Cycle 1
Contents
1. C CALCIA LJ K CA LJ K 12 After having written these variables to the result re start file after a model run further derived quantities are calculated from these variables and stored in the same arrays that now get new mnemotechnical names via an additional EQUIVALENCE statement according to COMDECK V12MNM2 Old name New name CA LJ K 1 SUPSAT LJ K CA LJ K 2 PHVALU 1 J K CA LJ K 3 CARION IJ K CA LJ K 4 SOLPRO LJ K CA LJ K 5 PREPHO LJ K CA LJ K 6 not used CA LI K 7 not used CA LJ K 8 not used CA LJ K 9 not used CA LJ K 10 not used CA LJ K 11 not used CA LJ K 12 not used PAGE 12 DKRZ OCEANIC CARBON CYCLE Model Documentation Several calcium carbonate cycle relevant quantities and the and organic carbon sediment pool values are found in the last COMDECK CACO3C Quantity Variable CO ion concentration CO2 LJ K H ion concentration HI 1 J K sediment pool CCSDI2 LJ K sediment pool CCSDI3 LJ K sediment pool CCSDIA LJ K POC C sediment pool OCSDI2 LJ K POC PC sediment pool OCSD13 LJ K POC C sediment pool OCSDIA LJ K PAGE 13 DKRZ OCEANIC CARBON CYCLE Model Documentation 3 4 THE PROGRAM Throughout this program the implicit type convention is used with variables beginning with A H O Z being of type REAL and variables beginning with I N being of type INTEGER Variables of type CHARACTER and LOGICAL are defined explic2. PAGE 3 DKRZ OCEANIC CARBON CYCLE Model Documentation 2 1 DISSOLUTION INORG PRECIPITATION OF CACO Degradation of CaCO is controlled by the degree of undersaturation of seawater with respect to calcite The destruction of aragonite the metastable modification of marine is accounted for in the model by allowing partial destruction of CaCO even in cases of calcite supersaturation After the ver tical redistribution of newly produced CaCO particles at first the deviation ACO3 from the saturation concentration is calculated Since the calcium concentration in seawater is almost constant and much higher than the CO3 concentration the marine CaCO saturation is almost entirely determined by the amount of ions in solution Then the amounts of total CaCO available in the respective grid box that are dissolved or can be precipitated E are determined and the concentrations for CO and at the new time level are accordingly t ACO C03 005 2 1 1 D caco 0 5 1 03 2 1 2 sai 31 ao 2 1 2 E max 0 2 1 3 t At t CO ED ue B 2 1 4 CaCO CaCO D c E 2 1 5 where I deviation of carbonate concentration from the saturation value C03 carbonate concentration at old time level COT saturation concentration of carbonate Dot amount of CaCO that reenters solution E amount of CaCO that can be precipitated
3. The inorganic chemistry varibles and constants are initialized in subroutine CHEMIN 3 4 2 3 Subroutine INIBIL initialization of geochemical inventories The model inventories for each geochemical variable and each reservoir as well the total model inven tories for each substance except oxygen are calculated These total inventories are used as reference for the subsequent check of conservation of matter by subroutine BILANZ The variables C12INV C13INV C14INV PHOINV ALKINV represent the total inventories of C C total alkalinity and phosphate in the model These values have to be conserved during the integration The oxygen inventory is allowed to fluctuate according to the amount of oxygen needed for remineralization of organic matter and according to the solubility at the see surface The ocean oxygen inventories are assumed to be com pensated by corresponding changes in the atmospheric oxygen content which is not modelled here 3 4 2 4 Subroutine BILANZ check of geochemical matter conservation BILANZ can be called at any position of the program of course NOT inside of LJ K DO loops to check conservation of matter C total alkalinity If IFULBI 1 in the main program BILANZ is called after every subroutine call in the time loop DO 1111 in the main program If IFULBI 0 in the main program BILANZ is only called once in each time step only after the ADVECT routine PAGE 17 DKRZ OCEANIC CARBON C
4. esac cft77 mapplo f case DEVICE in SU su segldr o runplo3 mapplo o 1gksg Incarg Incarg_no calc mpaint oplib deflib segldr runplo3 mapplo o lgksg Incarg calc oplib deflib esac runplo3 result gksm20 txt cat PROTOK cat GKS_ERROR PAGE 32 DKRZ OCEANIC CARBON CYCLE Model Documentation pwd 15 1 LLL ls grep gksm for GKSFIL in LLL do case DEVICE in SUN sun SUNC sunc GKSFIL iceage home k204002 tcolor ecolor pscm1 spl f GKSFIL d DEVICE scale 18 9 p pf m m211021 perm palettyn psz1 psm2 spl f GKSFIL d DEVICE scale 19 4 versat sp f GKSFIL d DEVICE scale 18 9 esac done exit PAGE 33 DKRZ OCEANIC CARBON CYCLE Model Documentation PAGE 34 DKRZ OCEANIC CARBON CYCLE Model Documentation Appendix C PLOT OUTPUT EXAMPLES In this section a subset of plots created by the capost job shell script see Appendix B is shown TOTAL CO2 MOLES LITER 10 6 195 2009 0 a J 20 50 9 50 0 250 m S NP un 21 500 4 m s a 5 o 750 4 L l l l l 0 2 20000 19500 DE 2050 90 60 30 EQ 30 N 60 90 ATLANTIC OCEAN Figure 4 Example for a plot output showing the GEOSECS cross section of the Western Atlantic for the total CO concentration 1076 moles liter PAGE 35 DKRZ OCEANIC CARBON CYCLE Model Documen
