 User Manual Draft 2 July 2007 Page 40 Figure Captions Figure 1 1 Photos of first and second generation APCT tools and components A First generation tool developed for use during DSDP and used in the first several years of ODP Horai 1985 Horai and Von Herzen 1985 Koehler and Von Herzen 1986 B Second generation tool dev
41. he coring shoe As of winter 2003 many of these second generation tools had been lost or damaged and the company that had built and serviced these tools had gone out of business Development of a third generation of APCT tools began in 2003 with support provided by the German Science Foundation to H Villinger University of Bremen and the U S National Science Foundation to A Fisher University of California Santa Cruz The technical development was completed in close collaboration with Fa Antares Stuhr Germany who had previously collaborated with H Villinger and colleagues on APCT 3 User Manual Draft 2 July 2007 Page 3 development of a Miniaturized Temperature Logger MTL project for use with collection of thermal data during conventional gravity and piston coring operations Pfender and Villinger 2002 Jannasch et al 2003 Hardware designs were discussed through 2003 and into 2004 and it was decided to retain as much as possible of the form and function of the second generation tools which had proven to be robust and easy to operate Designs for coring components were prepared by engineers working with the U S Implementing Organization US IO to IODP and new coring components were built by an established vendor Antares personnel created a series of prototype tool frames so that the fit into the coring components could be confirmed and produced a working prototype tool in advance of IODP Expedition 311 Cascadia Hydra
42. he measurement of thermal conductivity of deep sea sediments by a needle probe method J Geophys Res 64 1557 1563 1959 Von Herzen R P and A E Maxwell Measurements of heat flow at the preliminary Mohole site of Mexico J Geophys Res 69 741 748 1964 APCT 3 User Manual Draft 2 July 2007 Page 29 Appendices Al APCT 3 data sheet APCT 3 User Manual Draft 2 July 2007 Page 30 A2 Tool technical information Documents in this section comprise an assortment of drawings instructions packing slips and other information related to APCT 3 tool components APCT 3 User Manual Draft 2 July 2007 Page 31 A3 Calibration 1 Goals and procedures limitations APCT 3 tool calibration is an important part of tool production and maintenance but there are some common misunderstandings as to the need for calibration how it is done and its limitations This section discusses these issues and the next section reports on results of the laboratory calibration of the first three production APCT 3 tools during Summer 2006 A prototype tool was calibrated by A Trehu and colleagues at OSU prior to the expedition as described in Heesemann et al 2007 The determination of conductive seafloor heat flow requires measurements of the thermal gradient and thermal conductivity What matters most from the perspective of APCT 3 measurements used to determine the heat flux is the difference between adjacent measurements rather than their absolut
43. ined with a 10 point calibration as if they were detemined with a 3 point calibration APCT 3 User Manual Draft 2 July 2007 Page 38 Table A3 1 Summary of Summer 2006 calibration results tool 1858002C Tref Rooze Too2c orig Tref T002C orig T002C new Tref T002C new CC ohms CC CC CC CC 0 1992 94104 0 188 0 0112 0 1993 0 0001 4 9558 74614 4 954 0 0018 4 9561 0 0003 10 0300 58654 10 035 0 0050 10 0296 0 0004 14 9440 46760 14 955 0 0110 14 9437 0 0003 19 9130 37416 19 930 0 0170 19 9128 0 0002 24 9210 30070 24 941 0 0200 24 9209 0 0001 30 0050 24232 30 027 0 0220 30 0048 0 0002 35 0350 19684 35 059 0 0240 35 0363 0 0013 40 1180 16046 40 140 0 0220 40 1179 0 0001 45 1260 13189 45 146 0 0200 45 1255 0 0005 Table A3 2 Summary of Summer 2006 calibration results tool 1858004C Tref Roose T004C orig Tref T004C orig Tooac new Tref Tooac new CC ohms CC CC CC CC 0 1992 94211 0 165 0 034 0 1990 0 0002 4 9558 74692 4 932 0 024 4 9564 0 0006 10 0300 58711 10 014 0 016 10 0298 0 0002 14 9440 46801 14 936 0 008 14 9439 0 0001 19 9130 37445 19 913 0 000 19 9130 0 0000 24 9210 30090 24 926 0 005 24 9208 0 0002 30 0050 24245 30 015 0 010 30 0047 0 0003 35 0350 19692 35 050 0 015 35 0359 0 0009 40 1180 16050 40 134 0 016 40 1177 0 0003 45 1260 13190 45 144 0 018 45 1259 0 0001 Table A3 3 Summary of Summer 2006 calibration results tool 1858005C Tref Roosc Toosceori
44. intervals one for each calibration point Next data recovered from the APCT 3 tools were plotted to determine tool readings during the time periods corresponding to the times when the temperature reference was stable Curiously the three APCT 3 tools did not show the same equilibration response Tool 1858002C tended to overshoot the target APCT 3 User Manual Draft 2 July 2007 Page 35 temperature and generally took longer to equilibrate Fig A3 1 The first characteristic is consistent with Tool 1858002C being closer to a heater unit whereas the second characteristic may indicate that the sensor in this tool was not in as good thermal contact with the wall of the coring shoe sub as were the other tools We generally selected data intervals to process during which the reference probe and all of the APCT 3 tools were in rough equilibrium with the bath temperature measured tool responses oscillated but there was no measurable drift The latter was assessed by selecting a 15 20 minute interval and fitting the data to a straight line Intervals were selected so as to minimize the slope of this line It is not possible to determine prior to recovering the APCT 3 tools when they have achieved thermal equilibrium with the bath nor was it a simple matter to assess this with the reference probe Data from the latter were logged using terminal emulation so data could not be accessed until after the logging function was stopped and there was no capabi
45. irregular heating creation of a damaged zone around the coring shoe inside and or outside having different sediment properties fluid movement away from the tool for a brief period after penetration Experience has shown that it is often difficult to achieve a good fit between observations and modeled temperature decay without allowing for the time shift However this additional degree of freedom in data processing can also accommodate use of a theoretical model that is inconsistent with actual tool and formation geometry or properties We do not have much experience yet with the new APCT 3 cooling curves and there remains to be completed a detailed comparison of older and newer decay curves and their influence on inferred in situ temperature but it appears that time shifts required to best fit the data using the new model may be somewhat shorter than those needed with the older models This suggests that the newer models may do a better job representing experimental conditions It is also important in selecting a data interval during processing to examine the experimental data very carefully and to avoid data segments that show evidence of tool motion In some cases the tool is moved abruptly and this results in a second heating pulse that is clearly visible but in other cases there can be a subtle change in the rate of cooling If data are used in processing that include secondary heating because of tool motion a spurious formation temperature
46. lar program Use a spreadsheet to calculate three new R T pairs using the coefficients just determined spanning the full range of calibration For example during Summer 2006 calibration we use a range of 0 45 C thus we calculated three R T pairs for T 20 45 C Make sure to cover the full calibration range and to include values at the extreme ends and in the middle of the range Enter these R T pairs in the Calibration Temperature window and press OK The temperature values in the open wtf will be updated accordingly If you wish to save the new calibration coefficients choose Calibrtion gt Store from the main menu and name the wtc file accordingly NB Antares releases SZ wtc files as read only so you will need to change this to overwrite an existing wtc file Be sure to back up the old file first The method above was used for saving new coefficients based on Summer 2006 calibration of the first three APCT 3 tools Small errors were introduced in the specification of calibration coefficients A B and C which are slightly different as stored in the wtc files by WinTemp but additional spreadsheet calculations show that these additional errors result in calibrated temperatures that are lt 0 001 C different from those determined using the full 10 point calibration NB this does not mean that a 3 point calibration is as good as a 10 point calibration Rather the method above tricks WinTemp into using coefficients determ
47. lity to plot the data in real time without generating data gaps Nevertheless by waiting 20 30 minutes after temperatures appeared to stabilize we were able to assure that sufficiently stable data were acquired The APCT 3 tools were delivered from the contractor with calibration coefficients provided by the thermistor vendor These coefficients relate the resistance of the thermistor circuit to the measured temperature using the Steinhart Hart equation 1 a A B nR C nR A3 1 where T 15 temperature in Kelvin and R is resistance in ohms Comparison of mean reference temperatures during each stability period and apparent temperatures indicated by the APCT 3 tools based on factory calibration coefficients revealed absolute differences as great as 0 034 C Tables A3 1 to A3 3 Fig A3 2 Errors were systematically biased and tended to be largest for higher calibration temperatures but the offsets were inconsistent between tools We calculated new calibration coefficients for the three tools by fitting measured values of T and R with equation Tables A3 1 to A3 3 to derive new coefficients A B and C Table A3 4 Fig A3 2 Comparison of temperatures calculated with new coefficients to those determined with the reference probe indicates errors lt 0 002 C for all tools across the full range of calibration temperatures for most tools and temperatures APCT 3 User Manual Draft 2 July 2007 Page 36 the errors are lt 0 001 C Equ