5. input to plot software POIPRO Print depth profiles for regions of interest END Figure 3 Flow chart of the Hamburg Oceanic Carbon Cycle Model Part 3 PAGE 22 DKRZ OCEANIC CARBON CYCLE Model Documentation 4 USER S MANUAL 4 1 HOW TO RUN THE MODEL An example Bourne Shell script is available on the Hamburg CRAY2S The full path for this script is pool POST carun job To perform this script copy it wherever you like on your pf directory After doing this you have to change the outdir parameter which should be the path to your personal output directory on the mf disk For user m222222 a possible choice would be outdir mf m m222222 carbon_out Beware that this directory exists For further explanations look at the copy of the script which is shown in Appendix A 4 2 HOW TO GET OUTPUT PLOTS In principle there is a vast number of possible applications of the model So the output processing pre sented here is only a small part of many possible options that might be required However the way the output is handeled here should enable you to easily add your individual programs in analysing the results Three program packages are offered here 1 lyprof produces mean depth profiles of 5 4C rel to the model atmosphere value dissolved O gt gt and alkalinity of the model provinces Tropical Pacific Antarctica Northern Atlantic Southern Atlantic Northern Indian Ocean Tropical Indian O
6. CaCO flux here 4000 m By this formulation of the vertical redistribution of newly formed no degradation of is included yet that is performed separately in another step see below POC flux is assumed to follow the 1 z law after Suess 1980 with a modification of distributing about one third of the POC new production 28 7 Proc F 50m see below like the newly formed This addition is introduced to account for organic material coated by hard shells F F 2 2 2 with Proc P1 90238 2 0212 FER 2 4 F Ppoc 50M Spoc Spoc 2 2 4 where 7 depth Proc annual production of POC SPOC part of Ppoc that sinks immediately to the bottom layer here 5 7 that is 20 of those 28 7 of total POC produced that are not considered by the 1 z formulation of Suess 1980 dp e folding depth for CaCO flux here 4000 m PAGE 5 DKRZ OCEANIC CARBON CYCLE Model Documentation 2 3 REMINERALIZATION OF ORG C Remineralization of organic matter and corresponding oxygen consumption are modeled according to a fixed Redfield ratio of 1 172 Takahashi et al 1985 O concentration is not allowed to become negative In the case of full consumption POC degradation stops at the respective grid point After the determination of the amount of POC that is remineralized during one time step APOC the POC PO and O concentrations for the new time level are
7. Y vi I upstream formulation 2 5 2 At Ax t At 1 1 K c where c tracer concentration V velocity vector q term for sources and sinks V velocity component in the direction of grid point i Ax distance to neighboring grid point i tracer concentration at neighboring grid point 1 a 1 if is nutrient concentration in the surface layer 0 otherwise I light factor dependent on latitude Nn maximum velocity of nutrient uptake K half saturation constant PO concentration where dc dt c 2 Uptake of PO as biolimiting nutrient by phytoplankton in the surface layer is the only additional process included in the tracer transport equation second term on the right hand side of 2 5 2 The advection equation is solved iteratively by a single level scheme Uptake of nutrients by organisms is included in this equation to allow a shorter time constant for phytoplankton growth compared to the time step of 1 year All the other chemical interactions are calculated in separate routines time splitting method The biological POC production is assumed to follow Michaelis Menten kinetics for nutrient uptake e g Parsons and Takahashi 1973 For the light factor I the same latitudinal profile as in Bacastow and Maier Reimer 1990 is used It is coherent with the latitudinal distribution of the annual sum of solar radiation incident on the ocean surface layer For uptake of inorganically dissolved carbon by phy topla
8. YC O total dissolved inorganic CO2 at new and old time levels respectively CaCO calcium carbonate concentration at new and old time levels respectively Ci adjustable constants here c 10 1 in bottom layer and zero else PAGE 4 DKRZ OCEANIC CARBON CYCLE Model Documentation 2 2 ORG AND PRIMARY PRODUCTION the CaCO production in the surface ocean is calculated The CaCO production rate is coupled to the particulate organic carbon POC new production calculated in the advection step subroutine ADVECT After the production of biogenic particulate matter in the surface layer it is redistributed within the water column Biogenic particulate matter is produced only in the uppermost model layer and is immediately redistributed within the water column in amounts decreasing with depth The immediate redistribution is a reasonable assumption because the time scale for the particles sinking through the water column is shorter about 100 m day e g Suess 1980 than the time step of 1 year 20 of the CaCO production is assumed to fall immediately to the bottom layer while the remainder is distributed according to an exponentially decreasing vertical flux z d Fcaco 2 Peico 7 Scaco 2 2 1 where 7 depth annual production of CaCO3 Sc aCO part of aCO that sinks immediately to the bottom layer here 20 d e folding depth for
9. actual values for new production of particulate organic carbon and calcium carbonate and the carbon pool inventories atmosphere ocean sediment are printed Finally line printer plots of three dif ferent meridional western Atlantic western Pacific eastern Pacific are produced that help to interprete the result Examples for plot output are given in Appendix C The result re start file contains the result of the model integration with all basic geochemical fields of all model reservoirs and an indicator for the last year of integration From this basic file all relevant variables of the simulation can be derived This essential file is saved at the end of an integration The postprocessor input file contains the fields that can be analysed after a model run Besides the geochemical fields stored in ta similar way to the re start file it includes derived quantities as e g the primary production rate the CO3 ion concentration the difference in CO partial pressure between atmosphere and ocean etc One header line with basic information is preceeding every array From the postprocessor input file plots can be produced using of the postprocessor PLOFIL and the plot pro grams SECPLC and MAPPLC The profile file contains mean depth profiles of different geochemical quantities and specific ocean regions This file is the input file for program LYPROF which plots those depth profiles together with corresponding observed depth profiles fro