48. may be useful to know about in order to understand why the current system was designed and constructed the way that it is This section also contains a few references to previous scientific and technical studies Section II comprises an overview of APCT 3 system components and tool operation procedures These are summarized at the end of this section with two Quickstart documents that are intended to remind experienced users what steps to follow and in what order during routine operation of the tools Section III focuses on data processing and interpretation with an emphasis on a newly developed model representing tool response during deployment The new processing software includes a helpful graphical user interface and provides considerably greater control on parameter selection than did earlier software and the ability to explore parameter dependences of extrapolated temperatures Inexperienced users should pay particular attention to Section IIIA which discusses limitations of the modeling approach and ambiguities that are likely to remain in interpretation of formation temperatures even when the tool is deployed properly and works well Section IV comprises references cited throughout the manual Appendix A1 is the latest version of the tool data sheet used by the US IO when running the APCT 3 APCT 3 User Manual Draft 2 July 2007 Page 1 Appendix A2 contains technical documents machine drawings and other information provided by the ele
49. n extraction tool by the handle and position the electronics frame so that it is aligned with the annular cavity It may help to have someone else hold a flashlight or to use a camping light on your forehead during this process so that you can see to the base of the annular cavity As you lower the frame into the cavity in the coring shoe watch the alignment mark near the top of the insertion extraction tool This should align closely with the vertical mark on the coring shoe when the frame is oriented correctly The o rings on the electronics frame will cause a small amount of friction as the tool is lowered into the cavity but you should not have to push hard If there is much resistance extract the frame and examine the o rings and cavity in the shoe to see if there are any obstructions If the thermistor probe lands on the bottom of the annular cavity but misses the hole gently raise and lower the frame until you find the hole then lower the frame until it lands on the bottom of the cavity NB over time the APCT shoe or APCT 3 User Manual Draft 2 July 2007 Page 9 electronics frame may deform slightly requiring that smaller o rings or possibly no o rings be used on the frame 10 If you are preparing for an actual deployment as opposed to running a bench test clean and dress the o rings in the top ring Fill out the top of an APCT Data Sheet Appendix Al You will need to keep this sheet with you during the station filling it
50. n of ODP personnel The new tools were placed on the JOIDES Resolution for use during Leg 139 and operated for over 15 years The second generation APCT tools differed from first generation tools in several important ways The first generation tools were based on custom designed and constructed electronics bonded with epoxy into a form about the size of a small package of chewing gum Fig 1 1A A metal probe containing a thermistor extended from the base of the tool and a separate battery pack was attached with a small connector Both the tool and battery pack fit into a slots milled into the wall of a conventional APC coring shoe These first generation APCT tools were a marvel of technology especially considering that they were created in the early 1980 s but they were fragile instruments particularly the connectors and had to be removed from the coring shoe after each deployment in order to recover data The second generation tools were designed around a cylindrical tool frame that fit into an annular cavity in the base of a redesigned APC coring shoe Fig I 1B Two prongs extended from the base of the tool frame one of which contained a platinum resistance temperature device RTD the other prong helped to register the tool frame as it was lowered into the annular cavity Batteries were contained in two separate packs that fit into the tool frame and the tool could be programmed deployed and downloaded without removing the tool from t