10. calculated t t APOC r min 0 m O 2 3 1 POC POC APOC 2 3 2 PO PO APOC 2 3 3 APOC 03 0 1 5 2 3 4 Red where APOC amount of POC that can be remineralized during one time step r remineralization rate here 1 0 year 1 in the surface layer 0 05 year 1 elsewhere Rrea Redfield ratio P AO gt 0 1 oxygen concentration at the new and old time step respectively O E threshold value of oxygen concentration for bacterial decomposition PO phosphate concentration at the new and old time step respectively normalized to a POC concentration by the Redfield ratio P C POC particulate organic carbon concentration at the new and old time step respectively 2 4 GAS EXCHANGE OCEAN ATMOSPHERE Gas exchange between ocean and atmosphere is performed with a simple bulkformula F pCO air pCO water 2 4 1 where F is the gas exchange flux and is the gas exchange coefficient For A a value of 19 mol m yr at 270 ppm is adopted cf Broecker et al 1986 PAGE 6 DKRZ OCEANIC CARBON CYCLE Model Documentation 2 5 TRANSPORT OF TRACERS WITH OCEAN VELOCITY FIELD tracers are transported with the ocean velocity field An upstream formulation of the tracer equation continuity equation for amount of matter is applied d un SS div V c q tracer equation 2 5 1 2 t At t At t At ag dic V max
11. E 3 PHOSPHATE MOLES LITER 10 6 JAME 4 DISSOLVED OXYGEN MOLES LITER 10 6 JAME 5 POC MOLES LITER 10 6 JAME 6 CALCITE MOLES LITER 10 6 JAME 7 DELTA 13C JAME 8 DELTA 14C JAME 9 POC DELTA 13C JAME 10 POC DELTA 14C JAME 11 CALCITE DELTA 13C JAME 12 CALCITE DELTA 14C JAME 13 DEGREE OF CO3 SATURATION PERCENT JAME 14 PH VALUE JAME 15 CO3 MOLES LITER 10 6 JAME 16 SOLUBILITY PRODUCT A A A A A A A A A A A A A A ES 1 NO 0 JAME 17 PREFORMED MOLES LITER 10 6 TAME 18 TEMPERATURE DEG JAME 19 SALINITY PSS78 JAME 20 DISSOLVED GASEOUS CO2 SURFACE JAME 21 OCEAN ATMOSPHERE DIFFERENCE IN PCO JAME 22 PRIMARY PRODUCTION G M 2 MONTH JAME 23 CALCITE PRODUCTION G M 2 MONTH JAME 24 ORG C SEDIMENT POOL CONTENT MOLE M 2 25 SEDIMENT POOL CONTENT MOLE M 2 JAME 26 SIO4 MOLES LITER 10 6 999999999999999999999999999999 ZZAZZZZZZZZZZZZZZZZZZZZZZZZZZZ JAME 27 NN JAME 28 NN AME 29 NN JAME 30 NN EOF1 compile link and run the plot program case DEVICE in tcolor ecolor SUNC sunc pscm1 moddir map11 f mapplo f cp moddir map11_bw f mapplo f
12. ITE DELTA 13C 0 CNAME 12 CALCITE DELTA 14C 0 CNAME 13 DEGREE OF CO3 SATURATION PERCENT 0 CNAME 14 PH VALUE 0 CNAME 15 CO3 MOLES LITER 10 6 0 CNAME 16 SOLUBILITY PRODUCT 0 CNAME 17 PREFORMED MOLES LITER 10 6 0 CNAME 18 TEMPERATURE DEG C ST CNAME 19 SALINITY PSS78 0 CNAME 20 SIO4 MOLES LITER 10 6 0 EOF1 compile link and run the plot program case DEVICE in tcolor ecolor SUNC sunc pscm1 moddir sec11 f secplo f cp moddir sec11_bw f secplo f esac cft77 secplo f case DEVICE in SU su segldr o runplo2 secplo o lgksg Incarg Incarg_no calc mpaint oplib deflib segldr o runplo2 secplo o lgksg Incarg Incarg_no calc oplib deflib esac runplo2 result gksm18 txt cat PROTOK cat GKS_ERROR A A lee an e Plot horizontal maps map11 mapl11 bw cat gt MAPINP lt lt EOF1 INPUT FILE FOR PLOTTING HORIZONTAL PATTERNS FROM OUTPUT OF CMODEL TITLE TEST LAYER S TO BE PLOTTED YES 1 NO 0 25 M LAYER 1 75 M LAYER 2 150 M LAYER 3 250 M LAYER 4 450 M LAYER 5 700 M LAYER 6 1000 M LAYER 7 2000 M LAYER 8 2000000 RA PAGE 31 DKRZ OCEANIC CARBON CYCLE Model Documentation 3000 M LAYER 9 4000 M LAYER10 5000 M LAYER11 PARAMETER NAME 1 TOTAL CO2 MOLES LITER 10 6 JAME 2 ALKALINITY EQUIVALENTS LITER 10 6 JAM
13. LSE a complete new start of the model is performed Modifications in geochemical inventories can be made easily just after the READ statement for the re start file i e before the radiocarbon production rate is calculated After having fixed all geochemical inventories after reading of the re start values the production rate for radiocarbon is calculated It is set equal to the amount of radiocarbon that decays in the total model sys tem during one time step The inventory check is initated by call of subroutine INIBIL where all chemical inventories are fixed at the beginning of the model run without having modified one of the variables in any way by the simulation of the various processes The resulting inventories serve as a reference for subsequent checks of conser vation of matter during the model run Variable IFULBI should be set to zero usually In this case subroutine BILANZ that checks conservation of matter will be called only once per time step If IFULBI 1 is set the model inventories are checked after each subroutine Subroutine POOLS is called once before the time stepping loop It prints actual values of the carbon pool sizes for the different reservoirs Aditionally it can be called at arbitrary positions of the main program Most useful is to call POOLS at the beginning or end of one or several time steps at least once at the beginning and at the end of an integration The postprocessor input file is prepared in s
14. O supersaturation PH value CO ion concentration solubility product preformed land sea distribution actual thickness at topography scalar points zonal velocity component u meridional velocity component v potential temperature salinity depth at topography vector points vertical velocity component w PAGE 37 DKRZ OCEANIC CARBON CYCLE Model Documentation PAGE 38
15. RUNO001 Main Program 1 Set Common Blocks Initiate horizontal velocities and geometric variables INITIA2 BIOINI Initiate chemical and biological parameters Read restart values INIBIL Initiate balances inventories of parameters Continued with frame 2 Figure 1 Flow chart of the Hamburg Oceanic Carbon Cycle Model Part 1 PAGE 20 DKRZ OCEANIC CARBON CYCLE Model Documentation LYSOCL dissolution precipit according to saturation BIOSOF Production of soft tissue POC OXYCON Remineralization of soft tissue SURFCH pCO in surface layer and CO2 exchange ocean atmosph Y BIOTUR Bioturbation and POC re entering solution from sediment time step ADVECT loop Advection num Diff with 3 D ocean circulation field Year between 1820 and 1984 2 2 D meridional atmospheric transport decay Input from anthropogenic sources Forest Soil Fuel BILANZ Compares actual and basic inventories for correction Close of balances Maximum 2 continued with frame 3 INTSTP Figure 2 Flow chart of the Hamburg Oceanic Carbon Cycle Model Part 2 PAGE 21 DKRZ OCEANIC CARBON CYCLE Model Documentation BILANZ Compare actual and basic inventories for correction YES Write down restart values RESTART after this run Calculation of Delta C Delta TRN860 Prepare output files for
16. Report No 5 The Hamburg Ocean Carbon Cycle Circulation Model E Maier Reimer ax Planck I nstitut f r Meteorologie Bundesstra e 55 D 2000 Hamburg 13 C Heinze Institut f r Meereskunde der Universit t Hamburg Troplowitzstra e 7 D 2000 Hamburg 54 Edited by Modellberatungsgruppe Hamburg January 1992 1 SUMMARY PAGE DKRZ OCEANIC CARBON CYCLE Model Documentation Contents 1 1 MAIN AUTHORS OF THE MODEL 1 2 PERSON S RESPONSIBLE FOR MODEL SUPPORT AT THE DKRZ MODEL DESCRIPTION annually averaged version Cycle 1 2 1 DISSOLUTION INORG PRECIPITATION OF CACO3 2 2 ORG AND PRIMARY PRODUCTION 2 3 REMINERALIZATION OF ORG 2 4 GAS EXCHANGE OCEAN ATMOSPHERE 2 5 TRANSPORT OF TRACERS WITH OCEAN VELOCITY FIELD SYSTEM DESCRIPTION OX eh 3 1 INPUT FILES 3 2 OUTPUT FILES 3 3 COMMON BLOCKS 3 4 THE PROGRAM 3 4 1 Main Program 3 4 2 Subroutines 3 3 4 2 1 Subroutine INITIA 1 initialization of dal fields 3 4 2 2 Subroutine INITIA2 initialization of geochemical fields 3 4 2 3 Subroutine INIBIL initialization of geochemical inventories 3 4 2 4 Subroutine BILANZ check of geochemical matter conservation 3 4 2 5 Subroutine POOLS calculation of carbon pool sizes 3 4 2 6 Subroutine LYSOCL dissolution inorg precipitation of 3 4 2 7 Subroutine BIOSOF org C and CaCO primary production 3 4 2 8 Subroutine OXYCON remineralizati
17. YCLE Model Documentation 3 4 2 5 Subroutine POOLS calculation of carbon pool sizes POOLS calculates the actual values of new production of organic matter POC and calcite and the carbon contents of the various reservoirs This routine can be called at any instance within the main program 3 4 2 6 Subroutine LYSOCL dissolution inorg precipitation of CaCO Calculation dissolution and inorganic precipitation of CaCO according to section 2 1 3 4 2 7 Subroutine BIOSOF org C and primary production Here the CaCO production in the surface ocean is calculated The CaCO production rate is coupled to the POC new production calculated in the advection step see Subr ADVECT After the production of biogenic particulate matter in the surface layer it is redistributed within the water column Biogenic par ticulate matter is produced only in the uppermost model layer and is immediately redistributed within the water column in amounts decreasing with depth By this formulation of the vertical redistribution of newly formed no degradation of is included yet that is performed separately see section 2 2 3 4 2 8 Subroutine OXYCON remineralization of org Remineralization of organic matter and corresponding oxygen consumption are modeled according to a fixed Redfield ratio O concentration is not allowed to become negative In the case of full consump tion POC degradation stops
18. Z OCEANIC CARBON CYCLE Model Documentation All three postprocessing utilities reside as FORTRAN programs at the CRAY2S in the directory pool POST carbon An example Bourne Shell script is provided by pool POST capost job To perform this script copy it wherever you like on your pf directory After doing this you have to change the outdir parameter which should be the path to your personal output directory on the mf disk as decribed in section 4 1 For further explanations look at the copy of the script which is shown in Appendix B PAGE 24 DKRZ OCEANIC CARBON CYCLE Model Documentation 5 REFERENCES Bacastow R B and E Maier Reimer 1990 Circulation model of the oceanic carbon cycle Clim Dyn 4 Broecker W S and T H Peng 1982 Tracers in the Sea 690 pp ELDIGIO Press Lamont Doherty Geological Observatory Columbia University Palisades N Y Broecker W S J R Ledwell Takahashi R Weiss L Merlivat L Memery T H Peng J hne and K O Miinnich 1986 Isotopic versus micrometeorologic ocean CO2 fluxes A serious conflict J Geophy Res 91 10517 10527 Heinze C 1990 Zur Erniedrigung des atmosph rischen Kohlendioxidgehalts durch den Weltozean w hrend der letz ten Eiszeit Dissertation Max Planck Institut fir Meteorologie Examensarbeit No 3 180 pp Maier Reimer E and K Hasselmann 1987 Transport and storage of CO in the ocean an inorganic ocean circulation c
19. arbon cycle model Clim Dyn 2 63 90 Maier Reimer E and R Bacastow 1990 Modelling of geochemical tracers in the ocean in Climate Ocean Interaction edited by M E Schlesinger pp 233 267 Kluwer Acad Publ Dordrecht Maier Reimer E U Mikolajewicz and K Hasselmann 1991 On the sensitivity of the global ocean circulation to changes in the surface heat flux forcing Max Planck Institut fiir Meteorologie MPI Report No 68 Maier Reimer E and U Mikolajewicz 1991 The Hamburg Large Scale Geostrophic Ocean General Circulation Model Cycle 1 Deutsches Klimarechenzentrum Technical Report No 2 Parsons T R and M Takahashi 1973 Biological Oceanographic Processes 186 pp Pergamon New York PAGE 25 DKRZ OCEANIC CARBON CYCLE Model Documentation Suess E 1980 Particulate organic carbon flux in the oceans Surface productivity and oxygen utilization Nature 288 260 263 Takahashi T W S Broecker and S Langer 1985 Redfield ratio based on chemical data from isopycnal surfaces J Geophy Res 90 6907 6924 PAGE 26 DKRZ OCEANIC CARBON CYCLE Model Documentation Appendix A_JOB TO PERFORM A MODEL RUN QSUB q M4 QSUB eo standard error und output QSUB r car process name QSUB set x outdir mf b k204002 outcarb moddir pool POST carbon cd TMPDIR set e execution of script will be aborted if error occurs ja jacct New start from quasi steady state produced wit