51. nerally want to hand over the tool to the rig crew 20 40 minutes before they send the core barrel down the pipe and they will want to be ready before the driller announces that the last core is on deck The rig crew will make up the APCT 3 coring shoe and core catcher sub to a core barrel then will lower the barrel into the pipe on the sand line When the core barrel has been launched put on your steel toed boots grab a hard hat go to the driller s shack with the Data Sheet and let the driller know how you would like to run the station 3d The core barrel is usually pumped down the pipe on the sand line until the core barrel is a few tens of meters above mudline Let the driller know in advance if you would like to stop at mudline to record a bottom water temperature The APCT 3 tools have been carefully calibrated see Appendix A3 but it is good practice to verify bottom water temperature at each site at least once for each electronics set used during an expedition More frequent bottom water measurement may be desirable particularly when working in shallow water or in other environments where bottom water temperature variations are expected The drill pipe is an efficient heat exchanger so water in the pipe is generally close to bottom water temperature by the time the water reaches the bottom of the pipe provided that the water is sufficiently deep and that the surface water is not anomalously warm However depending on the pumping ra
52. o longer than 7 9 minutes sometimes less in part because of limited time with the tool motionless in the seafloor but also because deviations of tool cooling from the theoretical model tend to occur at later times Selection of formation properties is challenging for several reasons First sediment thermal conductivity is heterogeneous in many formations Second DSDP ODP and IODP scientists typically do not determine sediment heat capacity and there is no single relation between thermal conductivity and heat capacity that applies for all sediments Third thermal conductivity measurements are virtually never made at exactly the same location as the temperature probe and even if they are recovered sediments from the coring shoe are often highly disturbed Thus researchers must be prepared to process data using a variety of reasonable properties and to list in situ temperatures determined through processing with uncertainties that span a range of values APCT 3 User Manual Draft 2 July 2007 Page 20 The time shift applied during processing to optimize the statistical fit between observations and model calculations has a long history in analysis of seafloor heat flow data e g Bullard 1954 Davis et al 1997 Hartmann and Villinger 2002 Langseth 1965 Villinger and Davis 1987 The time shift is a heuristic representation of several properties and processes that are virtually impossible to predict a priori finite tool insertion time
53. on the insertion extraction tool and gently lift the tool vertically 4g Clean the surface of the electronics gently with a dry cloth Wipe off excess grease or heat sink compound Lower the clean electronics frame into the plastic cylindrical holder and screw on the cap Put the cylinder in a drawer or on the shelf Clean off the cutting shoes and sub s Put the interface box cables batteries and parts in Ziploc bags and place these in their boxes and or on the shelf Tell the ET lab tech or Lab Officer if supplies are needed APCT 3 User Manual Draft 2 July 2007 Page 16 C APCT 3 Operation Quickstart Deploy Tool assumes electronics frame is in shoe ready for deployment 1 Turn on computer launch WinTemp Attach curved connector to top of frame 2 Fill out top of Data Sheet 3 Choose Logger gt Battery and record the Voltage and Total Sample Count on Data Sheet 4 Choose Logger gt Clear data 5 Choose Logger gt Setup Check box for Synchronize Logger from PC Time 6 Set start time logging duration logging interval 7 Press Activate and confirm plan press OK 8 Disconnect connector from top of frame 9 Insert top ring Make up core catcher sub Hand to rig crew APCT 3 User Manual Draft 2 July 2007 Page 17 APCT 3 Operation Quickstart Recover Tool assumes coring shoe is clean open electronics frame is accessible 1 Turn on computer launch WinTemp Attach curved connector to top of frame 2 En