20. at the respective grid point After the determination of the amount of POC that is remineralized during one time step APOC the POC PO and concentrations for the new time level are calculated 3 4 2 9 Subroutine SURFCH gas exchange ocean atmosphere Gas exchange between ocean and atmosphere is performed with the bulkformula 2 4 1 3 4 2 10 Subroutine BIOTUR resuspension of sedimented matter The system of cycling constituents is closed here by resuspension of sedimented matter into the bottom layer at a fixed rate proportional to the sediment content of the respective grid cell Resuspension occurs in reality due to bioturbation in the uppermost sediment 3 4 2 11 Subroutine ADVECT transport of tracers with ocean velocity field Calculation of the advection of tracers with the 3 D ocean circulation field using an upstream formula tion of the tracer equation see section 2 5 PAGE 18 DKRZ OCEANIC CARBON CYCLE Model Documentation 3 5 PARAMETERS In namelist TUNE the following constants and variables can be set individually by the user INTSTP 3 number of time steps At 1 year TIMAX 1200 maximum CPU time in seconds Changes in the geophysical parameters must be done very carefully in the model source code Please contact the authors for such changes because a new spin up of the carbon cycle model might be neces sary PAGE 19 DKRZ OCEANIC CARBON CYCLE Model Documentation 3 6 FLOW CHARTS
21. cean Southern Indian Ocean Tropical Atlantic Southern Pacific and Northern Pacific and plots the respective mean profile of the GEOSECS data for a quick look of the model results 2 plofil11 is the interface between the main model postprocessor input file POSTIN and further treatment of the model results POSTIN contains all relevant parameters of the model run together in one file using the same standard format as the LSG model output for code numbers of the geochemical parameters see Appendix D This file is written in binary form Standard Fortran unformatted I O The carbon isotope values are uncalibrated in this file Program plofil11 cuts file POSTIN into single formatted files E10 4 for each parameter and calibrates the rare carbon isotopes for atmospheric values of AC 0 and 6 5 9 4 The resulting small parameter files are preceeded by one header line These files serve as input files for the plotting routines You may make use of these files for your individual treatment of the model results as well The plot routines now have to read only that parameter array that has to be plotted 3 Plot routines for merdional cross sections sec11 and sec11_bw and for horizontal maps map11 and map11_bw for colour and b w plots You have the choice of four different cross sections close to the GEOSECS sections eastern western Atlantic Pacific Every level of the model can be plotted inidividually with the map routines PAGE 23 DKR
22. d DLRU are needed for the meridional diffusive transport of CO in the atmosphere Following files are opened for input and output unit No 38 file VELOCI input unit No 36 file DPHILA input unit No 17 file MONITO input unit No 83 file RESTART input unit No 43 file INDLIS input unit No 87 file RESULT output PAGE 14 DKRZ OCEANIC CARBON CYCLE Model Documentation unit No 88 file POSTIN output e unit No 19 file PROFIL output Several counters concerning the time of integration are set The counter for Julian years is initialized by setting the variable ANNU This variable counts every year of integration Via ANNU certain input functions anthropogenic CO input e g can be activated at given years Time step counter NYETOT counts the total number of time steps of an integration It is set to zero at the start NYETOT is overwritten during re start runs when read from the re start file Variable INTSTP specifyies the number of time steps to be integrated For INTSTP 1 the time loop see below is carried out only once The variable TIMAX sets the maximum cpu time in seconds that is allowed to be used during the model run By setting TIMAX to an appropriate value the integration is stopped properly in the case that the run approaches the cpu time limit The run may not reach the number of integration time steps that are specified by variable INTSTP but save
23. d point lies in which ocean The code and the corresponding ocean regions are northern Atlantic equatorial Atlantic southern Atlantic northern Pacific equatorial Pacific southern Pacific northern Indian Ocean equatorial Indian Ocean southern Indian Ocean Arctic Ocean and European Polar Seas Southern Ocean ZZ O Q The re start file contains the result of the preceeding model integration with all basic geochemical fields of all model reservoirs and an indicator for the last year of integration A file with exactly the same for mat is produced at the end of the model run result re start file see below PAGE 9 DKRZ OCEANIC CARBON CYCLE Model Documentation 3 2 OUTPUT FILES Four output files are produced by the model and are saved after a run job flow control file dependent on run mode standard output written on file 6 or OUTPUT result re start file RESULT postprocessor input file POSTIN profile file PROFIL The job flow control file contains all control prints and all information about the job flow and the perfor mance of the integration All error messages are given here During the integration continuous informa tion about the conservation of the chemical inventories the number of iterations in the advection algorithm the year of integration and the atmospheric CO partial pressure is provided At the end of the run the