54. ors that have contributed to both the success and the enduring legacies of these programs One of the most innovative down hole tool developments in the latest years of DSDP was a piston coring shoe with temperature measurement capability Horai 1985 Horai and Von Herzen 1985 Koehler and Von Herzen 1986 This tool allowed DSDP and later ODP personnel to determine in situ temperatures within the undisturbed formation well ahead of the drilling bit without making a dedicated tool run These tools have been used successfully in many geological environments to evaluate thermal conditions within sub seafloor sediments and in open boreholes Although the piston coring system in DSDP was initially referred to as the HPC subsequent improvements created an advanced piston coring APC capability A temperature tool run with this system is herein referred to as an APCT tool APCT 3 User Manual Draft 2 July 2007 Page 2 Eight APCT tools based on the design introduced during DSDP were purchased by the ODP science operator Texas A amp M University TAMU in 1984 and were used extensively during the early years of the new program All of these tools were eventually lost or damaged over time and by ODP Leg 117 it was necessary to begin building a new set of instruments A second generation APCT tool development was completed in 1991 This tool system was designed and built on contract by a commercial engineering company under the supervisio
55. r filled squares and temperatures determined following calculation of new Steinhart Hart coefficients crosses In all cases the new coefficients provide residual errors lt 0 002 C C A Tool 1858002C B Tool 1858004C C Tool 1858005C APCT 3 User Manual Draft 2 July 2007 Page 42 Serial connector Ek Battery y j Sensor Ser CN serial connector Registration 4 T Main electronics Figure 1 1 1 ams WA 92 Og s ruo n y 099640 Joyojeo Jade L EE EES KUN EN XE ee ee Q HZ KE gt MEN GEN ES GSE BEN S o yanina T SN YS Ao WA WA WA WA WA WAA SIII ZLD Z aa NA A A ANA A AS De zz AY gt A EE z T T T T 1 TF All 221 222222022222222020 enemy N NOS 4 TOZOINO 2015 SUNOD E LIdV ZOLOWO qns 55 qns Joo c IDdV s dd 60 0 qns 4 TII m tq Bul dol oo awel 100 6 104 MEWA TIDE EN 3 2 X Pere 2 Bnjd eet seo 6 soluo1o l3 qoJd 61 L JO O uuoo elas SOUS LOdV 1 01 ons ty S SWI 008 0022 0012 0002 0092 0092 0061 euIjpnw Je vo 2 95
56. rocessing A Modeling and other considerations B TP Fit C APCT 3 Processing Quickstart IV References Appendices Al APCT 3 data sheet A2 Tool technical information 1 Coring shoe components 2 Electronics documentation A3 Calibration 1 Goals and procedures limitations 2 Summer 2006 calibration A4 TP Fit installation and operation APCT 3 User Manual Draft 2 July 2007 Page ti 1 Introduction A Goals and Organization This user manual accompanies the third generation of hardware and software to be used to determine subseafloor temperatures within sediments during piston coring operations This manual is intended to guide shipboard scientists and technicians in 1 the use of the APCT 3 tools to collect subseafloor thermal data and 2 application of software designed to help with interpretation of these data Although it seems like it should be a simple matter to determine the temperature of subseafloor sediments while coring in practice it can be challenging to collect high quality data and interpret this data correctly We have attempted to explain and summarize sufficient information so that a novice user can collect and interpret data with the APCT 3 system but it is important to discuss the information and recommendations in this manual with experienced scientists technicians and the drilling crew The rest of Section I contains background information on the history of temperature measurement while APC coring which
57. rs benefit from understanding how APCT coring components interface with regular coring components and operations In addition the APCT 3 includes a new option for running multiple tools during a single APC deployment this last capability remains to be tested The layout of the APCT 3 illustrates the primary coring components Fig II 1 APCT 3 electronics are deployed inside a coring shoe and optionally an upper tool sub The APCT 3 shoe differs from the shoe used with second generation tools only in the depth extent of the o ring surfaces they are slightly longer and in labeling instructions for the vendor During conventional use as with earlier generation APCT tools a regular APC core catcher sub forms the seal at the top of the annular cavity The APCT 3 tool prototype was deployed in this way during IODP Expedition 311 and the NGHP India Hydrate expeditions and it is anticipated that most future tool deployments will use this same configuration NB the deeper o ring surface inside the APCT 3 coring shoe should not lead to any incompatibilities with existing coring hardware but some hardware made for the new system may not fit properly with that for the second generation system Be sure to fit test any hardware as part of preparation in advance of deployment As part of the APCT 3 development an option was created to deploy two sets of APCT 3 electronics with a sensor to sensor spacing of approximately 57 2 cm 22 5 in APCT
58. s servicing or inspection If all goes well you will be able to collect data from dozens of deployments without removing the electronics from the coring shoe 4d Insert the electrical connector to allow the APCT 3 electronics to communicate with the computer If it is not already running start WinTemp Choose Logger gt Read data from the main menu If the tool is still running you will be asked to confirm that you would like to stop logging You may be asked to identify a calibration file for use with your tool Navigate to the appropriate directory probably c Program Files Antares and choose the wtc with the file name matching your tool number Data are downloaded and displayed in tabular form on the screen Choose File gt Save to save the data The file will automatically be named with the tool ID followed by the date and time at which the tool started and saved in WinTemp wtf format It is a good idea to also save the data in text format for use with processing software Choose File gt Export The data will be saved to an ASCII file dat using the same naming convention NB WinTemp defaults to saving data to the primary Antares directory You can save files to a different directory but then the program may ask you to APCT 3 User Manual Draft 2 July 2007 Page 15 locate a calibration file when you next recover data It is easier to just save to the Antares directory then to transfer the data to separate archive and
59. s were calibrated at the Hydraulics Laboratory at the Scripps Institution of Oceanography SIO in Summer 2006 Tools calibrated during this time have serial numbers 1858002C 1858004C and 1858005C A prototype APCT 3 tool was calibrated by A Trehu and colleagues at Oregon State University in Summer 2005 prior to deployment on IODP Expedition 311 as described elsewhere Heesemann et al 2007 The calibration tank used at SIO was custom built with internal dimensions of 50 cm width 172 cm length and 36 cm depth This tank was large enough to allow all three production tools to be submerged simultaneously Two of the tools were calibrated inside APCT coring shoes one new shoe and one older shoe on loan from the US IO and the third was calibrated inside a new upper sub Tank temperatures were controlled using competing water heating and chilling systems and spinners at each end of the tank kept the water well mixed during calibration Tank temperatures were monitored with a Hart Scientific Model AS125 temperature probe and a Model 1521 Digital Readout This measurement system which had been purchased in 2002 was sent to the manufacturer for recalibration immediately before the SIO calibration and was adjusted and certified to be accurate within an operating range of 10 50 C with accuracy of 0 001 0 002 C relative to an NIST certified reference Collection of APCT 3 calibration data required two days at SIO Calibration began on
60. te and the ambient hydrography water in the pipe may not equilibrate with bottom water if the pumps are APCT 3 User Manual Draft 2 July 2007 Page 12 running quickly In addition the complete APCT 3 system is thermally massive and the best bottom water temperature measurement will be made by holding the tool stationary a few meters above mudline for 10 15 minutes with the pumps off When positioning the tools at mudline be sure to take into account the length of the core barrel If the tool is inadvertently held below mudline a spurious bottom water temperature will be determined 3e After measuring the bottom water temperature the driller will lower the tool into the bit pressurize the drill string and fire the core barrel into the formation Wait 8 10 minutes for the tool to partly equilibrate with the formation The driller will pull the tool out and return it to the rig floor Some researchers like to pause again at mudline during tool recovery but the tool tends to equilibrate more slowing during this time because it is thermally more massive than during deployment because it contains sediment Your best bottom water temperature measurement is made prior to collection of a core Be sure to mark the data sheet to indicate the time of penetration and whether pressure bled off normally following APC deployment Complete bleed off of pressure generally indicates a normal deployment with the expectation that the APC coring sho
61. te dot will move and once again the Results plot is automatically updated 9 A few comments on selecting an equilibrium temperature None of the information shown on the contour plots can be used by itself to determine the true in situ temperature of the formation In many cases the properties that provide the best fit of the model to data may be unrealistic for example sometimes including very high values of k and pc The difficulty in selecting an appropriate model and equilibrium temperature is that although the new models are better than the old models in replicating the tool geometry there are aspects of each deployment that remain poorly constrained including the distribution of frictional heating heterogeneities in the formation the quality of the thermal contact between the shoe and sensor probe the creation of a damaged zone around the shoe Because these and likely other characteristics of each deployment are not well characterized available parameters k pc and the time shift may end up being adjusted to accommodate the data and improve the fit statistics In summary a good fit of the data to the model does not demonstrate that the model or the equilibrium temperature is correct Similarly the model that provides the statistical best fit to the data is not necessarily most likely to be correct Ultimately researchers will need to use all available data particularly physical properties measurements from around