24. deral Republic of Germany e Robert B Bacastow Scripps Institution of Oceanography La Jolla U S A Christoph Heinze Institut f r Meereskunde Hamburg Federal Republic of Germany 1 2 PERSON S RESPONSIBLE FOR MODEL SUPPORT AT THE DKRZ Michael Lautenschlager Deutsches Klimarechenzentrum Hamburg Federal Republic of Germany PAGEI DKRZ OCEANIC CARBON CYCLE Model Documentation PAGE 2 DKRZ OCEANIC CARBON CYCLE Model Documentation 2 MODEL DESCRIPTION annually averaged version Cycle 1 The model simulates the inorganic carbon cycle and part of the organic carbon cycle of the World Ocean Aditionally to the ocean water carbon reservoir the carbon pools of the atmosphere and marine sediment are considered The internal redistribution of tracers within the ocean water is based on the velocity field and the ther mohaline fields of the dynamical Hamburg Large Scale Geostrophic LSG Ocean General Circulation Model This dynamical model is described by Maier Reimer et al 1991 The carbon cycle model uses the same grid as the LSG model see Maier Reimer and Mikolajewicz 1991 The velocity and thermo haline fields are taken from the input files and are not modified by the carbon cycle model The carbon cycle model s basic structure is derived from the geochemical concept as described in the work of Broecker and Peng 1982 pp 2 11 The biological carbon pump is simulated with its two components the organic carbo
25. h standard velocity field cp moddir RESTART1 RESTART Restart from previous run cp outdir RESULT RESTART Model forcing standard output from lsg_ogcm1 annual mean cp moddir ST5499M VELOCI dk ocean basin identifiers cp moddir MONITO MONITO th geometrical variables from 152 ogcm1 cp moddir DPHILA DPHILA dk indices and wet points cp moddir INDLIS INDLIS 15 1 namelist for model input cat gt INPUT1 lt lt EOF1 amp TUNE INTSTP 3 TIMAX 1200 amp END EOF1 INTSTP number of time steps in this run DT 1 year max of CPU time in sec for this run moddir cc_ogem1 run cc_ogeml run lt INPUTI start carbon cycle model copy model output and restart file PROFIL mean GEOSECS profils POSTIN input for postprocessing RESULT restart file cp PROFIL POSTIN RESULT outdir 16 1 ja cfs jacct cd outdir pwd ls 1 exit PAGE 27 DKRZ OCEANIC CARBON CYCLE Model Documentation PAGE 28 DKRZ OCEANIC CARBON CYCLE Model Documentation Appendix B JOB TO PERFORM PLOTS OF MODEL RESULTS QSUB q 53 zeit limit QSUB eo standard error und output QSUB r process name QSUB set x outdir mf b k204002 outcarb moddir pool POST carbon cd TMPDIR split output of cc ogcml into separate files plofil11 cp moddir POSTIN POSTIN output corresp to stand restart cp moddir plof
26. il11 f plofil11 f cf77 Wf e mex plofil11 f o plofil11 run plofil11 run execute program cp ALKA outdir ALKA cp ATMOS outdir ATMOS cp BOTOPP outdir BOTOPP cp BOTOPU outdir BOTOPU cp CALC13 outdir CALC13 cp CALC14 outdir CALC14 cp CALCIT outdir CALCIT cp CALPRO outdir CALPRO cp CALSED outdir CALSED cp CO2SUR outdir CO2SUR cp outdir CO3 cp DC13 outdir DC13 cp DC14 outdir DC14 cp DDZINT outdir DDZINT cp DISC3 outdir DISC3 cp DISS3 outdir DISS3 cp DMIN3 outdir DMIN3 tcp KSP outdir KSP cp O2 outdir O2 cp OADIFF outdir OADIFF cp ORGSED outdir ORGSED cp PH outdir PH cp PHSURF outdir PHSURF cp PO4 outdir PO4 cp PO40 outdir PO40 cp POC outdir POC cp POCC13 outdir POCC13 cp POCC14 outdir POCC14 cp S outdir S cp 5 outdir SATCO3 cp SCO2 outdir SCO2 cp SEALAN outdir SEALAN cp SOFPRO outdir SOFPRO cp T outdir T cp U outdir U cp V outdir V cp W outdir W cp PM outdir PM cp C14AGE outdir C14AGE PAGE 29 DKRZ OCEANIC CARBON CYCLE Model Documentation cp 5104 outdir SIO4 PLOTTINGPART DEVICE SUNC versat PK1 ecolor tcolor SUN SUNC psm2 pscm1 psz1 case DEVICE in SUN sun ISUNC sunc cp pf m m211021 plot calc_cg calc cp pf m m211021 plot mpaint_SUN o mpaint cp pf m m211021 plot calc_cg calc esac get plot library for ocan data cp pf m m211021 plot oplib6 oplib getdefin
27. ition library case DEVICE in tcolor ecolor SUNC sunc pscm1 cp pf m m211021 plot deflibcn deflib cp pf m m211021 plot deflib deflib Plot GEOSECS profiles lyprof gt quicklook cp moddir PROFIL PROFIL cp moddir lyprof f PLOPRG cp moddir lyprof dat INP cft77 PLOPRG case DEVICE in SU su segldr o runplol PLOPRG o lgksg Incarg Incarg no calc mpaint oplib deflib segldr o runplol PLOPRG o lgksg Incarg Incarg no calc oplib esac runplol lt INP result gksm77 txt cat PROTOK cat GKS_ERROR Plot GEOSECS cross sections sec11 sec11_bw cat gt SECINP lt lt EOF1 INPUT FILE FOR PLOTTING VERTICAL CROSS SECTIONS FROM OUTPUT OF CMODEL TITLE TEST TYPE OF CROSS SECTION YES 1 NO 0 ATLANTICI 1 WESTERN ATLANTIC ATLANTIC2 0 EASTERN ATLANTIC PACIFICI 1 WESTERN PACIFIC PACIFIC2 0 EASTERN PACIFIC PARAMETER YES 1 0 PAGE 30 DKRZ OCEANIC CARBON CYCLE Model Documentation CNAME 1 TOTAL CO2 MOLES LITER 10 6 1 CNAME 2 ALKALINITY EQUIVALENTS LITER 10 6 0 CNAME 3 PHOSPHATE MOLES LITER 10 6 1 4 OXYGEN MOLES LITER 10 6 0 CNAME 5 POC MOLES LITER 10 6 0 CNAME 6 CALCITE MOLES LITER 10 6 0 CNAME 7 DELTA 13C 1 CNAME 8 DELTA 14C 1 CNAME 9 POC DELTA 13C 0 CNAME 10 POC DELTA 140 0 CNAME 11 CALC
28. itly 3 4 1 Main Program The main program is divided into three parts initialization time stepping loop output Most of the computing time is consumed within the time stepping loop The different biogeochemical and physical processes are simulated subsequently in separate routines time splitting method that are all part of the time stepping loop Only the advection algorithm transport of substances with the ocean velocity field and the extraction of biolimiting nutrients from the surface layer are carried out parallel in one subroutine The main program begins with a header containing basic general information about the program which in part is also given in this manual The header includes a schematic overview over the model grid a flow chart of the program numbers of the input output units references of literature sources relevant for the model an index of all variables that are used in the main program and in the COMMON blocks of the COMDECKS with indication of the variable type At the beginning of the FORTRAN code the LOGICAL variable RSTART is defined If RSTART is of value TRUE the model run is a re start run and a re start file is needed as additional input file If RSTART is of value FALSE no values are read from a re start file even if it had been opened and the initial values of the integration are used as given in the subroutines INITIA1 and INITIA2 The arrays UFF TD XX XB DLA DLRO an
29. m the GEOSECS expedition PAGE 10 DKRZ OCEANIC CARBON CYCLE Model Documentation 3 3 COMMON BLOCKS The COMMON blocks are summarized in four different COMDECKS COMDECK BLOCK COMDECK V12MNMT COMDECK V12MNM2 COMDECK CACO3C Every variable of the COMMON blocks is documented in the program header Therefore a full list of the variables is not repeated here In general following notation is used throughout the model e I zonal direction e J meridional direction e K vertical direction In COMDECK BLOCK the array boundaries for the model grid horizontal and vertical resolution and the number of tracers geochemical variables are stored IE number of grid points in zonal direction longitude bands JE total number of grid points in meridional direction latitude bands KE number of grid points in vertical direction layers The advection algorithm needs four latitude bands more two at the northern and two at the southern boundary than are actually needed to describe the model region The first beginning from north to south and last latitude bands that are limiting the actual model domain and the geochemical variables without dummies are specified by e JL1 first latitude band index northern boundary of model domain that contains valid information for the chemical variables JLE last latitude band index southern boundary of model domain that contains valid information for the chemical variables Fi
30. n pump and the calcium carbonate counterpump Phytoplankton organ isms grow in the ocean surface layer as a function of the concentration of dissolved biolimiting nutrients in sea water The soft tissue of the organisms is called particulate organic carbon Besides organic soft tissue the organisms produce hard parts in the form of calcium carbonate The ratio of nutrients to organically bound carbon Redfield ratio and the ratio of calcium carbonate carbon to organically bound carbon rain ratio within the newly formed biogenic material are fixed The remnants of the planktonic biota sink through the water column The organic material is remineralized parallel to oxygen consumption While most of the particulate organic carbon is remineralized within the upper 1000 m of the ocean the CaCO hard parts sink to greater depth before they undergo enhanced degradation by inor ganic solution Superimposed on the production and degradation of biogenic matter is the transport of dissolved and suspended matter by the oceanic velocity field Biogenic matter is partly lost to sediment pools for organic carbon The cycling of matter in the model is closed by resuspension of sedimented matter back into the water column The carbon cycle model includes a simple atmosphere model with only diffusive transport of CO and only in meridonal directions Gas transfer between ocean and atmosphere is performed via a simple bulk formula
31. nally with parameter NV the number of geochemical key variables is specified Example Ifthe model hasa 72x72 grid points horizontal resolution 11 layers and 12 geochemical key variables we have to specify 72 76 JL1 3 JLE 74 11 NV 12 11 DKRZ OCEANIC CARBON CYCLE Model Documentation The geochemical key variables for ocean and atmosphere are contained in COMDECK V12MNMT For mnemotechnical reasons all variables have two different names introduced by EQUIVALENCE state ments one that shows the actual meaning of the variable and one that allows to handle the variables easily in DO loops For atmospheric the three carbon isotopes CO and are specified by the mnemotech nical names and DO loop names Quantity Variable DO loop variable CO ATCI2 1J ATC LJ 1 BCO ATC13 1 J ATC 1 2 4CO ATC14 1 J ATC LJ 3 The geochemical variables for seawater are represented by the following mnemotechnical names and the DO loop names Quantity Variable DO loop variable 5 SCO212 LJ K CA LJ K 1 total alkalinity ALKALI IJ K CA 1 J K 2 dissolved phosphate PHOSPH I J K CA 1 J K 3 dissolved oxygen OXYGEN LJ K CA 1 J K 4 POC C POCI2 LJ K CA 1 J K 5 CALCI2 LJ K CA LJ K 6 YBCO SCO213 LJ K CA LJ K 7 SCO214 1 J K CA LJ K 8 POCI3 LJ K CA LJ K 9 C POCIA LJ K CA LJ K 10 C CALCI3 LJ K CA LJ K 11
32. nkton a Redfield ratio of P C 1 122 Takahashi et al 1985 is prescribed production is set proportional to the production of POC according to the rain ratio close to zero at temperatures below 2 C sani chosen A maximum of 1 4 is used with strong reduction of calcite production PAGE 7 DKRZ OCEANIC CARBON CYCLE Model Documentation PAGE 8 DKRZ OCEANIC CARBON CYCLE Model Documentation 3 SYSTEM DESCRIPTION 3 1 INPUT FILES The model is started with initial conditions on four input files in the subroutines INITIA1 and INITIA2 1 velocity field file VELOCI 2 geometry file DPHILA 3 ocean identifiers file MONITO 4 index file for control maps file INDLIS If the model is re started an additional input file is needed 5 re start file with actual values of concentrations file RESTART The velocity field file contains all information about all three velocity components convective adjust ment convective mixing temperature salinity bottom topography land sea distribution velocity points pressure points layer thicknesses velocity points pressure points and ice cover thickness In the geometry file the geographic variables for latitudinal and longitudinal size of the grid point boxes are specified as given from the dynamical model 1 56 In the input file with ocean identifiers every grid point has been assigned to a certain code that indicates which gri