62. ter time on Data Sheet 3 Choose Logger gt Read Data Confirm you wish to stop logging if necessary 4 Choose File gt Save to save the data in binary WinTemp format 5 Choose File gt Export to save the data in ASCII format 6 Copy and or backup data to archive and working directories APCT 3 User Manual Draft 2 July 2007 Page 18 HL APCT 3 Data Processing A Modeling and other considerations Processing APCT 3 temperature data to determine in situ conditions cannot be done automatically but requires careful and somewhat subjective fitting of measured temperatures to theoretical decay curves Some general understanding of the physics involved is required to make good interpretations The description of processing steps in the following section assumes that the reader understands the general theory behind APCT measurement processing as described by Horai and Von Herzen 1985 and Horai 1985 and Heeseman et al 2007 Additional insight is provided by papers describing processing of subseafloor probe data using tools with differing geometries e g Bullard 1954 Davis et al 1997 Hartmann and Villinger 2002 Langseth 1965 Villinger and Davis 1987 Discussing the procedure requires a brief review of tool responses during typical deployments Fig 1 1 Measured temperatures drop as the APCT 3 is deployed from the ship and lowered to the seafloor The lowest measured temperature may be found close to the seafloor but as
63. tes APCT 3 project co PIs and colleagues worked closely with Expedition 311 researchers who calibrated and field tested the prototype tool which worked extremely well and generated useful thermal data Heesemann et al 2007 On the basis of this experience project researchers requested several important design and functional changes to the APCT 3 electronics and Antares personnel responded by producing redesigned tools in Spring 2006 These instruments were taken to the Hydraulics Laboratory at the Scripps Institution of Oceanography in Summer 2006 and calibrated across a working range of 0 45 C see Appendix A3 for a discussion of calibration procedures and examples of results from the 2006 calibration effort This user manual was assembled in Spring and Summer 2007 APCT 3 User Manual Draft 2 July 2007 Page 4 II APCT 3 Components and Operation A APCT 3 Components 1 Introduction The APCT 3 system comprises three main components coring hardware electronics and operating software The first two sets of components are discussed in this section and operating software is discussed in the next section in the context of running an APCT 3 measurement station Chapter III discusses processing and interpretation of APCT 3 data and data collected with earlier generation tools using newly designed software 2 Coring hardware The US IO drilling crew and technicians handle almost all aspects of coring operations but APCT 3 operato
64. the APCT measurement depth and empirical relations between k and pc and consider whether an inferred equilibrium value makes sense on the context of other measurements APCT 3 User Manual Draft 2 July 2007 Page 26 C APCT 3 Processing Quickstart 1 Put APCT 3 data in a working directory with the 7PFit m code and subdirectories and start Matlab Run 7PFit 2 Select Load Data to load a data file 3 Select Edit Meta Data and enter appropriate values Be sure to enter values of k and pc most consistent with initial expectations 4 Select Pick and choose the tool penetration time 70 the initial data point to fit to the model Data Start and the final data point to fit to the model Data Stop 5 Select Show Fit and examine the Results plot window Return to Edit Meta Data and Pick as needed to examine different properties and data intervals 6 Select Compute Contours and the program will complete the same calculations using all available values of k and pc When this is complete select Explore to evaluate the influence of sediment physical properties in fit statistics equilibrium temperatures and other parameters 7 Select Save Session to create a Matlab mat file or Make Report to generate text output for later plotting APCT 3 User Manual Draft 2 July 2007 Page 27 IV References Bullard E C The flow of heat through the floor of the Atlantic Ocean Proc Royal Soc Lond Ser A 222 408 429 1954 Davis E E

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