33. on of org C 3 4 2 9 Subroutine SURFCH gas exchange ocean atmosphere 3 4 2 10 Subroutine BIOTUR resuspension of sedimented matter 3 4 2 11 Subroutine ADVECT transport of tracers with ocean velocity field 3 5 PARAMETERS 3 6 FLOW CHARTS 18 18 18 18 18 18 19 20 DKRZ OCEANIC CARBON CYCLE Model Documentation 4 USER S MANUAL 2 a Be 4 1 HOW TO RUN THE MODEL 4 2 HOW TO GET OUTPUT PLOTS 5 REFERENCES o eee ne Be BA i Appendix A JOB TO PERFORM A MODEL Appendix JOB TO PERFORM PLOTS OF MODEL RESULTS Appendix PLOT OUTPUT EXAMPLES Appendix D CODE NUMBERS USED BY POSTPROCESSING PACKAGE 23 23 25 27 29 35 297 DKRZ OCEANIC CARBON CYCLE Model Documentation 1 SUMMARY PAGE The carbon cycle model calculates the prognostic fields of oceanic geochemical carbon cycle tracers making use of a frozen velocity field provided by a run of the LSG oceanic circulation model see the corresponding manual LSG Large Scale Geostrophic The carbon cycle model includes a crude approximation of interactions between sediment and bottom layer water A simple meridionally diffusive one layer atmosphere model allows to calculate the CO airborne fraction resulting from the oceanic biogeochemical interactions 1 1 MAIN AUTHORS OF THE MODEL Ernst Maier Reimer Max Planck Institut fiir Meteorologie Hamburg Fe
34. s that part of the required integration that has been produced up to the cpu threshold value TIMA X The rest of the integration can be carried out afterwards by an additional re start of the program With the statement DO 1111 the program enters the time loop and starts simulation of the various bio geochemical processes by subsequent call of subroutines for the different processes Before the end of the time stepping loop the meridional transport of the different isotopes of CO in the atmosphere is performed After having finished the time loop at statement 1111 CONTINUE a final calculation of the various carbon pool sizes CALL POOLS and the inventories CALL BILANZ is carried out and all geochem ical key variables are written to the result re start file The main program ends with CLOSE statements for the files attached during the run PAGE 15 DKRZ OCEANIC CARBON CYCLE Model Documentation 3 4 2 Subroutines Two subroutines are called for initiation of variables and tunable parameters In subroutine INITIA1 the velocity field and the geometrical variables in subroutine INITIA2 the biogeochemical variables are ini tialized The vertical velocity component is calculated newly from the horizontal velocities using the continuity equation Now LOGICAL varibale RSTART is set If RSTART is set TRUE the time step counter NYETOT and all relevant geochemical key values read from the re start file If RSTART is set FA
35. tation TOTAL CO2 MOLES LITER 10 6 l l 90 J SSS SS s ss N 60 4 E 30 4 0 id gt ea 2 m Ni Js sul 60 5 90 y T T T T T 1 25E 85E 145E 155W 95W 35W 25E DEPTH M 25 DELTA 25 Figure 5 Example for a plot output showing the world map of the total concentration 107 moles liter for a depth of 23 meters TOTAL CO2 MOLES LITER 10 6 l 60 4 30 4 30 4 60 4 V 90 25E 85E 145E 155W 95W 35W 25 DEPTH M 2000 DELTA 25 Figure 6 Example for a plot output showingthe world map of the total concentration 107 moles liter for a depth of 2000 meters PAGE 36 DKRZ OCEANIC CARBON CYCLE Model Documentation Appendix D CODE NUMBERS USED BY POSTPROCESSING PACKAGE Code OO CN Q UU SS sN D oN D I i ID SS 10 Q Q NE 10 tU DU N Quantity 2200 CO total alkalinity dissolved phosphate dissolved oxygen YBCO PC pCO at the ocean surface pCO air pCO water pH value at the ocean surface new production of POC new production of CaCO POC C sediment pool sediment pool depth at topography scalar points C
36. ubroutine TRN860 In this part of the program also derived quantities are calculated based on the geochemical key variables and a suite of control output is produced to provide a quicklook onto the model results line printer plots Subroutine POIPRO is called in order to give depth profiles of geochemical tracers for special regions of the model ocean PAGE 16 DKRZ OCEANIC CARBON CYCLE Model Documentation 3 4 2 1 Subroutine INITIA 1 initialization of physical fields The geometrical parameters areas volumes are set The velocity field of the dynamical ocean model is read from the input file via subroutine REACIR In subroutine REACIR the velocity layer thickness convective adjustment temperature salinity topogra phy and ice thickness arrays are read from file VELOCI prepared by the standard I O as described in Maier Reimer and Mikolajewicz 1991 The values of and AA of the geographical boundaries of the grid point boxes are read from file DPHILA Furthermore the following parameters are specified in this routine the time step DT the decay rate for 4C during one time step DECCON and the diffusion coefficient DIFF for the advection routine see Subroutine ADVECT 3 4 2 2 Subroutine INITIA2 initialization of geochemical fields Currently this routine performs the initialization of the meridional transport of CO in the atmosphere The biological parameters and chemical inventories are set in subroutine BIOINI
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